Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
CCNL2	81669	broad.mit.edu	37	1	1333666	1333666	+	Silent	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr1:1333666G>A	uc001afi.2	-	3	452	c.420C>T	c.(418-420)CGC>CGT	p.R140R	CCNL2_uc001afg.1_5'UTR|CCNL2_uc001afh.2_Silent_p.R140R|CCNL2_uc001afj.2_Silent_p.R140R|CCNL2_uc001afk.2_Silent_p.R140R|LOC148413_uc001afm.2_5'Flank|LOC148413_uc001afn.1_5'Flank|LOC148413_uc009vkc.1_5'Flank|LOC148413_uc009vkd.2_5'Flank	NM_030937	NP_112199	Q96S94	CCNL2_HUMAN	cyclin L2 isoform A	140	Cyclin-like 1.				regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|RNA processing|transcription, DNA-dependent	nuclear speck	protein kinase binding			ovary(2)|central_nervous_system(1)	3	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.03e-36)|OV - Ovarian serous cystadenocarcinoma(86;4.17e-22)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.0023)|BRCA - Breast invasive adenocarcinoma(365;0.00465)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.146)		CGTCCCGTATGCGTCTTGGGG	0.502													51	195	---	---	---	---	PASS
RERE	473	broad.mit.edu	37	1	8420609	8420609	+	Silent	SNP	T	G	G			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr1:8420609T>G	uc001ape.2	-	19	3768	c.2958A>C	c.(2956-2958)CCA>CCC	p.P986P	RERE_uc001apf.2_Silent_p.P986P|RERE_uc010nzx.1_Silent_p.P718P|RERE_uc001apd.2_Silent_p.P432P	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	986	Pro-rich.				multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GTTGCAGGGGTGGGGGGTGAG	0.706													6	31	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16918514	16918514	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr1:16918514C>A	uc009vos.1	-	7	891	c.3G>T	c.(1-3)ATG>ATT	p.M1I	NBPF1_uc010oce.1_Intron	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672	1						cytoplasm					0				UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		CTGATACCACCATGCTGACGT	0.483													33	696	---	---	---	---	PASS
ZBTB7B	51043	broad.mit.edu	37	1	154988948	154988948	+	Silent	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr1:154988948C>A	uc001fgk.3	+	4	1565	c.1407C>A	c.(1405-1407)CCC>CCA	p.P469P	ZBTB7B_uc009wpa.2_Silent_p.P469P|ZBTB7B_uc001fgj.3_Silent_p.P503P|ZBTB7B_uc010peq.1_Silent_p.P503P|ZBTB7B_uc001fgl.3_Silent_p.P469P	NM_015872	NP_056956	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	469					cell differentiation|ectoderm development|multicellular organismal development|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding				0	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			ATGCACCACCCCACTACCCAC	0.652													3	56	---	---	---	---	PASS
COPA	1314	broad.mit.edu	37	1	160276964	160276964	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr1:160276964G>A	uc009wti.2	-	14	1685	c.1291C>T	c.(1291-1293)CGG>TGG	p.R431W	COPA_uc001fvv.3_Missense_Mutation_p.R431W|COPA_uc009wtj.1_Missense_Mutation_p.R377W	NM_004371	NP_004362	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha isoform	431					COPI coating of Golgi vesicle|intracellular protein transport|pancreatic juice secretion|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat|cytosol|extracellular space|microsome|soluble fraction	hormone activity|structural molecule activity			ovary(1)|skin(1)	2	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GAATGCATCCGATCTAGGACA	0.478													7	297	---	---	---	---	PASS
CEP170	9859	broad.mit.edu	37	1	243354360	243354360	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr1:243354360G>T	uc001hzs.2	-	8	1476	c.1068C>A	c.(1066-1068)AGC>AGA	p.S356R	CEP170_uc001hzt.2_Missense_Mutation_p.S356R|CEP170_uc001hzu.2_Missense_Mutation_p.S356R	NM_014812	NP_055627	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa isoform alpha	356						centriole|microtubule|spindle				ovary(1)|haematopoietic_and_lymphoid_tissue(1)	2	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			CACTTTTAATGCTTTTAGAAT	0.378													3	41	---	---	---	---	PASS
