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
INPP5B	3633	broad.mit.edu	37	1	38344007	38344007	+	Intron	SNP	A	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38344007A>G	uc001ccg.1	-						INPP5B_uc009vvk.1_Intron|INPP5B_uc001ccf.1_Intron|INPP5B_uc010oij.1_RNA	NM_005540	NP_005531	P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			urinary_tract(1)	1	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TGAAATGCAAAGTCCACACTG	0.557													16	72	---	---	---	---	PASS
DMAP1	55929	broad.mit.edu	37	1	44684379	44684379	+	Silent	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44684379A>T	uc001clq.1	+	6	752	c.672A>T	c.(670-672)CGA>CGT	p.R224R	DMAP1_uc010okt.1_3'UTR|DMAP1_uc001clr.1_Silent_p.R224R|DMAP1_uc001cls.1_Silent_p.R224R|DMAP1_uc010oku.1_Silent_p.R214R	NM_001034024	NP_001029196	Q9NPF5	DMAP1_HUMAN	DNA methyltransferase 1 associated protein 1	224					DNA methylation|histone H2A acetylation|histone H4 acetylation|negative regulation of transcription, DNA-dependent|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex	DNA binding|protein binding				0	Acute lymphoblastic leukemia(166;0.155)					GGCACGAACGACGGCGGAAGG	0.562											OREG0013437	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	28	126	---	---	---	---	PASS
CYP2J2	1573	broad.mit.edu	37	1	60373477	60373477	+	Silent	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:60373477G>T	uc001czq.2	-	6	989	c.984C>A	c.(982-984)GCC>GCA	p.A328A		NM_000775	NP_000766	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J,	328					epoxygenase P450 pathway|linoleic acid metabolic process|regulation of heart contraction|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	arachidonic acid 11,12-epoxygenase activity|arachidonic acid 14,15-epoxygenase activity|aromatase activity|electron carrier activity|heme binding|linoleic acid epoxygenase activity			ovary(1)	1	all_cancers(7;0.000396)					CTGGGTAGAGGGCCATATAAA	0.527													6	144	---	---	---	---	PASS
DOCK7	85440	broad.mit.edu	37	1	63084419	63084419	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:63084419T>C	uc001daq.2	-	14	1674	c.1640A>G	c.(1639-1641)GAG>GGG	p.E547G	DOCK7_uc001dan.2_Missense_Mutation_p.E439G|DOCK7_uc001dao.2_Missense_Mutation_p.E439G|DOCK7_uc001dap.2_Missense_Mutation_p.E547G|DOCK7_uc009wah.1_Missense_Mutation_p.E547G	NM_033407	NP_212132	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	547					activation of Rac GTPase activity|axonogenesis|establishment of neuroblast polarity|microtubule cytoskeleton organization|positive regulation of peptidyl-serine phosphorylation	axon|basal part of cell|growth cone	GTP binding|guanyl-nucleotide exchange factor activity|Rac GTPase binding			ovary(2)	2						TGCGGGAAACTCTAAGATTTC	0.388													52	114	---	---	---	---	PASS
SERBP1	26135	broad.mit.edu	37	1	67891959	67891959	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67891959C>A	uc001ddv.2	-	2	463	c.323G>T	c.(322-324)CGA>CTA	p.R108L	SERBP1_uc001ddx.2_Missense_Mutation_p.R108L|SERBP1_uc001ddy.2_Missense_Mutation_p.R108L|SERBP1_uc001ddw.2_Missense_Mutation_p.R108L	NM_001018067	NP_001018077	Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1 isoform 1	108					regulation of mRNA stability	nucleus|perinuclear region of cytoplasm	mRNA 3'-UTR binding|protein binding			skin(1)	1						TCTTCCAACTCGTCTTATTCC	0.403													5	255	---	---	---	---	PASS
LMO4	8543	broad.mit.edu	37	1	87805242	87805242	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:87805242G>C	uc001dmi.2	+	3	1040	c.260G>C	c.(259-261)TGC>TCC	p.C87S	LMO4_uc001dmj.2_Missense_Mutation_p.C87S	NM_006769	NP_006760	P61968	LMO4_HUMAN	LIM domain only 4	87	LIM zinc-binding 2.				neural tube closure|transcription from RNA polymerase II promoter	transcription factor complex	sequence-specific DNA binding transcription factor activity|transcription factor binding|zinc ion binding				0		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		AGCGGTGCTTGCAGCGCTTGC	0.423													16	75	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144951999	144951999	+	Intron	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144951999C>A	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emg.1_3'UTR|PDE4DIP_uc001emh.2_3'UTR	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CGCTATTTGCCCACTGAATCC	0.259			T	PDGFRB	MPD								12	178	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145536947	145536947	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145536947C>A	uc001eoa.2	+	18	2403	c.2327C>A	c.(2326-2328)CCC>CAC	p.P776H	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.P645H|ITGA10_uc009wiw.2_Missense_Mutation_p.P633H|ITGA10_uc010oyw.1_Missense_Mutation_p.P721H	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	776	Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GAGGGCTCACCCACCTCTATA	0.542													7	230	---	---	---	---	PASS
SELENBP1	8991	broad.mit.edu	37	1	151337664	151337664	+	Splice_Site	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151337664C>G	uc001exx.2	-	10	1184	c.1137_splice	c.e10+1	p.K379_splice	SELENBP1_uc010pcy.1_Splice_Site_p.K421_splice|SELENBP1_uc001exy.2_Splice_Site_p.K276_splice|SELENBP1_uc001exz.2_Splice_Site_p.K276_splice|SELENBP1_uc010pcz.1_Splice_Site_p.K317_splice|SELENBP1_uc009wms.2_Splice_Site_p.K215_splice|SELENBP1_uc009wmt.2_Splice_Site_p.K276_splice|SELENBP1_uc001eya.2_Splice_Site_p.K315_splice|SELENBP1_uc009wmu.2_Splice_Site_p.G248_splice	NM_003944	NP_003935	Q13228	SBP1_HUMAN	selenium binding protein 1						protein transport	cytosol|membrane|nucleolus	protein binding|selenium binding				0	Lung SC(34;0.00471)|Ovarian(49;0.00871)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GAGGCTCTTACCTTGACCACT	0.577													13	39	---	---	---	---	PASS
C1orf114	57821	broad.mit.edu	37	1	169391155	169391155	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:169391155A>C	uc001gga.1	-	3	682	c.514T>G	c.(514-516)TTT>GTT	p.F172V	C1orf114_uc001gfz.1_Missense_Mutation_p.F172V|C1orf114_uc009wvq.1_Missense_Mutation_p.F172V|C1orf114_uc001ggb.2_Missense_Mutation_p.F172V|C1orf114_uc001ggc.1_Missense_Mutation_p.F172V	NM_021179	NP_067002	Q5TID7	CA114_HUMAN	hypothetical protein LOC57821	172											0	all_hematologic(923;0.208)					TAATTTTTAAAAGTAGTAGTG	0.353													37	91	---	---	---	---	PASS
C1orf129	80133	broad.mit.edu	37	1	170914697	170914697	+	5'UTR	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:170914697C>T	uc001ghg.2	+	2					C1orf129_uc009wvy.2_5'UTR|C1orf129_uc010plz.1_5'UTR	NM_025063	NP_079339	Q5TGP6	CA129_HUMAN	hypothetical protein LOC80133 isoform 2								binding			pancreas(1)	1	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCTCTGTCAGCATGTTGACAA	0.338													14	53	---	---	---	---	PASS
CHIT1	1118	broad.mit.edu	37	1	203186906	203186906	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:203186906C>T	uc001gzn.2	-	10	1213	c.1117G>A	c.(1117-1119)GGC>AGC	p.G373S	FMOD_uc010pqi.1_Intron|CHIT1_uc001gzm.1_RNA|CHIT1_uc009xal.1_Missense_Mutation_p.G135S|CHIT1_uc009xam.1_RNA|CHIT1_uc009xan.1_RNA|CHIT1_uc001gzo.2_Missense_Mutation_p.G364S	NM_003465	NP_003456	Q13231	CHIT1_HUMAN	chitotriosidase precursor	373					chitin catabolic process|immune response|response to bacterium	extracellular space|lysosome	cation binding|chitin binding|endochitinase activity				0						GGGTATCGGCCCTGGTTGCAG	0.592													13	48	---	---	---	---	PASS
SLC45A3	85414	broad.mit.edu	37	1	205628353	205628353	+	3'UTR	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205628353G>T	uc001hda.1	-	5					SLC45A3_uc010prn.1_Intron|SLC45A3_uc010pro.1_Intron|SLC45A3_uc010prp.1_Intron|ELK4_uc010prq.1_Intron	NM_033102	NP_149093	Q96JT2	S45A3_HUMAN	prostein						transmembrane transport	integral to membrane			SLC45A3/BRAF(2)	ovary(2)|prostate(2)	4	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			CCAATGTGCTGGAAGTTTTCT	0.592			T	ETV1|ETV5|ELK4|ERG	prostate 						OREG0014161	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	114	---	---	---	---	PASS
KCNH1	3756	broad.mit.edu	37	1	211307396	211307396	+	5'UTR	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:211307396C>T	uc001hib.2	-	1					KCNH1_uc001hic.2_5'UTR	NM_172362	NP_758872	O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H,						myoblast fusion|regulation of transcription, DNA-dependent	voltage-gated potassium channel complex	calmodulin binding|delayed rectifier potassium channel activity|two-component sensor activity			ovary(4)|central_nervous_system(1)	5				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		CCCCATGCGCCCGGCGGGGAT	0.756											OREG0014229	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	16	---	---	---	---	PASS
PREPL	9581	broad.mit.edu	37	2	44554022	44554022	+	Silent	SNP	T	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44554022T>A	uc002ruf.2	-	10	1610	c.1575A>T	c.(1573-1575)CTA>CTT	p.L525L	PREPL_uc002rug.2_Silent_p.L459L|PREPL_uc002ruh.2_Silent_p.L463L|PREPL_uc010fax.2_Silent_p.L525L|PREPL_uc002rui.3_Silent_p.L436L|PREPL_uc002ruj.1_Silent_p.L436L|PREPL_uc002ruk.1_Silent_p.L525L	NM_006036	NP_006027	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like isoform C	525					proteolysis	cytosol	serine-type endopeptidase activity			ovary(1)	1		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GTTTTTTAGTTAGGCGGCCAT	0.448													21	60	---	---	---	---	PASS
SMEK2	57223	broad.mit.edu	37	2	55813757	55813757	+	Silent	SNP	T	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:55813757T>A	uc002rzc.2	-	6	1488	c.1113A>T	c.(1111-1113)GTA>GTT	p.V371V	SMEK2_uc002rzb.2_Silent_p.V371V|SMEK2_uc002rzd.2_Silent_p.V371V|SMEK2_uc002rza.2_Silent_p.V247V	NM_001122964	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 isoform 1	371						microtubule organizing center|nucleus	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TAATTACCATTACAATTTCAA	0.294													72	203	---	---	---	---	PASS
CNRIP1	25927	broad.mit.edu	37	2	68520911	68520911	+	3'UTR	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68520911C>A	uc002sek.3	-	3					CNRIP1_uc002sej.3_Intron|CNRIP1_uc002sem.1_RNA|CNRIP1_uc002sel.3_RNA	NM_015463	NP_056278	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1								protein binding			liver(1)	1						AATGGTGTGGCATGCCTTGTT	0.433													5	34	---	---	---	---	PASS
ANKRD36	375248	broad.mit.edu	37	2	97784175	97784175	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:97784175A>T	uc010yva.1	+	3	651	c.407A>T	c.(406-408)CAC>CTC	p.H136L	ANKRD36_uc002sxn.2_Missense_Mutation_p.H136L|ANKRD36_uc010yuz.1_RNA|ANKRD36_uc010fic.2_5'UTR|ANKRD36_uc002sxo.2_Missense_Mutation_p.H136L|ANKRD36_uc002sxp.3_RNA	NM_001164315	NP_001157787	A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	136	ANK 4.										0						ACTGCTCTGCACTACGCTGTG	0.413													26	71	---	---	---	---	PASS
ST6GAL2	84620	broad.mit.edu	37	2	107460218	107460218	+	Silent	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:107460218C>G	uc002tdq.2	-	2	335	c.216G>C	c.(214-216)GGG>GGC	p.G72G	ST6GAL2_uc002tdr.2_Silent_p.G72G|ST6GAL2_uc002tds.3_Silent_p.G72G	NM_001142351	NP_001135823	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	72	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(4)|skin(1)	11						CGTCCAGGCCCCCAGGCGGGG	0.701													18	64	---	---	---	---	PASS
NPHP1	4867	broad.mit.edu	37	2	110927475	110927475	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:110927475C>A	uc002tfn.3	-	5	524	c.430G>T	c.(430-432)GAG>TAG	p.E144*	NPHP1_uc002tfm.3_Nonsense_Mutation_p.E144*|NPHP1_uc002tfl.3_Nonsense_Mutation_p.E144*|NPHP1_uc002tfo.3_Nonsense_Mutation_p.E82*|NPHP1_uc010ywx.1_Nonsense_Mutation_p.E144*|NPHP1_uc010fjv.1_Nonsense_Mutation_p.E144*	NM_207181	NP_997064	O15259	NPHP1_HUMAN	nephrocystin 1 isoform 2	144	Potential.|Glu-rich.				actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cell-cell junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2						tcattttcctctttctcttcc	0.229													5	85	---	---	---	---	PASS
RIF1	55183	broad.mit.edu	37	2	152320194	152320194	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152320194A>C	uc002txm.2	+	30	4290	c.4160A>C	c.(4159-4161)AAT>ACT	p.N1387T	RIF1_uc002txl.2_Missense_Mutation_p.N1387T|RIF1_uc002txn.2_Missense_Mutation_p.N1387T|RIF1_uc002txo.2_Missense_Mutation_p.N1387T|RIF1_uc002txp.2_RNA	NM_018151	NP_060621	Q5UIP0	RIF1_HUMAN	RAP1 interacting factor 1	1387					cell cycle|response to DNA damage stimulus	chromosome, telomeric region|cytoplasm|nucleus|spindle	binding	p.N1387D(1)		ovary(5)|breast(4)|skin(3)|lung(2)|kidney(1)	15				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TCCAAAGAGAATACACCCCCA	0.363													44	145	---	---	---	---	PASS
