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
ARHGEF16	27237	broad.mit.edu	37	1	3390011	3390011	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:3390011G>T	uc001akg.3	+	8	1478	c.1230G>T	c.(1228-1230)GCG>GCT	p.A410A	ARHGEF16_uc001aki.2_Silent_p.A122A|ARHGEF16_uc001akj.2_Silent_p.A122A|ARHGEF16_uc009vli.1_Silent_p.A114A|ARHGEF16_uc010nzh.1_Silent_p.A114A	NM_014448	NP_055263	Q5VV41	ARHGG_HUMAN	Rho guanine exchange factor 16	410	DH.|Required for RHOG activation and mediates interaction with EPHA2.				activation of Cdc42 GTPase activity|activation of Rac GTPase activity|apoptosis|cell chemotaxis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of establishment of protein localization in plasma membrane|small GTPase mediated signal transduction	cytosol	PDZ domain binding|receptor tyrosine kinase binding|Rho GTPase binding|Rho guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(77;0.00276)|all_epithelial(69;0.00102)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.101)	all_epithelial(116;7.14e-21)|all_lung(118;2.24e-08)|Lung NSC(185;3.55e-06)|Breast(487;0.000765)|Renal(390;0.00121)|Hepatocellular(190;0.0046)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.211)		Epithelial(90;8.62e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.62e-22)|GBM - Glioblastoma multiforme(42;2.49e-12)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.000681)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		GGCGGCCGGCGTGCGGGGGCC	0.662													6	30	---	---	---	---	PASS
CASZ1	54897	broad.mit.edu	37	1	10715789	10715789	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:10715789G>A	uc001aro.2	-	9	1902	c.1582C>T	c.(1582-1584)CGT>TGT	p.R528C	CASZ1_uc001arp.1_Missense_Mutation_p.R528C|CASZ1_uc009vmx.2_Missense_Mutation_p.R552C	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	castor homolog 1, zinc finger isoform a	528					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			skin(1)	1	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GGGCTGAAACGCATGAAGCCG	0.607													6	46	---	---	---	---	PASS
FBLIM1	54751	broad.mit.edu	37	1	16101265	16101265	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:16101265G>T	uc001axd.1	+	8	1307	c.864G>T	c.(862-864)GAG>GAT	p.E288D	FBLIM1_uc001axe.1_Missense_Mutation_p.E288D|FBLIM1_uc001axf.2_RNA|FBLIM1_uc001axg.1_Missense_Mutation_p.E288D|FBLIM1_uc001axh.1_Missense_Mutation_p.E191D|FBLIM1_uc001axi.1_Missense_Mutation_p.E191D	NM_017556	NP_060026	Q8WUP2	FBLI1_HUMAN	filamin-binding LIM protein-1 isoform a	288	PLEKHC1-binding.|LIM zinc-binding 2.				cell adhesion|cell junction assembly|regulation of cell shape	cell cortex|cytoskeleton|cytosol|focal adhesion|intracellular membrane-bounded organelle	zinc ion binding			skin(1)	1		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		GCCAGAACGAGGTGTACTGCC	0.632													8	108	---	---	---	---	PASS
NBPF1	55672	broad.mit.edu	37	1	16907280	16907280	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:16907280G>T	uc009vos.1	-	16	2439	c.1551C>A	c.(1549-1551)TCC>TCA	p.S517S	NBPF1_uc009vot.1_Intron|NBPF1_uc001ayz.1_Intron|NBPF1_uc010oce.1_Silent_p.S246S	NM_017940	NP_060410	Q3BBV0	NBPF1_HUMAN	hypothetical protein LOC55672	517	NBPF 2.					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)		CATCATGAGAGGATTCTCTGT	0.453													15	740	---	---	---	---	PASS
PADI1	29943	broad.mit.edu	37	1	17566199	17566199	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:17566199G>T	uc001bah.1	+	14	1645	c.1553G>T	c.(1552-1554)GGG>GTG	p.G518V	PADI1_uc010oco.1_Missense_Mutation_p.G75V|PADI1_uc010ocp.1_Missense_Mutation_p.G75V|PADI1_uc010ocq.1_5'UTR|PADI1_uc009vpb.1_5'UTR	NM_013358	NP_037490	Q9ULC6	PADI1_HUMAN	peptidylarginine deiminase type I	518					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	CTTCTTGCAGGGTTAAAACAC	0.522													6	62	---	---	---	---	PASS
ACTL8	81569	broad.mit.edu	37	1	18152822	18152822	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:18152822C>A	uc001bat.2	+	3	1125	c.909C>A	c.(907-909)CTC>CTA	p.L303L		NM_030812	NP_110439	Q9H568	ACTL8_HUMAN	actin-like 8	303						cytoplasm|cytoskeleton				ovary(4)	4		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00186)|all_lung(284;0.0054)|Lung NSC(340;0.00566)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;6.43e-06)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.00652)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)		GCAACACCCTCTATCCCGGGT	0.612											OREG0013157	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	51	---	---	---	---	PASS
KIF17	57576	broad.mit.edu	37	1	21009181	21009181	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:21009181C>T	uc001bdr.3	-	11	2546	c.2428G>A	c.(2428-2430)GCC>ACC	p.A810T	KIF17_uc001bdp.3_Missense_Mutation_p.A88T|KIF17_uc001bdq.3_Missense_Mutation_p.A88T|KIF17_uc009vpx.2_Missense_Mutation_p.A180T|KIF17_uc001bds.3_Missense_Mutation_p.A810T	NM_020816	NP_065867	Q9P2E2	KIF17_HUMAN	kinesin family member 17 isoform a	810	Potential.				microtubule-based movement|protein transport	cytoplasm|microtubule	ATP binding			ovary(3)|skin(1)	4		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TTGCTCTTGGCCCGCACTTCC	0.637													6	79	---	---	---	---	PASS
USP48	84196	broad.mit.edu	37	1	22079485	22079485	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:22079485C>A	uc001bfb.2	-	4	778	c.540G>T	c.(538-540)CAG>CAT	p.Q180H	USP48_uc010odq.1_Missense_Mutation_p.Q180H|USP48_uc009vqc.2_Missense_Mutation_p.Q180H|USP48_uc001bfc.2_Missense_Mutation_p.Q180H|USP48_uc001bfe.1_Missense_Mutation_p.Q180H|USP48_uc001bff.2_Missense_Mutation_p.Q180H	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	180					ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)		CAGTTCTTACCTGCTGTTGTC	0.353													9	24	---	---	---	---	PASS
S100PBP	64766	broad.mit.edu	37	1	33291859	33291859	+	Silent	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:33291859C>T	uc001bvz.2	+	3	436	c.159C>T	c.(157-159)TAC>TAT	p.Y53Y	S100PBP_uc001bwa.1_Silent_p.Y53Y|S100PBP_uc001bwb.1_Silent_p.Y53Y|S100PBP_uc001bwc.2_Silent_p.Y53Y|S100PBP_uc001bwd.2_RNA	NM_022753	NP_073590	Q96BU1	S1PBP_HUMAN	S100P binding protein isoform a	53						nucleus	calcium-dependent protein binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				ATGTAAATTACACAGAGGAAG	0.473													7	58	---	---	---	---	PASS
THRAP3	9967	broad.mit.edu	37	1	36755023	36755023	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:36755023C>A	uc001cae.3	+	5	1627	c.1403C>A	c.(1402-1404)TCA>TAA	p.S468*	THRAP3_uc001caf.3_Nonsense_Mutation_p.S468*|THRAP3_uc001cag.1_Nonsense_Mutation_p.S468*	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	468					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			ovary(5)|lung(3)|breast(1)	9		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GAGGAGAAGTCAGGCAAATGG	0.453			T	USP6	aneurysmal bone cysts								14	61	---	---	---	---	PASS
MACF1	23499	broad.mit.edu	37	1	39801599	39801599	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:39801599C>A	uc010oiu.1	+	1	4790	c.4659C>A	c.(4657-4659)CAC>CAA	p.H1553Q	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc001cdb.1_Intron	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	3118					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AAGGATTGCACTACCAGGAAT	0.468													4	72	---	---	---	---	PASS
HIVEP3	59269	broad.mit.edu	37	1	42048104	42048104	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:42048104C>G	uc001cgz.3	-	4	3578	c.2365G>C	c.(2365-2367)GAG>CAG	p.E789Q	HIVEP3_uc001cha.3_Missense_Mutation_p.E789Q|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	789	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN (By similarity).				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GTTCTCCTCTCCTTCCCTGAT	0.542													11	43	---	---	---	---	PASS
TIE1	7075	broad.mit.edu	37	1	43782880	43782880	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:43782880C>T	uc001ciu.2	+	15	2499	c.2420C>T	c.(2419-2421)ACC>ATC	p.T807I	TIE1_uc010oke.1_Missense_Mutation_p.T762I|TIE1_uc009vwq.2_Missense_Mutation_p.T763I|TIE1_uc010okg.1_Missense_Mutation_p.T452I	NM_005424	NP_005415	P35590	TIE1_HUMAN	tyrosine kinase with immunoglobulin-like and	807	Cytoplasmic (Potential).				mesoderm development	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity			lung(3)|stomach(1)|salivary_gland(1)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GGCGAGGAGACCATCCTGCAG	0.607													5	48	---	---	---	---	PASS
STIL	6491	broad.mit.edu	37	1	47717149	47717149	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:47717149G>T	uc001crc.1	-	17	3678	c.3523C>A	c.(3523-3525)CAT>AAT	p.H1175N	TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Missense_Mutation_p.H1129N|STIL_uc010omo.1_Missense_Mutation_p.H1158N|STIL_uc001crd.1_Missense_Mutation_p.H1176N|STIL_uc001cre.1_Missense_Mutation_p.H1175N	NM_003035	NP_003026	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 2	1175					cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				ATTATTTCATGGTCATTCTTA	0.383													6	91	---	---	---	---	PASS
LRP8	7804	broad.mit.edu	37	1	53728158	53728158	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:53728158C>A	uc001cvi.1	-	11	1876	c.1734G>T	c.(1732-1734)CTG>CTT	p.L578L	LRP8_uc001cvh.1_Silent_p.L131L|LRP8_uc001cvk.1_Silent_p.L408L|LRP8_uc001cvj.1_Silent_p.L578L|LRP8_uc001cvl.1_Silent_p.L449L|LRP8_uc001cvm.1_Silent_p.L163L	NM_004631	NP_004622	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein	578	LDL-receptor class B 3.|Extracellular (Potential).				cytokine-mediated signaling pathway|endocytosis|lipid metabolic process|platelet activation|proteolysis	caveola	calcium ion binding|very-low-density lipoprotein particle receptor activity				0						TGTCTGACACCAGTGTTTGCC	0.512													10	236	---	---	---	---	PASS
C8B	732	broad.mit.edu	37	1	57409428	57409428	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:57409428A>T	uc001cyp.2	-	8	1242	c.1175T>A	c.(1174-1176)GTC>GAC	p.V392D	C8B_uc010oon.1_Missense_Mutation_p.V330D|C8B_uc010ooo.1_Missense_Mutation_p.V340D	NM_000066	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	392	MACPF.				complement activation, alternative pathway|complement activation, classical pathway|cytolysis	membrane attack complex				central_nervous_system(2)|large_intestine(1)|ovary(1)	4						ACTGACGTAGACCTCTTCAAT	0.408													13	85	---	---	---	---	PASS
PHGDH	26227	broad.mit.edu	37	1	120263815	120263815	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:120263815G>C	uc001ehz.2	+	2	388	c.161G>C	c.(160-162)CGC>CCC	p.R54P	PHGDH_uc009whl.2_5'UTR|PHGDH_uc009whm.2_5'UTR|PHGDH_uc001eia.2_Missense_Mutation_p.R54P|PHGDH_uc009whn.2_Missense_Mutation_p.R54P|PHGDH_uc001eib.2_Missense_Mutation_p.R20P	NM_006623	NP_006614	O43175	SERA_HUMAN	phosphoglycerate dehydrogenase	54					brain development|L-serine biosynthetic process		electron carrier activity|NAD binding|phosphoglycerate dehydrogenase activity			ovary(1)	1	all_cancers(5;1.18e-09)|all_epithelial(5;2.16e-10)|Melanoma(3;1.93e-05)|all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0347)		Lung(183;0.0111)|LUSC - Lung squamous cell carcinoma(189;0.0593)	NADH(DB00157)	CTTATTGTTCGCTCTGCCACC	0.522													22	81	---	---	---	---	PASS
ANKRD35	148741	broad.mit.edu	37	1	145561622	145561622	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:145561622G>T	uc001eob.1	+	10	1418	c.1310G>T	c.(1309-1311)AGG>ATG	p.R437M	NBPF10_uc001emp.3_Intron|ANKRD35_uc010oyx.1_Missense_Mutation_p.R280M	NM_144698	NP_653299	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	437										ovary(4)|skin(1)	5	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GAGACCATCAGGAAAGCCACA	0.572													6	85	---	---	---	---	PASS
RPTN	126638	broad.mit.edu	37	1	152128552	152128552	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:152128552G>T	uc001ezs.1	-	3	1088	c.1023C>A	c.(1021-1023)TCC>TCA	p.S341S		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	341	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0						GACCATAGTGGGAACTCTGAC	0.498													12	476	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152285911	152285911	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:152285911C>G	uc001ezu.1	-	3	1487	c.1451G>C	c.(1450-1452)CGG>CCG	p.R484P	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	484	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGTCCCGGTCCGTCCATGGGC	0.607									Ichthyosis				37	201	---	---	---	---	PASS
LCE3D	84648	broad.mit.edu	37	1	152552178	152552178	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:152552178C>A	uc001fab.2	-	2	292	c.235G>T	c.(235-237)GGC>TGC	p.G79C		NM_032563	NP_115952	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	79					keratinization						0	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		GAGCCCCCGCCTTGCTGACCA	0.647													9	49	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155448861	155448861	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:155448861C>A	uc009wqq.2	-	3	4280	c.3800G>T	c.(3799-3801)AGG>ATG	p.R1267M	ASH1L_uc001fkt.2_Missense_Mutation_p.R1267M|ASH1L_uc009wqr.1_Missense_Mutation_p.R1267M	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	1267					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TCGTTTCTGCCTTTTCATCTT	0.408													27	108	---	---	---	---	PASS
KIRREL	55243	broad.mit.edu	37	1	158057651	158057651	+	Splice_Site	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:158057651G>C	uc001frn.3	+	6	1171	c.767_splice	c.e6+1	p.R256_splice	KIRREL_uc010pib.1_Splice_Site_p.R156_splice|KIRREL_uc009wsq.2_Splice_Site_p.R92_splice|KIRREL_uc001fro.3_Splice_Site_p.R54_splice	NM_018240	NP_060710	Q96J84	KIRR1_HUMAN	kin of IRRE like precursor							integral to membrane				ovary(1)	1	all_hematologic(112;0.0378)					TGGGCTACAGGTGAGGGGGTC	0.587											OREG0013906	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	23	---	---	---	---	PASS
MNDA	4332	broad.mit.edu	37	1	158815425	158815425	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:158815425C>T	uc001fsz.1	+	5	819	c.619C>T	c.(619-621)CCC>TCC	p.P207S		NM_002432	NP_002423	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	207	HIN-200.				B cell receptor signaling pathway|cellular defense response|negative regulation of B cell proliferation|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			ovary(2)|skin(2)	4	all_hematologic(112;0.0378)					AAGAAATGTTCCCCAAAACGA	0.443													6	40	---	---	---	---	PASS