FIGN	55137	broad.mit.edu	37	2	164467945	164467945	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr2:164467945C>T	uc002uck.1	-	3	708	c.397G>A	c.(397-399)GCT>ACT	p.A133T		NM_018086	NP_060556	Q5HY92	FIGN_HUMAN	fidgetin	133						nuclear matrix	ATP binding|nucleoside-triphosphatase activity			large_intestine(2)|ovary(1)|skin(1)	4						CTGACTCCAGCTTTGCTGGCA	0.498													80	230	---	---	---	---	PASS
ALS2	57679	broad.mit.edu	37	2	202626025	202626025	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr2:202626025C>A	uc002uyo.2	-	4	1048	c.692G>T	c.(691-693)CGA>CTA	p.R231L	ALS2_uc002uyp.3_Missense_Mutation_p.R231L|ALS2_uc002uyq.2_Missense_Mutation_p.R231L|ALS2_uc002uyr.2_Missense_Mutation_p.R231L	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	231					cell death|endosome organization|positive regulation of Rac GTPase activity|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(5)|lung(1)|breast(1)	7						CTGGTTGCATCGTTCTGGGAC	0.498													5	121	---	---	---	---	PASS
GPC1	2817	broad.mit.edu	37	2	241404317	241404317	+	Silent	SNP	C	T	T	rs2229458	by1000genomes	TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr2:241404317C>T	uc002vyw.3	+	6	1280	c.1059C>T	c.(1057-1059)CCC>CCT	p.P353P		NM_002081	NP_002072	P35052	GPC1_HUMAN	glypican 1 precursor	353					axon guidance	anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			breast(1)	1		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		CCCAGGGCCCCGGGCCTGAGG	0.701													3	2	---	---	---	---	PASS
ANO7	50636	broad.mit.edu	37	2	242138766	242138766	+	Silent	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr2:242138766C>T	uc002wax.2	+	5	610	c.507C>T	c.(505-507)TAC>TAT	p.Y169Y		NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN	transmembrane protein 16G isoform NGEP long	169	Cytoplasmic (Potential).					cell junction|chloride channel complex|cytosol	chloride channel activity			pancreas(2)|central_nervous_system(1)	3						CAGTGCACTACGCCCTCCTCA	0.637													17	74	---	---	---	---	PASS
ZNF197	10168	broad.mit.edu	37	3	44672664	44672664	+	Silent	SNP	G	A	A	rs150727145	byFrequency	TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr3:44672664G>A	uc003cnm.2	+	3	707	c.501G>A	c.(499-501)CCG>CCA	p.P167P	ZNF197_uc003cnn.2_Silent_p.P167P|ZNF197_uc003cno.2_RNA|ZNF197_uc003cnp.2_Silent_p.P167P	NM_006991	NP_008922	O14709	ZN197_HUMAN	zinc finger protein 197 isoform 1	167					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|skin(1)	4				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		AAATTTGCCCGCATCCTCCTA	0.527													4	179	---	---	---	---	PASS
LRRC2	79442	broad.mit.edu	37	3	46592966	46592966	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr3:46592966G>A	uc010hji.2	-	2	480	c.116C>T	c.(115-117)GCC>GTC	p.A39V	LRRC2_uc003cpu.3_Missense_Mutation_p.A39V	NM_024512	NP_078788	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	39										ovary(1)	1		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		CTTCTCCAAGGCGCTCTTCTC	0.468													4	164	---	---	---	---	PASS
DOCK3	1795	broad.mit.edu	37	3	51413195	51413195	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr3:51413195G>A	uc011bds.1	+	51	5452	c.5429G>A	c.(5428-5430)CGA>CAA	p.R1810Q		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1810						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		AATTTCCAGCGAGCCCTGTTC	0.527													6	220	---	---	---	---	PASS
FLJ10213	55096	broad.mit.edu	37	3	73111759	73111759	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr3:73111759C>T	uc003dpj.2	+	1	950	c.527C>T	c.(526-528)GCC>GTC	p.A176V	PPP4R2_uc003dph.1_Intron|PPP4R2_uc003dpi.1_Intron	NM_018029	NP_060499	Q6P2I7	EBLN2_HUMAN	hypothetical protein LOC55096	176				A -> G (in Ref. 1; AAK83528).			protein binding				0		Prostate(10;0.0187)|Lung SC(41;0.236)		Epithelial(33;3.9e-05)|BRCA - Breast invasive adenocarcinoma(55;7.72e-05)|LUSC - Lung squamous cell carcinoma(21;0.00156)|Lung(16;0.00487)|KIRC - Kidney renal clear cell carcinoma(39;0.012)|Kidney(39;0.0139)		AACTTTATTGCCCTTGAGAAG	0.463													4	131	---	---	---	---	PASS