CHRNA1	1134	broad.mit.edu	37	2	175612868	175612868	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:175612868A>T	uc002ujd.2	-	10	1511	c.1433T>A	c.(1432-1434)TTA>TAA	p.L478*	uc002uiw.2_Intron|CHRNA1_uc002uje.2_Nonsense_Mutation_p.L453*	NM_001039523	NP_001034612	P02708	ACHA_HUMAN	nicotinic cholinergic receptor alpha 1 isoform a	478					muscle cell homeostasis|neuromuscular junction development|neuromuscular process|neuromuscular synaptic transmission|neuron homeostasis|regulation of action potential in neuron|skeletal muscle contraction|skeletal muscle tissue growth	cell junction|cell surface|neuromuscular junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	acetylcholine receptor activity|nicotinic acetylcholine-activated cation-selective channel activity			ovary(2)|central_nervous_system(1)|skin(1)	4						TTGCTGATTTAATTCAATGAG	0.488													28	102	---	---	---	---	PASS
PECR	55825	broad.mit.edu	37	2	216908708	216908708	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:216908708G>A	uc002vft.2	-	7	813	c.745C>T	c.(745-747)CCT>TCT	p.P249S	PECR_uc010zjq.1_RNA|PECR_uc002vfr.2_Missense_Mutation_p.P111S|PECR_uc002vfs.2_Missense_Mutation_p.P103S	NM_018441	NP_060911	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	249					fatty acid biosynthetic process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Adenine(DB00173)	GAAGCTGCAGGAGACAGTAGG	0.512													12	36	---	---	---	---	PASS
ZFAND2B	130617	broad.mit.edu	37	2	220072989	220072989	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220072989T>C	uc002vka.2	+	5	618	c.446T>C	c.(445-447)ATC>ACC	p.I149T	ZFAND2B_uc010zkt.1_Missense_Mutation_p.I149T|ZFAND2B_uc010fwd.1_Missense_Mutation_p.I149T|ZFAND2B_uc002vjy.1_Missense_Mutation_p.I149T|ZFAND2B_uc002vjz.1_Missense_Mutation_p.I149T|ZFAND2B_uc002vkb.1_Missense_Mutation_p.I40T	NM_138802	NP_620157	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	149						endoplasmic reticulum	protein binding|zinc ion binding				0		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTGCTGCCATCTCCAGAGCA	0.532													23	54	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52438515	52438515	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52438515C>A	uc003ddx.2	-	12	1319	c.1204G>T	c.(1204-1206)GAG>TAG	p.E402*	BAP1_uc003ddw.2_5'Flank|BAP1_uc010hmg.2_5'Flank|BAP1_uc010hmh.2_RNA	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	402					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		tcgtcatcctcatagtcatcc	0.483			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								21	48	---	---	---	---	PASS
ABTB1	80325	broad.mit.edu	37	3	127399635	127399635	+	3'UTR	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:127399635C>A	uc003ejt.2	+	12					ABTB1_uc003ejr.2_3'UTR|ABTB1_uc003ejs.2_3'UTR|ABTB1_uc003eju.2_3'UTR|ABTB1_uc010hsm.2_3'UTR	NM_172027	NP_742024	Q969K4	ABTB1_HUMAN	ankyrin repeat and BTB (POZ) domain containing 1							cytoplasm|nucleolus|plasma membrane	translation elongation factor activity				0						CCACCCCAGTCCCAAATCCAG	0.597													7	8	---	---	---	---	PASS
SAMD7	344658	broad.mit.edu	37	3	169644942	169644942	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:169644942C>A	uc003fgd.2	+	6	1159	c.892C>A	c.(892-894)CCT>ACT	p.P298T	SAMD7_uc003fge.2_Missense_Mutation_p.P298T|SAMD7_uc011bpo.1_Missense_Mutation_p.P199T	NM_182610	NP_872416	Q7Z3H4	SAMD7_HUMAN	sterile alpha motif domain containing 7	298										skin(1)	1	all_cancers(22;1.55e-22)|all_epithelial(15;2.41e-27)|all_lung(20;3.52e-17)|Lung NSC(18;1.44e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0106)			TGGGGTTTGCCCTCCAGTTCC	0.512													39	70	---	---	---	---	PASS
ENPEP	2028	broad.mit.edu	37	4	111463966	111463966	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111463966C>T	uc003iab.3	+	12	2209	c.1867C>T	c.(1867-1869)CAT>TAT	p.H623Y		NM_001977	NP_001968	Q07075	AMPE_HUMAN	glutamyl aminopeptidase	623	Extracellular (Potential).				cell migration|cell proliferation|cell-cell signaling|proteolysis	integral to plasma membrane	aminopeptidase activity|metalloexopeptidase activity|zinc ion binding			skin(3)|ovary(1)|breast(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)	L-Glutamic Acid(DB00142)	AAACCCAGATCATATTGGGTT	0.378													38	118	---	---	---	---	PASS
SPCS3	60559	broad.mit.edu	37	4	177248330	177248330	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:177248330C>T	uc003iur.3	+	4	450	c.312C>T	c.(310-312)GTC>GTT	p.V104V		NM_021928	NP_068747	P61009	SPCS3_HUMAN	signal peptidase complex subunit 3	104	Lumenal (Potential).				energy reserve metabolic process|regulation of insulin secretion|signal peptide processing	integral to membrane|microsome|signal peptidase complex	peptidase activity			ovary(1)	1		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.43e-19)|Epithelial(43;1.84e-16)|OV - Ovarian serous cystadenocarcinoma(60;4.51e-09)|GBM - Glioblastoma multiforme(59;0.000142)|STAD - Stomach adenocarcinoma(60;0.00279)|LUSC - Lung squamous cell carcinoma(193;0.0319)		ACCAAGTTGTCCTATGGGACA	0.308													9	18	---	---	---	---	PASS
RWDD4A	201965	broad.mit.edu	37	4	184562425	184562425	+	3'UTR	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184562425G>T	uc003ivt.1	-	7						NM_152682	NP_689895	Q6NW29	RWDD4_HUMAN	RWD domain containing 4A												0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;7.35e-27)|Epithelial(43;1.49e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.76e-10)|GBM - Glioblastoma multiforme(59;5.54e-06)|Colorectal(24;7.92e-06)|STAD - Stomach adenocarcinoma(60;2.35e-05)|COAD - Colon adenocarcinoma(29;6.26e-05)|LUSC - Lung squamous cell carcinoma(40;0.00935)|READ - Rectum adenocarcinoma(43;0.166)		AATACAACAAGATCTCTTCAT	0.279													6	11	---	---	---	---	PASS
RWDD4A	201965	broad.mit.edu	37	4	184562426	184562426	+	3'UTR	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:184562426A>T	uc003ivt.1	-	7						NM_152682	NP_689895	Q6NW29	RWDD4_HUMAN	RWD domain containing 4A												0		all_lung(41;4.4e-14)|Lung NSC(41;1.03e-13)|Colorectal(36;0.00139)|all_hematologic(60;0.00756)|Hepatocellular(41;0.00826)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.202)		all cancers(43;7.35e-27)|Epithelial(43;1.49e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.76e-10)|GBM - Glioblastoma multiforme(59;5.54e-06)|Colorectal(24;7.92e-06)|STAD - Stomach adenocarcinoma(60;2.35e-05)|COAD - Colon adenocarcinoma(29;6.26e-05)|LUSC - Lung squamous cell carcinoma(40;0.00935)|READ - Rectum adenocarcinoma(43;0.166)		ATACAACAAGATCTCTTCATG	0.279													7	11	---	---	---	---	PASS
FAT1	2195	broad.mit.edu	37	4	187530344	187530344	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:187530344C>A	uc003izf.2	-	16	10387	c.10199G>T	c.(10198-10200)CGA>CTA	p.R3400L		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	3400	Extracellular (Potential).|Cadherin 31.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						TACCGTTTCTCGGTCGAGAAG	0.453										HNSCC(5;0.00058)			4	117	---	---	---	---	PASS
SEMA5A	9037	broad.mit.edu	37	5	9154665	9154665	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:9154665G>T	uc003jek.2	-	12	2128	c.1416C>A	c.(1414-1416)TTC>TTA	p.F472L		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	472	Sema.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						GCAGGCCCACGAACAGGACAC	0.612													5	216	---	---	---	---	PASS
TTC33	23548	broad.mit.edu	37	5	40716581	40716581	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:40716581A>C	uc003jma.2	-	5	603	c.455T>G	c.(454-456)GTA>GGA	p.V152G	TTC33_uc011cpm.1_Missense_Mutation_p.V44G|TTC33_uc010ivg.2_Nonstop_Mutation_p.*81E	NM_012382	NP_036514	Q6PID6	TTC33_HUMAN	tetratricopeptide repeat domain 33	152	TPR 3.						binding			ovary(1)	1						GTGAAGGGCTACTTGAAAACT	0.373													54	197	---	---	---	---	PASS
ITGA1	3672	broad.mit.edu	37	5	52221113	52221113	+	Silent	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:52221113C>G	uc003jou.2	+	19	2461	c.2409C>G	c.(2407-2409)CCC>CCG	p.P803P	ITGA1_uc003jov.2_RNA|ITGA1_uc003jow.2_Silent_p.P334P	NM_181501	NP_852478	P56199	ITA1_HUMAN	integrin, alpha 1 precursor	803	Extracellular (Potential).				axon guidance|cell-matrix adhesion|integrin-mediated signaling pathway|muscle contraction	integrin complex	collagen binding|receptor activity			ovary(2)|lung(1)	3		Lung NSC(810;5.05e-05)|Breast(144;0.0851)				TTCAGATTCCCTTTGCCAAAG	0.393													22	77	---	---	---	---	PASS
ARSB	411	broad.mit.edu	37	5	78076227	78076227	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:78076227C>T	uc003kfq.2	-	8	2881	c.1595G>A	c.(1594-1596)TGG>TAG	p.W532*		NM_000046	NP_000037	P15848	ARSB_HUMAN	arylsulfatase B isoform 1 precursor	532					lysosomal transport|lysosome organization	lysosome	arylsulfatase activity|metal ion binding|N-acetylgalactosamine-4-sulfatase activity			upper_aerodigestive_tract(1)	1		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		ATCCTACATCCAAGGGCCCCA	0.532													48	144	---	---	---	---	PASS
ERAP1	51752	broad.mit.edu	37	5	96139528	96139528	+	Silent	SNP	G	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:96139528G>A	uc003kmm.2	-	2	449	c.102C>T	c.(100-102)AGC>AGT	p.S34S	ERAP1_uc003kml.2_Silent_p.S34S|ERAP1_uc010jbm.1_Intron|ERAP1_uc003kmn.2_Silent_p.S34S	NM_001040458	NP_001035548	Q9NZ08	ERAP1_HUMAN	type 1 tumor necrosis factor receptor shedding	34	Lumenal (Potential).				angiogenesis|antigen processing and presentation of endogenous peptide antigen via MHC class I|fat cell differentiation|membrane protein ectodomain proteolysis|regulation of blood pressure|regulation of innate immune response|response to bacterium	cytosol|endoplasmic reticulum lumen|endoplasmic reticulum membrane|extracellular region|integral to membrane	aminopeptidase activity|interleukin-1, Type II receptor binding|interleukin-6 receptor binding|metalloexopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		all_cancers(142;1.75e-06)|all_epithelial(76;3.08e-09)|all_lung(232;0.000435)|Lung NSC(167;0.000601)|Ovarian(225;0.024)|Colorectal(57;0.0432)|Breast(839;0.244)		all cancers(79;7.26e-15)|COAD - Colon adenocarcinoma(37;0.071)		ATGCTTCAGTGCTCTGACACC	0.453													35	78	---	---	---	---	PASS
PDLIM4	8572	broad.mit.edu	37	5	131607572	131607572	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:131607572C>T	uc003kwn.2	+	6	836	c.759C>T	c.(757-759)CCC>CCT	p.P253P	uc003kwm.3_Intron|PDLIM4_uc003kwp.2_Intron|PDLIM4_uc003kwo.2_Silent_p.P361P	NM_003687	NP_003678	P50479	PDLI4_HUMAN	PDZ and LIM domain 4 isoform 1	253	LIM zinc-binding.						protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGGGGCTGCCCGAGTGCACGC	0.736													24	16	---	---	---	---	PASS
PCDHA5	56143	broad.mit.edu	37	5	140202644	140202644	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140202644C>T	uc003lhl.2	+	1	1284	c.1284C>T	c.(1282-1284)GAC>GAT	p.D428D	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Silent_p.D428D|PCDHA5_uc003lhj.1_Silent_p.D428D	NM_018908	NP_061731	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5 isoform 1 precursor	428	Extracellular (Potential).|Cadherin 4.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(1)|breast(1)|skin(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCGCGGGACGGGGGCTCGC	0.647													106	147	---	---	---	---	PASS
HDAC3	8841	broad.mit.edu	37	5	141014600	141014600	+	Intron	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141014600C>A	uc003llf.2	-						HDAC3_uc003lle.1_5'UTR|HDAC3_uc010jgd.1_Intron|HDAC3_uc010jge.1_Intron|RELL2_uc003lli.2_5'Flank|RELL2_uc003llh.2_5'Flank|RELL2_uc003llg.2_5'Flank|RELL2_uc010jgf.2_5'Flank	NM_003883	NP_003874	O15379	HDAC3_HUMAN	histone deacetylase 3						anti-apoptosis|cellular lipid metabolic process|negative regulation of cell cycle|negative regulation of JNK cascade|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|spindle assembly|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|spindle microtubule|transcriptional repressor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|transcription corepressor activity|transcription factor binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Vorinostat(DB02546)	TGAACCCAGTCCTGGAGACTA	0.507													9	58	---	---	---	---	PASS
ARAP3	64411	broad.mit.edu	37	5	141049604	141049604	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:141049604C>A	uc003llm.2	-	15	2212	c.2134G>T	c.(2134-2136)GGA>TGA	p.G712*	ARAP3_uc011dbe.1_Nonsense_Mutation_p.G374*|ARAP3_uc003lln.2_Nonsense_Mutation_p.G614*	NM_022481	NP_071926	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	712					cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			breast(5)|ovary(1)|large_intestine(1)	7						AGAGCTGCTCCCAGCACACAC	0.562													5	106	---	---	---	---	PASS