MYOC	4653	broad.mit.edu	37	1	171621186	171621186	+	Missense_Mutation	SNP	C	A	A	rs144579767		TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:171621186C>A	uc001ghu.2	-	1	588	c.566G>T	c.(565-567)CGA>CTA	p.R189L	MYOC_uc010pmk.1_Missense_Mutation_p.R131L	NM_000261	NP_000252	Q99972	MYOC_HUMAN	myocilin precursor	189			R -> Q.		anatomical structure morphogenesis	cilium|extracellular space|rough endoplasmic reticulum	structural molecule activity			lung(1)	1	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					AGCAGTGTCTCGGGTCTGGGG	0.567													52	164	---	---	---	---	PASS
MRPS14	63931	broad.mit.edu	37	1	174987652	174987652	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:174987652G>T	uc001gkk.2	-	2	123	c.106C>A	c.(106-108)CGC>AGC	p.R36S	MRPS14_uc009wwr.2_Missense_Mutation_p.R21S	NM_022100	NP_071383	O60783	RT14_HUMAN	mitochondrial ribosomal protein S14	36					translation	mitochondrial ribosome	protein binding|structural constituent of ribosome				0						TTCACATCGCGCCACATTCTC	0.443													4	61	---	---	---	---	PASS
TNN	63923	broad.mit.edu	37	1	175053048	175053048	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:175053048C>G	uc001gkl.1	+	5	1324	c.1211C>G	c.(1210-1212)CCC>CGC	p.P404R	TNN_uc010pmx.1_Missense_Mutation_p.P404R	NM_022093	NP_071376	Q9UQP3	TENN_HUMAN	tenascin N precursor	404	Fibronectin type-III 2.				cell growth|cell migration|signal transduction	extracellular space|proteinaceous extracellular matrix				large_intestine(5)|ovary(3)|central_nervous_system(1)	9		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		AGCAGTGACCCCAAGAGCCGA	0.542													9	37	---	---	---	---	PASS
ASTN1	460	broad.mit.edu	37	1	177001635	177001635	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:177001635G>T	uc001glc.2	-	3	1034	c.822C>A	c.(820-822)TCC>TCA	p.S274S	ASTN1_uc001glb.1_Silent_p.S274S|ASTN1_uc001gld.1_Silent_p.S274S|ASTN1_uc009wwx.1_Silent_p.S274S|ASTN1_uc001gle.3_RNA	NM_004319	NP_004310	O14525	ASTN1_HUMAN	astrotactin isoform 1	274					cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15						AGCCCTGCAGGGAGTCGAGGG	0.587													6	75	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186147831	186147831	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:186147831C>A	uc001grq.1	+	104	16456	c.16227C>A	c.(16225-16227)TCC>TCA	p.S5409S	HMCN1_uc001grs.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	5409					response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						CATCTCTCTCCAGGACTAGAA	0.438													6	100	---	---	---	---	PASS
CFHR4	10877	broad.mit.edu	37	1	196871656	196871656	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:196871656G>T	uc001gto.2	+	2	236	c.167G>T	c.(166-168)TGT>TTT	p.C56F	CFHR4_uc009wyy.2_Missense_Mutation_p.C55F|CFHR4_uc001gtp.2_Missense_Mutation_p.C56F	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor	56	Sushi 1.					extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3						TCCTATTACTGTGATCAAAAT	0.403													4	43	---	---	---	---	PASS
PIK3C2B	5287	broad.mit.edu	37	1	204433648	204433648	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:204433648C>A	uc001haw.2	-	5	1598	c.1119G>T	c.(1117-1119)GGG>GGT	p.G373G	PIK3C2B_uc010pqv.1_Silent_p.G373G|PIK3C2B_uc001hax.1_Silent_p.G373G|PIK3C2B_uc009xbd.1_RNA	NM_002646	NP_002637	O00750	P3C2B_HUMAN	phosphoinositide-3-kinase, class 2 beta	373					cell communication|phosphatidylinositol-mediated signaling	endoplasmic reticulum|microsome|nucleus|phosphatidylinositol 3-kinase complex|plasma membrane	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity|protein binding			lung(2)|breast(2)|stomach(1)|prostate(1)|central_nervous_system(1)	7	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TGACCTCATCCCCGAGGTGCT	0.527													16	77	---	---	---	---	PASS
CR2	1380	broad.mit.edu	37	1	207643415	207643415	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:207643415C>A	uc001hfw.2	+	6	1287	c.1193C>A	c.(1192-1194)ACA>AAA	p.T398K	CR2_uc001hfv.2_Missense_Mutation_p.T398K|CR2_uc009xch.2_Missense_Mutation_p.T398K|CR2_uc009xci.1_5'Flank	NM_001877	NP_001868	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus)	398	Sushi 6.|Extracellular (Potential).				complement activation, classical pathway|innate immune response	integral to membrane|plasma membrane	complement receptor activity|protein homodimerization activity			upper_aerodigestive_tract(3)|skin(3)|urinary_tract(1)|ovary(1)	8						GCCCAAGGCACATGGGAGCCA	0.458													8	28	---	---	---	---	PASS
TATDN3	128387	broad.mit.edu	37	1	212988413	212988413	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:212988413G>T	uc001hjo.2	+	10	834	c.740G>T	c.(739-741)GGG>GTG	p.G247V	TATDN3_uc010ptj.1_3'UTR|TATDN3_uc010ptk.1_Missense_Mutation_p.G254V|TATDN3_uc001hjp.2_Missense_Mutation_p.G246V|TATDN3_uc010ptl.1_Missense_Mutation_p.G226V|TATDN3_uc010ptm.1_Missense_Mutation_p.G194V	NM_001042552	NP_001036017	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3 isoform 1	247						nucleus	endodeoxyribonuclease activity, producing 5'-phosphomonoesters|metal ion binding				0				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)		CAGGTGAAAGGGATCTCAGTG	0.423													7	98	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237666802	237666802	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:237666802C>A	uc001hyl.1	+	22	2730	c.2610C>A	c.(2608-2610)AGC>AGA	p.S870R		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	870	Cytoplasmic (By similarity).|1.|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGGATACCAGCCAGGTACCAA	0.418													18	66	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237670108	237670108	+	Silent	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:237670108T>C	uc001hyl.1	+	23	2832	c.2712T>C	c.(2710-2712)TAT>TAC	p.Y904Y		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	904	Cytoplasmic (By similarity).|1.|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GCTGGCAGTATGGTCCGGTAT	0.373													14	48	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237813369	237813369	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:237813369A>T	uc001hyl.1	+	50	7825	c.7705A>T	c.(7705-7707)ATA>TTA	p.I2569L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2569	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GCGGGATTCCATAGAAGTTTG	0.398													16	86	---	---	---	---	PASS
OR2G3	81469	broad.mit.edu	37	1	247768907	247768907	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:247768907G>T	uc010pyz.1	+	1	20	c.20G>T	c.(19-21)AGT>ATT	p.S7I		NM_001001914	NP_001001914	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G,	7	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			GGCAATGAGAGTTCCCTAATG	0.463													5	27	---	---	---	---	PASS
TRIM58	25893	broad.mit.edu	37	1	248039414	248039414	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr1:248039414G>T	uc001ido.2	+	6	1132	c.1084G>T	c.(1084-1086)GTC>TTC	p.V362F	OR2W3_uc001idp.1_Intron	NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	362	B30.2/SPRY.					intracellular	zinc ion binding			skin(3)|ovary(1)|pancreas(1)|lung(1)|central_nervous_system(1)	7	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGGTTTAGGGGTCTGTCAAGA	0.552													6	26	---	---	---	---	PASS
YIPF4	84272	broad.mit.edu	37	2	32526505	32526505	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:32526505G>C	uc002rok.2	+	5	805	c.538G>C	c.(538-540)GTA>CTA	p.V180L		NM_032312	NP_115688	Q9BSR8	YIPF4_HUMAN	Yip1 domain family, member 4	180	Helical; (Potential).					endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)					TCCTCTCATTGTAATAGCCCC	0.318													18	57	---	---	---	---	PASS
TTC27	55622	broad.mit.edu	37	2	32855589	32855589	+	Splice_Site	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:32855589G>T	uc002rom.2	+	2	320	c.89_splice	c.e2-1	p.E30_splice	TTC27_uc010ymx.1_Splice_Site	NM_017735	NP_060205	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27								protein binding			central_nervous_system(1)	1						TTATATTACAGAGAGTGGATC	0.303													8	36	---	---	---	---	PASS
C2orf61	285051	broad.mit.edu	37	2	47378423	47378423	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:47378423G>C	uc002rvs.2	-	3	500	c.373C>G	c.(373-375)CCC>GCC	p.P125A	C2orf61_uc010fbd.2_RNA|C2orf61_uc010yog.1_Missense_Mutation_p.P125A	NM_173649	NP_775920	Q8N801	CB061_HUMAN	hypothetical protein LOC285051 isoform 2	125								p.0?(2)			0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			AGTGTGCTGGGGCTTGGCCGT	0.453													8	57	---	---	---	---	PASS
LRRTM1	347730	broad.mit.edu	37	2	80529786	80529786	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:80529786G>A	uc002sok.1	-	2	1429	c.1159C>T	c.(1159-1161)CCT>TCT	p.P387S	CTNNA2_uc010yse.1_Intron|CTNNA2_uc010ysf.1_Intron|CTNNA2_uc010ysg.1_Intron|CTNNA2_uc010ysh.1_Intron|CTNNA2_uc010ysi.1_5'Flank|LRRTM1_uc002soj.3_RNA	NM_178839	NP_849161	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	387	Lumenal (Potential).					axon|endoplasmic reticulum membrane|growth cone|integral to membrane				ovary(3)|upper_aerodigestive_tract(1)|skin(1)	5						GAGCTGGCAGGGGGCCCCAGA	0.726										HNSCC(69;0.2)			7	11	---	---	---	---	PASS
EIF2AK3	9451	broad.mit.edu	37	2	88874860	88874860	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:88874860G>T	uc002stc.3	-	13	2343	c.2141C>A	c.(2140-2142)CCT>CAT	p.P714H		NM_004836	NP_004827	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha	714	Cytoplasmic (Potential).|Protein kinase.				activation of caspase activity|bone mineralization|calcium-mediated signaling|chondrocyte development|endocrine pancreas development|endoplasmic reticulum organization|endoplasmic reticulum unfolded protein response|ER overload response|insulin secretion|insulin-like growth factor receptor signaling pathway|negative regulation of myelination|negative regulation of translational initiation in response to stress|protein autophosphorylation|protein homooligomerization	endoplasmic reticulum membrane|integral to membrane	ATP binding|eukaryotic translation initiation factor 2alpha kinase activity|identical protein binding			ovary(3)	3						TTGTGGTGAAGGAGCTATGAT	0.453													7	117	---	---	---	---	PASS
BUB1	699	broad.mit.edu	37	2	111398613	111398613	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:111398613G>T	uc002tgc.2	-	23	3065	c.2953C>A	c.(2953-2955)CAG>AAG	p.Q985K	BUB1_uc010yxh.1_Missense_Mutation_p.Q965K|BUB1_uc010fkb.2_Missense_Mutation_p.Q928K	NM_004336	NP_004327	O43683	BUB1_HUMAN	budding uninhibited by benzimidazoles 1	985	Protein kinase.				apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		TTTTATACCTGGTAGTTCCAT	0.368													5	49	---	---	---	---	PASS
INHBB	3625	broad.mit.edu	37	2	121106938	121106938	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:121106938T>G	uc002tmn.2	+	2	758	c.712T>G	c.(712-714)TTG>GTG	p.L238V		NM_002193	NP_002184	P09529	INHBB_HUMAN	inhibin beta B subunit preproprotein	238					activin receptor signaling pathway|cellular response to insulin stimulus|cellular response to starvation|defense response|fat cell differentiation|growth|negative regulation of follicle-stimulating hormone secretion|negative regulation of hepatocyte growth factor biosynthetic process|negative regulation of insulin secretion|ovarian follicle development|positive regulation of follicle-stimulating hormone secretion|positive regulation of ovulation	extracellular region|perinuclear region of cytoplasm	cytokine activity|growth factor activity|hormone activity|host cell surface receptor binding|protein homodimerization activity			pancreas(2)|skin(1)	3		Prostate(154;0.122)				CATCCAGGCCTTGTTTGAGCG	0.647													7	82	---	---	---	---	PASS
GLI2	2736	broad.mit.edu	37	2	121742113	121742113	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:121742113C>A	uc010flp.2	+	11	1780	c.1750C>A	c.(1750-1752)CAT>AAT	p.H584N	GLI2_uc002tmq.1_Missense_Mutation_p.H256N|GLI2_uc002tmr.1_Missense_Mutation_p.H239N|GLI2_uc002tmt.3_Missense_Mutation_p.H256N|GLI2_uc002tmu.3_Missense_Mutation_p.H239N|GLI2_uc002tmw.1_Missense_Mutation_p.H567N	NM_005270	NP_005261	P10070	GLI2_HUMAN	GLI-Kruppel family member GLI2	584	C2H2-type 5.				axon guidance|branching morphogenesis of a tube|cell proliferation|cerebellar cortex morphogenesis|developmental growth|embryonic digestive tract development|epidermal cell differentiation|floor plate formation|heart development|hindgut morphogenesis|kidney development|lung development|negative regulation of transcription from RNA polymerase II promoter|odontogenesis of dentine-containing tooth|osteoblast development|osteoblast differentiation|pituitary gland development|positive regulation of DNA replication|positive regulation of T cell differentiation in thymus|positive regulation of transcription from RNA polymerase II promoter|proximal/distal pattern formation|skeletal system development|smoothened signaling pathway involved in ventral spinal cord interneuron specification|spinal cord ventral commissure morphogenesis	nucleus|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|lung(2)|breast(1)|central_nervous_system(1)|pancreas(1)	13	Renal(3;0.0496)	Prostate(154;0.0623)				TCTCCGGAAGCATGTGAAAAC	0.572													20	199	---	---	---	---	PASS
GALNT13	114805	broad.mit.edu	37	2	155158018	155158018	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:155158018G>T	uc002tyr.3	+	9	1639	c.1072G>T	c.(1072-1074)GGT>TGT	p.G358C	GALNT13_uc002tyt.3_Missense_Mutation_p.G358C|GALNT13_uc010foc.1_Missense_Mutation_p.G177C|GALNT13_uc010fod.2_Missense_Mutation_p.G111C	NM_052917	NP_443149	Q8IUC8	GLT13_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	358	Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			ovary(2)|pancreas(2)|central_nervous_system(1)|skin(1)	6						TGGTGGCACTGGTCATGTCAT	0.438													7	85	---	---	---	---	PASS
GPD2	2820	broad.mit.edu	37	2	157425354	157425354	+	Silent	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:157425354C>T	uc002tzf.3	+	10	1543	c.1183C>T	c.(1183-1185)CTG>TTG	p.L395L	GPD2_uc010zch.1_Silent_p.L168L|GPD2_uc002tzd.3_Silent_p.L395L|GPD2_uc002tze.1_RNA	NM_001083112	NP_001076581	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2,	395					cellular lipid metabolic process	glycerol-3-phosphate dehydrogenase complex|mitochondrial inner membrane	calcium ion binding|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity			ovary(1)	1						AGGGGATGTCCTGGCAGCATG	0.398													8	34	---	---	---	---	PASS