ROBO2	6092	broad.mit.edu	37	3	77147227	77147227	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr3:77147227G>A	uc003dpy.3	+	2	767	c.124G>A	c.(124-126)GTC>ATC	p.V42I	ROBO2_uc003dpz.2_Missense_Mutation_p.V42I|ROBO2_uc011bgj.1_RNA|ROBO2_uc011bgk.1_Missense_Mutation_p.V42I	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	42	Ig-like C2-type 1.|Extracellular (Potential).				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CGATGTCATCGTCTCTAAGGG	0.547													12	36	---	---	---	---	PASS
OCIAD1	54940	broad.mit.edu	37	4	48851971	48851971	+	Silent	SNP	T	C	C			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr4:48851971T>C	uc003gyo.2	+	6	506	c.249T>C	c.(247-249)TGT>TGC	p.C83C	OCIAD1_uc011bzk.1_RNA|OCIAD1_uc003gyr.2_Silent_p.C83C|OCIAD1_uc003gyp.2_Silent_p.C83C|OCIAD1_uc003gys.2_Silent_p.C83C|OCIAD1_uc003gyq.2_Silent_p.C83C|OCIAD1_uc010igk.2_Silent_p.C88C	NM_017830	NP_060300	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1 isoform 1	83	OCIA.					endosome	protein binding				0						AAGTTGCTTGTATCATGGGAT	0.318													39	128	---	---	---	---	PASS
HMGCR	3156	broad.mit.edu	37	5	74646121	74646121	+	Silent	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr5:74646121G>A	uc003kdp.2	+	8	858	c.702G>A	c.(700-702)CAG>CAA	p.Q234Q	HMGCR_uc011cst.1_Silent_p.Q254Q|HMGCR_uc003kdq.2_Silent_p.Q234Q|HMGCR_uc010izn.1_Intron	NM_000859	NP_000850	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	234					cholesterol biosynthetic process|coenzyme A metabolic process|germ cell migration|gonad development|isoprenoid biosynthetic process	endoplasmic reticulum membrane|integral to membrane|peroxisomal membrane	hydroxymethylglutaryl-CoA reductase (NADPH) activity|NADP binding			ovary(1)	1		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Bezafibrate(DB01393)|Cerivastatin(DB00439)|Fluvastatin(DB01095)|Lovastatin(DB00227)|NADH(DB00157)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	CAATTTGGCAGCTCAGCCATT	0.413													3	101	---	---	---	---	PASS
PCDHGA3	56112	broad.mit.edu	37	5	140725403	140725403	+	Silent	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr5:140725403C>T	uc003ljm.1	+	1	1803	c.1803C>T	c.(1801-1803)AAC>AAT	p.N601N	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Silent_p.N361N|PCDHGA3_uc011dap.1_Silent_p.N601N	NM_018916	NP_061739	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3 isoform 1	601	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGCCAGAACGCCTGGCTGT	0.697													11	39	---	---	---	---	PASS
PCDHGA4	56111	broad.mit.edu	37	5	140735373	140735373	+	Silent	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr5:140735373C>T	uc003ljq.1	+	1	606	c.606C>T	c.(604-606)CGC>CGT	p.R202R	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljp.1_Silent_p.R202R	NM_018917	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4 isoform 1	202	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTAGATCGCGAGGAAGAGG	0.552													6	21	---	---	---	---	PASS
KCTD16	57528	broad.mit.edu	37	5	143586927	143586927	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr5:143586927G>A	uc003lnm.1	+	3	1279	c.650G>A	c.(649-651)CGA>CAA	p.R217Q	KCTD16_uc003lnn.1_Missense_Mutation_p.R217Q	NM_020768	NP_065819	Q68DU8	KCD16_HUMAN	potassium channel tetramerisation domain	217						cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	voltage-gated potassium channel activity	p.R217G(1)		large_intestine(2)|ovary(1)|skin(1)	4		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			GACCCTGATCGAGCCCCAGAA	0.453													6	141	---	---	---	---	PASS
CYP21A2	1589	broad.mit.edu	37	6	32008267	32008267	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr6:32008267C>T	uc003nze.1	+	8	1142	c.1024C>T	c.(1024-1026)CGG>TGG	p.R342W	CYP21A2_uc003nzf.1_Missense_Mutation_p.R312W	NM_000500	NP_000491	P08686	CP21A_HUMAN	cytochrome P450, family 21, subfamily A,	341			R -> W (in AH3; non-classic form; mild).|R -> P (in AH3; simple virilizing form).		glucocorticoid biosynthetic process|mineralocorticoid biosynthetic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	electron carrier activity|heme binding|steroid 21-monooxygenase activity|steroid binding				0						GGACCGTGCACGGCTGCCCTT	0.667													7	36	---	---	---	---	PASS