TTC1	7265	broad.mit.edu	37	5	159437519	159437519	+	5'UTR	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159437519C>G	uc003lxu.2	+	2						NM_003314	NP_003305	Q99614	TTC1_HUMAN	tetratricopeptide repeat domain 1						protein folding		unfolded protein binding			skin(1)	1	Renal(175;0.00196)	all_hematologic(541;0.00014)|Breast(839;0.0101)|all_neural(177;0.0281)|Medulloblastoma(196;0.0425)|Lung NSC(249;0.119)|all_lung(500;0.163)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	Epithelial(171;8.37e-05)|all cancers(165;0.000694)|OV - Ovarian serous cystadenocarcinoma(192;0.0402)		TTAGCGTCACCTCCCTCACTG	0.433													20	100	---	---	---	---	PASS
PROP1	5626	broad.mit.edu	37	5	177421243	177421243	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:177421243C>T	uc003mif.1	-	2	515	c.206G>A	c.(205-207)CGG>CAG	p.R69Q		NM_006261	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	69	Homeobox.				central nervous system development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTGGCGGCGCCGGGAGTGCGG	0.652													33	113	---	---	---	---	PASS
FAM8A1	51439	broad.mit.edu	37	6	17606158	17606158	+	Silent	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17606158G>C	uc003ncc.2	+	4	1134	c.1011G>C	c.(1009-1011)GGG>GGC	p.G337G		NM_016255	NP_057339	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	337	RDD.					integral to membrane					0	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			TCCTGCTGGGGCTTCGAGTTG	0.423													4	123	---	---	---	---	PASS
FAM8A1	51439	broad.mit.edu	37	6	17606162	17606162	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:17606162C>T	uc003ncc.2	+	4	1138	c.1015C>T	c.(1015-1017)CGA>TGA	p.R339*		NM_016255	NP_057339	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	339	RDD.					integral to membrane					0	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			GCTGGGGCTTCGAGTTGTGAC	0.423													5	115	---	---	---	---	PASS
BTN2A1	11120	broad.mit.edu	37	6	26469143	26469143	+	3'UTR	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:26469143G>C	uc003nib.1	+	8					BTN2A1_uc003nic.1_3'UTR|BTN2A1_uc003nid.1_3'UTR|BTN2A1_uc011dko.1_3'UTR	NM_007049	NP_008980	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1 isoform 1						lipid metabolic process	integral to plasma membrane				ovary(1)|skin(1)	2						TATGGACTTGGAATGAGGCCT	0.488													2	9	---	---	---	---	PASS
WDR46	9277	broad.mit.edu	37	6	33248690	33248690	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33248690G>A	uc003ods.2	-	11	1234	c.1190C>T	c.(1189-1191)ACT>ATT	p.T397I	WDR46_uc011dra.1_Missense_Mutation_p.T343I	NM_005452	NP_005443	O15213	WDR46_HUMAN	WD repeat domain 46 isoform 1	397											0						CAGGGTCCGAGTGCTCAGAGG	0.602													52	136	---	---	---	---	PASS
WDR46	9277	broad.mit.edu	37	6	33248691	33248691	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33248691T>A	uc003ods.2	-	11	1233	c.1189A>T	c.(1189-1191)ACT>TCT	p.T397S	WDR46_uc011dra.1_Missense_Mutation_p.T343S	NM_005452	NP_005443	O15213	WDR46_HUMAN	WD repeat domain 46 isoform 1	397											0						AGGGTCCGAGTGCTCAGAGGC	0.597													52	139	---	---	---	---	PASS
KIFC1	3833	broad.mit.edu	37	6	33374604	33374604	+	Silent	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33374604G>T	uc003oef.3	+	10	2379	c.1929G>T	c.(1927-1929)CTG>CTT	p.L643L	KIFC1_uc011drf.1_Silent_p.L635L	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1	643					blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0						TTTCTCCACTGGAAGAGAACG	0.547													17	63	---	---	---	---	PASS
LPA	4018	broad.mit.edu	37	6	161032706	161032706	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:161032706C>A	uc003qtl.2	-	17	2611	c.2491G>T	c.(2491-2493)GGA>TGA	p.G831*		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	3339	Kringle 30.				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TAACTCTGTCCATTACCGTGG	0.478													73	144	---	---	---	---	PASS
RAC1	5879	broad.mit.edu	37	7	6442071	6442071	+	Silent	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6442071G>C	uc003spx.2	+	6	814	c.573G>C	c.(571-573)CTG>CTC	p.L191L	RAC1_uc003spw.2_Silent_p.L210L	NM_006908	NP_008839	P63000	RAC1_HUMAN	ras-related C3 botulinum toxin substrate 1	191					actin filament polymerization|apoptosis|axon guidance|cell motility|cell-matrix adhesion|induction of apoptosis by extracellular signals|inflammatory response|lamellipodium assembly|localization within membrane|negative regulation of interleukin-23 production|negative regulation of receptor-mediated endocytosis|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of lamellipodium assembly|positive regulation of Rho protein signal transduction|regulation of cell migration|regulation of defense response to virus by virus|regulation of hydrogen peroxide metabolic process|regulation of respiratory burst|ruffle organization|small GTPase mediated signal transduction|T cell costimulation|viral reproduction	cytosol|melanosome|plasma membrane	GTP binding|GTP-dependent protein binding|GTPase activity|thioesterase binding			lung(2)	2		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.104)	Pravastatin(DB00175)|Simvastatin(DB00641)	AATGCCTGCTGTTGTAAATGT	0.458													13	31	---	---	---	---	PASS
ZNF12	7559	broad.mit.edu	37	7	6731607	6731607	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6731607C>T	uc003sqt.1	-	5	1520	c.966G>A	c.(964-966)GAG>GAA	p.E322E	ZNF12_uc011jxa.1_Silent_p.E160E|ZNF12_uc003sqs.1_Silent_p.E284E	NM_016265	NP_057349	P17014	ZNF12_HUMAN	zinc finger protein 12 isoform a	322					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0231)		CATAGGGCTTCTCCCCTGTGT	0.453													32	140	---	---	---	---	PASS
OGDH	4967	broad.mit.edu	37	7	44685072	44685072	+	Silent	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:44685072C>A	uc003tln.2	+	3	478	c.369C>A	c.(367-369)CTC>CTA	p.L123L	OGDH_uc003tlm.2_Silent_p.L123L|OGDH_uc011kbx.1_Silent_p.L123L|OGDH_uc011kby.1_Intron|OGDH_uc003tlp.2_Silent_p.L123L|OGDH_uc011kbz.1_5'UTR|OGDH_uc003tlo.1_5'UTR	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	123					glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)	TGGACAAGCTCGTGGAGGACC	0.612													5	222	---	---	---	---	PASS
CDC14C	168448	broad.mit.edu	37	7	48965048	48965048	+	Silent	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48965048C>A	uc010kyv.1	+	1	892	c.780C>A	c.(778-780)ACC>ACA	p.T260T		NR_003595				SubName: Full=Putative uncharacterized protein MGC26484;												0						ATGGCAGCACCCCTACTGATG	0.453													6	42	---	---	---	---	PASS
SPDYE6	729597	broad.mit.edu	37	7	101987641	101987641	+	3'UTR	SNP	A	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:101987641A>G	uc011kkp.1	-	8					SPDYE6_uc003uzb.2_3'UTR	NM_001146210	NP_001139682	P0CI01	SPDE6_HUMAN	speedy homolog E6												0						GAAAATCCACATCTCCCCTGG	0.483													7	30	---	---	---	---	PASS
SGCZ	137868	broad.mit.edu	37	8	14181623	14181623	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:14181623G>T	uc003wwq.2	-	3	985	c.325C>A	c.(325-327)CAT>AAT	p.H109N	SGCZ_uc010lss.2_Intron	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta	96	Extracellular (Potential).				cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		TTTCGAGAATGAATTTCTTTC	0.378													4	87	---	---	---	---	PASS
TUSC3	7991	broad.mit.edu	37	8	15531300	15531300	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:15531300C>T	uc003wwt.2	+	6	963	c.753C>T	c.(751-753)ATC>ATT	p.I251I	TUSC3_uc003wwr.2_Silent_p.I251I|TUSC3_uc003wws.2_Silent_p.I251I|TUSC3_uc003wwu.2_Silent_p.I251I|TUSC3_uc003wwv.2_Silent_p.I251I|TUSC3_uc003www.2_Silent_p.I251I|TUSC3_uc003wwx.2_RNA|TUSC3_uc003wwy.2_Silent_p.I251I	NM_006765	NP_006756	Q13454	TUSC3_HUMAN	tumor suppressor candidate 3 isoform a	251					cell redox homeostasis|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				ovary(2)|central_nervous_system(1)	3				Colorectal(111;0.113)		GGAACCATATCCGTGGACCTC	0.383													24	96	---	---	---	---	PASS
MLLT3	4300	broad.mit.edu	37	9	20346394	20346394	+	3'UTR	SNP	A	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:20346394A>C	uc003zoe.2	-	11					MLLT3_uc011lne.1_3'UTR|MLLT3_uc011lnf.1_3'UTR	NM_004529	NP_004520	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		aaaaaaaaccaaaaaaaaaaa	0.299			T	MLL	ALL								4	24	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66499680	66499680	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66499680C>A	uc004aee.1	+	1	490	c.490C>A	c.(490-492)CCC>ACC	p.P164T	LOC442421_uc004aed.1_RNA					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0						TCATGTTAACCCCTTCCCAGG	0.582													17	61	---	---	---	---	PASS
NOTCH1	4851	broad.mit.edu	37	9	139410507	139410507	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139410507C>T	uc004chz.2	-	10	1595	c.1595G>A	c.(1594-1596)TGT>TAT	p.C532Y	NOTCH1_uc004cia.1_5'Flank	NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	532	Extracellular (Potential).|EGF-like 14; calcium-binding (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity			haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GGTGCTGGCACACTCGTCCAC	0.647			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			16	46	---	---	---	---	PASS
C10orf76	79591	broad.mit.edu	37	10	103750317	103750317	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103750317T>C	uc009xwy.1	-	19	1499	c.1397A>G	c.(1396-1398)GAT>GGT	p.D466G	C10orf76_uc009xwx.1_RNA	NM_024541	NP_078817	Q5T2E6	CJ076_HUMAN	hypothetical protein LOC79591	466						integral to membrane					0		Colorectal(252;0.123)		Epithelial(162;2.41e-08)|all cancers(201;6.41e-07)		CATATAGAGATCCATAGGAAA	0.294													74	196	---	---	---	---	PASS
VENTX	27287	broad.mit.edu	37	10	135053527	135053527	+	Missense_Mutation	SNP	C	A	A	rs150065198	byFrequency	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135053527C>A	uc010quy.1	+	3	505	c.494C>A	c.(493-495)GCG>GAG	p.A165E		NM_014468	NP_055283	O95231	VENTX_HUMAN	VENT homeobox	165					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)		TCTCTCCATGCGCCCCCAGCT	0.597													33	113	---	---	---	---	PASS
CARS	833	broad.mit.edu	37	11	3050597	3050597	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3050597G>C	uc001lxh.2	-	7	703	c.629C>G	c.(628-630)TCC>TGC	p.S210C	CARS_uc001lxe.2_Missense_Mutation_p.S200C|CARS_uc001lxf.2_Missense_Mutation_p.S293C|CARS_uc001lxg.2_Missense_Mutation_p.S210C|CARS_uc010qxo.1_Missense_Mutation_p.S293C|CARS_uc010qxp.1_Missense_Mutation_p.S223C|uc001lxi.1_5'Flank	NM_001751	NP_001742	P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase isoform b	210					cysteinyl-tRNA aminoacylation	cytoplasm|cytosol	ATP binding|cysteine-tRNA ligase activity|metal ion binding|protein homodimerization activity|protein homodimerization activity|tRNA binding|tRNA binding		CARS/ALK(5)	soft_tissue(5)|ovary(2)	7		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;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	GGAGAAGATGGAATTGTCAGT	0.483			T	ALK	ALCL								26	99	---	---	---	---	PASS
SLC6A5	9152	broad.mit.edu	37	11	20676346	20676346	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20676346C>T	uc001mqd.2	+	16	2599	c.2326C>T	c.(2326-2328)CCC>TCC	p.P776S	SLC6A5_uc009yic.2_Missense_Mutation_p.P541S	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	776	Cytoplasmic (Potential).				synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	CATGATCGACCCCTTGGGAAC	0.562													100	272	---	---	---	---	PASS
SLC6A5	9152	broad.mit.edu	37	11	20676347	20676347	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20676347C>T	uc001mqd.2	+	16	2600	c.2327C>T	c.(2326-2328)CCC>CTC	p.P776L	SLC6A5_uc009yic.2_Missense_Mutation_p.P541L	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	776	Cytoplasmic (Potential).				synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	ATGATCGACCCCTTGGGAACC	0.557													101	279	---	---	---	---	PASS
ACCS	84680	broad.mit.edu	37	11	44096169	44096169	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44096169G>A	uc009yks.1	+	5	571	c.427G>A	c.(427-429)GAG>AAG	p.E143K	EXT2_uc010rfo.1_5'Flank|ACCS_uc010rfm.1_Missense_Mutation_p.E70K|ACCS_uc010rfn.1_Missense_Mutation_p.G119E|ACCS_uc001mxx.2_Missense_Mutation_p.E143K	NM_001127219	NP_001120691	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase	143							1-aminocyclopropane-1-carboxylate synthase activity|protein homodimerization activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups			breast(2)|ovary(1)|lung(1)	4						CAGCCTCCGGGAGGAAGTGGC	0.562													53	170	---	---	---	---	PASS
GIF	2694	broad.mit.edu	37	11	59611470	59611470	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:59611470C>T	uc001noi.2	-	2	186	c.138G>A	c.(136-138)TCG>TCA	p.S46S	GIF_uc010rkz.1_Silent_p.S46S	NM_005142	NP_005133	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	46			S -> L (in IFD).		cobalamin metabolic process|cobalamin transport|cobalt ion transport	apical plasma membrane|endosome|extracellular space|microvillus	cobalamin binding			ovary(1)|liver(1)	2						ATGAAGTCACCGAGTTCTCCA	0.512													21	66	---	---	---	---	PASS