XIRP2	129446	broad.mit.edu	37	2	168097247	168097247	+	Splice_Site	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:168097247G>A	uc002udx.2	+	6	1060	c.1042_splice	c.e6+1	p.V348_splice	XIRP2_uc010fpn.2_Splice_Site_p.V381_splice|XIRP2_uc010fpo.2_Splice_Site_p.V348_splice|XIRP2_uc010fpp.2_Splice_Site_p.V348_splice|XIRP2_uc002udy.2_Splice_Site_p.V173_splice|XIRP2_uc010fpq.2_Splice_Site_p.V126_splice|XIRP2_uc010fpr.2_Splice_Site_p.V126_splice	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1						actin cytoskeleton organization	cell junction	actin binding			skin(7)|ovary(6)|pancreas(1)	14						CAAGAAACTGGTAAGAGTCTG	0.373													5	48	---	---	---	---	PASS
LRP2	4036	broad.mit.edu	37	2	170030452	170030452	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:170030452G>T	uc002ues.2	-	56	11204	c.10991C>A	c.(10990-10992)TCG>TAG	p.S3664*		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3664	LDL-receptor class A 29.|Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	GGGCTCATCCGAGTGGTCTCC	0.577													5	69	---	---	---	---	PASS
HJURP	55355	broad.mit.edu	37	2	234762542	234762542	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:234762542G>C	uc002vvg.2	-	2	198	c.132C>G	c.(130-132)TTC>TTG	p.F44L	HJURP_uc010znd.1_Missense_Mutation_p.F37L|HJURP_uc010zne.1_Missense_Mutation_p.F37L	NM_018410	NP_060880	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	44					cell cycle|CenH3-containing nucleosome assembly at centromere|centromeric core chromatin assembly|chromosome segregation|regulation of DNA binding|regulation of protein complex assembly	condensed chromosome kinetochore|cytoplasm|nucleolus|nucleoplasm	DNA binding|histone binding			ovary(1)	1		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		GGGTGTCCTCGAAGGGCTGGT	0.642													4	69	---	---	---	---	PASS
FARP2	9855	broad.mit.edu	37	2	242373648	242373648	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr2:242373648G>T	uc002wbi.1	+	10	1060	c.943G>T	c.(943-945)GAG>TAG	p.E315*	FARP2_uc010zoq.1_Nonsense_Mutation_p.E315*|FARP2_uc010zor.1_Nonsense_Mutation_p.E315*	NM_014808	NP_055623	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	315	FERM.				axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		GATTTGTGTGGAGTATCACAC	0.428													6	74	---	---	---	---	PASS
EDEM1	9695	broad.mit.edu	37	3	5249922	5249922	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:5249922G>T	uc003bqi.2	+	8	1615	c.1483G>T	c.(1483-1485)GTG>TTG	p.V495L	EDEM1_uc011asz.1_Missense_Mutation_p.V273L|EDEM1_uc003bqh.2_Missense_Mutation_p.V495L	NM_014674	NP_055489	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like	495	Lumenal (Potential).				ER-associated protein catabolic process|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|response to unfolded protein	integral to endoplasmic reticulum membrane	calcium ion binding|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity|misfolded protein binding			ovary(2)|breast(1)	3				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		ACCAGAGTTAGTGGAATCCAC	0.463													17	37	---	---	---	---	PASS
SH3BP5	9467	broad.mit.edu	37	3	15301308	15301308	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:15301308G>T	uc003bzp.1	-	6	818	c.629C>A	c.(628-630)CCT>CAT	p.P210H	SH3BP5_uc010hem.1_Intron|SH3BP5_uc003bzq.1_Missense_Mutation_p.P53H|SH3BP5_uc003bzr.1_Missense_Mutation_p.P53H|uc003bzo.1_RNA	NM_004844	NP_004835	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	210					intracellular signal transduction	mitochondrion	protein kinase inhibitor activity|SH3 domain binding				0						TTCAAAATAAGGCCTGCAGAA	0.448													9	164	---	---	---	---	PASS
SCN10A	6336	broad.mit.edu	37	3	38805039	38805039	+	Silent	SNP	T	G	G	rs150977149	byFrequency	TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:38805039T>G	uc003ciq.2	-	5	648	c.648A>C	c.(646-648)ACA>ACC	p.T216T		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	216	I.|Helical; Voltage-sensor; Name=S4 of repeat I; (Potential).				sensory perception	voltage-gated sodium channel complex				ovary(5)|skin(3)|large_intestine(1)|kidney(1)	10				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	GAACTCTGAATGTCCGCAGGC	0.403													11	54	---	---	---	---	PASS
CELSR3	1951	broad.mit.edu	37	3	48664368	48664368	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:48664368T>C	uc003cuf.1	-	53	12172	c.12172A>G	c.(12172-12174)ATC>GTC	p.I4058V	SLC26A6_uc003cug.2_Missense_Mutation_p.I651V|SLC26A6_uc003cuh.2_Missense_Mutation_p.I672V|SLC26A6_uc010hke.2_Missense_Mutation_p.I504V|SLC26A6_uc003cuk.2_Missense_Mutation_p.I564V|SLC26A6_uc003cui.2_Missense_Mutation_p.I671V|SLC26A6_uc003cuj.2_Missense_Mutation_p.I653V|SLC26A6_uc011bbp.1_Missense_Mutation_p.I636V	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	Error:Variant_position_missing_in_Q9NYQ7_after_alignment					homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AGGTCCAGGATGAGGCTGTGG	0.597													10	50	---	---	---	---	PASS
IQCF2	389123	broad.mit.edu	37	3	51895936	51895936	+	Silent	SNP	A	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:51895936A>C	uc003dbt.1	+	2	119	c.81A>C	c.(79-81)ACA>ACC	p.T27T	IQCF1_uc003dbq.3_Intron|IQCF2_uc003dbu.1_RNA	NM_203424	NP_982248	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	27											0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		AATGGAAGACATTGCAGAAGA	0.328													10	43	---	---	---	---	PASS
GNL3	26354	broad.mit.edu	37	3	52724612	52724612	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:52724612G>T	uc003dfd.2	+	7	719	c.546G>T	c.(544-546)CTG>CTT	p.L182L	GNL3_uc011beh.1_RNA|GNL3_uc003dfe.2_Silent_p.L170L|GNL3_uc003dff.2_Silent_p.L170L|SNORD19B_uc010hml.1_5'Flank|SNORD69_uc003dfh.1_5'Flank	NM_014366	NP_055181	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3	182					regulation of cell proliferation	nucleolus	GTP binding|protein binding				0				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		TATCAGATCTGGTACCAAAGG	0.254													8	284	---	---	---	---	PASS
CACNA2D3	55799	broad.mit.edu	37	3	54905622	54905622	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:54905622G>T	uc003dhf.2	+	18	1731	c.1683G>T	c.(1681-1683)GAG>GAT	p.E561D	CACNA2D3_uc011beu.1_RNA|CACNA2D3_uc003dhg.1_Missense_Mutation_p.E467D|CACNA2D3_uc003dhh.1_RNA|CACNA2D3_uc010hmv.1_Missense_Mutation_p.E295D	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha	561	Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)		ACCTCTCTGAGGTGGAGTGGG	0.473													6	86	---	---	---	---	PASS
C3orf63	23272	broad.mit.edu	37	3	56661628	56661628	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:56661628G>T	uc003did.3	-	19	3930	c.3829C>A	c.(3829-3831)CCA>ACA	p.P1277T	C3orf63_uc003dib.3_Missense_Mutation_p.P396T|C3orf63_uc003dic.3_Missense_Mutation_p.P901T|C3orf63_uc003die.3_Missense_Mutation_p.P1338T	NM_015224	NP_056039	Q9UK61	CC063_HUMAN	retinoblastoma-associated protein 140 isoform b	1338										ovary(3)|kidney(1)|central_nervous_system(1)	5				KIRC - Kidney renal clear cell carcinoma(284;0.0126)|Kidney(284;0.0147)		ACAACCTCTGGGTTTAGAATT	0.353													5	49	---	---	---	---	PASS
DZIP3	9666	broad.mit.edu	37	3	108373066	108373066	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:108373066A>T	uc003dxd.2	+	19	2530	c.2108A>T	c.(2107-2109)AAA>ATA	p.K703I	DZIP3_uc003dxf.1_Missense_Mutation_p.K703I|DZIP3_uc011bhm.1_Missense_Mutation_p.K154I|DZIP3_uc003dxg.1_Missense_Mutation_p.K426I	NM_014648	NP_055463	Q86Y13	DZIP3_HUMAN	DAZ interacting protein 3, zinc finger	703					protein polyubiquitination	cytoplasm	polyubiquitin binding|RNA binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2						AGACTTATAAAAGATGATGCA	0.403													11	37	---	---	---	---	PASS
SLC35A5	55032	broad.mit.edu	37	3	112300035	112300035	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:112300035G>T	uc003dze.2	+	6	1316	c.1071G>T	c.(1069-1071)CTG>CTT	p.L357L		NM_017945	NP_060415	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	357	Helical; (Potential).					Golgi membrane|integral to membrane	nucleotide-sugar transmembrane transporter activity|sugar:hydrogen symporter activity			ovary(1)	1						GGCCCTCCCTGGAATTTTTCT	0.458													5	31	---	---	---	---	PASS
CCDC80	151887	broad.mit.edu	37	3	112357818	112357818	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:112357818T>A	uc003dzf.2	-	2	1153	c.935A>T	c.(934-936)AAA>ATA	p.K312I	CCDC80_uc011bhv.1_Missense_Mutation_p.K312I|CCDC80_uc003dzg.2_Missense_Mutation_p.K312I|CCDC80_uc003dzh.1_Missense_Mutation_p.K312I	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor	312										ovary(2)	2						TGGGTCCTCTTTCTTCTTCTC	0.607													21	62	---	---	---	---	PASS
POLQ	10721	broad.mit.edu	37	3	121206859	121206859	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:121206859G>T	uc003eee.3	-	16	5048	c.4919C>A	c.(4918-4920)CCA>CAA	p.P1640Q	POLQ_uc003eed.2_Missense_Mutation_p.P812Q	NM_199420	NP_955452	O75417	DPOLQ_HUMAN	DNA polymerase theta	1640					DNA repair|DNA replication	nucleoplasm	ATP binding|ATP-dependent helicase activity|damaged DNA binding|DNA-directed DNA polymerase activity|single-stranded DNA-dependent ATPase activity			ovary(4)|breast(3)|lung(2)|upper_aerodigestive_tract(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.0915)		TTGCAGTCCTGGACTTAGATC	0.348								DNA_polymerases_(catalytic_subunits)					6	90	---	---	---	---	PASS
SEMA5B	54437	broad.mit.edu	37	3	122641184	122641184	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:122641184C>A	uc003efz.1	-	11	1687	c.1383G>T	c.(1381-1383)GAG>GAT	p.E461D	SEMA5B_uc011bju.1_Missense_Mutation_p.E403D|SEMA5B_uc003ega.1_RNA|SEMA5B_uc003egb.1_Missense_Mutation_p.E461D|SEMA5B_uc010hro.1_Missense_Mutation_p.E403D|SEMA5B_uc010hrp.1_RNA	NM_001031702	NP_001026872	Q9P283	SEM5B_HUMAN	semaphorin 5B isoform 1	461	Extracellular (Potential).|Sema.				cell differentiation|nervous system development	integral to membrane	receptor activity			ovary(2)|breast(2)|pancreas(2)|central_nervous_system(1)	7				GBM - Glioblastoma multiforme(114;0.0367)		TGACACAGGGCTCGGGTGTCA	0.637													7	19	---	---	---	---	PASS
MYLK	4638	broad.mit.edu	37	3	123339143	123339143	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:123339143G>T	uc003ego.2	-	32	5561	c.5279C>A	c.(5278-5280)TCT>TAT	p.S1760Y	uc003egk.2_Intron|MYLK_uc003egl.2_5'UTR|MYLK_uc003egm.2_5'UTR|MYLK_uc010hrr.2_Missense_Mutation_p.S195Y|MYLK_uc011bjv.1_Missense_Mutation_p.S560Y|MYLK_uc011bjw.1_Missense_Mutation_p.S1760Y|MYLK_uc003egp.2_Missense_Mutation_p.S1691Y|MYLK_uc003egq.2_Missense_Mutation_p.S1709Y|MYLK_uc003egr.2_Missense_Mutation_p.S1640Y|MYLK_uc003egs.2_Missense_Mutation_p.S1584Y	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	1760	Calmodulin-binding.				aorta smooth muscle tissue morphogenesis|muscle contraction	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)|skin(2)|stomach(1)	9		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CATTGCCATAGAGGACAGTCT	0.522													8	219	---	---	---	---	PASS
KALRN	8997	broad.mit.edu	37	3	124380707	124380707	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:124380707G>T	uc003ehg.2	+	45	6401	c.6274G>T	c.(6274-6276)GAG>TAG	p.E2092*	KALRN_uc003ehi.2_Nonsense_Mutation_p.E433*|KALRN_uc003ehk.2_Nonsense_Mutation_p.E395*|KALRN_uc011bjz.1_Nonsense_Mutation_p.E184*	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	2091	DH 2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)|skin(1)	6						GAAAGCAGTGGAGTTAATGTG	0.483													13	104	---	---	---	---	PASS
SEC61A1	29927	broad.mit.edu	37	3	127786843	127786843	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:127786843G>T	uc003ekb.2	+	11	1369	c.1185G>T	c.(1183-1185)AAG>AAT	p.K395N	RUVBL1_uc003eke.2_Intron|RUVBL1_uc003ekf.2_Intron|SEC61A1_uc003ekc.2_Missense_Mutation_p.K342N|SEC61A1_uc003ekd.2_Missense_Mutation_p.K275N|SEC61A1_uc003ekg.2_Missense_Mutation_p.K89N	NM_013336	NP_037468	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit	395	Cytoplasmic (Potential).				protein targeting to ER	integral to endoplasmic reticulum membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity|protein binding|ribosome binding			ovary(1)	1						AGCAGCTGAAGGAGCAGCAGA	0.567											OREG0015775	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	80	---	---	---	---	PASS
RAB43	339122	broad.mit.edu	37	3	128848948	128848948	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:128848948T>G	uc003elo.1	-	11	1045	c.834A>C	c.(832-834)GAA>GAC	p.E278D	ISY1_uc010hsz.1_Missense_Mutation_p.E98D|ISY1_uc003elp.1_Missense_Mutation_p.E278D|ISY1_uc010hta.1_Missense_Mutation_p.E300D	NM_020701	NP_065752	Q86YS6	RAB43_HUMAN	ISY1 splicing factor homolog	Error:Variant_position_missing_in_Q86YS6_after_alignment					protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			lung(1)	1						GCCTTCTGGCTTCTTCACTTT	0.552													29	48	---	---	---	---	PASS
MRPL3	11222	broad.mit.edu	37	3	131181652	131181652	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:131181652G>T	uc003eoh.2	-	10	1126	c.962C>A	c.(961-963)CCT>CAT	p.P321H	MRPL3_uc011blo.1_Missense_Mutation_p.P216H|MRPL3_uc011blp.1_Missense_Mutation_p.P348H	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	321					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0						ATCTCCATCAGGAAAATATGT	0.413													5	35	---	---	---	---	PASS
SOX14	8403	broad.mit.edu	37	3	137484005	137484005	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:137484005G>A	uc003erm.1	+	1	427	c.379G>A	c.(379-381)GCC>ACC	p.A127T		NM_004189	NP_004180	O95416	SOX14_HUMAN	SRY-box 14	127					negative regulation of transcription from RNA polymerase II promoter|nervous system development|transcription, DNA-dependent	nucleus	sequence-specific DNA binding				0						GAAAGCCCGGGCCTTCTTGCC	0.716													5	13	---	---	---	---	PASS
PHC3	80012	broad.mit.edu	37	3	169835124	169835124	+	Missense_Mutation	SNP	T	A	A	rs138410529	by1000genomes	TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:169835124T>A	uc010hws.1	-	10	2111	c.2047A>T	c.(2047-2049)AGT>TGT	p.S683C	PHC3_uc003fgl.2_Missense_Mutation_p.S695C|PHC3_uc011bpq.1_Missense_Mutation_p.S642C	NM_024947	NP_079223	Q8NDX5	PHC3_HUMAN	polyhomeotic like 3	683					multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			GGAATGCTACTGTGCATAGAT	0.433													23	43	---	---	---	---	PASS
ZNF639	51193	broad.mit.edu	37	3	179051978	179051978	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr3:179051978G>T	uc003fjq.1	+	6	1569	c.1226G>T	c.(1225-1227)GGG>GTG	p.G409V	ZNF639_uc003fjr.1_Missense_Mutation_p.G409V	NM_016331	NP_057415	Q9UID6	ZN639_HUMAN	zinc finger protein 639	409	Interaction with CTNNA2.|C2H2-type 6.				initiation of viral infection|negative regulation by host of viral transcription|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of cell growth|positive regulation of transcription, DNA-dependent	nucleus	protein self-association|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|zinc ion binding				0	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			GATGACTGTGGGAAAGGCTTT	0.328													6	62	---	---	---	---	PASS