ASCC3	10973	broad.mit.edu	37	6	101166013	101166013	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr6:101166013C>A	uc003pqk.2	-	12	2346	c.2017G>T	c.(2017-2019)GAT>TAT	p.D673Y	ASCC3_uc011eai.1_Missense_Mutation_p.D575Y|ASCC3_uc003pql.2_Missense_Mutation_p.D673Y	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN	activating signal cointegrator 1 complex subunit	673					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(5)|skin(1)	6		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		AAACGGCCATCAAAGAAGAAA	0.343													44	117	---	---	---	---	PASS
DLGAP2	9228	broad.mit.edu	37	8	1497834	1497834	+	Silent	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr8:1497834G>A	uc003wpl.2	+	2	1072	c.975G>A	c.(973-975)CCG>CCA	p.P325P	DLGAP2_uc003wpm.2_Silent_p.P325P	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	404					neuron-neuron synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		CCCTGAGGCCGTGCCACTACC	0.567													4	4	---	---	---	---	PASS
CSMD1	64478	broad.mit.edu	37	8	2910129	2910129	+	Silent	SNP	T	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr8:2910129T>A	uc011kwk.1	-	50	7908	c.7518A>T	c.(7516-7518)TCA>TCT	p.S2506S	CSMD1_uc011kwj.1_Silent_p.S1835S|CSMD1_uc010lrg.2_Silent_p.S574S	NM_033225	NP_150094	Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1 precursor	2506	Extracellular (Potential).|Sushi 15.					integral to membrane				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TCCCGGTAAATGAACCGTTTC	0.428													7	27	---	---	---	---	PASS
ANK1	286	broad.mit.edu	37	8	41572581	41572581	+	Silent	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr8:41572581G>A	uc003xok.2	-	15	1698	c.1614C>T	c.(1612-1614)ACC>ACT	p.T538T	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoi.2_Silent_p.T538T|ANK1_uc003xoj.2_Silent_p.T538T|ANK1_uc003xol.2_Silent_p.T538T|ANK1_uc003xom.2_Silent_p.T571T	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	538	89 kDa domain.|ANK 16.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CGTGCAGAGGGGTAAATCCTT	0.627													22	91	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66500937	66500937	+	RNA	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr9:66500937C>T	uc004aed.1	+	3		c.1030C>T								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						AAGAGCGCCGCGGAGCGCCTG	0.607													3	26	---	---	---	---	PASS
LOC442421	442421	broad.mit.edu	37	9	66500939	66500939	+	RNA	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr9:66500939G>A	uc004aed.1	+	3		c.1032G>A								Homo sapiens similar to prostaglandin E receptor 4, subtype EP4; PGE receptor, EP4 subtype; prostaglandin E2 receptor, mRNA (cDNA clone IMAGE:5288780).												0						GAGCGCCGCGGAGCGCCTGAA	0.602													3	28	---	---	---	---	PASS
MAMDC4	158056	broad.mit.edu	37	9	139751941	139751941	+	Silent	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr9:139751941C>T	uc004cjs.2	+	18	2279	c.2229C>T	c.(2227-2229)TTC>TTT	p.F743F	MAMDC4_uc011mej.1_Silent_p.F80F	NM_206920	NP_996803	Q6UXC1	AEGP_HUMAN	apical early endosomal glycoprotein precursor	822	MAM 5.|Extracellular (Potential).				protein transport	integral to membrane				breast(4)|upper_aerodigestive_tract(2)|central_nervous_system(1)	7	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		ACTGCGGCTTCTCCCCTGGAG	0.657													5	78	---	---	---	---	PASS
CELF2	10659	broad.mit.edu	37	10	11330491	11330491	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr10:11330491G>A	uc001iki.3	+	9	1023	c.931G>A	c.(931-933)GCC>ACC	p.A311T	CELF2_uc010qbi.1_Missense_Mutation_p.A83T|CELF2_uc010qbj.1_Missense_Mutation_p.A311T|CELF2_uc001ikk.2_Missense_Mutation_p.A318T|CELF2_uc001ikl.3_Missense_Mutation_p.A318T|CELF2_uc010qbk.1_RNA|CELF2_uc010qbl.1_Missense_Mutation_p.A287T|CELF2_uc010qbm.1_Missense_Mutation_p.A83T|CELF2_uc001iko.3_Missense_Mutation_p.A287T|CELF2_uc001ikp.3_Missense_Mutation_p.A287T|CELF2_uc010qbn.1_Missense_Mutation_p.A295T|CELF2_uc010qbo.1_Missense_Mutation_p.A200T|CELF2_uc010qbp.1_Missense_Mutation_p.A83T	NM_001025077	NP_001020248	O95319	CELF2_HUMAN	CUG triplet repeat, RNA binding protein 2	311	Ala-rich.				mRNA processing|regulation of heart contraction	cytoplasm|nucleus	nucleotide binding|protein binding|RNA binding				0						CACGAGCAGCGCCCTGGGAGC	0.637													10	45	---	---	---	---	PASS