BEST1	7439	broad.mit.edu	37	11	61722613	61722613	+	Nonsense_Mutation	SNP	G	T	T	rs62637053		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:61722613G>T	uc001nss.2	+	3	767	c.187G>T	c.(187-189)GAG>TAG	p.E63*	BEST1_uc010rlp.1_Nonsense_Mutation_p.E3*|BEST1_uc001nsq.2_5'UTR|BEST1_uc010rlq.1_Nonsense_Mutation_p.E3*|BEST1_uc010rlr.1_Nonsense_Mutation_p.E63*|BEST1_uc010rls.1_5'UTR|BEST1_uc001nsr.2_Nonsense_Mutation_p.E3*|BEST1_uc009ynt.2_RNA|BEST1_uc010rlt.1_Nonsense_Mutation_p.E3*|BEST1_uc001nst.2_Nonsense_Mutation_p.E3*|BEST1_uc010rlu.1_5'UTR|BEST1_uc010rlv.1_5'Flank	NM_004183	NP_004174	O76090	BEST1_HUMAN	bestrophin 1 isoform 1	63	Extracellular (Potential).				response to stimulus|transepithelial chloride transport|visual perception	basolateral plasma membrane|chloride channel complex|cytosol|membrane fraction	chloride channel activity			central_nervous_system(1)	1						GCTGATGTTTGAGAAACTGAC	0.512													5	115	---	---	---	---	PASS
ATG2A	23130	broad.mit.edu	37	11	64673943	64673943	+	Nonsense_Mutation	SNP	G	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64673943G>A	uc001obx.2	-	21	3161	c.3046C>T	c.(3046-3048)CAG>TAG	p.Q1016*		NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1016							protein binding			ovary(1)|central_nervous_system(1)	2						GGGGCCAGCTGAGCCGGGGGA	0.687													22	59	---	---	---	---	PASS
RPS6KB2	6199	broad.mit.edu	37	11	67200888	67200888	+	Silent	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:67200888C>A	uc001old.2	+	10	958	c.876C>A	c.(874-876)CTC>CTA	p.L292L	RPS6KB2_uc001olf.2_Silent_p.L92L|RPS6KB2_uc001olg.2_Silent_p.L292L|RPS6KB2_uc009yrq.2_Silent_p.L92L|RPS6KB2_uc001ole.2_RNA|RPS6KB2_uc001olh.2_Intron|RPS6KB2_uc009yrr.2_Silent_p.L123L	NM_003952	NP_003943	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide	292	Protein kinase.				nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of translational initiation|translation	nucleoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)|salivary_gland(1)	7			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			CCCCCTACCTCACCCCAGATG	0.602													5	167	---	---	---	---	PASS
THYN1	29087	broad.mit.edu	37	11	134122802	134122802	+	5'UTR	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134122802C>G	uc001qhf.2	-	2					THYN1_uc001qhg.2_5'UTR|THYN1_uc001qhh.2_5'UTR|THYN1_uc001qhi.2_5'UTR|THYN1_uc001qhj.2_5'UTR|THYN1_uc009zdb.2_5'UTR|ACAD8_uc009zdc.2_5'Flank|ACAD8_uc010sco.1_5'Flank|ACAD8_uc010scp.1_5'Flank|ACAD8_uc010scq.1_5'Flank|ACAD8_uc001qhk.2_5'Flank|ACAD8_uc001qhl.2_5'Flank	NM_001037305	NP_001032382	Q9P016	THYN1_HUMAN	thymocyte nuclear protein 1 isoform 1							nucleus					0	all_hematologic(175;0.127)	all_cancers(12;1.1e-21)|all_epithelial(12;3.77e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;1.68e-10)|all cancers(11;1.95e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00148)|Lung(977;0.207)		GACTTTAGTGCGGACGATTCT	0.572													31	121	---	---	---	---	PASS
DDX23	9416	broad.mit.edu	37	12	49231789	49231789	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49231789C>A	uc001rsm.2	-	6	646	c.555G>T	c.(553-555)CAG>CAT	p.Q185H		NM_004818	NP_004809	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	185	Glu-rich.					catalytic step 2 spliceosome|nucleoplasm|U5 snRNP	ATP binding|ATP-dependent RNA helicase activity|nucleic acid binding|protein binding			kidney(3)|ovary(1)|lung(1)|skin(1)	6						CAAGCATCCTCTGCCGCTCTT	0.488													8	295	---	---	---	---	PASS
ACCN2	41	broad.mit.edu	37	12	50453582	50453582	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:50453582C>T	uc001rvw.2	+	3	632	c.403C>T	c.(403-405)CTG>TTG	p.L135L	ACCN2_uc001rvv.2_Silent_p.L135L|ACCN2_uc009zln.2_5'UTR|ACCN2_uc009zlo.2_Silent_p.L135L	NM_001095	NP_001086	P78348	ACCN2_HUMAN	amiloride-sensitive cation channel 2, neuronal	135	Extracellular (By similarity).				calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)	TGAAAAGCAGCTGGAGATACT	0.537													12	25	---	---	---	---	PASS
TBC1D15	64786	broad.mit.edu	37	12	72278663	72278663	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:72278663A>G	uc001swu.2	+	5	491	c.482A>G	c.(481-483)AAG>AGG	p.K161R	TBC1D15_uc009zrv.2_Missense_Mutation_p.K40R|TBC1D15_uc010stt.1_Missense_Mutation_p.K147R|TBC1D15_uc001swv.2_Missense_Mutation_p.K161R|TBC1D15_uc001sww.2_Intron	NM_022771	NP_073608	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15 isoform 1	139							protein binding|Rab GTPase activator activity				0						AAATCAATCAAGCAAAACAAA	0.403													23	77	---	---	---	---	PASS
SLITRK1	114798	broad.mit.edu	37	13	84455734	84455734	+	5'UTR	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:84455734C>A	uc001vlk.2	-	1						NM_052910	NP_443142	Q96PX8	SLIK1_HUMAN	slit and trk like 1 protein precursor							integral to membrane				ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	5	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		ATTTAGTGCTCCAATGTCCGA	0.522													4	60	---	---	---	---	PASS
FARP1	10160	broad.mit.edu	37	13	99098408	99098408	+	Silent	SNP	G	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:99098408G>A	uc001vnj.2	+	25	3189	c.2853G>A	c.(2851-2853)AAG>AAA	p.K951K	FARP1_uc001vnh.2_Silent_p.K982K	NM_005766	NP_005757	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF, and pleckstrin domain protein 1	951	PH 2.				regulation of Rho protein signal transduction	cytoplasm|cytoskeleton|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(2)	2	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			GGTGGCAGAAGCTGTGGGTGG	0.552											OREG0022474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	40	85	---	---	---	---	PASS
PCCA	5095	broad.mit.edu	37	13	100925589	100925589	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:100925589A>T	uc001voo.2	+	12	1092	c.1054A>T	c.(1054-1056)ACA>TCA	p.T352S	PCCA_uc010aga.2_Missense_Mutation_p.T326S|PCCA_uc010tiz.1_Missense_Mutation_p.T352S	NM_000282	NP_000273	P05165	PCCA_HUMAN	propionyl-Coenzyme A carboxylase, alpha	352	ATP-grasp.|Biotin carboxylation.				fatty acid beta-oxidation	mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|enzyme binding|metal ion binding|propionyl-CoA carboxylase activity			skin(2)	2	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	GGAAATGAATACAAGACTCCA	0.378													13	81	---	---	---	---	PASS
PABPN1	8106	broad.mit.edu	37	14	23794353	23794353	+	Intron	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23794353C>A	uc001wjk.2	+						PABPN1_uc001wjh.3_Intron|PABPN1_uc001wjj.2_3'UTR	NM_004643	NP_004634	Q86U42	PABP2_HUMAN	poly(A) binding protein, nuclear 1						modification by virus of host mRNA processing|mRNA 3'-end processing|muscle contraction|nuclear mRNA splicing, via spliceosome|poly(A)+ mRNA export from nucleus|termination of RNA polymerase II transcription|viral infectious cycle	cytoplasm|nucleoplasm|ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			ovary(2)	2	all_cancers(95;6.69e-06)			GBM - Glioblastoma multiforme(265;0.00643)		ACTTCTTTTCCCCCCTTCCCT	0.517													6	100	---	---	---	---	PASS
IPO4	79711	broad.mit.edu	37	14	24657425	24657425	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24657425G>C	uc001wmv.1	-	4	406	c.275C>G	c.(274-276)ACA>AGA	p.T92R	IPO4_uc001wmu.2_5'UTR|IPO4_uc001wmx.1_5'UTR|IPO4_uc001wmy.1_5'UTR|IPO4_uc010tnz.1_RNA|IPO4_uc001wmw.1_RNA|IPO4_uc001wmz.1_Missense_Mutation_p.T92R	NM_024658	NP_078934	Q8TEX9	IPO4_HUMAN	importin 4	92					intracellular protein transport	cytoplasm|nucleus	protein binding|protein transporter activity			kidney(1)	1				GBM - Glioblastoma multiforme(265;0.0087)		TACTTACTCTGTTTCTCTCTG	0.567													10	9	---	---	---	---	PASS
TINF2	26277	broad.mit.edu	37	14	24710922	24710922	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24710922G>T	uc001woa.3	-	3	700	c.358C>A	c.(358-360)CAG>AAG	p.Q120K	TINF2_uc010alm.2_5'UTR|TINF2_uc001wob.3_Missense_Mutation_p.Q120K|TINF2_uc010tof.1_Missense_Mutation_p.Q85K|TINF2_uc001woc.3_Missense_Mutation_p.Q120K	NM_001099274	NP_001092744	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	120					negative regulation of epithelial cell proliferation|negative regulation of protein ADP-ribosylation|negative regulation of telomere maintenance via telomerase|positive regulation of telomere maintenance|protein localization to chromosome, telomeric region|telomere assembly|telomere maintenance via telomere lengthening	nuclear telomere cap complex|nucleoplasm|perinucleolar chromocenter	protein binding|protein binding|telomeric DNA binding				0				GBM - Glioblastoma multiforme(265;0.0185)		TCTGACAGCTGCTTCACCTGC	0.438									Ataxia_Pancytopenia_syndrome|Congenital_Dyskeratosis				19	25	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33068660	33068660	+	Silent	SNP	T	A	A	rs144892695		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33068660T>A	uc001wrq.2	+	6	2684	c.2514T>A	c.(2512-2514)GCT>GCA	p.A838A	AKAP6_uc010aml.2_Silent_p.A835A	NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	838	Spectrin 1.				protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TCAAGGAAGCTGTGGAGGAGG	0.398													43	80	---	---	---	---	PASS
SLC8A3	6547	broad.mit.edu	37	14	70633975	70633975	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70633975C>T	uc001xly.2	-	2	1919	c.1165G>A	c.(1165-1167)GAT>AAT	p.D389N	SLC8A3_uc001xlw.2_Missense_Mutation_p.D389N|SLC8A3_uc001xlx.2_Missense_Mutation_p.D389N|SLC8A3_uc001xlz.2_Missense_Mutation_p.D389N|SLC8A3_uc010ara.2_RNA	NM_183002	NP_892114	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium	389	Calx-beta 1.|Cytoplasmic (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(2)|breast(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		TCAGGCTCATCGGTGTGCACC	0.512													87	156	---	---	---	---	PASS
AMN	81693	broad.mit.edu	37	14	103389067	103389067	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:103389067C>T	uc001ymg.3	+	1	75	c.42C>T	c.(40-42)TGC>TGT	p.C14C	AMN_uc001ymh.3_5'Flank	NM_030943	NP_112205	Q9BXJ7	AMNLS_HUMAN	amnionless protein precursor	14					lipid metabolic process|lipoprotein metabolic process|multicellular organismal development	integral to membrane|plasma membrane					0				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGCAGCTCTGCGGTGAGCCGG	0.692													7	4	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	107062402	107062402	+	RNA	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:107062402G>C	uc010tyt.1	-	131		c.6193C>G								Parts of antibodies, mostly variable regions.												0						TCCTGGGCCCGACTCCTGCAG	0.597													3	78	---	---	---	---	PASS
HERC2	8924	broad.mit.edu	37	15	28514431	28514431	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28514431C>A	uc001zbj.2	-	11	1515	c.1409G>T	c.(1408-1410)GGC>GTC	p.G470V	HERC2_uc001zbl.1_Missense_Mutation_p.G165V	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	470					DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	nucleus	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)	13		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GTACACGCGGCCATTGCGTGA	0.562													26	52	---	---	---	---	PASS
EIF2AK4	440275	broad.mit.edu	37	15	40299227	40299227	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:40299227C>G	uc001zkm.1	+	24	3418	c.3368C>G	c.(3367-3369)GCA>GGA	p.A1123G	EIF2AK4_uc010bbj.1_Missense_Mutation_p.A824G|EIF2AK4_uc001zkn.1_Missense_Mutation_p.A223G|EIF2AK4_uc001zko.1_Missense_Mutation_p.A61G|EIF2AK4_uc010bbk.1_RNA	NM_001013703	NP_001013725	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha	1123	Histidyl-tRNA synthetase-like.				translation	cytosolic ribosome	aminoacyl-tRNA ligase activity|ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|protein homodimerization activity			lung(2)|stomach(1)|skin(1)	4		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		ATCCCTTTTGCAAGATATGTG	0.229													9	49	---	---	---	---	PASS
GANC	2595	broad.mit.edu	37	15	42584934	42584934	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:42584934C>G	uc001zpi.2	+	5	645	c.331C>G	c.(331-333)CTG>GTG	p.L111V	GANC_uc001zph.2_Missense_Mutation_p.L111V|GANC_uc001zpj.1_5'UTR	NM_198141	NP_937784	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	111					carbohydrate metabolic process		carbohydrate binding|maltose alpha-glucosidase activity			central_nervous_system(2)	2		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)		GTTTTCTAGGCTGATTTCATG	0.403													4	127	---	---	---	---	PASS