BEND4	389206	broad.mit.edu	37	4	42145654	42145654	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:42145654A>C	uc003gwn.2	-	3	1425	c.845T>G	c.(844-846)CTG>CGG	p.L282R	BEND4_uc003gwm.2_Missense_Mutation_p.L282R|BEND4_uc011byy.1_Missense_Mutation_p.L282R	NM_207406	NP_997289	Q6ZU67	BEND4_HUMAN	BEN domain containing 4 isoform a	282											0						AGAGGTTGACAGAGGATCCAC	0.498													10	24	---	---	---	---	PASS
PDGFRA	5156	broad.mit.edu	37	4	55131190	55131190	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:55131190C>A	uc003han.3	+	5	1064	c.733C>A	c.(733-735)CTT>ATT	p.L245I	PDGFRA_uc003haa.2_Intron|PDGFRA_uc003hal.2_3'UTR|PDGFRA_uc010igq.1_Missense_Mutation_p.L139I|PDGFRA_uc003ham.2_RNA	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	245	Ig-like C2-type 3.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	GGTGGTTGACCTTCAATGGAC	0.333			Mis|O|T	FIP1L1	GIST|idiopathic hypereosinophilic syndrome				Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	TSP Lung(21;0.16)			5	48	---	---	---	---	PASS
SMR3A	26952	broad.mit.edu	37	4	71232555	71232555	+	Silent	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:71232555C>G	uc003hfg.1	+	3	330	c.249C>G	c.(247-249)CCC>CCG	p.P83P	SMR3B_uc011cas.1_Intron	NM_012390	NP_036522	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3	83	Pro-rich.|Poly-Pro.					extracellular region					0		all_hematologic(202;0.196)				CTCCTCCACCCTATGGTCCAG	0.567													8	38	---	---	---	---	PASS
CDS1	1040	broad.mit.edu	37	4	85525418	85525418	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:85525418A>G	uc011ccv.1	+	2	638	c.140A>G	c.(139-141)TAT>TGT	p.Y47C		NM_001263	NP_001254	Q92903	CDS1_HUMAN	CDP-diacylglycerol synthase 1	47					signal transduction|visual perception	endoplasmic reticulum membrane|integral to membrane	diacylglycerol cholinephosphotransferase activity|phosphatidate cytidylyltransferase activity			large_intestine(2)|ovary(1)|breast(1)	4		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		GATGACAGATATGGAGATTTG	0.348													15	31	---	---	---	---	PASS
PDHA2	5161	broad.mit.edu	37	4	96761394	96761394	+	Missense_Mutation	SNP	C	A	A	rs143281239		TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:96761394C>A	uc003htr.3	+	1	156	c.93C>A	c.(91-93)GAC>GAA	p.D31E		NM_005390	NP_005381	P29803	ODPAT_HUMAN	pyruvate dehydrogenase E1 alpha 2 precursor	31					glycolysis	mitochondrial matrix	pyruvate dehydrogenase (acetyl-transferring) activity			central_nervous_system(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)	NADH(DB00157)	CCTCAAATGACGCTACATTTG	0.502													5	15	---	---	---	---	PASS
FAT4	79633	broad.mit.edu	37	4	126242434	126242434	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:126242434G>T	uc003ifj.3	+	1	4868	c.4868G>T	c.(4867-4869)GGC>GTC	p.G1623V		NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	1623	Cadherin 15.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						ATTCTTCAGGGCCTTGATGGA	0.433													16	37	---	---	---	---	PASS
INTU	27152	broad.mit.edu	37	4	128564999	128564999	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:128564999G>T	uc003ifk.1	+	2	540	c.470G>T	c.(469-471)CGG>CTG	p.R157L	INTU_uc011cgq.1_RNA	NM_015693	NP_056508	Q9ULD6	PDZD6_HUMAN	PDZ domain containing 6	157										ovary(1)	1						GTCCAACAGCGATACAAAGAT	0.393													4	45	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	4	165981199	165981199	+	Silent	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:165981199T>A	uc011cjl.1	+	1	900	c.900T>A	c.(898-900)CCT>CCA	p.P300P		NM_001105575	NP_001099045			tripartite motif-containing 75																		TTCTAGACCCTGAAACAGCAC	0.343													12	33	---	---	---	---	PASS
ZFP42	132625	broad.mit.edu	37	4	188924324	188924324	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:188924324A>T	uc003izg.1	+	3	608	c.363A>T	c.(361-363)GAA>GAT	p.E121D	ZFP42_uc003izh.1_Missense_Mutation_p.E121D|ZFP42_uc003izi.1_Missense_Mutation_p.E121D	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	121					female gonad development|male gonad development|meiosis	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|skin(1)	2		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		GTTCTTTGGAATACATGAAAA	0.408													26	74	---	---	---	---	PASS
SEMA5A	9037	broad.mit.edu	37	5	9202246	9202246	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:9202246G>T	uc003jek.2	-	9	1465	c.753C>A	c.(751-753)GCC>GCA	p.A251A		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	251	Sema.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2						TGCACACCCGGGCAGCTCTGG	0.502													5	31	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13719032	13719032	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:13719032G>T	uc003jfd.2	-	72	12500	c.12458C>A	c.(12457-12459)CCT>CAT	p.P4153H	DNAH5_uc003jfc.2_Missense_Mutation_p.P321H	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4153	AAA 6 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					TCCTTGTGGAGGATCGTTGGC	0.453									Kartagener_syndrome				11	39	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13719033	13719033	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:13719033G>T	uc003jfd.2	-	72	12499	c.12457C>A	c.(12457-12459)CCT>ACT	p.P4153T	DNAH5_uc003jfc.2_Missense_Mutation_p.P321T	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4153	AAA 6 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)					CCTTGTGGAGGATCGTTGGCA	0.453									Kartagener_syndrome				10	40	---	---	---	---	PASS
PRDM9	56979	broad.mit.edu	37	5	23523402	23523402	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:23523402C>A	uc003jgo.2	+	9	1067	c.885C>A	c.(883-885)ATC>ATA	p.I295I		NM_020227	NP_064612	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	295	SET.			I -> VRRACHF (in Ref. 4; AAF87242).	meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleoplasm	histone-lysine N-methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(3)|large_intestine(2)|pancreas(1)	6						AAACTCAGATCACCAAGGGGA	0.443										HNSCC(3;0.000094)			14	47	---	---	---	---	PASS
LMBRD2	92255	broad.mit.edu	37	5	36105250	36105250	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:36105250T>C	uc003jkb.1	-	17	2362	c.1947A>G	c.(1945-1947)ATA>ATG	p.I649M	uc003jka.1_5'Flank	NM_001007527	NP_001007528	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	649	Cytoplasmic (Potential).					integral to membrane					0	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GGAGAAGTTCTATCCGGTCCC	0.408													9	31	---	---	---	---	PASS
NIPBL	25836	broad.mit.edu	37	5	37024753	37024753	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:37024753A>G	uc003jkl.3	+	30	6140	c.5641A>G	c.(5641-5643)ACA>GCA	p.T1881A	NIPBL_uc003jkk.3_Missense_Mutation_p.T1881A	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	1881	HEAT 2.				brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TGAACAACCAACATTTCCAAA	0.313													11	19	---	---	---	---	PASS
GHR	2690	broad.mit.edu	37	5	42695076	42695076	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:42695076G>T	uc003jmt.2	+	5	367	c.324G>T	c.(322-324)GGG>GGT	p.G108G	GHR_uc011cpq.1_5'UTR	NM_000163	NP_000154	P10912	GHR_HUMAN	growth hormone receptor precursor	108	Extracellular (Potential).				2-oxoglutarate metabolic process|activation of JAK2 kinase activity|activation of MAPK activity|allantoin metabolic process|citrate metabolic process|creatine metabolic process|creatinine metabolic process|endocytosis|fatty acid metabolic process|growth hormone receptor signaling pathway|insulin-like growth factor receptor signaling pathway|isoleucine metabolic process|JAK-STAT cascade|multicellular organismal metabolic process|oxaloacetate metabolic process|positive regulation of multicellular organism growth|positive regulation of tyrosine phosphorylation of Stat3 protein|positive regulation of tyrosine phosphorylation of Stat5 protein|receptor internalization|response to cycloheximide|response to estradiol stimulus|succinate metabolic process|taurine metabolic process|valine metabolic process	cell surface|extracellular space|growth hormone receptor complex|integral to plasma membrane	growth factor binding|peptide hormone binding|proline-rich region binding|protein homodimerization activity|protein kinase binding			lung(4)|kidney(1)|skin(1)	6		Myeloproliferative disorder(839;0.00878)			Pegvisomant(DB00082)|Somatropin recombinant(DB00052)	TTTCTGCTGGGGAAAACAGCT	0.308													4	14	---	---	---	---	PASS
GZMA	3001	broad.mit.edu	37	5	54401310	54401310	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:54401310G>A	uc003jpm.2	+	2	116	c.79G>A	c.(79-81)GAA>AAA	p.E27K		NM_006144	NP_006135	P12544	GRAA_HUMAN	granzyme A precursor	27					cleavage of lamin|cytolysis|immune response|negative regulation of DNA binding|negative regulation of endodeoxyribonuclease activity|negative regulation of oxidoreductase activity|positive regulation of apoptosis	extracellular region|immunological synapse|nucleus	protein homodimerization activity|serine-type endopeptidase activity			ovary(2)|pancreas(1)|skin(1)	4		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				AGATGTCTGTGAAAAAATTAT	0.413													9	32	---	---	---	---	PASS
DDX4	54514	broad.mit.edu	37	5	55075836	55075836	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:55075836A>G	uc003jqg.3	+	8	513	c.439A>G	c.(439-441)AGA>GGA	p.R147G	DDX4_uc010ivz.2_Missense_Mutation_p.R127G|DDX4_uc003jqh.3_Intron|DDX4_uc003jqj.2_Intron	NM_001136034	NP_001129506	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 isoform	147	Gly-rich.				multicellular organismal development|sperm motility	perinuclear region of cytoplasm|pi-body|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding			ovary(1)|skin(1)	2		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				GCCATACAGAAGAGGTGGAAG	0.373													4	18	---	---	---	---	PASS
BDP1	55814	broad.mit.edu	37	5	70806897	70806897	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:70806897C>A	uc003kbp.1	+	17	4241	c.3978C>A	c.(3976-3978)ACC>ACA	p.T1326T	BDP1_uc003kbn.1_Silent_p.T1326T|BDP1_uc003kbo.2_Silent_p.T1326T	NM_018429	NP_060899	A6H8Y1	BDP1_HUMAN	transcription factor-like nuclear regulator	1326	9; approximate.|9 X 55 AA repeats of G-R-R-X-I-S-P-X-E-N- G-X-E-E-V-K-P-X-X-E-M-E-T-D-L-K-X-T-G-R- E-X-X-X-R-E-K-T-X-E-X-X-D-A-X-E-E-I-D-X- D-L-E-E-T.				regulation of transcription, DNA-dependent|transcription from RNA polymerase III promoter	nucleoplasm	DNA binding			skin(2)	2		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TAGAGGAGACCAGTACCTCAA	0.423													6	57	---	---	---	---	PASS
PDE8B	8622	broad.mit.edu	37	5	76646894	76646894	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:76646894G>T	uc003kfa.2	+	9	1067	c.1022G>T	c.(1021-1023)TGG>TTG	p.W341L	PDE8B_uc003kfb.2_Missense_Mutation_p.W321L|PDE8B_uc003kfc.2_Missense_Mutation_p.W341L|PDE8B_uc003kfd.2_Missense_Mutation_p.W294L|PDE8B_uc003kfe.2_Intron	NM_003719	NP_003710	O95263	PDE8B_HUMAN	phosphodiesterase 8B isoform 1	341					cyclic nucleotide metabolic process|regulation of transcription, DNA-dependent	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|two-component response regulator activity				0		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)		ATGTAGGAGTGGCAGGGGGTT	0.517													9	20	---	---	---	---	PASS
DDX46	9879	broad.mit.edu	37	5	134153324	134153324	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:134153324G>T	uc003kzw.2	+	20	2917	c.2749G>T	c.(2749-2751)GAA>TAA	p.E917*		NM_014829	NP_055644	Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	917					mRNA processing|RNA splicing	Cajal body|nuclear speck	ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGAGAAACAAGAAGAAGAGAG	0.408													7	51	---	---	---	---	PASS
PCDHB11	56125	broad.mit.edu	37	5	140579904	140579904	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:140579904C>A	uc003liy.2	+	1	557	c.557C>A	c.(556-558)CCA>CAA	p.P186Q	PCDHB11_uc011daj.1_Intron	NM_018931	NP_061754	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11 precursor	186	Extracellular (Potential).|Cadherin 2.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(3)|ovary(2)|upper_aerodigestive_tract(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGAGTCATTCCAGACAATAGG	0.438													5	51	---	---	---	---	PASS
PCDH12	51294	broad.mit.edu	37	5	141337102	141337102	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:141337102C>A	uc003llx.2	-	1	1526	c.315G>T	c.(313-315)CTG>CTT	p.L105L		NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor	105	Cadherin 1.|Extracellular (Potential).				neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAAAGGAAACCAGGCAGGGAT	0.587													6	83	---	---	---	---	PASS
ADRB2	154	broad.mit.edu	37	5	148207268	148207268	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:148207268G>A	uc003lpr.1	+	1	1113	c.874G>A	c.(874-876)GTT>ATT	p.V292I	SH3TC2_uc003lpp.1_Intron	NM_000024	NP_000015	P07550	ADRB2_HUMAN	adrenergic, beta-2-, receptor, surface	292	Helical; Name=6.|Agonist and antagonist binding.				activation of transmembrane receptor protein tyrosine kinase activity|desensitization of G-protein coupled receptor protein signaling pathway by arrestin|endosome to lysosome transport|positive regulation of MAPKKK cascade|receptor-mediated endocytosis	endosome|integral to plasma membrane|lysosome|receptor complex	beta2-adrenergic receptor activity|norepinephrine binding|potassium channel regulator activity|protein homodimerization activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Alprenolol(DB00866)|Arformoterol(DB01274)|Bambuterol(DB01408)|Bisoprolol(DB00612)|Bitolterol(DB00901)|Bretylium(DB01158)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Isoproterenol(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Metipranolol(DB01214)|Nadolol(DB01203)|Norepinephrine(DB00368)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Terbutaline(DB00871)|Timolol(DB00373)	CTTCTTCATCGTTAACATTGT	0.463													8	65	---	---	---	---	PASS
GFPT2	9945	broad.mit.edu	37	5	179757699	179757699	+	Splice_Site	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:179757699C>A	uc003mlw.1	-	6	632	c.534_splice	c.e6+1	p.L178_splice		NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2						dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	TTGTAACTCACCAACTGCTGA	0.378													15	74	---	---	---	---	PASS