GHITM	27069	broad.mit.edu	37	10	85904774	85904774	+	Splice_Site	SNP	T	C	C			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr10:85904774T>C	uc001kcs.1	+	5	687	c.483_splice	c.e5+2	p.V161_splice	GHITM_uc010qma.1_Splice_Site_p.V92_splice|GHITM_uc010qmb.1_Splice_Site_p.V91_splice	NM_014394	NP_055209	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein						apoptosis	integral to membrane|mitochondrial inner membrane					0						TCTTGGGTGGTAAGTCAGCTG	0.368													3	176	---	---	---	---	PASS
OR5L2	26338	broad.mit.edu	37	11	55594892	55594892	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr11:55594892G>T	uc001nhy.1	+	1	198	c.198G>T	c.(196-198)TTG>TTT	p.L66F		NM_001004739	NP_001004739	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L,	66	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		all_epithelial(135;0.208)				TCAGCCACTTGTCCTTTGTAG	0.473										HNSCC(27;0.073)			6	486	---	---	---	---	PASS
OR8J1	219477	broad.mit.edu	37	11	56128312	56128312	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr11:56128312C>T	uc010rjh.1	+	1	590	c.590C>T	c.(589-591)ACA>ATA	p.T197I		NM_001005205	NP_001005205	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J,	197	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					TTACCAGAAACAGTTGTCTTT	0.294													50	140	---	---	---	---	PASS
CCDC88B	283234	broad.mit.edu	37	11	64109490	64109490	+	Silent	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr11:64109490C>A	uc001nzy.2	+	8	744	c.700C>A	c.(700-702)CGA>AGA	p.R234R	CCDC88B_uc009ypo.1_Silent_p.R231R|CCDC88B_uc001nzz.1_5'Flank	NM_032251	NP_115627	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88	234					microtubule cytoskeleton organization	cytoplasm	microtubule binding			ovary(3)|skin(1)	4						GCTGCTGGAGCGAGAACCCCT	0.632													3	46	---	---	---	---	PASS
SLC22A20	440044	broad.mit.edu	37	11	64981472	64981472	+	Silent	SNP	G	C	C	rs239258	by1000genomes	TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr11:64981472G>C	uc010roc.1	+	1	126	c.123G>C	c.(121-123)ACG>ACC	p.T41T	SLC22A20_uc010rob.1_Silent_p.T41T	NM_001004326	NP_001004326	A6NK97	S22AK_HUMAN	solute carrier family 22, member 20	41	Helical; (Potential).				ion transport	integral to membrane	transmembrane transporter activity			central_nervous_system(1)	1						AGAACTTCACGGCCGCTGTCC	0.687													2	3	---	---	---	---	PASS
DYRK2	8445	broad.mit.edu	37	12	68050894	68050894	+	Silent	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr12:68050894C>A	uc001str.3	+	3	609	c.207C>A	c.(205-207)GGC>GGA	p.G69G	DYRK2_uc001sts.3_5'UTR	NM_006482	NP_006473	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	69					apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|positive regulation of glycogen biosynthetic process|smoothened signaling pathway	cytoplasm|nucleus	ATP binding|magnesium ion binding|manganese ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(1)|central_nervous_system(1)	4			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		AGATTGGCGGCAGTAAGCACA	0.473													3	90	---	---	---	---	PASS
UTP20	27340	broad.mit.edu	37	12	101764854	101764854	+	Silent	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr12:101764854C>T	uc001tia.1	+	51	6862	c.6706C>T	c.(6706-6708)CTG>TTG	p.L2236L		NM_014503	NP_055318	O75691	UTP20_HUMAN	down-regulated in metastasis	2236					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|negative regulation of cell proliferation	90S preribosome|cytoplasm|nucleolus|nucleoplasm|preribosome, small subunit precursor|small-subunit processome	protein binding			ovary(2)|breast(2)	4						ATCAAGAAAGCTGTTGGTCCC	0.448													56	218	---	---	---	---	PASS