SPESP1	246777	broad.mit.edu	37	15	69238023	69238023	+	Silent	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:69238023G>T	uc002arn.1	+	2	278	c.150G>T	c.(148-150)GGG>GGT	p.G50G	NOX5_uc002arp.1_Intron|NOX5_uc002arq.1_Intron|NOX5_uc010bid.1_Intron|NOX5_uc002aro.2_Intron	NM_145658	NP_663633	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1 precursor	50					multicellular organismal development	acrosomal vesicle					0						TTCCCTCTGGGGAGCCAGGTC	0.383													6	184	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	76074431	76074431	+	Missense_Mutation	SNP	C	T	T	rs149323153	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76074431C>T	uc010umm.1	+	8	610	c.533C>T	c.(532-534)TCG>TTG	p.S178L	uc002bba.1_5'Flank					SubName: Full=cDNA FLJ59077, highly similar to Golgin subfamily A member 6;																		CTCCAGTCCTCGAGCTGCAGA	0.547													6	48	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	76074441	76074441	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76074441A>T	uc010umm.1	+	8	620	c.543A>T	c.(541-543)AGA>AGT	p.R181S	uc002bba.1_5'Flank					SubName: Full=cDNA FLJ59077, highly similar to Golgin subfamily A member 6;																		CGAGCTGCAGAGAAGCGGTCC	0.557													6	48	---	---	---	---	PASS
LINGO1	84894	broad.mit.edu	37	15	77906716	77906716	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77906716G>T	uc002bct.1	-	2	1585	c.1533C>A	c.(1531-1533)CAC>CAA	p.H511Q	LINGO1_uc002bcu.1_Missense_Mutation_p.H505Q	NM_032808	NP_116197	Q96FE5	LIGO1_HUMAN	leucine-rich repeat neuronal 6A	511	Extracellular (Potential).|Ig-like C2-type.				negative regulation of axonogenesis|nerve growth factor receptor signaling pathway	integral to membrane|plasma membrane				ovary(1)|lung(1)	2						GCACATGCAGGTGGGCGGGCA	0.662													26	70	---	---	---	---	PASS
C16orf5	29965	broad.mit.edu	37	16	4562433	4562433	+	3'UTR	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4562433G>C	uc002cwu.2	-	5					C16orf5_uc002cwv.2_3'UTR|C16orf5_uc002cww.2_3'UTR|C16orf5_uc010uxl.1_3'UTR|C16orf5_uc010uxm.1_3'UTR|C16orf5_uc010btu.2_RNA	NM_013399	NP_037531	Q9H305	LITFL_HUMAN	cell death inducing protein						apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|tumor necrosis factor-mediated signaling pathway	nucleus				ovary(1)	1		Ovarian(90;0.17)				AGGTAGGGCAGGGTGAAGAGG	0.587													4	4	---	---	---	---	PASS
C16orf71	146562	broad.mit.edu	37	16	4794979	4794979	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4794979C>T	uc002cxn.2	+	6	1472	c.1010C>T	c.(1009-1011)CCC>CTC	p.P337L		NM_139170	NP_631909	Q8IYS4	CP071_HUMAN	hypothetical protein LOC146562	337										central_nervous_system(1)	1						GCCGACACTCCCCAGGACACC	0.592													20	65	---	---	---	---	PASS
DNAH3	55567	broad.mit.edu	37	16	21033334	21033334	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21033334T>G	uc010vbe.1	-	40	5735	c.5735A>C	c.(5734-5736)CAC>CCC	p.H1912P		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1912					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		GAAGGCAAGGTGGATGGGAGA	0.468													24	56	---	---	---	---	PASS
TNRC6A	27327	broad.mit.edu	37	16	24800756	24800756	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:24800756G>T	uc002dmm.2	+	6	907	c.793G>T	c.(793-795)GAG>TAG	p.E265*	TNRC6A_uc010bxs.2_Nonsense_Mutation_p.E12*|TNRC6A_uc010vcc.1_Nonsense_Mutation_p.E12*|TNRC6A_uc002dmn.2_Nonsense_Mutation_p.E12*|TNRC6A_uc002dmo.2_Nonsense_Mutation_p.E12*	NM_014494	NP_055309	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	265	Ser-rich.|Sufficient for interaction with EIF2C1, EIF2C3 and EIF2C4.				negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|micro-ribonucleoprotein complex	nucleotide binding|RNA binding			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0394)		TTCTGAATCAGAGAGAAACAT	0.483													7	178	---	---	---	---	PASS
ABCC11	85320	broad.mit.edu	37	16	48265825	48265825	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48265825C>A	uc002eff.1	-	1	358	c.8G>T	c.(7-9)AGG>ATG	p.R3M	ABCC11_uc002efg.1_Missense_Mutation_p.R3M|ABCC11_uc002efh.1_Missense_Mutation_p.R3M|ABCC11_uc010vgl.1_Missense_Mutation_p.R3M	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	3	Cytoplasmic (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				TGTCCTCTTCCTAGTCATTTT	0.458									Cerumen_Type				6	231	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61689382	61689382	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61689382A>C	uc002eog.1	-	11	2150	c.1898T>G	c.(1897-1899)TTG>TGG	p.L633W		NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	633	Helical; (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		ACCTAACAGCAAAATGATGCA	0.423													34	124	---	---	---	---	PASS
DDX28	55794	broad.mit.edu	37	16	68055763	68055763	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68055763C>A	uc002evh.1	-	1	2197	c.1343G>T	c.(1342-1344)CGA>CTA	p.R448L	DUS2L_uc002evi.2_5'Flank|DUS2L_uc002evj.2_5'Flank|DUS2L_uc010vkk.1_5'Flank	NM_018380	NP_060850	Q9NUL7	DDX28_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	448	Helicase C-terminal.					mitochondrial nucleoid|nucleus	ATP binding|ATP-dependent helicase activity|RNA binding			skin(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0116)|Epithelial(162;0.0474)|all cancers(182;0.233)		AAGTATGTCTCGGGAGCTCTT	0.507													5	124	---	---	---	---	PASS
CLEC18B	497190	broad.mit.edu	37	16	74445808	74445808	+	Intron	SNP	T	C	C	rs146209466	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:74445808T>C	uc002fct.2	-						CLEC18B_uc002fcu.2_Intron|CLEC18B_uc010vmu.1_3'UTR|CLEC18B_uc010vmv.1_Intron	NM_001011880	NP_001011880	Q6UXF7	CL18B_HUMAN	C-type lectin domain family 18, member B							extracellular region	sugar binding				0						GGGTcaggagtgagctggtca	0.294													4	31	---	---	---	---	PASS
CNTNAP4	85445	broad.mit.edu	37	16	76486631	76486631	+	Missense_Mutation	SNP	A	C	C	rs150449060		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:76486631A>C	uc002feu.1	+	10	1683	c.1298A>C	c.(1297-1299)TAC>TCC	p.Y433S	CNTNAP4_uc002fev.1_Missense_Mutation_p.Y297S|CNTNAP4_uc010chb.1_Missense_Mutation_p.Y360S|CNTNAP4_uc002fex.1_Missense_Mutation_p.Y436S|CNTNAP4_uc002few.2_Missense_Mutation_p.Y408S	NM_033401	NP_207837	Q9C0A0	CNTP4_HUMAN	cell recognition protein CASPR4 isoform 1	433	Extracellular (Potential).|Laminin G-like 2.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(1)|pancreas(1)	2						TCGAATCTCTACCAGCCAGGA	0.433													8	34	---	---	---	---	PASS
MTHFSD	64779	broad.mit.edu	37	16	86565766	86565766	+	Silent	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:86565766G>T	uc002fjn.2	-	8	1054	c.1003C>A	c.(1003-1005)CGG>AGG	p.R335R	MTHFSD_uc010voo.1_Silent_p.R315R|MTHFSD_uc002fjo.2_Silent_p.R172R|MTHFSD_uc002fjm.2_Silent_p.R334R|MTHFSD_uc010vop.1_Silent_p.R172R|MTHFSD_uc010voq.1_Silent_p.R334R|MTHFSD_uc010vor.1_Silent_p.R335R	NM_001159377	NP_001152849	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain	335	RRM.				folic acid-containing compound biosynthetic process		5-formyltetrahydrofolate cyclo-ligase activity|ATP binding|RNA binding				0						CAGGTGAGCCGCAGGGGCACG	0.701													10	23	---	---	---	---	PASS
KIF1C	10749	broad.mit.edu	37	17	4926964	4926964	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4926964C>G	uc002gan.1	+	23	3156	c.2830C>G	c.(2830-2832)CAG>GAG	p.Q944E		NM_006612	NP_006603	O43896	KIF1C_HUMAN	kinesin family member 1C	944					microtubule-based movement|retrograde vesicle-mediated transport, Golgi to ER	endoplasmic reticulum|Golgi apparatus|microtubule	ATP binding|microtubule motor activity			breast(2)	2						CTGGCTCAAGCAGGAGCAGCT	0.711													18	36	---	---	---	---	PASS
LRRC37A4	55073	broad.mit.edu	37	17	43587576	43587576	+	Intron	SNP	A	G	G	rs2684618		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587576A>G	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						tctgaaaagaaaagaaaaaaa	0.154													3	71	---	---	---	---	PASS
CD300A	11314	broad.mit.edu	37	17	72480255	72480255	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72480255G>T	uc002jkv.2	+	7	1211	c.890G>T	c.(889-891)AGG>ATG	p.R297M	CD300A_uc002jkw.2_Missense_Mutation_p.R184M|CD300A_uc010dfr.2_Missense_Mutation_p.R148M|CD300A_uc010dfs.2_Missense_Mutation_p.R101M	NM_007261	NP_009192	Q9UGN4	CLM8_HUMAN	leukocyte membrane antigen	297	Cytoplasmic (Potential).				cell adhesion	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2						AGTGTGATAAGGAAGACATAG	0.542													5	114	---	---	---	---	PASS
PRPSAP1	5635	broad.mit.edu	37	17	74324943	74324943	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74324943C>G	uc010wta.1	-	7	1082	c.636G>C	c.(634-636)AGG>AGC	p.R212S	PRPSAP1_uc010wtb.1_Missense_Mutation_p.R109S	NM_002766	NP_002757	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate	183					nucleotide biosynthetic process		enzyme inhibitor activity|identical protein binding|magnesium ion binding|ribose phosphate diphosphokinase activity			ovary(1)	1						AGGACTGGGCCCTAGAAGGAC	0.493													11	57	---	---	---	---	PASS
SEC14L1	6397	broad.mit.edu	37	17	75209549	75209549	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:75209549G>T	uc002jto.2	+	16	2284	c.2017G>T	c.(2017-2019)GAG>TAG	p.E673*	SEC14L1_uc010dhc.2_Nonsense_Mutation_p.E673*|SEC14L1_uc010wth.1_Nonsense_Mutation_p.E673*|SEC14L1_uc002jtm.2_Nonsense_Mutation_p.E673*|SEC14L1_uc010wti.1_Nonsense_Mutation_p.E639*|SEC14L1_uc010wtj.1_3'UTR|SEC14L1_uc002jtr.2_Nonsense_Mutation_p.E67*	NM_003003	NP_002994	Q92503	S14L1_HUMAN	SEC14 (S. cerevisiae)-like 1 isoform a	673	GOLD.				transport	Golgi apparatus|integral to membrane	binding			ovary(2)	2						GTACTACACCGAGGTGATCGG	0.647													4	62	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	76497744	76497744	+	RNA	SNP	T	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76497744T>G	uc002jvt.1	+	2		c.3203T>G								Homo sapiens cDNA FLJ45552 fis, clone BRTHA2038279.																		AGTGGCAGGGTCTGAAGTCCC	0.627													9	27	---	---	---	---	PASS
CBX8	57332	broad.mit.edu	37	17	77768913	77768913	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:77768913G>C	uc002jxd.1	-	5	784	c.691C>G	c.(691-693)CTG>GTG	p.L231V		NM_020649	NP_065700	Q9HC52	CBX8_HUMAN	chromobox homolog 8	231					negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear chromatin|PcG protein complex	methylated histone residue binding				0			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GTGTCGTCCAGCTTCCTGCCC	0.662													11	32	---	---	---	---	PASS
FASN	2194	broad.mit.edu	37	17	80041257	80041257	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:80041257G>T	uc002kdu.2	-	32	5503	c.5386C>A	c.(5386-5388)CTG>ATG	p.L1796M	FASN_uc002kdv.1_5'Flank	NM_004104	NP_004095	P49327	FAS_HUMAN	fatty acid synthase	1796	Enoyl reductase (By similarity).				energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|pantothenate metabolic process|positive regulation of cellular metabolic process|triglyceride biosynthetic process	cytosol|Golgi apparatus|melanosome|plasma membrane	3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity|3-oxoacyl-[acyl-carrier-protein] synthase activity|[acyl-carrier-protein] S-acetyltransferase activity|[acyl-carrier-protein] S-malonyltransferase activity|acyl carrier activity|cofactor binding|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity|myristoyl-[acyl-carrier-protein] hydrolase activity|oleoyl-[acyl-carrier-protein] hydrolase activity|palmitoyl-[acyl-carrier-protein] hydrolase activity|phosphopantetheine binding|protein binding|zinc ion binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)|Pyrazinamide(DB00339)	AACGCATCCAGTAGGACCCCG	0.642													21	58	---	---	---	---	PASS
DSC2	1824	broad.mit.edu	37	18	28651758	28651758	+	Silent	SNP	A	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28651758A>G	uc002kwl.3	-	13	2392	c.1938T>C	c.(1936-1938)TAT>TAC	p.Y646Y	DSC2_uc002kwk.3_Silent_p.Y646Y	NM_024422	NP_077740	Q02487	DSC2_HUMAN	desmocollin 2 isoform Dsc2a preproprotein	646	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)			TAGGTACTACATATGAGCCAA	0.368													18	63	---	---	---	---	PASS
MBD1	4152	broad.mit.edu	37	18	47799982	47799982	+	Silent	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:47799982A>T	uc010dow.1	-	12	1835	c.1398T>A	c.(1396-1398)CCT>CCA	p.P466P	MBD1_uc002lef.2_Silent_p.P217P|MBD1_uc002leg.2_Silent_p.P416P|MBD1_uc010xdi.1_Silent_p.P517P|MBD1_uc002leh.3_Silent_p.P410P|MBD1_uc002len.2_Silent_p.P466P|MBD1_uc002lei.3_Silent_p.P466P|MBD1_uc002lej.3_Silent_p.P410P|MBD1_uc002lek.3_Silent_p.P417P|MBD1_uc002lel.3_Silent_p.P443P|MBD1_uc002lem.3_Silent_p.P466P|MBD1_uc010xdj.1_Silent_p.P410P|MBD1_uc010xdk.1_Silent_p.P491P|MBD1_uc010dox.1_Silent_p.P443P|MBD1_uc002leo.2_Silent_p.P466P	NM_015846	NP_056671	Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1 isoform 1	466					negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|nuclear speck	methyl-CpG binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						GCACCTGCACAGGACTGCTTG	0.632													23	49	---	---	---	---	PASS