GFPT2	9945	broad.mit.edu	37	5	179757700	179757700	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:179757700C>A	uc003mlw.1	-	6	632	c.534G>T	c.(532-534)TTG>TTT	p.L178F		NM_005110	NP_005101	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	178	Glutamine amidotransferase type-2.				dolichol-linked oligosaccharide biosynthetic process|energy reserve metabolic process|fructose 6-phosphate metabolic process|glutamine metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine|UDP-N-acetylglucosamine biosynthetic process	cytosol	glutamine-fructose-6-phosphate transaminase (isomerizing) activity|sugar binding			ovary(1)|skin(1)	2	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	TGTAACTCACCAACTGCTGAA	0.373													15	74	---	---	---	---	PASS
KAAG1	353219	broad.mit.edu	37	6	24358065	24358065	+	Silent	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:24358065G>A	uc003ndz.1	+	1	935	c.198G>A	c.(196-198)GCG>GCA	p.A66A	DCDC2_uc003ndx.2_5'UTR|DCDC2_uc003ndy.2_5'UTR	NM_181337	NP_851854	Q9UBP8	KAAG1_HUMAN	kidney associated antigen 1	66					immune response						0						CCCAGGGCGCGGGATCGCCTC	0.662													6	25	---	---	---	---	PASS
SLC17A1	6568	broad.mit.edu	37	6	25819768	25819768	+	Missense_Mutation	SNP	C	A	A	rs146175657	byFrequency	TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:25819768C>A	uc003nfh.3	-	5	616	c.500G>T	c.(499-501)CGA>CTA	p.R167L	SLC17A1_uc011djy.1_RNA|SLC17A1_uc010jqb.1_Missense_Mutation_p.R165L|SLC17A1_uc010jqc.1_Missense_Mutation_p.R165L	NM_005074	NP_005065	Q14916	NPT1_HUMAN	solute carrier family 17 (sodium phosphate),	167					sodium ion transport|urate metabolic process	integral to plasma membrane|membrane fraction	sodium-dependent phosphate transmembrane transporter activity|symporter activity			ovary(3)|pancreas(1)	4						AAGTCGGCCTCGTTCCAGGGG	0.393													4	50	---	---	---	---	PASS
TRIM38	10475	broad.mit.edu	37	6	25967109	25967109	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:25967109A>T	uc003nfm.2	+	3	794	c.359A>T	c.(358-360)CAG>CTG	p.Q120L	TRIM38_uc003nfn.2_Missense_Mutation_p.Q120L	NM_006355	NP_006346	O00635	TRI38_HUMAN	tripartite motif-containing 38	120	B box-type.				positive regulation of I-kappaB kinase/NF-kappaB cascade	intracellular	signal transducer activity|zinc ion binding				0						CGGGCACCACAGCACAAAGGG	0.557													12	49	---	---	---	---	PASS
C2	717	broad.mit.edu	37	6	31902047	31902047	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:31902047A>G	uc003nyf.2	+	6	1084	c.820A>G	c.(820-822)AAG>GAG	p.K274E	C2_uc003nyc.2_Intron|C2_uc011doo.1_Intron|C2_uc011dop.1_Intron|C2_uc003nye.3_Missense_Mutation_p.K274E|C2_uc010jtk.2_Missense_Mutation_p.K142E|C2_uc011doq.1_Missense_Mutation_p.K245E|C2_uc003nyg.2_Intron|CFB_uc011dor.1_Intron|C2_uc003nyh.1_5'Flank	NM_000063	NP_000054	P06681	CO2_HUMAN	complement component 2 isoform 1 preproprotein	274	VWFA.				complement activation, classical pathway|innate immune response|proteolysis	extracellular space	serine-type endopeptidase activity			ovary(1)|skin(1)	2		Ovarian(999;0.00965)		LUAD - Lung adenocarcinoma(999;0.247)		TCTCATCTTCAAGGAGAGCGC	0.547													38	177	---	---	---	---	PASS
SPDEF	25803	broad.mit.edu	37	6	34507062	34507062	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:34507062T>C	uc003ojq.1	-	5	1209	c.794A>G	c.(793-795)TAT>TGT	p.Y265C	SPDEF_uc011dsq.1_Missense_Mutation_p.Y249C	NM_012391	NP_036523	O95238	SPDEF_HUMAN	SAM pointed domain containing ets transcription	265	ETS.				negative regulation of survival gene product expression|negative regulation of transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			skin(3)|ovary(1)|central_nervous_system(1)	5						GAAGCGGCCATAGCTGTGGGG	0.617													15	114	---	---	---	---	PASS
SCUBE3	222663	broad.mit.edu	37	6	35214015	35214015	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:35214015C>T	uc003okf.1	+	21	2791	c.2785C>T	c.(2785-2787)CGA>TGA	p.R929*	SCUBE3_uc003okg.1_Nonsense_Mutation_p.R928*|SCUBE3_uc003okh.1_Nonsense_Mutation_p.R816*	NM_152753	NP_689966	Q8IX30	SCUB3_HUMAN	signal peptide, CUB domain, EGF-like 3	929					protein heterooligomerization|protein homooligomerization	cell surface|extracellular region	calcium ion binding|protein binding			skin(1)	1						AGACATTGTGCGAGATGGCCG	0.418													24	151	---	---	---	---	PASS
PI16	221476	broad.mit.edu	37	6	36931007	36931007	+	Silent	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:36931007C>T	uc003ona.2	+	5	1217	c.889C>T	c.(889-891)CTG>TTG	p.L297L	PI16_uc003omz.1_Intron|PI16_uc003onb.2_Intron|PI16_uc011dts.1_Silent_p.L68L	NM_153370	NP_699201	Q6UXB8	PI16_HUMAN	protease inhibitor 16 precursor	297	Extracellular (Potential).					extracellular region|integral to membrane	peptidase inhibitor activity				0						AGCTCACAGCCTGCCCTCCTT	0.532													22	65	---	---	---	---	PASS
TREML2	79865	broad.mit.edu	37	6	41168703	41168703	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:41168703C>A	uc010jxm.1	-	1	223	c.44G>T	c.(43-45)GGT>GTT	p.G15V		NM_024807	NP_079083	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid	15					T cell activation	cell surface|integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)					TGAGACGCAACCCTGTGGCCA	0.622													4	7	---	---	---	---	PASS
TREML2	79865	broad.mit.edu	37	6	41168707	41168707	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:41168707G>T	uc010jxm.1	-	1	219	c.40C>A	c.(40-42)CAG>AAG	p.Q14K		NM_024807	NP_079083	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid	14					T cell activation	cell surface|integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)					ACGCAACCCTGTGGCCACAGC	0.622													4	8	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51774224	51774224	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:51774224G>T	uc003pah.1	-	40	6815	c.6539C>A	c.(6538-6540)TCC>TAC	p.S2180Y	PKHD1_uc010jzn.1_Missense_Mutation_p.S205Y|PKHD1_uc003pai.2_Missense_Mutation_p.S2180Y	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	2180	Extracellular (Potential).				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity			lung(15)|ovary(15)|large_intestine(5)|central_nervous_system(3)|skin(3)|breast(2)|upper_aerodigestive_tract(1)	44	Lung NSC(77;0.0605)					CATATCCCTGGATCCTAGCAT	0.483													13	76	---	---	---	---	PASS
GFRAL	389400	broad.mit.edu	37	6	55264165	55264165	+	Splice_Site	SNP	A	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:55264165A>G	uc003pcm.1	+	8	1135	c.1049_splice	c.e8-2	p.G350_splice		NM_207410	NP_997293	Q6UXV0	GFRAL_HUMAN	GDNF family receptor alpha like precursor							integral to membrane	receptor activity			ovary(1)|breast(1)	2	Lung NSC(77;0.0875)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			TTCTTTTTCTAGGAGAAGTAA	0.313													4	14	---	---	---	---	PASS
IBTK	25998	broad.mit.edu	37	6	82909856	82909856	+	Splice_Site	SNP	A	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:82909856A>C	uc003pjl.1	-	21	3552	c.3025_splice	c.e21+1	p.G1009_splice	IBTK_uc011dyu.1_Splice_Site|IBTK_uc011dyv.1_Splice_Site_p.E1009_splice|IBTK_uc011dyw.1_Splice_Site_p.G808_splice|IBTK_uc010kbi.1_Splice_Site_p.G703_splice|IBTK_uc003pjm.2_Splice_Site_p.G1009_splice	NM_015525	NP_056340	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton's tyrosine kinase						negative regulation of protein phosphorylation|release of sequestered calcium ion into cytosol	cytoplasm|membrane|nucleus	protein kinase binding|protein tyrosine kinase inhibitor activity			ovary(2)|central_nervous_system(2)	4		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		CTTTCCACGAACCTGTAGATG	0.378													12	42	---	---	---	---	PASS
PRSS35	167681	broad.mit.edu	37	6	84234230	84234230	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:84234230C>A	uc003pjz.2	+	2	1233	c.1070C>A	c.(1069-1071)CCA>CAA	p.P357Q	PRSS35_uc010kbm.2_Missense_Mutation_p.P357Q	NM_153362	NP_699193	Q8N3Z0	PRS35_HUMAN	protease, serine, 35 precursor	357	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			ovary(1)	1		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		CTGAAAGATCCAGACAAAAAG	0.517													18	52	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90471376	90471376	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:90471376G>T	uc003pnn.1	-	17	2564	c.2448C>A	c.(2446-2448)TTC>TTA	p.F816L	MDN1_uc003pno.1_Missense_Mutation_p.F234L	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	816					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTACAAATGCGAACAATAAGG	0.333													4	31	---	---	---	---	PASS
MDN1	23195	broad.mit.edu	37	6	90499528	90499528	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:90499528C>A	uc003pnn.1	-	7	1317	c.1201G>T	c.(1201-1203)GAG>TAG	p.E401*	MDN1_uc003pnp.1_Nonsense_Mutation_p.E401*	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	401					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)|skin(2)	10		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCAATATCCTCCAGAAGGATC	0.468													5	56	---	---	---	---	PASS
BACH2	60468	broad.mit.edu	37	6	90718521	90718521	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:90718521C>G	uc011eab.1	-	6	852	c.43G>C	c.(43-45)GAG>CAG	p.E15Q	BACH2_uc003pnw.2_Missense_Mutation_p.E15Q|BACH2_uc010kch.2_Missense_Mutation_p.E15Q	NM_021813	NP_068585	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper	15						nucleus	protein dimerization activity|sequence-specific DNA binding			ovary(3)|pancreas(1)|lung(1)|skin(1)	6		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		ACTGTGGACTCATACACATAC	0.423													8	54	---	---	---	---	PASS
BCLAF1	9774	broad.mit.edu	37	6	136597032	136597032	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:136597032C>T	uc003qgx.1	-	5	1884	c.1631G>A	c.(1630-1632)CGT>CAT	p.R544H	BCLAF1_uc003qgw.1_Missense_Mutation_p.R371H|BCLAF1_uc003qgy.1_Missense_Mutation_p.R542H|BCLAF1_uc011edc.1_RNA|BCLAF1_uc011edd.1_RNA|BCLAF1_uc011ede.1_Missense_Mutation_p.R542H	NM_014739	NP_055554	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1 isoform	544					induction of apoptosis|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding			ovary(1)	1	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		GACTTCAGGACGGTGAGAATC	0.433													7	67	---	---	---	---	PASS
TNFAIP3	7128	broad.mit.edu	37	6	138200413	138200413	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:138200413G>A	uc003qhr.2	+	7	1897	c.1831G>A	c.(1831-1833)GGC>AGC	p.G611S	TNFAIP3_uc003qhs.2_Missense_Mutation_p.G611S	NM_006290	NP_006281	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	611	Interaction with NAF1 (By similarity).|A20-type 4.				anti-apoptosis|apoptosis|B-1 B cell homeostasis|negative regulation of B cell activation|negative regulation of bone resorption|negative regulation of CD40 signaling pathway|negative regulation of endothelial cell apoptosis|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of inflammatory response|negative regulation of interleukin-2 production|negative regulation of interleukin-6 production|negative regulation of NF-kappaB transcription factor activity|negative regulation of osteoclast proliferation|negative regulation of protein ubiquitination|negative regulation of smooth muscle cell proliferation|negative regulation of toll-like receptor 2 signaling pathway|negative regulation of toll-like receptor 3 signaling pathway|negative regulation of tumor necrosis factor production|negative regulation of type I interferon production|positive regulation of protein catabolic process|protein K48-linked ubiquitination|protein K63-linked deubiquitination|protein oligomerization|regulation of defense response to virus by host|regulation of germinal center formation|regulation of vascular wound healing|tolerance induction to lipopolysaccharide	centrosome|cytosol|nucleus	caspase inhibitor activity|DNA binding|protease binding|protein self-association|ubiquitin binding|ubiquitin thiolesterase activity|ubiquitin-protein ligase activity|ubiquitin-specific protease activity|zinc ion binding	p.0?(22)		haematopoietic_and_lymphoid_tissue(133)|lung(3)|ovary(1)	137	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CAGAAAAGCCGGCTGCGTGTA	0.532			D|N|F		marginal zone B-cell lymphomas|Hodgkin's lymphoma|primary mediastinal B cell lymphoma								13	110	---	---	---	---	PASS
TAB2	23118	broad.mit.edu	37	6	149700403	149700403	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:149700403C>A	uc003qmj.2	+	3	1530	c.1352C>A	c.(1351-1353)CCT>CAT	p.P451H	TAB2_uc011eec.1_Missense_Mutation_p.P419H|TAB2_uc010kia.1_Missense_Mutation_p.P451H|TAB2_uc010kib.1_Missense_Mutation_p.P451H|TAB2_uc003qmk.3_RNA	NM_015093	NP_055908	Q9NYJ8	TAB2_HUMAN	mitogen-activated protein kinase kinase kinase 7	451					activation of MAPK activity|heart development|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	K63-linked polyubiquitin binding|zinc ion binding				0						GCAACCTCTCCTCGAGTGGTA	0.507													6	79	---	---	---	---	PASS
FTSJ2	29960	broad.mit.edu	37	7	2275030	2275030	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:2275030C>A	uc003slm.2	-	3	497	c.468G>T	c.(466-468)GCG>GCT	p.A156A	MAD1L1_uc003slh.1_5'Flank|MAD1L1_uc003slf.1_5'Flank|MAD1L1_uc003slg.1_5'Flank|MAD1L1_uc010ksh.1_5'Flank|MAD1L1_uc003sli.1_5'Flank|MAD1L1_uc010ksi.1_5'Flank|MAD1L1_uc010ksj.2_5'Flank|FTSJ2_uc003slk.2_Silent_p.A2A|FTSJ2_uc003sll.2_Silent_p.A2A|FTSJ2_uc003sln.2_RNA|FTSJ2_uc003slo.2_Silent_p.A2A	NM_013393	NP_037525	Q9UI43	RRMJ2_HUMAN	FtsJ homolog 2	156					cell proliferation	mitochondrion|nucleolus	nucleic acid binding|rRNA (uridine-2'-O-)-methyltransferase activity			ovary(1)	1		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0822)|OV - Ovarian serous cystadenocarcinoma(56;2.7e-14)		TGGCATTGGGCGCCATGTCGC	0.592													10	46	---	---	---	---	PASS
STK31	56164	broad.mit.edu	37	7	23793980	23793980	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:23793980A>C	uc003sws.3	+	10	1247	c.1180A>C	c.(1180-1182)ATA>CTA	p.I394L	STK31_uc003swt.3_Missense_Mutation_p.I371L|STK31_uc011jze.1_Missense_Mutation_p.I394L|STK31_uc010kuq.2_Missense_Mutation_p.I371L	NM_031414	NP_113602	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31 isoform a	394							ATP binding|nucleic acid binding|protein serine/threonine kinase activity			skin(3)|lung(2)|ovary(2)|stomach(2)	9						TTCAGATGCTATACAAGTGTT	0.373													16	42	---	---	---	---	PASS
HOXA3	3200	broad.mit.edu	37	7	27150165	27150165	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:27150165G>T	uc011jzl.1	-	2	295	c.95C>A	c.(94-96)CCG>CAG	p.P32Q	HOXA3_uc011jzk.1_Intron|HOXA3_uc003syk.2_Missense_Mutation_p.P32Q	NM_030661	NP_109377	O43365	HXA3_HUMAN	homeobox A3 isoform a	32					angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(2)	2						CGCCGGGTACGGCTGCTGATT	0.657													3	6	---	---	---	---	PASS