WASF3	10810	broad.mit.edu	37	13	27256797	27256797	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr13:27256797C>T	uc001uqv.2	+	9	1262	c.1037C>T	c.(1036-1038)CCG>CTG	p.P346L	WASF3_uc001uqw.2_Missense_Mutation_p.P343L	NM_006646	NP_006637	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	346	Poly-Pro.				actin filament polymerization	cytoplasm|cytoskeleton	actin binding			pancreas(1)	1	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		CCACCTCCTCCGCCACCTCCT	0.572													105	238	---	---	---	---	PASS
TNFAIP2	7127	broad.mit.edu	37	14	103599852	103599852	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr14:103599852C>A	uc001ymm.1	+	9	1830	c.1699C>A	c.(1699-1701)CAC>AAC	p.H567N	TNFAIP2_uc010awo.1_Intron|TNFAIP2_uc010txz.1_Missense_Mutation_p.H236N|TNFAIP2_uc010tya.1_Missense_Mutation_p.H50N	NM_006291	NP_006282	Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2	567					angiogenesis|cell differentiation	extracellular space				central_nervous_system(1)	1		Melanoma(154;0.155)	Epithelial(46;0.191)			CTGCACCCAGCACGTAAGCCG	0.627													3	50	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105415557	105415557	+	Silent	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr14:105415557G>A	uc010axc.1	-	7	6351	c.6231C>T	c.(6229-6231)CCC>CCT	p.P2077P	AHNAK2_uc001ypx.2_Silent_p.P1977P	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2077						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TCTTCAAACTGGGCATCTCCA	0.612													2	2	---	---	---	---	PASS
SECISBP2L	9728	broad.mit.edu	37	15	49329843	49329843	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr15:49329843T>A	uc001zxe.1	-	2	282	c.148A>T	c.(148-150)ATT>TTT	p.I50F	SECISBP2L_uc001zxd.1_Missense_Mutation_p.I50F|SECISBP2L_uc010bep.1_5'UTR|SECISBP2L_uc010beq.1_Missense_Mutation_p.I50F	NM_014701	NP_055516	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	50										breast(1)|skin(1)	2						TAGCTGGGAATTGGAGTTGGT	0.398													34	82	---	---	---	---	PASS
ATP8B4	79895	broad.mit.edu	37	15	50190384	50190384	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr15:50190384A>G	uc001zxu.2	-	22	2496	c.2354T>C	c.(2353-2355)GTA>GCA	p.V785A	ATP8B4_uc010ber.2_Missense_Mutation_p.V658A|ATP8B4_uc010ufd.1_Missense_Mutation_p.V595A|ATP8B4_uc010ufe.1_RNA|ATP8B4_uc001zxv.1_Missense_Mutation_p.V83A	NM_024837	NP_079113	Q8TF62	AT8B4_HUMAN	ATPase class I type 8B member 4	785	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			skin(3)|ovary(2)|breast(2)|large_intestine(1)	8		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		GCAGCAAATTACAGTCTTACA	0.423													4	154	---	---	---	---	PASS
LOC220594	220594	broad.mit.edu	37	17	18416592	18416592	+	RNA	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr17:18416592G>A	uc010cqe.2	-	5		c.2759C>T			LOC220594_uc010cqf.2_RNA|LOC220594_uc002gty.2_RNA	NR_003554				Homo sapiens mRNA for TL132.												0						CAGCCAGAGTGGTAGCTTTAC	0.428													13	54	---	---	---	---	PASS
FAM83G	644815	broad.mit.edu	37	17	18874710	18874710	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr17:18874710G>A	uc002guw.2	-	6	2601	c.2434C>T	c.(2434-2436)CGG>TGG	p.R812W	SLC5A10_uc002gur.1_Intron|SLC5A10_uc002guu.1_Intron|SLC5A10_uc002gut.1_Intron|SLC5A10_uc002guv.1_Intron|SLC5A10_uc010vyl.1_Intron	NM_001039999	NP_001035088	A6ND36	FA83G_HUMAN	hypothetical protein LOC644815	812										ovary(1)|central_nervous_system(1)	2						TGAGCCCTCCGTTTAGAATCC	0.622													14	69	---	---	---	---	PASS
CDK5RAP3	80279	broad.mit.edu	37	17	46053334	46053334	+	Silent	SNP	A	G	G			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr17:46053334A>G	uc002imr.2	+	8	837	c.753A>G	c.(751-753)GAA>GAG	p.E251E	CDK5RAP3_uc010wlc.1_Silent_p.E271E|CDK5RAP3_uc002imq.1_Silent_p.E26E|CDK5RAP3_uc002imu.2_Silent_p.E95E|CDK5RAP3_uc002ims.2_Silent_p.E164E|CDK5RAP3_uc002imv.2_Silent_p.E95E|CDK5RAP3_uc002imw.2_Silent_p.E95E|CDK5RAP3_uc002imx.2_Silent_p.E26E	NM_176096	NP_788276	Q96JB5	CK5P3_HUMAN	CDK5 regulatory subunit associated protein 3	251					brain development|regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation		neuronal Cdc2-like kinase binding				0						CTGTGGTGGAACGACCCCACC	0.602													3	95	---	---	---	---	PASS