MKNK2	2872	broad.mit.edu	37	19	2039896	2039896	+	Intron	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2039896C>T	uc002lus.2	-						MKNK2_uc002luq.1_Intron|MKNK2_uc010xgu.1_Intron|MKNK2_uc010xgv.1_Intron|MKNK2_uc002lur.2_Intron|MKNK2_uc002lut.1_3'UTR	NM_199054	NP_951009	Q9HBH9	MKNK2_HUMAN	MAP kinase-interacting serine/threonine kinase 2						cell surface receptor linked signaling pathway|intracellular protein kinase cascade|regulation of translation		ATP binding|metal ion binding|protein serine/threonine kinase activity			lung(1)|breast(1)	2		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAAGAGGCACCCCTCAGGGGA	0.677													27	72	---	---	---	---	PASS
KDM4B	23030	broad.mit.edu	37	19	5137677	5137677	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:5137677A>T	uc002mbq.3	+	17	2657	c.2431A>T	c.(2431-2433)ACC>TCC	p.T811S	KDM4B_uc010xim.1_Missense_Mutation_p.T845S|KDM4B_uc002mbr.3_Missense_Mutation_p.T569S	NM_015015	NP_055830	O94953	KDM4B_HUMAN	jumonji domain containing 2B	811					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|zinc ion binding			lung(1)	1						GCAGATGACCACCGATAGGAG	0.687													5	23	---	---	---	---	PASS
TNPO2	30000	broad.mit.edu	37	19	12813644	12813644	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12813644T>A	uc002muo.2	-	20	2483	c.2298A>T	c.(2296-2298)GAA>GAT	p.E766D	TNPO2_uc002mup.2_Missense_Mutation_p.E858D|TNPO2_uc002muq.2_Missense_Mutation_p.E766D|TNPO2_uc002mur.2_Missense_Mutation_p.E766D	NM_001136196	NP_001129668	O14787	TNPO2_HUMAN	transportin 2 (importin 3, karyopherin beta 2b)	766	HEAT 13.				intracellular protein transport	cytoplasm|nucleus	nuclear localization sequence binding|protein binding|protein transporter activity			ovary(1)	1						CACCTGTGTTTTCCAGCAGTG	0.592													73	152	---	---	---	---	PASS
SFRS14	10147	broad.mit.edu	37	19	19136452	19136452	+	Silent	SNP	G	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19136452G>A	uc002nkx.2	-	3	851	c.705C>T	c.(703-705)CTC>CTT	p.L235L	SFRS14_uc002nkz.1_Silent_p.L249L|SFRS14_uc002nla.1_Silent_p.L235L|SFRS14_uc002nlb.2_Silent_p.L235L|SFRS14_uc010xqk.1_Intron	NM_014884	NP_055699	Q8IX01	SUGP2_HUMAN	splicing factor, arginine/serine-rich 14	235					mRNA processing|RNA splicing	nucleus	RNA binding				0			OV - Ovarian serous cystadenocarcinoma(5;3.05e-05)|Epithelial(12;0.00161)			CCTTAGCTGTGAGCAGGCCCT	0.517													57	186	---	---	---	---	PASS
CILP2	148113	broad.mit.edu	37	19	19653420	19653420	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19653420G>A	uc002nmv.3	+	5	914	c.829G>A	c.(829-831)GGA>AGA	p.G277R	CILP2_uc002nmw.3_Missense_Mutation_p.G283R	NM_153221	NP_694953	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	277						proteinaceous extracellular matrix	carbohydrate binding|carboxypeptidase activity			ovary(1)	1						CCAGGCCAACGGATCCATCTC	0.597													34	83	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	19	34584130	34584130	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:34584130G>T	uc002nuz.2	-	1	84	c.32C>A	c.(31-33)GCT>GAT	p.A11D						full-length cDNA clone CS0DE007YF24 of Placenta of Homo sapiens (human).																		GGATGGACGAGCAGCAAACAC	0.502													6	12	---	---	---	---	PASS
LRFN3	79414	broad.mit.edu	37	19	36430547	36430547	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36430547G>C	uc002oco.2	+	2	672	c.220G>C	c.(220-222)GTG>CTG	p.V74L		NM_024509	NP_078785	Q9BTN0	LRFN3_HUMAN	leucine rich repeat and fibronectin type III	74	LRR 1.|Extracellular (Potential).				cell adhesion	axon|cell junction|dendrite|integral to membrane|postsynaptic membrane|presynaptic membrane					0	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CATCGCCTCCGTGCGCCGCCG	0.706													5	22	---	---	---	---	PASS
LYPD5	284348	broad.mit.edu	37	19	44303017	44303017	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44303017T>A	uc002oxm.3	-	3	398	c.317A>T	c.(316-318)GAC>GTC	p.D106V	LYPD5_uc002oxn.3_Missense_Mutation_p.D63V	NM_001031749	NP_001026919	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5 isoform A	106						anchored to membrane|plasma membrane					0		Prostate(69;0.0352)				GTTGCATTTGTCAGTTGTGCA	0.687													4	18	---	---	---	---	PASS
ZNF221	7638	broad.mit.edu	37	19	44471370	44471370	+	Silent	SNP	C	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:44471370C>T	uc002oxx.2	+	6	2044	c.1716C>T	c.(1714-1716)GGC>GGT	p.G572G	ZNF221_uc010ejb.1_Silent_p.G572G|ZNF221_uc010xws.1_Silent_p.G572G	NM_013359	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	572	C2H2-type 15.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1		Prostate(69;0.0352)				AGAGCTTTGGCTGGGCTTCAT	0.453													9	184	---	---	---	---	PASS
KLK10	5655	broad.mit.edu	37	19	51517901	51517901	+	3'UTR	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51517901G>T	uc002puy.2	-	6					KLK10_uc002puz.2_3'UTR|KLK10_uc002pva.2_3'UTR	NM_145888	NP_665895	O43240	KLK10_HUMAN	kallikrein-related peptidase 10 preproprotein						cell cycle|proteolysis	extracellular region	serine-type endopeptidase activity			lung(2)	2		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00885)		TGAGAGGGGAGATGTTTAGAG	0.552													4	9	---	---	---	---	PASS
ZNF606	80095	broad.mit.edu	37	19	58490271	58490271	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58490271C>A	uc002qqw.2	-	7	2395	c.1777G>T	c.(1777-1779)GAG>TAG	p.E593*	ZNF606_uc010yhp.1_Nonsense_Mutation_p.E503*	NM_025027	NP_079303	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	593					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		TATGGTTTCTCTCCCGTGTGA	0.418													6	225	---	---	---	---	PASS
KCNQ2	3785	broad.mit.edu	37	20	62065065	62065065	+	Intron	SNP	T	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62065065T>G	uc002yey.1	-						KCNQ2_uc002yez.1_Intron|KCNQ2_uc002yfa.1_Intron|KCNQ2_uc002yfb.1_Intron|KCNQ2_uc011aax.1_Intron|KCNQ2_uc002yfc.1_3'UTR	NM_172107	NP_742105	O43526	KCNQ2_HUMAN	potassium voltage-gated channel KQT-like protein						axon guidance|synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			upper_aerodigestive_tract(1)|ovary(1)	2	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)	AGAAAAAAAATCAATCAAAAT	0.393													44	103	---	---	---	---	PASS
APP	351	broad.mit.edu	37	21	27269956	27269956	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:27269956C>A	uc002ylz.2	-	16	2193	c.1993G>T	c.(1993-1995)GAG>TAG	p.E665*	APP_uc011acg.1_Nonsense_Mutation_p.E173*|APP_uc010glk.2_Nonsense_Mutation_p.E641*|APP_uc002yma.2_Nonsense_Mutation_p.E646*|APP_uc011ach.1_Nonsense_Mutation_p.E609*|APP_uc002ymb.2_Nonsense_Mutation_p.E590*|APP_uc010glj.2_Nonsense_Mutation_p.E534*|APP_uc011aci.1_Nonsense_Mutation_p.E555*	NM_000484	NP_000475	P05067	A4_HUMAN	amyloid beta A4 protein isoform a precursor	665	Extracellular (Potential).		E -> D (in a patient with late onset Alzheimer disease).		adult locomotory behavior|axon cargo transport|axon midline choice point recognition|cell adhesion|cellular copper ion homeostasis|collateral sprouting in absence of injury|dendrite development|endocytosis|extracellular matrix organization|G2 phase of mitotic cell cycle|innate immune response|ionotropic glutamate receptor signaling pathway|mating behavior|mRNA polyadenylation|neuron apoptosis|neuron remodeling|Notch signaling pathway|platelet activation|platelet degranulation|positive regulation of mitotic cell cycle|protein phosphorylation|regulation of epidermal growth factor receptor activity|regulation of multicellular organism growth|regulation of synapse structure and activity|regulation of translation|visual learning	axon|cell surface|coated pit|dendritic shaft|dendritic spine|extracellular region|Golgi apparatus|integral to plasma membrane|platelet alpha granule lumen	acetylcholine receptor binding|DNA binding|heparin binding|identical protein binding|metal ion binding|protein binding|protein binding|PTB domain binding|serine-type endopeptidase inhibitor activity			ovary(1)	1		Breast(209;0.00295)				TCAGAGATCTCCTCCGTCTTG	0.343													7	287	---	---	---	---	PASS
PLAC4	191585	broad.mit.edu	37	21	42551343	42551343	+	Silent	SNP	G	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42551343G>C	uc002yyz.2	-	1	5824	c.213C>G	c.(211-213)CTC>CTG	p.L71L	BACE2_uc002yyw.2_Intron|BACE2_uc002yyx.2_Intron|BACE2_uc002yyy.2_Intron	NM_182832	NP_878252	Q8WY50	PLAC4_HUMAN	placenta-specific 4	71											0		Prostate(19;2.29e-06)				cagggtgagtgagggtgtcag	0.249													2	8	---	---	---	---	PASS
TRAPPC10	7109	broad.mit.edu	37	21	45522670	45522670	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:45522670A>T	uc002zea.2	+	22	3527	c.3358A>T	c.(3358-3360)AGT>TGT	p.S1120C	TRAPPC10_uc010gpo.2_Missense_Mutation_p.S831C|TRAPPC10_uc011afa.1_Missense_Mutation_p.S498C	NM_003274	NP_003265	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1120					vesicle-mediated transport	Golgi apparatus|integral to membrane	binding|sodium ion transmembrane transporter activity			ovary(1)|skin(1)	2						TGTCGACAACAGTAGCAACTG	0.577													47	261	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38121873	38121873	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38121873G>T	uc003atr.2	+	7	3581	c.3310G>T	c.(3310-3312)GAG>TAG	p.E1104*	TRIOBP_uc003atu.2_Nonsense_Mutation_p.E932*|TRIOBP_uc003atq.1_Nonsense_Mutation_p.E1104*|TRIOBP_uc003ats.1_Nonsense_Mutation_p.E932*	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	1104					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					CCCCCAACACGAGCCCCTTCA	0.652													5	233	---	---	---	---	PASS
BMX	660	broad.mit.edu	37	X	15549469	15549469	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:15549469A>G	uc004cww.2	+	11	1146	c.958A>G	c.(958-960)ATG>GTG	p.M320V	BMX_uc004cwx.3_Missense_Mutation_p.M320V|BMX_uc004cwy.3_Missense_Mutation_p.M320V	NM_203281	NP_975010	P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	320	SH2.				cellular component disassembly involved in apoptosis|intracellular signal transduction|mesoderm development	cytosol	ATP binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding|signal transducer activity			lung(3)|ovary(2)	5	Hepatocellular(33;0.183)					AGGAGCATTTATGGTTAGAAA	0.343													61	76	---	---	---	---	PASS
GAB3	139716	broad.mit.edu	37	X	153906344	153906344	+	3'UTR	SNP	A	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:153906344A>C	uc004fmj.1	-	10					GAB3_uc004fmk.1_3'UTR|GAB3_uc010nve.1_3'UTR|GAB3_uc004fml.1_3'UTR	NM_080612	NP_542179	Q8WWW8	GAB3_HUMAN	Gab3 protein isoform 2											ovary(1)	1	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CTTGGTTTTGACCTGTGTTGA	0.383													29	22	---	---	---	---	PASS
PRKCZ	5590	broad.mit.edu	37	1	1988169	1988169	+	Intron	DEL	T	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:1988169delT	uc001aiq.2	+							NM_002744	NP_002735	Q05513	KPCZ_HUMAN	protein kinase C, zeta isoform 1						anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)		tttctttgacttttttttttt	0.169													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	20200621	20200623	+	IGR	DEL	CAC	-	-	rs144954291		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20200621_20200623delCAC								RNF186 (58850 upstream) : OTUD3 (8265 downstream)																							ccaccaccatcaccaccaccacc	0.202													5	3	---	---	---	---	
C1orf177	163747	broad.mit.edu	37	1	55279346	55279352	+	Intron	DEL	CCGGCCT	-	-	rs67384270		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55279346_55279352delCCGGCCT	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2												0						TGAGGCTGGCCCGGCCTCCGGCCTCCG	0.604													4	6	---	---	---	---	
IL23R	149233	broad.mit.edu	37	1	67672567	67672568	+	Intron	INS	-	T	T	rs79547341		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:67672567_67672568insT	uc001ddo.2	+						IL23R_uc009waz.2_Intron|IL23R_uc001ddp.2_Intron|IL23R_uc010opi.1_Intron|IL23R_uc010opj.1_Intron|IL23R_uc010opk.1_Intron|IL23R_uc010opl.1_Intron|IL23R_uc010opm.1_Intron|IL23R_uc001ddq.2_Intron|IL23R_uc010opn.1_Intron|IL23R_uc001ddr.2_Intron|IL23R_uc010opo.1_Intron|IL23R_uc010opp.1_Intron|IL23R_uc010opq.1_Intron|IL23R_uc010opr.1_Intron|IL23R_uc010ops.1_Intron|IL23R_uc010opt.1_Intron|IL23R_uc010opu.1_Intron|IL23R_uc010opv.1_Intron|IL23R_uc010opw.1_Intron|IL23R_uc010opx.1_Intron|IL23R_uc010opy.1_Intron|IL23R_uc010opz.1_Intron|IL23R_uc010oqa.1_Intron|IL23R_uc010oqb.1_Intron|IL23R_uc010oqc.1_Intron|IL23R_uc010oqd.1_Intron|IL23R_uc010oqe.1_Intron|IL23R_uc010oqf.1_Intron|IL23R_uc010oqg.1_Intron|IL23R_uc010oqh.1_Intron|IL23R_uc001dds.2_5'Flank|IL23R_uc001ddt.2_5'Flank	NM_144701	NP_653302	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor precursor						inflammatory response|negative regulation of interleukin-10 production|positive regulation of defense response to virus by host|positive regulation of interferon-gamma production|positive regulation of interleukin-12 production|positive regulation of memory T cell differentiation|positive regulation of T cell mediated cytotoxicity|positive regulation of T-helper 1 type immune response|positive regulation of T-helper 17 cell lineage commitment|positive regulation of T-helper 17 type immune response|response to interferon-gamma|response to lipopolysaccharide	interleukin-23 receptor complex	receptor activity				0						ACAGCCAGGTCttttttttttt	0.351													8	7	---	---	---	---	