HOXA7	3204	broad.mit.edu	37	7	27194745	27194745	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:27194745C>A	uc003sys.2	-	2	608	c.476G>T	c.(475-477)CGC>CTC	p.R159L	HOXA6_uc003syq.1_5'Flank|uc003syr.1_3'UTR	NM_006896	NP_008827	P31268	HXA7_HUMAN	homeobox A7	159	Poly-Arg.|Homeobox.				angiogenesis|negative regulation of cell-matrix adhesion|negative regulation of keratinocyte differentiation|negative regulation of leukocyte migration|negative regulation of monocyte differentiation|negative regulation of transcription from RNA polymerase II promoter		sequence-specific DNA binding|transcription factor binding				0						TTCAATGCGGCGGCGCCGCGT	0.602													29	120	---	---	---	---	PASS
FAM188B	84182	broad.mit.edu	37	7	30831048	30831048	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:30831048G>T	uc003tbt.2	+	5	1008	c.931G>T	c.(931-933)GAG>TAG	p.E311*	FAM188B_uc010kwe.2_Nonsense_Mutation_p.E282*	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182	311											0						GGATCCCTCCGAGGACACCCC	0.622													4	39	---	---	---	---	PASS
ADCY1	107	broad.mit.edu	37	7	45725621	45725621	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:45725621T>A	uc003tne.3	+	13	2152	c.2134T>A	c.(2134-2136)TCT>ACT	p.S712T		NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1	712					activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GGTCCTTTCGTCTGGGGGCCA	0.652													5	25	---	---	---	---	PASS
GTF2IRD1	9569	broad.mit.edu	37	7	74016709	74016709	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:74016709G>T	uc003uaq.2	+	27	3222	c.2829G>T	c.(2827-2829)ATG>ATT	p.M943I	GTF2IRD1_uc010lbq.2_Missense_Mutation_p.M960I|GTF2IRD1_uc003uap.2_Missense_Mutation_p.M928I|GTF2IRD1_uc003uar.1_3'UTR	NM_016328	NP_057412	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1 isoform 1	943				Missing: Cytoplasmic localization.		nucleus	DNA binding|protein binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			ovary(4)	4						CAATGTACATGGTGGACTATG	0.478													5	68	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100680080	100680080	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:100680080G>T	uc003uxp.1	+	3	5436	c.5383G>T	c.(5383-5385)GGT>TGT	p.G1795C	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1795	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|28.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					AACTGCTGAAGGTACCAGCAT	0.517													11	318	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100685234	100685234	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:100685234G>T	uc003uxp.1	+	3	10590	c.10537G>T	c.(10537-10539)GGT>TGT	p.G3513C	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	3513	Extracellular (Potential).|Ser-rich.|57.|59 X approximate tandem repeats.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity	p.G3513V(1)		ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					ATCAACTGCTGGTGAAGGAAG	0.493													12	418	---	---	---	---	PASS
NUP205	23165	broad.mit.edu	37	7	135277850	135277850	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:135277850G>T	uc003vsw.2	+	12	1771	c.1740G>T	c.(1738-1740)CAG>CAT	p.Q580H		NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	580					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6						ATAGTGTCCAGTACCGTCACC	0.488													14	70	---	---	---	---	PASS
CNTNAP2	26047	broad.mit.edu	37	7	146805264	146805264	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:146805264C>A	uc003weu.1	+	5	1092	c.576C>A	c.(574-576)GGC>GGA	p.G192G		NM_014141	NP_054860	Q9UHC6	CNTP2_HUMAN	cell recognition molecule Caspr2 precursor	192	Extracellular (Potential).				behavior|cell adhesion|clustering of voltage-gated potassium channels|limbic system development|neuron recognition|signal transduction|striatum development|superior temporal gyrus development|thalamus development|transmission of nerve impulse	axolemma|cell body fiber|dendrite|juxtaparanode region of axon|voltage-gated potassium channel complex	receptor binding			ovary(9)|central_nervous_system(1)|pancreas(1)	11	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			ACTTTGATGGCCATGTTGTAT	0.358										HNSCC(39;0.1)			5	12	---	---	---	---	PASS
INTS9	55756	broad.mit.edu	37	8	28651468	28651468	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:28651468G>T	uc003xha.2	-	10	1192	c.893C>A	c.(892-894)CCC>CAC	p.P298H	INTS9_uc011lav.1_Missense_Mutation_p.P274H|INTS9_uc011law.1_Missense_Mutation_p.P277H|INTS9_uc011lax.1_Missense_Mutation_p.P191H|INTS9_uc010lvc.2_RNA|INTS9_uc003xhb.2_Missense_Mutation_p.P298H	NM_018250	NP_060720	Q9NV88	INT9_HUMAN	integrator complex subunit 9 isoform 1	298					snRNA processing	integrator complex	protein binding			central_nervous_system(1)|pancreas(1)	2		Ovarian(32;0.0439)		KIRC - Kidney renal clear cell carcinoma(542;0.127)|Kidney(114;0.152)		AGGGTAGCAGGGAACCAACAC	0.483													6	65	---	---	---	---	PASS
RB1CC1	9821	broad.mit.edu	37	8	53573532	53573532	+	Silent	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:53573532T>C	uc003xre.3	-	11	2139	c.1581A>G	c.(1579-1581)TTA>TTG	p.L527L	RB1CC1_uc003xrf.3_Silent_p.L527L	NM_014781	NP_055596	Q8TDY2	RBCC1_HUMAN	Rb1-inducible coiled coil protein 1 isoform 1	527					autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	11		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CTGCTTCATATAATCTCTTTC	0.279													6	15	---	---	---	---	PASS
RB1CC1	9821	broad.mit.edu	37	8	53573823	53573823	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:53573823C>G	uc003xre.3	-	10	1935	c.1377G>C	c.(1375-1377)ATG>ATC	p.M459I	RB1CC1_uc003xrf.3_Missense_Mutation_p.M459I	NM_014781	NP_055596	Q8TDY2	RBCC1_HUMAN	Rb1-inducible coiled coil protein 1 isoform 1	459					autophagy|cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus|pre-autophagosomal structure|ULK1-ATG13-FIP200 complex	protein binding			ovary(8)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	11		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				CAGCATGAAGCATTACAAAGC	0.358													5	22	---	---	---	---	PASS
ARFGEF1	10565	broad.mit.edu	37	8	68204208	68204208	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:68204208C>A	uc003xxo.1	-	6	1180	c.790G>T	c.(790-792)GAC>TAC	p.D264Y		NM_006421	NP_006412	Q9Y6D6	BIG1_HUMAN	brefeldin A-inhibited guanine	264					exocytosis|regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity|myosin binding			ovary(4)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|kidney(1)	8	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			AGGTCAAGGTCCCCTTCGTGT	0.423													13	59	---	---	---	---	PASS
CRISPLD1	83690	broad.mit.edu	37	8	75941732	75941732	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:75941732G>T	uc003yan.2	+	14	1806	c.1431G>T	c.(1429-1431)CAG>CAT	p.Q477H	CRISPLD1_uc011lfk.1_Missense_Mutation_p.Q289H|CRISPLD1_uc011lfl.1_Missense_Mutation_p.Q289H	NM_031461	NP_113649	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain	477	LCCL 2.					extracellular region				ovary(1)|central_nervous_system(1)	2	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			CTTCTTTTCAGAATGGAATCT	0.373													5	21	---	---	---	---	PASS
ZFHX4	79776	broad.mit.edu	37	8	77766784	77766784	+	Missense_Mutation	SNP	A	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:77766784A>C	uc003yav.2	+	10	7879	c.7492A>C	c.(7492-7494)AAC>CAC	p.N2498H	ZFHX4_uc003yau.1_Missense_Mutation_p.N2543H|ZFHX4_uc003yaw.1_Missense_Mutation_p.N2498H	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2498						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ATTTGACCCCAACAATCCGCT	0.547										HNSCC(33;0.089)			31	153	---	---	---	---	PASS
PEX2	5828	broad.mit.edu	37	8	77895842	77895842	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:77895842C>A	uc003yax.2	-	4	1031	c.573G>T	c.(571-573)ATG>ATT	p.M191I	PEX2_uc003yay.2_Missense_Mutation_p.M191I|PEX2_uc003yaz.2_Missense_Mutation_p.M191I	NM_000318	NP_000309	P28328	PEX2_HUMAN	peroxin 2	191					peroxisome organization	integral to peroxisomal membrane	protein binding|zinc ion binding			ovary(1)	1						GTTCCCTATTCATGTATTCAA	0.388													10	78	---	---	---	---	PASS
UBR5	51366	broad.mit.edu	37	8	103301779	103301779	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:103301779T>C	uc003ykr.1	-	35	4648	c.4615A>G	c.(4615-4617)ATC>GTC	p.I1539V	UBR5_uc003yks.1_Missense_Mutation_p.I1539V	NM_015902	NP_056986	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin	1539					cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)			TTCCTGATGATGTAGGATGAC	0.468													8	55	---	---	---	---	PASS
SLC30A8	169026	broad.mit.edu	37	8	118184797	118184797	+	Silent	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:118184797G>A	uc003yoh.2	+	8	1217	c.987G>A	c.(985-987)GTG>GTA	p.V329V	SLC30A8_uc010mcz.2_Silent_p.V280V|SLC30A8_uc011lia.1_Silent_p.V280V|SLC30A8_uc003yog.2_Silent_p.V280V	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8	329	Cytoplasmic (Potential).				insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion transmembrane transporter activity			ovary(2)|skin(2)	4	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			ACAGCCAAGTGGTTCGGAGAG	0.507													12	46	---	---	---	---	PASS
FAM135B	51059	broad.mit.edu	37	8	139190841	139190841	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:139190841C>A	uc003yuy.2	-	10	1137	c.966G>T	c.(964-966)CTG>CTT	p.L322L	FAM135B_uc003yux.2_Silent_p.L223L|FAM135B_uc003yuz.2_RNA	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	322										ovary(7)|skin(2)	9	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TGACTGTGTCCAGGAACTGGG	0.532										HNSCC(54;0.14)			6	31	---	---	---	---	PASS
COL22A1	169044	broad.mit.edu	37	8	139606266	139606266	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr8:139606266G>T	uc003yvd.2	-	63	5056	c.4609C>A	c.(4609-4611)CCC>ACC	p.P1537T	COL22A1_uc011ljo.1_Missense_Mutation_p.P817T	NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1537	Pro-rich.|Gly-rich.|Collagen-like 15.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCACCTTTGGGACCTATGGGT	0.632										HNSCC(7;0.00092)			6	34	---	---	---	---	PASS
MPDZ	8777	broad.mit.edu	37	9	13176150	13176150	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr9:13176150G>T	uc010mia.1	-	19	2973	c.2916C>A	c.(2914-2916)CCC>CCA	p.P972P	MPDZ_uc003zkz.3_5'Flank|MPDZ_uc010mhy.2_Silent_p.P972P|MPDZ_uc010mhz.2_Silent_p.P972P|MPDZ_uc011lmn.1_Silent_p.P972P|MPDZ_uc003zlb.3_Silent_p.P972P	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	972					interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6				GBM - Glioblastoma multiforme(50;2.03e-06)		CAGCTGAATCGGGTAGCACAG	0.348													3	6	---	---	---	---	PASS
FAM154A	158297	broad.mit.edu	37	9	18928305	18928305	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr9:18928305C>A	uc003zni.1	-	4	1448	c.1170G>T	c.(1168-1170)AAG>AAT	p.K390N	FAM154A_uc010mip.1_Missense_Mutation_p.K198N	NM_153707	NP_714918	Q8IYX7	F154A_HUMAN	hypothetical protein LOC158297	390										pancreas(1)	1				GBM - Glioblastoma multiforme(50;6.53e-16)		ACCAATGAGGCTTACAGCTTT	0.577													5	22	---	---	---	---	PASS
IFNA16	3449	broad.mit.edu	37	9	21217192	21217192	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr9:21217192A>G	uc003zor.1	-	1	119	c.113T>C	c.(112-114)TTG>TCG	p.L38S	IFNA14_uc003zoo.1_Intron	NM_002173	NP_002164	P05015	IFN16_HUMAN	interferon, alpha 16 precursor	38					blood coagulation|regulation of type I interferon-mediated signaling pathway|response to virus|type I interferon-mediated signaling pathway	extracellular space	cytokine activity|interferon-alpha/beta receptor binding			skin(1)	1				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		CAGGAGTATCAAGGCCCTCCT	0.498													7	25	---	---	---	---	PASS
ZNF782	158431	broad.mit.edu	37	9	99580443	99580443	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr9:99580443T>C	uc004awp.1	-	6	2143	c.1862A>G	c.(1861-1863)AAT>AGT	p.N621S	ZNF782_uc011lup.1_Missense_Mutation_p.N489S	NM_001001662	NP_001001662	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	621	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)				TCCACATTCATTACATTCATA	0.433													9	22	---	---	---	---	PASS
TMEM38B	55151	broad.mit.edu	37	9	108467943	108467943	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr9:108467943G>T	uc004bcu.1	+	2	295	c.178G>T	c.(178-180)GGT>TGT	p.G60C	TMEM38B_uc010mtn.1_Missense_Mutation_p.G60C	NM_018112	NP_060582	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	60	Helical; (Potential).					integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2						CCACTGTTTTGGTGGAGGAAT	0.418													6	64	---	---	---	---	PASS
GDI2	2665	broad.mit.edu	37	10	5836916	5836916	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:5836916C>A	uc001iil.3	-	4	611	c.320G>T	c.(319-321)GGG>GTG	p.G107V	GDI2_uc001iim.3_Intron|GDI2_uc009xid.2_Missense_Mutation_p.G111V	NM_001494	NP_001485	P50395	GDIB_HUMAN	GDP dissociation inhibitor 2 isoform 1	107					protein transport|small GTPase mediated signal transduction	cell surface|cytosol|membrane	protein binding|Rab GDP-dissociation inhibitor activity				0						GACAAAGCTCCCTTCAGTCAC	0.373													6	70	---	---	---	---	PASS
ZEB1	6935	broad.mit.edu	37	10	31809717	31809717	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:31809717T>A	uc001ivs.3	+	7	1517	c.1454T>A	c.(1453-1455)CTT>CAT	p.L485H	ZEB1_uc001ivr.3_Missense_Mutation_p.L267H|ZEB1_uc010qee.1_Missense_Mutation_p.L267H|ZEB1_uc010qef.1_Missense_Mutation_p.L267H|ZEB1_uc009xlj.1_Missense_Mutation_p.L411H|ZEB1_uc010qeg.1_Missense_Mutation_p.L344H|ZEB1_uc009xlk.1_Missense_Mutation_p.L267H|ZEB1_uc001ivt.3_Missense_Mutation_p.L267H|ZEB1_uc001ivu.3_Missense_Mutation_p.L486H|ZEB1_uc001ivv.3_Missense_Mutation_p.L465H|ZEB1_uc010qeh.1_Missense_Mutation_p.L418H|ZEB1_uc009xlo.1_Missense_Mutation_p.L468H|ZEB1_uc009xlp.2_Missense_Mutation_p.L469H	NM_030751	NP_110378	P37275	ZEB1_HUMAN	zinc finger E-box binding homeobox 1 isoform b	485					cell proliferation|immune response|negative regulation of transcription from RNA polymerase II promoter|positive regulation of neuron differentiation	cytoplasm	E-box binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(3)|central_nervous_system(2)	5		Prostate(175;0.0156)				CCTAGCCAACTTCAAGTTGTT	0.373													10	51	---	---	---	---	PASS