LPO	4025	broad.mit.edu	37	17	56345181	56345181	+	Silent	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr17:56345181C>T	uc002ivt.2	+	13	2281	c.1965C>T	c.(1963-1965)AAC>AAT	p.N655N	LPO_uc010wns.1_Silent_p.N596N|LPO_uc010dcp.2_Silent_p.N572N|LPO_uc010dcq.2_Silent_p.N326N|LPO_uc010dcr.2_Silent_p.N218N	NM_006151	NP_006142	P22079	PERL_HUMAN	lactoperoxidase isoform 1 preproprotein	655					hydrogen peroxide catabolic process	extracellular space	heme binding|peroxidase activity			ovary(1)|breast(1)	2						TCTTCACGAACGAGCAGAAGG	0.577													19	83	---	---	---	---	PASS
PRAM1	84106	broad.mit.edu	37	19	8564163	8564163	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr19:8564163C>T	uc002mkd.2	-	2	549	c.529G>A	c.(529-531)GCC>ACC	p.A177T	PRAM1_uc002mkc.2_Missense_Mutation_p.A177T	NM_032152	NP_115528	Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	225	Pro-rich.						lipid binding|protein binding				0						GGGGGTCTGGCGGGGTGACTG	0.697													5	21	---	---	---	---	PASS
LYL1	4066	broad.mit.edu	37	19	13211896	13211896	+	Silent	SNP	T	G	G			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr19:13211896T>G	uc002mwi.2	-	2	451	c.90A>C	c.(88-90)CCA>CCC	p.P30P		NM_005583	NP_005574	P12980	LYL1_HUMAN	lymphoblastic leukemia derived sequence 1	30					B cell differentiation|blood vessel maturation|definitive hemopoiesis|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding				0			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)			GCTTAGGGGGTGGGGCAGGCG	0.706			T	TRB@	T-ALL								3	8	---	---	---	---	PASS
POLD1	5424	broad.mit.edu	37	19	50902196	50902196	+	Missense_Mutation	SNP	C	T	T	rs3218772	byFrequency	TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr19:50902196C>T	uc002psb.3	+	2	144	c.88C>T	c.(88-90)CGG>TGG	p.R30W	POLD1_uc002psc.3_Missense_Mutation_p.R30W|POLD1_uc010enx.2_RNA|POLD1_uc010eny.2_Missense_Mutation_p.R30W	NM_002691	NP_002682	P28340	DPOD1_HUMAN	DNA-directed DNA polymerase delta 1	30					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|DNA synthesis involved in DNA repair|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|response to UV|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	delta DNA polymerase complex|nucleoplasm|nucleotide-excision repair complex	3'-5'-exodeoxyribonuclease activity|chromatin binding|DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding|protein binding			upper_aerodigestive_tract(1)|central_nervous_system(1)	2		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		TGATGCACCTCGGCCATCCCA	0.662								DNA_polymerases_(catalytic_subunits)					10	7	---	---	---	---	PASS
MORC3	23515	broad.mit.edu	37	21	37716975	37716975	+	Silent	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr21:37716975C>A	uc002yvi.2	+	7	931	c.855C>A	c.(853-855)ATC>ATA	p.I285I		NM_015358	NP_056173	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	285					cell aging|maintenance of protein location in nucleus|negative regulation of fibroblast proliferation|peptidyl-serine phosphorylation|protein stabilization	aggresome|intermediate filament cytoskeleton|PML body	ATP binding|zinc ion binding			ovary(2)	2						TTGCCTACATCGAACGTGATG	0.383													3	135	---	---	---	---	PASS
ABCG1	9619	broad.mit.edu	37	21	43702403	43702403	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr21:43702403C>A	uc002zaq.2	+	6	714	c.608C>A	c.(607-609)GCG>GAG	p.A203E	ABCG1_uc002zan.2_Missense_Mutation_p.A205E|ABCG1_uc002zam.2_Missense_Mutation_p.A181E|ABCG1_uc002zao.2_Missense_Mutation_p.A200E|ABCG1_uc002zap.2_Missense_Mutation_p.A203E|ABCG1_uc002zar.2_Missense_Mutation_p.A214E|ABCG1_uc011aev.1_Missense_Mutation_p.A214E	NM_004915	NP_004906	P45844	ABCG1_HUMAN	ATP-binding cassette sub-family G member 1	203	Cytoplasmic (Potential).|ABC transporter.				