C1orf59	113802	broad.mit.edu	37	1	109191118	109191119	+	3'UTR	INS	-	A	A			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109191118_109191119insA	uc001dvt.3	-	8					C1orf59_uc001dvu.3_3'UTR|C1orf59_uc009wer.2_3'UTR	NM_001102592	NP_001096062	Q5T8I9	HENMT_HUMAN	hypothetical protein LOC113802						gene silencing by RNA|piRNA metabolic process	P granule	metal ion binding|O-methyltransferase activity|RNA binding|RNA methyltransferase activity				0		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0152)|Lung(183;0.0895)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.163)		TAGGATTACACAAAAAAAACTA	0.351													18	8	---	---	---	---	
LGTN	1939	broad.mit.edu	37	1	206770284	206770284	+	Intron	DEL	C	-	-	rs138836612		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:206770284delC	uc001heh.2	-						LGTN_uc009xbw.2_Intron	NM_006893	NP_008824	P41214	EIF2D_HUMAN	ligatin						intracellular protein transport	cytoplasm	protein binding|receptor activity|translation initiation factor activity				0	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			GTTCCAAAGACCCCCCCAAAT	0.313													3	6	---	---	---	---	
GPN1	11321	broad.mit.edu	37	2	27852150	27852151	+	Intron	INS	-	G	G	rs146892484	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27852150_27852151insG	uc010ymc.1	+						ZNF512_uc010yly.1_Intron|CCDC121_uc010eze.2_5'Flank|CCDC121_uc002rld.2_5'Flank|CCDC121_uc002rle.2_5'Flank|GPN1_uc010ezf.2_Intron|GPN1_uc010yma.1_Intron|GPN1_uc010ymb.1_Intron|GPN1_uc010ymd.1_Intron|GPN1_uc010yme.1_Intron|GPN1_uc010ezg.1_5'UTR	NM_007266	NP_009197	Q9HCN4	GPN1_HUMAN	GPN-loop GTPase 1 isoform a							cytoplasm	GTP binding|nucleoside-triphosphatase activity|protein binding				0						GCATGGCTTTCGGGGGCTTCCC	0.589													12	6	---	---	---	---	
USP34	9736	broad.mit.edu	37	2	61527959	61527959	+	Intron	DEL	A	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61527959delA	uc002sbe.2	-							NM_014709	NP_055524	Q70CQ2	UBP34_HUMAN	ubiquitin specific protease 34						positive regulation of canonical Wnt receptor signaling pathway|protein K48-linked deubiquitination|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(8)|breast(5)|skin(3)|lung(2)|prostate(1)	19			Epithelial(17;0.229)			aaaaaTGAACAAAAAAAAAAA	0.114													3	3	---	---	---	---	
LYG2	254773	broad.mit.edu	37	2	99870873	99870893	+	Intron	DEL	AGATAGTATTCTCACAGGCTC	-	-	rs80345491		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99870873_99870893delAGATAGTATTCTCACAGGCTC	uc002szw.1	-						MRPL30_uc002szl.1_Intron|LYG2_uc010fip.1_5'Flank|LYG2_uc002szx.1_Intron	NM_175735	NP_783862	Q86SG7	LYG2_HUMAN	lysozyme G-like 2 precursor						cell wall macromolecule catabolic process|peptidoglycan catabolic process	extracellular region	lysozyme activity			ovary(1)	1						CCCTGTTTCAAGATAGTATTCTCACAGGCTCAGTACATAGT	0.308													6	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	113104223	113104224	+	IGR	INS	-	AT	AT			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113104223_113104224insAT								ZC3H6 (6583 upstream) : RGPD8 (21742 downstream)																							ccatcaccaccaccaccaccat	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	129098917	129098919	+	IGR	DEL	GTG	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:129098917_129098919delGTG								HS6ST1 (22746 upstream) : None (None downstream)																							ggtattggtagtggtggtgatgg	0.103													4	2	---	---	---	---	
PTH2R	5746	broad.mit.edu	37	2	209346020	209346021	+	Intron	INS	-	GCAACCTC	GCAACCTC	rs61511423		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:209346020_209346021insGCAACCTC	uc002vdb.2	+						PTH2R_uc010zjb.1_Intron	NM_005048	NP_005039	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor precursor							integral to plasma membrane	parathyroid hormone receptor activity			ovary(1)|breast(1)|skin(1)	3				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)		ctcggctcactcgcctcccggg	0.015													4	3	---	---	---	---	
EPHA3	2042	broad.mit.edu	37	3	89448278	89448278	+	Intron	DEL	A	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:89448278delA	uc003dqy.2	+						EPHA3_uc003dqx.1_Intron|EPHA3_uc010hon.1_Intron	NM_005233	NP_005224	P29320	EPHA3_HUMAN	ephrin receptor EphA3 isoform a precursor							extracellular region|integral to plasma membrane	ATP binding			lung(17)|ovary(7)|large_intestine(4)|central_nervous_system(2)|stomach(1)|skin(1)|pancreas(1)	33	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		gactttgtctaaaaaaaaaaa	0.109										TSP Lung(6;0.00050)			6	3	---	---	---	---	
SMC4	10051	broad.mit.edu	37	3	160146393	160146393	+	Intron	DEL	T	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:160146393delT	uc003fdh.2	+						IFT80_uc003fda.2_Intron|SMC4_uc003fdi.2_Intron|SMC4_uc003fdj.2_Intron|SMC4_uc010hwd.2_Intron|SMC4_uc003fdl.2_Intron	NM_001002800	NP_001002800	Q9NTJ3	SMC4_HUMAN	SMC4 structural maintenance of chromosomes						cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CAGGATATCGTTTTTTTTTTT	0.299													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	18147069	18147070	+	IGR	INS	-	TTCC	TTCC	rs56073401		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:18147069_18147070insTTCC								LCORL (123684 upstream) : None (None downstream)																							tccttccttcctctcttccttc	0.149													4	2	---	---	---	---	
DCLK2	166614	broad.mit.edu	37	4	151120062	151120063	+	Intron	INS	-	C	C	rs71596224		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:151120062_151120063insC	uc003ilm.3	+						DCLK2_uc003iln.3_Intron|DCLK2_uc003ilo.3_Intron|DCLK2_uc003ilp.3_Intron	NM_001040260	NP_001035350	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2 isoform a						intracellular signal transduction	cytoplasm|cytoskeleton	ATP binding|protein serine/threonine kinase activity			ovary(3)	3	all_hematologic(180;0.151)					CCCTTTCAGCACCCCCCCCCCC	0.446													4	2	---	---	---	---	
NKD2	85409	broad.mit.edu	37	5	1036608	1036609	+	Intron	DEL	CC	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:1036608_1036609delCC	uc003jbt.1	+						NKD2_uc010itf.1_Intron	NM_033120	NP_149111	Q969F2	NKD2_HUMAN	naked cuticle homolog 2						exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding				0	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			ccctgccccgcccccccccaac	0.480													4	2	---	---	---	---	
HCN1	348980	broad.mit.edu	37	5	45396488	45396489	+	Intron	INS	-	T	T			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:45396488_45396489insT	uc003jok.2	-							NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic							integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						CATTTTATCTCTTTTTTTTTTT	0.287													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	127980064	127980065	+	IGR	DEL	AC	-	-	rs34273754		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127980064_127980065delAC								FBN2 (106148 upstream) : SLC27A6 (321145 downstream)																							ttatattgctacacacacacac	0.109													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	134723987	134723998	+	IGR	DEL	TCCTTCCCTCCC	-	-	rs148190110	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:134723987_134723998delTCCTTCCCTCCC								SGK1 (84791 upstream) : ALDH8A1 (514531 downstream)																							cttccttccttccttccctccctccctccctc	0.000													3	4	---	---	---	---	
TRA2A	29896	broad.mit.edu	37	7	23545204	23545205	+	Intron	INS	-	A	A	rs34037907		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:23545204_23545205insA	uc003swi.2	-						TRA2A_uc011jzb.1_Intron|TRA2A_uc011jzc.1_Intron|TRA2A_uc011jzd.1_Intron	NM_013293	NP_037425	Q13595	TRA2A_HUMAN	transformer-2 alpha						nuclear mRNA splicing, via spliceosome	nucleus	nucleotide binding|RNA binding			ovary(1)	1						agagaaaaagcaaaaaaaaaaa	0.223													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	67206114	67206117	+	IGR	DEL	TTCT	-	-	rs56895053		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:67206114_67206117delTTCT								STAG3L4 (419602 upstream) : None (None downstream)																							ccttccttccttctttccttcctt	0.113													4	3	---	---	---	---	
TFR2	7036	broad.mit.edu	37	7	100230357	100230357	+	Intron	DEL	G	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100230357delG	uc003uvv.1	-						TFR2_uc010lhc.1_Intron|TFR2_uc003uvu.1_Intron	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2						cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					aaaaaaaaaagaacctttttt	0.000													4	2	---	---	---	---	
PUS7	54517	broad.mit.edu	37	7	105146876	105146876	+	Intron	DEL	T	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:105146876delT	uc003vcx.2	-						PUS7_uc010lji.2_Intron|PUS7_uc003vcy.2_Intron|PUS7_uc003vcz.1_Intron	NM_019042	NP_061915	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 homolog						pseudouridine synthesis|tRNA processing		pseudouridine synthase activity|RNA binding			breast(1)	1						tttttttttcttttttttttt	0.129													6	3	---	---	---	---	
ATG9B	285973	broad.mit.edu	37	7	150719079	150719080	+	Intron	DEL	TT	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:150719079_150719080delTT	uc011kvc.1	-						ATG9B_uc003wig.3_Intron	NM_173681	NP_775952	Q674R7	ATG9B_HUMAN	ATG9 autophagy related 9 homolog B						autophagic vacuole assembly	autophagic vacuole membrane|cytoplasmic vesicle|integral to membrane				ovary(1)	1	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AAtttccttctttttttttttt	0.069													6	3	---	---	---	---	
KIAA0146	23514	broad.mit.edu	37	8	48614647	48614660	+	Intron	DEL	TCTCTCTCTCTCTT	-	-	rs35588989	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48614647_48614660delTCTCTCTCTCTCTT	uc003xqd.2	+						KIAA0146_uc011ldb.1_Intron|KIAA0146_uc010lxs.2_Intron|KIAA0146_uc011ldc.1_Intron|KIAA0146_uc011ldd.1_Intron|KIAA0146_uc003xqe.2_Intron|KIAA0146_uc003xqf.2_Intron|KIAA0146_uc011lde.1_Intron|KIAA0146_uc010lxt.2_Intron|KIAA0146_uc011ldf.1_Intron|KIAA0146_uc011ldg.1_Intron	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514												0		Lung NSC(58;0.175)				tctctctctctctctctctctctTacacacacac	0.173													6	3	---	---	---	---	
TG	7038	broad.mit.edu	37	8	134052199	134052200	+	Intron	DEL	CA	-	-	rs3835182		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:134052199_134052200delCA	uc003ytw.2	+						TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc003ytz.2_Intron|SLA_uc011lje.1_Intron|SLA_uc011ljf.1_Intron|SLA_uc011ljg.1_Intron|SLA_uc011ljd.1_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor						hormone biosynthetic process|signal transduction|thyroid gland development|thyroid hormone generation	extracellular space	hormone activity			ovary(8)|breast(4)|pancreas(1)|central_nervous_system(1)|skin(1)	15	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CACTTGCATGcacacacacaca	0.460													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	142359627	142359628	+	IGR	INS	-	AC	AC	rs148211915	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142359627_142359628insAC								LOC731779 (4908 upstream) : GPR20 (6961 downstream)																							agtagactgagacacacacaca	0.000													4	2	---	---	---	---	
FGD3	89846	broad.mit.edu	37	9	95772799	95772800	+	Intron	INS	-	AGAGAC	AGAGAC	rs151317911	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95772799_95772800insAGAGAC	uc004asw.2	+						FGD3_uc004asx.2_Intron|FGD3_uc004asz.2_Intron|FGD3_uc004ata.2_Intron	NM_001083536	NP_001077005	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3						actin cytoskeleton organization|apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Cdc42 GTPase activity|regulation of cell shape|small GTPase mediated signal transduction	cytoskeleton|cytosol|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(1)|breast(1)	2						accagagggaaagagacagaga	0.238													3	3	---	---	---	---	
SLC16A9	220963	broad.mit.edu	37	10	61444172	61444172	+	Intron	DEL	A	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:61444172delA	uc010qig.1	-							NM_194298	NP_919274	Q7RTY1	MOT9_HUMAN	solute carrier family 16 (monocarboxylic acid						urate metabolic process	integral to membrane|plasma membrane	symporter activity			skin(2)|ovary(1)	3						TCCTAAAGTGAAAAAAAAAAA	0.323													4	7	---	---	---	---	