GDF10	2662	broad.mit.edu	37	10	48429216	48429216	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:48429216G>C	uc001jfb.2	-	2	1126	c.670C>G	c.(670-672)CAG>GAG	p.Q224E	GDF10_uc009xnp.2_Missense_Mutation_p.Q223E|GDF10_uc009xnq.1_Missense_Mutation_p.Q224E	NM_004962	NP_004953	P55107	BMP3B_HUMAN	growth differentiation factor 10 precursor	224					growth|skeletal system development|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			lung(1)|central_nervous_system(1)	2						GAATCCAGCTGGGCGGAGAGG	0.697													3	4	---	---	---	---	PASS
ANK3	288	broad.mit.edu	37	10	61835767	61835767	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:61835767G>T	uc001jky.2	-	37	5064	c.4872C>A	c.(4870-4872)ACC>ACA	p.T1624T	ANK3_uc001jkw.2_Intron|ANK3_uc009xpa.2_Intron|ANK3_uc001jkx.2_Intron|ANK3_uc010qih.1_Intron|ANK3_uc001jkz.3_Intron|ANK3_uc001jkv.2_Intron|ANK3_uc009xpb.1_Intron	NM_020987	NP_066267	Q12955	ANK3_HUMAN	ankyrin 3 isoform 1	1624	Ser-rich.				establishment of protein localization|signal transduction	basolateral plasma membrane|cytoplasm|cytoskeleton	protein binding			skin(9)|ovary(6)|pancreas(2)|central_nervous_system(2)	19						TCACTGGAGAGGTTCGAGAGG	0.478													5	44	---	---	---	---	PASS
ZNF365	22891	broad.mit.edu	37	10	64159292	64159292	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:64159292G>T	uc001jly.3	+	5	1075	c.1013G>T	c.(1012-1014)CGA>CTA	p.R338L	ZNF365_uc001jmb.3_Intron|ZNF365_uc001jmc.2_Intron|ZNF365_uc001jlz.3_Missense_Mutation_p.R323L|ZNF365_uc001jma.3_RNA	NM_014951	NP_055766	Q70YC4	TALAN_HUMAN	zinc finger protein 365 isoform A	Error:Variant_position_missing_in_Q70YC4_after_alignment										ovary(1)|skin(1)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					TGTAGAAGCCGAGGGCACCCG	0.483													4	84	---	---	---	---	PASS
TCF7L2	6934	broad.mit.edu	37	10	114911628	114911628	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:114911628G>T	uc001lae.3	+	10	1653	c.1146G>T	c.(1144-1146)CAG>CAT	p.Q382H	TCF7L2_uc001lac.3_Missense_Mutation_p.Q359H|TCF7L2_uc010qrk.1_Missense_Mutation_p.Q359H|TCF7L2_uc010qrl.1_Missense_Mutation_p.Q359H|TCF7L2_uc010qrm.1_Missense_Mutation_p.Q382H|TCF7L2_uc010qrn.1_Missense_Mutation_p.Q325H|TCF7L2_uc001lad.3_Missense_Mutation_p.Q355H|TCF7L2_uc001lag.3_Missense_Mutation_p.Q406H|TCF7L2_uc001laf.3_Missense_Mutation_p.Q359H|TCF7L2_uc010qro.1_Missense_Mutation_p.Q359H|TCF7L2_uc001lah.2_Missense_Mutation_p.Q364H|TCF7L2_uc010qrp.1_Missense_Mutation_p.Q359H|TCF7L2_uc010qrq.1_Missense_Mutation_p.Q355H|TCF7L2_uc010qrr.1_Missense_Mutation_p.Q297H|TCF7L2_uc010qrs.1_Missense_Mutation_p.Q253H|TCF7L2_uc010qrt.1_Missense_Mutation_p.Q253H|TCF7L2_uc010qru.1_Missense_Mutation_p.Q281H|TCF7L2_uc010qrv.1_Missense_Mutation_p.Q199H|TCF7L2_uc010qrw.1_Missense_Mutation_p.Q86H|TCF7L2_uc010qrx.1_Missense_Mutation_p.Q239H	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1	382	Mediates interaction with MAD2L2.|HMG box.				anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		CCATCAACCAGATCCTTGGGC	0.532													8	50	---	---	---	---	PASS
CLRN3	119467	broad.mit.edu	37	10	129676511	129676511	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:129676511C>A	uc001lka.1	-	3	746	c.583G>T	c.(583-585)GTA>TTA	p.V195L	CLRN3_uc001ljz.1_Missense_Mutation_p.V127L	NM_152311	NP_689524	Q8NCR9	CLRN3_HUMAN	clarin 3	195	Helical; (Potential).					integral to membrane				skin(1)	1		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				ATGATGGTTACAGTGACTATA	0.453													18	99	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	10	134650410	134650410	+	Silent	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:134650410T>C	uc010qux.1	-	37	5625	c.5625A>G	c.(5623-5625)CAA>CAG	p.Q1875Q		NM_017609	NP_060079			Homo sapiens cDNA, FLJ17989.																		CGCAGAGATTTTGCCAAGCCT	0.537													10	69	---	---	---	---	PASS
MUC6	4588	broad.mit.edu	37	11	1016592	1016592	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:1016592C>A	uc001lsw.2	-	31	6260	c.6209G>T	c.(6208-6210)GGG>GTG	p.G2070V		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	2070	Ser-rich.|Thr-rich.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TTGGCTGGTCCCACTGGTGGT	0.577													9	143	---	---	---	---	PASS
KRTAP5-3	387266	broad.mit.edu	37	11	1629296	1629296	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:1629296G>A	uc001ltw.1	-	1	398	c.320C>T	c.(319-321)TCC>TTC	p.S107F		NM_001012708	NP_001012726	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	107	11 X 4 AA repeats of C-C-X-P.					keratin filament				ovary(2)	2		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		GACCCCCTTGGAACCCCCACA	0.662													10	53	---	---	---	---	PASS
OR56B4	196335	broad.mit.edu	37	11	6129132	6129132	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:6129132C>A	uc010qzx.1	+	1	124	c.124C>A	c.(124-126)CTC>ATC	p.L42I		NM_001005181	NP_001005181	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B,	42	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCTGCTCTACCTCTTAGCTCT	0.502													6	42	---	---	---	---	PASS
OR2AG2	338755	broad.mit.edu	37	11	6789336	6789336	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:6789336G>C	uc001meq.1	-	1	853	c.853C>G	c.(853-855)CTG>GTG	p.L285V		NM_001004490	NP_001004490	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG,	285	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)|ovary(1)|central_nervous_system(1)	4		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AGTGGATTCAGGGCTGGAGTG	0.502													6	47	---	---	---	---	PASS
STK33	65975	broad.mit.edu	37	11	8414154	8414154	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:8414154C>A	uc001mgi.1	-	12	2367	c.1448G>T	c.(1447-1449)GGA>GTA	p.G483V	STK33_uc001mgj.1_Missense_Mutation_p.G483V|STK33_uc001mgk.1_Missense_Mutation_p.G483V|STK33_uc010rbn.1_Missense_Mutation_p.G442V|STK33_uc001mgl.3_Missense_Mutation_p.G296V	NM_030906	NP_112168	Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	483						Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|pancreas(1)|central_nervous_system(1)|skin(1)	7				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		CTCCATTTCTCCCTTGATTTC	0.448													7	89	---	---	---	---	PASS
ASCL3	56676	broad.mit.edu	37	11	8959439	8959439	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:8959439G>T	uc001mhd.1	-	2	330	c.270C>A	c.(268-270)TAC>TAA	p.Y90*		NM_020646	NP_065697	Q9NQ33	ASCL3_HUMAN	ASCL3	89					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus	DNA binding				0				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)		AGGCTGGCCCGTAGGAGTACT	0.542													18	90	---	---	---	---	PASS
MRGPRX1	259249	broad.mit.edu	37	11	18956275	18956275	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:18956275C>A	uc001mpg.2	-	1	275	c.57G>T	c.(55-57)GAG>GAT	p.E19D		NM_147199	NP_671732	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	19	Extracellular (Potential).				acute-phase response	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(2)|central_nervous_system(1)	3						AAAGAGTCTCCTCAGTTCCGT	0.527													10	373	---	---	---	---	PASS
TTC17	55761	broad.mit.edu	37	11	43515348	43515348	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:43515348G>T	uc001mxi.2	+	24	3334	c.3320G>T	c.(3319-3321)TGG>TTG	p.W1107L	TTC17_uc010rfj.1_Missense_Mutation_p.W1107L|TTC17_uc001mxl.2_Missense_Mutation_p.W163L|TTC17_uc001mxm.2_Missense_Mutation_p.W88L	NM_018259	NP_060729	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	1107	TPR 6.						binding			ovary(5)	5						GCACTGGTGTGGTATGAATCC	0.478													8	178	---	---	---	---	PASS
MADD	8567	broad.mit.edu	37	11	47307069	47307069	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:47307069C>A	uc001ner.1	+	14	2670	c.2479C>A	c.(2479-2481)CGG>AGG	p.R827R	MADD_uc001neq.2_Silent_p.R827R|MADD_uc001nev.1_Silent_p.R784R|MADD_uc001nes.1_Silent_p.R784R|MADD_uc001net.1_Silent_p.R827R|MADD_uc009yln.1_Silent_p.R784R|MADD_uc001neu.1_Silent_p.R784R|MADD_uc001nex.2_Silent_p.R827R|MADD_uc001nez.2_Silent_p.R784R|MADD_uc001new.2_Silent_p.R827R	NM_003682	NP_003673	Q8WXG6	MADD_HUMAN	MAP-kinase activating death domain-containing	827					activation of MAPK activity|apoptosis|cell surface receptor linked signaling pathway|regulation of apoptosis|regulation of cell cycle	cytoplasm|integral to membrane|plasma membrane	death receptor binding|protein kinase activator activity|Rab guanyl-nucleotide exchange factor activity			ovary(5)|skin(4)|central_nervous_system(2)	11				Lung(87;0.182)		GTCAGACTCTCGGGCAAGCTC	0.567													7	204	---	---	---	---	PASS
OR5AS1	219447	broad.mit.edu	37	11	55798388	55798388	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:55798388G>C	uc010riw.1	+	1	494	c.494G>C	c.(493-495)AGG>ACG	p.R165T		NM_001001921	NP_001001921	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS,	165	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|liver(1)|skin(1)	5	Esophageal squamous(21;0.00693)					CTCACATTCAGGCTGTCATTT	0.428													6	65	---	---	---	---	PASS
OR8I2	120586	broad.mit.edu	37	11	55861505	55861505	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:55861505C>A	uc010rix.1	+	1	722	c.722C>A	c.(721-723)GCA>GAA	p.A241E		NM_001003750	NP_001003750	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I,	241	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(1)	1	Esophageal squamous(21;0.00693)					TCCACCTGCGCATCCCACCTC	0.498													4	29	---	---	---	---	PASS
OR10V1	390201	broad.mit.edu	37	11	59481101	59481101	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:59481101T>C	uc001nof.1	-	1	218	c.218A>G	c.(217-219)TAT>TGT	p.Y73C		NM_001005324	NP_001005324	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V,	73	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						GGAAGATGTATAGAAGATTTC	0.453													6	36	---	---	---	---	PASS
MS4A7	58475	broad.mit.edu	37	11	60160167	60160167	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:60160167G>T	uc001npe.2	+	6	701	c.556G>T	c.(556-558)GTG>TTG	p.V186L	MS4A7_uc001npf.2_Missense_Mutation_p.V186L|MS4A7_uc001npg.2_Missense_Mutation_p.V141L|MS4A7_uc001nph.2_Missense_Mutation_p.V141L|MS4A14_uc001npi.2_Intron	NM_206939	NP_996822	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member	186	Helical; (Potential).					integral to membrane	receptor activity			ovary(1)|central_nervous_system(1)	2						GGGTGTCCTAGTGGTGATGCT	0.512													24	83	---	---	---	---	PASS
DDB1	1642	broad.mit.edu	37	11	61083759	61083759	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:61083759G>T	uc001nrc.3	-	12	1634	c.1408C>A	c.(1408-1410)CAG>AAG	p.Q470K	DDB1_uc010rle.1_Intron|DDB1_uc010rlf.1_Missense_Mutation_p.Q470K|DDB1_uc010rlg.1_RNA|DDB1_uc001nrd.2_Missense_Mutation_p.Q470K	NM_001923	NP_001914	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1	470	Interaction with CDT1.|Interaction with CUL4A.				cell cycle checkpoint|interspecies interaction between organisms|nucleotide-excision repair, DNA damage removal|proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex|Cul4B-RING ubiquitin ligase complex|cytoplasm|nucleoplasm	damaged DNA binding|protein binding			ovary(2)|lung(1)|central_nervous_system(1)	4						GTTATCACCTGGATAAGCTGC	0.438								NER					10	295	---	---	---	---	PASS
KDM2A	22992	broad.mit.edu	37	11	66947553	66947553	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:66947553G>T	uc001ojw.2	+	3	910	c.46G>T	c.(46-48)GGT>TGT	p.G16C	KDM2A_uc001ojx.2_RNA	NM_012308	NP_036440	Q9Y2K7	KDM2A_HUMAN	F-box and leucine-rich repeat protein 11	16					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(4)|lung(3)|breast(1)|skin(1)	9						TTCCTAGCGTGGTACCATGCG	0.398													5	54	---	---	---	---	PASS
DSCAML1	57453	broad.mit.edu	37	11	117307860	117307860	+	Silent	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:117307860G>A	uc001prh.1	-	26	4880	c.4878C>T	c.(4876-4878)TTC>TTT	p.F1626F		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1566	Extracellular (Potential).|Fibronectin type-III 6.				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CCAGGGTGGCGAACTGGGCTG	0.617													13	58	---	---	---	---	PASS
BCL9L	283149	broad.mit.edu	37	11	118769284	118769284	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:118769284C>A	uc001pug.2	-	8	5305	c.4340G>T	c.(4339-4341)AGC>ATC	p.S1447I	BCL9L_uc009zal.2_Missense_Mutation_p.S1442I	NM_182557	NP_872363	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1447					negative regulation of transforming growth factor beta receptor signaling pathway|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent		transcription coactivator activity			ovary(1)|pancreas(1)	2	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GGGCGGCTGGCTGTAGACCTC	0.672													3	9	---	---	---	---	PASS
UBASH3B	84959	broad.mit.edu	37	11	122653771	122653771	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:122653771G>T	uc001pyi.3	+	5	972	c.612G>T	c.(610-612)GTG>GTT	p.V204V		NM_032873	NP_116262	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing,	204						cytoplasm|nucleus	protein tyrosine phosphatase activity			central_nervous_system(1)	1		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		AAGTGCATGTGGAACCTCATA	0.463													9	280	---	---	---	---	PASS
GRAMD1B	57476	broad.mit.edu	37	11	123489412	123489412	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:123489412T>C	uc001pyx.2	+	18	2242	c.1913T>C	c.(1912-1914)CTG>CCG	p.L638P	GRAMD1B_uc001pyw.2_Missense_Mutation_p.L645P|GRAMD1B_uc010rzw.1_Missense_Mutation_p.L594P|GRAMD1B_uc010rzx.1_Missense_Mutation_p.L598P|GRAMD1B_uc001pyy.2_Missense_Mutation_p.L325P	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	638	Helical; (Potential).					integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CTGGTGCTGCTGGTCATCCTT	0.522													5	17	---	---	---	---	PASS
OR6M1	390261	broad.mit.edu	37	11	123676931	123676931	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:123676931T>C	uc010rzz.1	-	1	127	c.127A>G	c.(127-129)ATC>GTC	p.I43V		NM_001005325	NP_001005325	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M,	43	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(2)	2		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		AGGGAGATGATGGTGATGTTT	0.418													10	65	---	---	---	---	PASS
OR8B4	283162	broad.mit.edu	37	11	124294684	124294684	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:124294684G>T	uc010sak.1	-	1	84	c.84C>A	c.(82-84)TTC>TTA	p.F28L		NM_001005196	NP_001005196	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B,	28	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AGAATAGAAGGAAAAGAGGGA	0.468													14	48	---	---	---	---	PASS