amyloid precursor protein catabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|detection of hormone stimulus|high-density lipoprotein particle remodeling|intracellular cholesterol transport|lipoprotein metabolic process|low-density lipoprotein particle remodeling|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|positive regulation of cholesterol biosynthetic process|regulation of cholesterol esterification|regulation of transcription, DNA-dependent|response to lipid|reverse cholesterol transport	endoplasmic reticulum membrane|external side of plasma membrane|Golgi membrane|recycling endosome	ADP binding|ATP binding|cholesterol transporter activity|glycoprotein transporter activity|phospholipid transporter activity|protein heterodimerization activity|protein homodimerization activity|sterol-transporting ATPase activity|toxin transporter activity			ovary(2)|central_nervous_system(1)	3					Adenosine triphosphate(DB00171)	ATACTGACAGCGCTGGGCTTG	0.637													5	80	---	---	---	---	PASS
PIWIL3	440822	broad.mit.edu	37	22	25144942	25144942	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr22:25144942C>A	uc003abd.1	-	12	1798	c.1381G>T	c.(1381-1383)GAT>TAT	p.D461Y	PIWIL3_uc011ajx.1_Missense_Mutation_p.D352Y|PIWIL3_uc011ajy.1_Missense_Mutation_p.D352Y|PIWIL3_uc010gut.1_Missense_Mutation_p.D461Y	NM_001008496	NP_001008496	Q7Z3Z3	PIWL3_HUMAN	piwi-like 3	461					cell differentiation|gene silencing by RNA|meiosis|multicellular organismal development|regulation of translation|spermatogenesis	cytoplasm	RNA binding			ovary(3)|central_nervous_system(1)	4						AAATTGGTATCAAATTTCAAA	0.348													46	137	---	---	---	---	PASS
ASPHD2	57168	broad.mit.edu	37	22	26830386	26830386	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr22:26830386G>A	uc003acg.2	+	2	1202	c.805G>A	c.(805-807)GCG>ACG	p.A269T		NM_020437	NP_065170	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	269	Lumenal (Potential).				peptidyl-amino acid modification	integral to endoplasmic reticulum membrane	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|peptide-aspartate beta-dioxygenase activity			ovary(1)	1						TTTTGGGAACGCGTGCATCTC	0.547													51	206	---	---	---	---	PASS
TRIOBP	11078	broad.mit.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr22:38119902A>G	uc003atr.2	+	7	1610	c.1339A>G	c.(1339-1341)ACA>GCA	p.T447A	TRIOBP_uc003atu.2_Missense_Mutation_p.T275A|TRIOBP_uc003atq.1_Missense_Mutation_p.T447A|TRIOBP_uc003ats.1_Missense_Mutation_p.T275A	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	447					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)					CAGTAGAGCTACACGAGACAA	0.587													4	84	---	---	---	---	PASS
CCNB3	85417	broad.mit.edu	37	X	50054016	50054016	+	Silent	SNP	A	G	G			TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chrX:50054016A>G	uc004dox.3	+	6	3145	c.2847A>G	c.(2845-2847)TTA>TTG	p.L949L	CCNB3_uc004doy.2_Silent_p.L949L|CCNB3_uc004doz.2_Intron|CCNB3_uc010njq.2_Intron	NM_033031	NP_149020	Q8WWL7	CCNB3_HUMAN	cyclin B3 isoform 3	949					cell division|meiosis|regulation of cyclin-dependent protein kinase activity|regulation of G2/M transition of mitotic cell cycle	nucleus	protein kinase binding			ovary(4)|lung(3)|large_intestine(1)|pancreas(1)	9	Ovarian(276;0.236)					AGGAGCCATTAGCCTTACAAG	0.483													3	98	---	---	---	---	PASS
DAPK1	1612	broad.mit.edu	37	9	90321801	90321802	+	Frame_Shift_Ins	INS	-	G	G	rs56169226		TCGA-EJ-5522-01A-01D-1576-08	TCGA-EJ-5522-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	b4a89182-c17c-42a8-af9e-4fcc861e336c	9b4b6723-8e0e-4e98-a726-c023723e08b1	g.chr9:90321801_90321802insG	uc004apc.2	+	26	3953_3954	c.3815_3816insG	c.(3814-3816)ATGfs	p.M1272fs	DAPK1_uc004apd.2_Frame_Shift_Ins_p.M1272fs|DAPK1_uc011ltg.1_Frame_Shift_Ins_p.M1206fs|DAPK1_uc011lth.1_Frame_Shift_Ins_p.M1009fs|DAPK1_uc004apg.2_Frame_Shift_Ins_p.M249fs	NM_004938	NP_004929	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1272					apoptosis|induction of apoptosis by extracellular signals|intracellular protein kinase cascade	actin cytoskeleton|cytoplasm	ATP binding|calmodulin binding|protein serine/threonine kinase activity			ovary(1)|breast(1)	2						ACCAACACCATGGGGGGGTACA	0.584									Chronic_Lymphocytic_Leukemia_Familial_Clustering_of				126	28	---	---	---	---	