POLR3A	11128	broad.mit.edu	37	10	79770063	79770063	+	Intron	DEL	A	-	-	rs3832673		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:79770063delA	uc001jzn.2	-							NM_007055	NP_008986	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide						innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity|ribonucleoside binding|zinc ion binding				0	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			aaaaaaaaagaaaaaaaaaaa	0.179													8	5	---	---	---	---	
PLEKHA7	144100	broad.mit.edu	37	11	16996173	16996174	+	Intron	INS	-	T	T	rs140380478		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:16996173_16996174insT	uc001mmo.2	-						PLEKHA7_uc010rcu.1_Intron	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A						epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						gatttcacaggttttttttttt	0.124													9	4	---	---	---	---	
MS4A12	54860	broad.mit.edu	37	11	60269262	60269282	+	Intron	DEL	AAATTAAGGAAAAGAAAATAA	-	-	rs3831398		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60269262_60269282delAAATTAAGGAAAAGAAAATAA	uc001npr.2	+							NM_017716	NP_060186	Q9NXJ0	M4A12_HUMAN	membrane-spanning 4-domains, subfamily A, member							integral to membrane	receptor activity				0						CATAGGCCAGAAATTAAGGAAAAGAAAATAAAAAAGAAGTC	0.326													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	31269805	31269806	+	Intron	INS	-	AAG	AAG	rs10650892		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:31269805_31269806insAAG	uc010sjy.1	-						uc001rjy.2_Intron|uc001rjz.2_Intron					RecName: Full=Ovostatin homolog 1; Flags: Precursor;																		CAATATTCCTCAAACTTCTCTT	0.307													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	40842476	40842477	+	IGR	INS	-	C	C			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40842476_40842477insC								LRRK2 (79392 upstream) : CNTN1 (243881 downstream)																							cttccttccttcttctttcctt	0.050													4	3	---	---	---	---	
STAT6	6778	broad.mit.edu	37	12	57505929	57505930	+	5'Flank	INS	-	AC	AC	rs138188494	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57505929_57505930insAC	uc009zpe.2	-						STAT6_uc009zpf.2_5'Flank|STAT6_uc001sna.2_5'Flank|STAT6_uc010srb.1_5'Flank|STAT6_uc010src.1_5'Flank|STAT6_uc010srd.1_5'Flank|STAT6_uc009zpg.2_Intron	NM_003153	NP_003144	P42226	STAT6_HUMAN	signal transducer and activator of transcription						regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	calcium ion binding|DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(2)|lung(1)|skin(1)	4						ACCACAAGACTacacacacaca	0.228											OREG0021933	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
ACACB	32	broad.mit.edu	37	12	109660099	109660100	+	Intron	INS	-	GAGTGAGTGAGTGAGTGAGT	GAGTGAGTGAGTGAGTGAGT	rs142886669	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109660099_109660100insGAGTGAGTGAGTGAGTGAGT	uc001tob.2	+						ACACB_uc001toc.2_Intron	NM_001093	NP_001084	O00763	ACACB_HUMAN	acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)	aatgggtggccgagtgagtgag	0.356													4	2	---	---	---	---	
RNF34	80196	broad.mit.edu	37	12	121840361	121840361	+	Intron	DEL	A	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:121840361delA	uc001ual.1	+						RNF34_uc010szw.1_Intron|RNF34_uc001uak.1_Intron|RNF34_uc001uam.1_Intron	NM_025126	NP_079402	Q969K3	RNF34_HUMAN	ring finger protein 34 isoform 2						apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		ATAAGGGATTAAAAAAAAAAA	0.303													4	2	---	---	---	---	
RSRC2	65117	broad.mit.edu	37	12	123003139	123003140	+	Intron	INS	-	A	A	rs139622590		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:123003139_123003140insA	uc001ucr.2	-						RSRC2_uc001uco.2_Intron|RSRC2_uc001ucp.2_Intron|RSRC2_uc001ucq.2_Intron|RSRC2_uc001ucs.2_Intron|RSRC2_uc001uct.2_Intron|RSRC2_uc001ucu.2_Intron	NM_023012	NP_075388	Q7L4I2	RSRC2_HUMAN	arginine/serine-rich coiled-coil 2 isoform a											ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.14e-05)|Epithelial(86;0.000183)|BRCA - Breast invasive adenocarcinoma(302;0.201)		gactccgtgtcaaaaaaaaaaa	0.163													4	3	---	---	---	---	
TPTE2P1	646405	broad.mit.edu	37	13	25527490	25527491	+	Intron	INS	-	AAAAAG	AAAAAG			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25527490_25527491insAAAAAG	uc010tdh.1	-						TPTE2P1_uc001upx.3_Intron	NR_026730				RecName: Full=C2 tensin-type domain-containing protein ENSP00000371290;												0						AGGAAGGTTCTAAAAAAAATTT	0.252													11	5	---	---	---	---	
SLTM	79811	broad.mit.edu	37	15	59200201	59200202	+	Intron	INS	-	GTGT	GTGT	rs140029214	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59200201_59200202insGTGT	uc002afp.2	-						SLTM_uc002afo.2_Intron|SLTM_uc002afq.2_Intron|SLTM_uc010bgd.2_Intron|SLTM_uc002afr.1_Intron	NM_024755	NP_079031	Q9NWH9	SLTM_HUMAN	modulator of estrogen induced transcription						apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			ovary(1)	1						AAACATGCtgcgtgtgtgtgtg	0.188													3	3	---	---	---	---	
WDR61	80349	broad.mit.edu	37	15	78587083	78587083	+	Intron	DEL	T	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78587083delT	uc002bdn.2	-						WDR61_uc002bdo.2_Intron|WDR61_uc010umz.1_Intron|WDR61_uc010una.1_Intron|WDR61_uc010blc.1_3'UTR	NM_025234	NP_079510	Q9GZS3	WDR61_HUMAN	WD repeat domain 61								protein binding			ovary(1)|skin(1)	2						TGATGACTGCTTTTTTTTTTT	0.358													4	2	---	---	---	---	
CCDC78	124093	broad.mit.edu	37	16	773319	773320	+	Intron	INS	-	A	A	rs60065133		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:773319_773320insA	uc002cjg.2	-						CCDC78_uc002cjf.2_Intron|CCDC78_uc002cji.3_3'UTR|CCDC78_uc002cjj.3_3'UTR|CCDC78_uc002cjh.2_Intron	NM_001031737	NP_001026907	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78											central_nervous_system(1)	1		Hepatocellular(780;0.0218)				TGGCGCCCCCCCCAGGCCTTGG	0.688													2	4	---	---	---	---	
PRSS21	10942	broad.mit.edu	37	16	2867531	2867531	+	Intron	DEL	A	-	-	rs111876704		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2867531delA	uc002crt.2	+						PRSS21_uc002crs.2_Intron|PRSS21_uc002crr.2_Intron	NM_006799	NP_006790	Q9Y6M0	TEST_HUMAN	testisin isoform 1						proteolysis	anchored to membrane|cytoplasm|membrane fraction|plasma membrane	serine-type endopeptidase activity			ovary(1)|skin(1)	2						GAGGGGGTAGAGGGGGGCCTT	0.697													7	6	---	---	---	---	
LPCAT2	54947	broad.mit.edu	37	16	55571300	55571300	+	Intron	DEL	C	-	-	rs111668979		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55571300delC	uc002eie.3	+						LPCAT2_uc002eic.2_Intron	NM_017839	NP_060309	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2						cellular membrane organization|platelet activating factor biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|Golgi stack|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding				0						aagaccctgtccccaaaaaaa	0.144													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	57355160	57355160	+	IGR	DEL	A	-	-	rs68058611		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57355160delA								PLLP (36589 upstream) : CCL22 (37558 downstream)																							actttgtctcaaaaaaaaaaa	0.090													3	4	---	---	---	---	
PKD1L2	114780	broad.mit.edu	37	16	81228329	81228330	+	Intron	INS	-	AA	AA			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81228329_81228330insAA	uc002fgh.1	-						PKD1L2_uc002fgj.2_Intron	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a						neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3						gactccatctcaaaaaaaaaaa	0.129													4	2	---	---	---	---	
STX8	9482	broad.mit.edu	37	17	9317326	9317329	+	Intron	DEL	TCCA	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:9317326_9317329delTCCA	uc002glx.2	-							NM_004853	NP_004844	Q9UNK0	STX8_HUMAN	syntaxin 8						transport	endoplasmic reticulum|integral to plasma membrane				central_nervous_system(1)	1						tacccatctgtccatccatccatc	0.000													4	2	---	---	---	---	
SCPEP1	59342	broad.mit.edu	37	17	55064829	55064829	+	Intron	DEL	T	-	-	rs113438881		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:55064829delT	uc002iuv.3	+						SCPEP1_uc010dcl.2_Intron|SCPEP1_uc010wnk.1_Intron	NM_021626	NP_067639	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1 precursor						proteolysis	extracellular region	serine-type carboxypeptidase activity			skin(1)	1	Breast(9;2.86e-08)					TGCCTCTCCCTTTTTTTTTTT	0.378													8	4	---	---	---	---	
NOL11	25926	broad.mit.edu	37	17	65731846	65731846	+	Intron	DEL	A	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:65731846delA	uc002jgd.1	+						NOL11_uc010wql.1_Intron|NOL11_uc010deu.1_Intron	NM_015462	NP_056277	Q9H8H0	NOL11_HUMAN	nucleolar protein 11							nucleolus					0	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			AGACTTGGGCAAAAATAAGAG	0.264													5	5	---	---	---	---	
ZNF532	55205	broad.mit.edu	37	18	56606479	56606487	+	Intron	DEL	AAAAAAAAA	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56606479_56606487delAAAAAAAAA	uc002lho.2	+						ZNF532_uc002lhp.2_Intron|ZNF532_uc010xeg.1_Intron|ZNF532_uc002lhr.2_Intron|ZNF532_uc002lhs.2_Intron	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|skin(1)	2						acgttgtctcaaaaaaaaaaaaaaaaaaa	0.115													4	2	---	---	---	---	
OR1M1	125963	broad.mit.edu	37	19	9203785	9203786	+	5'Flank	INS	-	AT	AT	rs4804096	by1000genomes	TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:9203785_9203786insAT	uc010xkj.1	+							NM_001004456	NP_001004456	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M,						sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(3)	3						cacacacacacatatatatata	0.223													2	5	---	---	---	---	
CCDC105	126402	broad.mit.edu	37	19	15131120	15131120	+	Intron	DEL	A	-	-	rs112998351		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15131120delA	uc002nae.2	+							NM_173482	NP_775753	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105						microtubule cytoskeleton organization	microtubule				ovary(1)	1						attttgtctcaaaaaaaaaaa	0.194													4	2	---	---	---	---	
GPATCH1	55094	broad.mit.edu	37	19	33586469	33586469	+	Intron	DEL	T	-	-	rs79024536		TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:33586469delT	uc002nug.1	+							NM_018025	NP_060495	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1							catalytic step 2 spliceosome	nucleic acid binding			skin(1)	1	Esophageal squamous(110;0.137)					gcgcccagccTTTTTTttttt	0.000													7	4	---	---	---	---	
ZMYND8	23613	broad.mit.edu	37	20	45918760	45918772	+	Intron	DEL	AGCTCATACCTTA	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:45918760_45918772delAGCTCATACCTTA	uc002xta.1	-						ZMYND8_uc010ghr.1_Intron|ZMYND8_uc002xst.1_Intron|ZMYND8_uc002xsu.1_Intron|ZMYND8_uc002xsv.1_Intron|ZMYND8_uc002xsw.1_Intron|ZMYND8_uc002xsx.1_Intron|ZMYND8_uc002xsy.1_Intron|ZMYND8_uc002xsz.1_Intron|ZMYND8_uc010zxy.1_Intron|ZMYND8_uc002xtb.1_Intron|ZMYND8_uc002xss.2_Intron|ZMYND8_uc010zxz.1_Intron|ZMYND8_uc002xtc.1_Intron|ZMYND8_uc002xtd.1_Intron|ZMYND8_uc002xte.1_Intron|ZMYND8_uc010zya.1_Intron|ZMYND8_uc002xtf.1_Intron|ZMYND8_uc002xtg.2_Intron|ZMYND8_uc010ghs.1_Intron	NM_012408	NP_036540	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8 isoform b								protein binding|zinc ion binding			central_nervous_system(2)|urinary_tract(1)|ovary(1)|skin(1)	5			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			TTTAGATGTCAGCTCATACCTTAAAATGAACTT	0.324													6	4	---	---	---	---	
TAF9B	51616	broad.mit.edu	37	X	77387403	77387405	+	Intron	DEL	ATC	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77387403_77387405delATC	uc004eda.2	-							NM_015975	NP_057059	Q9HBM6	TAF9B_HUMAN	transcription associated factor 9B						negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell growth|transcription initiation, DNA-dependent	transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding				0						GTGCAACTATATCATAGAAGAAA	0.232													1	5	---	---	---	---	
STAG2	10735	broad.mit.edu	37	X	123217328	123217328	+	Frame_Shift_Del	DEL	T	-	-			TCGA-A3-3317-01A-01D-0966-08	TCGA-A3-3317-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:123217328delT	uc004etz.3	+	28	3321	c.2982delT	c.(2980-2982)CCTfs	p.P994fs	STAG2_uc004eua.2_Frame_Shift_Del_p.P994fs|STAG2_uc004eub.2_Frame_Shift_Del_p.P994fs|STAG2_uc004euc.2_Frame_Shift_Del_p.P994fs|STAG2_uc004eud.2_Frame_Shift_Del_p.P994fs|STAG2_uc004eue.2_Frame_Shift_Del_p.P994fs	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	994					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						GCCATCCACCTTTAAATTTGG	0.338													51	58	---	---	---	---	