OR8B8	26493	broad.mit.edu	37	11	124310527	124310527	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:124310527C>T	uc010sal.1	-	1	455	c.455G>A	c.(454-456)GGG>GAG	p.G152E		NM_012378	NP_036510	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B,	152	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CCCAGCAAACCCCATCCCATA	0.522													10	82	---	---	---	---	PASS
KIRREL3	84623	broad.mit.edu	37	11	126333056	126333056	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:126333056G>T	uc001qea.2	-	6	1099	c.738C>A	c.(736-738)ATC>ATA	p.I246I	KIRREL3_uc001qeb.2_Silent_p.I246I|KIRREL3_uc001qec.1_Silent_p.I246I	NM_032531	NP_115920	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 isoform 1	246	Extracellular (Potential).				hemopoiesis	extracellular region|integral to membrane|plasma membrane	protein binding			ovary(3)	3	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		ACTCACGCTGGATGTCAATGG	0.607													6	21	---	---	---	---	PASS
NTM	50863	broad.mit.edu	37	11	132177606	132177606	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr11:132177606G>T	uc001qgp.2	+	4	1214	c.550G>T	c.(550-552)GAA>TAA	p.E184*	NTM_uc001qgm.2_Nonsense_Mutation_p.E184*|NTM_uc010sch.1_Nonsense_Mutation_p.E175*|NTM_uc010sci.1_Nonsense_Mutation_p.E184*|NTM_uc010scj.1_Nonsense_Mutation_p.E143*|NTM_uc001qgo.2_Nonsense_Mutation_p.E184*|NTM_uc001qgq.2_Nonsense_Mutation_p.E184*|NTM_uc001qgr.2_5'UTR	NM_016522	NP_057606	Q9P121	NTRI_HUMAN	neurotrimin isoform 1	184	Ig-like C2-type 2.				cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)|skin(1)	6						GAGTGAAGACGAATACTTGGA	0.493													4	57	---	---	---	---	PASS
DCP1B	196513	broad.mit.edu	37	12	2062441	2062441	+	Missense_Mutation	SNP	T	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:2062441T>G	uc001qjx.1	-	7	745	c.665A>C	c.(664-666)GAA>GCA	p.E222A	DCP1B_uc010sdy.1_Missense_Mutation_p.E120A	NM_152640	NP_689853	Q8IZD4	DCP1B_HUMAN	decapping enzyme Dcp1b	222					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	hydrolase activity|protein binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			GTGTTGGGGTTCAGGGTCTAA	0.398													6	46	---	---	---	---	PASS
NDUFA9	4704	broad.mit.edu	37	12	4791398	4791398	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:4791398G>T	uc001qnc.2	+	9	838	c.828G>T	c.(826-828)CTG>CTT	p.L276L	NDUFA9_uc010ses.1_Silent_p.L57L	NM_005002	NP_004993	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	276					mitochondrial electron transport, NADH to ubiquinone|sodium ion transport	mitochondrial matrix|mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity|protein binding			ovary(1)	1					NADH(DB00157)	TTTTCCACCTGGTGAAGTACA	0.418													5	54	---	---	---	---	PASS
PRB3	5544	broad.mit.edu	37	12	11420857	11420857	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:11420857T>A	uc001qzs.2	-	3	364	c.326A>T	c.(325-327)CAG>CTG	p.Q109L	PRB4_uc001qzf.1_Intron	NM_006249	NP_006240	Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	109	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.|3.					extracellular region	Gram-negative bacterial cell surface binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(49;0.201)			ACCTTGGGACTGGTTTCCTCC	0.627													28	160	---	---	---	---	PASS
GUCY2C	2984	broad.mit.edu	37	12	14766078	14766078	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:14766078G>T	uc001rcd.2	-	27	3332	c.3195C>A	c.(3193-3195)ACC>ACA	p.T1065T		NM_004963	NP_004954	P25092	GUC2C_HUMAN	guanylate cyclase 2C precursor	1065	Cytoplasmic (Potential).				intracellular signal transduction|receptor guanylyl cyclase signaling pathway	integral to membrane	ATP binding|GTP binding|guanylate cyclase activity|protein binding|protein kinase activity|receptor activity			ovary(4)|skin(2)	6						CCTTGTCTGTGGTATTCAGCT	0.438													5	73	---	---	---	---	PASS
PTPRO	5800	broad.mit.edu	37	12	15733040	15733040	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:15733040C>A	uc001rcv.1	+	21	3162	c.2988C>A	c.(2986-2988)AAC>AAA	p.N996K	PTPRO_uc001rcw.1_Missense_Mutation_p.N968K|PTPRO_uc001rcx.1_Missense_Mutation_p.N185K|PTPRO_uc001rcy.1_Missense_Mutation_p.N185K|PTPRO_uc001rcz.1_Missense_Mutation_p.N157K|PTPRO_uc001rda.1_Missense_Mutation_p.N157K	NM_030667	NP_109592	Q16827	PTPRO_HUMAN	receptor-type protein tyrosine phosphatase O	996	Cytoplasmic (Potential).|Tyrosine-protein phosphatase.					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)	9		Hepatocellular(102;0.244)				TCAATGCCAACTATATTCCTG	0.378													6	20	---	---	---	---	PASS
C12orf35	55196	broad.mit.edu	37	12	32138230	32138230	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:32138230G>T	uc001rks.2	+	4	4755	c.4341G>T	c.(4339-4341)AAG>AAT	p.K1447N	C12orf35_uc001rkt.2_5'Flank	NM_018169	NP_060639	Q9HCM1	CL035_HUMAN	hypothetical protein LOC55196	1447										ovary(1)|skin(1)	2	all_cancers(9;3.36e-11)|all_epithelial(9;2.56e-11)|all_lung(12;5.67e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0114)			TAACTCCTAAGGAGTATTTAC	0.353													7	71	---	---	---	---	PASS
PLEKHA9	51054	broad.mit.edu	37	12	45568068	45568068	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:45568068G>T	uc001rom.1	-	3	618	c.81C>A	c.(79-81)TCC>TCA	p.S27S	PLEKHA9_uc009zke.2_Silent_p.S27S	NM_015899	NP_056983			pleckstrin homology domain containing, family A												0	Lung SC(27;0.192)|Renal(347;0.236)			GBM - Glioblastoma multiforme(48;0.173)		CCTCAGAATTGGACACACCAG	0.408													7	179	---	---	---	---	PASS
ASB8	140461	broad.mit.edu	37	12	48547277	48547277	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:48547277C>A	uc001rrh.2	-	2	172	c.3G>T	c.(1-3)ATG>ATT	p.M1I	ASB8_uc010slr.1_5'UTR	NM_024095	NP_077000	Q9H765	ASB8_HUMAN	ankyrin repeat and SOCS box-containing 8	1					intracellular signal transduction	cytoplasm|nucleus				kidney(1)	1						TACTGGAACTCATCAAGGCTC	0.448													5	51	---	---	---	---	PASS
GRASP	160622	broad.mit.edu	37	12	52404685	52404685	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:52404685A>T	uc001rzo.1	+	3	373	c.317A>T	c.(316-318)AAG>ATG	p.K106M	GRASP_uc001rzp.1_Translation_Start_Site	NM_181711	NP_859062	Q7Z6J2	GRASP_HUMAN	GRP1 (general receptor for phosphoinositides	106	PDZ.					cell junction|perinuclear region of cytoplasm|postsynaptic membrane				central_nervous_system(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(357;0.0967)		ACGTTGGAGAAGGAGGATAAC	0.532													26	161	---	---	---	---	PASS
DGKA	1606	broad.mit.edu	37	12	56330863	56330863	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:56330863G>A	uc001sij.2	+	3	391	c.127G>A	c.(127-129)GTC>ATC	p.V43I	DGKA_uc009zoc.1_Missense_Mutation_p.V43I|DGKA_uc001sih.1_5'UTR|DGKA_uc001sii.1_5'UTR|DGKA_uc009zod.1_Intron|DGKA_uc009zoe.1_Missense_Mutation_p.V43I|DGKA_uc001sik.2_Missense_Mutation_p.V43I|DGKA_uc001sil.2_Missense_Mutation_p.V43I|DGKA_uc001sim.2_Missense_Mutation_p.V43I|DGKA_uc001sin.2_Missense_Mutation_p.V43I|DGKA_uc009zof.2_5'UTR|DGKA_uc001sio.2_5'UTR	NM_001345	NP_001336	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	43					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|platelet activation	plasma membrane	ATP binding|calcium ion binding|diacylglycerol kinase activity			ovary(3)|pancreas(1)	4					Vitamin E(DB00163)	GGCTAAATATGTCCAAGGAGA	0.448													27	86	---	---	---	---	PASS
ATP5B	506	broad.mit.edu	37	12	57039026	57039026	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:57039026G>T	uc001slr.2	-	2	344	c.239C>A	c.(238-240)CCA>CAA	p.P80Q	SNORD59B_uc001sls.1_5'Flank|SNORD59A_uc001slt.1_5'Flank	NM_001686	NP_001677	P06576	ATPB_HUMAN	mitochondrial ATP synthase beta subunit	80					angiogenesis|ATP hydrolysis coupled proton transport|regulation of intracellular pH|respiratory electron transport chain	cell surface|mitochondrial nucleoid|mitochondrial proton-transporting ATP synthase, catalytic core|plasma membrane	ATP binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|hydrogen-exporting ATPase activity, phosphorylative mechanism|MHC class I protein binding|proton-transporting ATPase activity, rotational mechanism			ovary(1)	1						TAGAATTGGTGGTAGTCCCTC	0.557													5	72	---	---	---	---	PASS
LRP1	4035	broad.mit.edu	37	12	57595586	57595586	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:57595586G>T	uc001snd.2	+	67	10958	c.10492G>T	c.(10492-10494)GAG>TAG	p.E3498*		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	3498	Extracellular (Potential).|LDL-receptor class A 25.				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(8)|lung(3)|breast(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(2)	22				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TGGTGTGGACGAGTTCCGCTG	0.632													4	78	---	---	---	---	PASS
DPY19L2	283417	broad.mit.edu	37	12	64061895	64061895	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:64061895C>A	uc001srp.1	-	1	460	c.279G>T	c.(277-279)CGG>CGT	p.R93R	DPY19L2_uc009zqk.1_RNA	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2	93					multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GCACCTTTTCCCGGAGCTGCG	0.607													22	61	---	---	---	---	PASS
DPY19L2	283417	broad.mit.edu	37	12	64061896	64061896	+	Missense_Mutation	SNP	C	T	T	rs111719532		TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:64061896C>T	uc001srp.1	-	1	459	c.278G>A	c.(277-279)CGG>CAG	p.R93Q	DPY19L2_uc009zqk.1_RNA	NM_173812	NP_776173	Q6NUT2	D19L2_HUMAN	dpy-19-like 2	93					multicellular organismal development|spermatid development	integral to membrane				central_nervous_system(1)|skin(1)	2			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		CACCTTTTCCCGGAGCTGCGC	0.607													20	61	---	---	---	---	PASS
ACTR6	64431	broad.mit.edu	37	12	100617613	100617613	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:100617613G>T	uc001thb.1	+	11	1167	c.1111G>T	c.(1111-1113)GAT>TAT	p.D371Y	ACTR6_uc001thc.1_Missense_Mutation_p.D263Y|ACTR6_uc001thd.1_Missense_Mutation_p.D351Y|ACTR6_uc009ztu.1_Intron|ACTR6_uc001the.1_Missense_Mutation_p.D289Y|ACTR6_uc001thf.1_Missense_Mutation_p.D269Y|uc001thg.1_5'Flank	NM_022496	NP_071941	Q9GZN1	ARP6_HUMAN	ARP6 actin-related protein 6 homolog	371						cytoplasm|cytoskeleton				ovary(1)	1						AGAGAATGATGATTTTGAAGA	0.328													6	63	---	---	---	---	PASS
CMKLR1	1240	broad.mit.edu	37	12	108686289	108686289	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:108686289G>A	uc009zuw.2	-	3	642	c.451C>T	c.(451-453)CGC>TGC	p.R151C	CMKLR1_uc001tmw.2_Missense_Mutation_p.R151C|CMKLR1_uc001tmv.2_Missense_Mutation_p.R149C|CMKLR1_uc009zuv.2_Missense_Mutation_p.R151C	NM_001142345	NP_001135817	Q99788	CML1_HUMAN	chemokine-like receptor 1 isoform a	151	Cytoplasmic (Potential).				chemotaxis|immune response|negative regulation of interleukin-12 production|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage chemotaxis|regulation of calcium-mediated signaling|skeletal system development	integral to plasma membrane	chemokine receptor activity			lung(3)|ovary(1)|pancreas(1)	5						CGAACGCTGCGGTGGTTCTGG	0.572													6	65	---	---	---	---	PASS
NAA25	80018	broad.mit.edu	37	12	112486193	112486193	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:112486193C>A	uc001ttm.2	-	16	1803	c.1783G>T	c.(1783-1785)GAG>TAG	p.E595*	NAA25_uc001ttn.3_RNA|NAA25_uc009zvz.1_Nonsense_Mutation_p.E567*|NAA25_uc009zwa.1_Nonsense_Mutation_p.E595*	NM_024953	NP_079229	Q14CX7	NAA25_HUMAN	mitochondrial distribution and morphology 20	595						cytoplasm	protein binding			ovary(1)|breast(1)|pancreas(1)	3						GCGATAAACTCTGGGATCTTC	0.373													9	58	---	---	---	---	PASS
PTPN11	5781	broad.mit.edu	37	12	112926888	112926888	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:112926888G>T	uc001ttx.2	+	13	1888	c.1508G>T	c.(1507-1509)GGG>GTG	p.G503V		NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type	507	Tyrosine-protein phosphatase.		G -> A (in JMML).|G -> R (in patients with growth retardation, pulmonic stenosis and juvenile myelomonocytic leukemia).		axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	p.G503A(14)|p.G503V(8)|p.G503E(2)|p.G503L(1)|p.G503R(1)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392						CAGAGGTCAGGGATGGTCCAG	0.468			Mis		JMML|AML|MDS		Noonan Syndrome		Noonan_syndrome				31	174	---	---	---	---	PASS
NOS1	4842	broad.mit.edu	37	12	117768764	117768764	+	Missense_Mutation	SNP	A	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr12:117768764A>T	uc001twm.1	-	2	797	c.111T>A	c.(109-111)AGT>AGA	p.S37R		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1, neuronal	37	Interaction with NOSIP (By similarity).|PDZ.				multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(3)|skin(3)|pancreas(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)	L-Citrulline(DB00155)	CGGGCGGCTTACTGACCCGCT	0.577													8	41	---	---	---	---	PASS
BRCA2	675	broad.mit.edu	37	13	32900678	32900678	+	Nonsense_Mutation	SNP	G	T	T	rs80358780		TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr13:32900678G>T	uc001uub.1	+	7	786	c.559G>T	c.(559-561)GAG>TAG	p.E187*	BRCA2_uc001uua.1_Nonsense_Mutation_p.E64*	NM_000059	NP_000050	P51587	BRCA2_HUMAN	breast cancer 2, early onset	187					cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding	p.E187K(1)		ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TCTAGGAGCTGAGGTGGATCC	0.378			D|Mis|N|F|S		breast|ovarian|pancreatic	breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)		Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	TCGA Ovarian(8;0.087)			5	66	---	---	---	---	PASS
LCP1	3936	broad.mit.edu	37	13	46730577	46730577	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr13:46730577G>T	uc001vaz.3	-	5	613	c.487C>A	c.(487-489)CTT>ATT	p.L163I	LCP1_uc001vba.3_Missense_Mutation_p.L163I	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin	163	Actin-binding 1.|CH 1.				regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		ATTTACCAAAGGACAATGCCA	0.383			T	BCL6	NHL 								6	92	---	---	---	---	PASS
UTP14C	9724	broad.mit.edu	37	13	52603078	52603078	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr13:52603078G>T	uc001vgb.2	+	2	673	c.138G>T	c.(136-138)CTG>CTT	p.L46L	UTP14C_uc001vga.2_3'UTR|UTP14C_uc001vgc.2_RNA	NM_021645	NP_067677	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein,	46					cell differentiation|meiosis|multicellular organismal development|rRNA processing|spermatogenesis	nucleolus|small-subunit processome				ovary(3)|large_intestine(1)|breast(1)	5		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.3e-08)		AAAAGCTTCTGGAAGCAATCA	0.453													8	149	---	---	---	---	PASS
MYCBP2	23077	broad.mit.edu	37	13	77699588	77699588	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr13:77699588C>T	uc001vkf.2	-	55	7877	c.7786G>A	c.(7786-7788)GGG>AGG	p.G2596R	MYCBP2_uc010aev.2_Missense_Mutation_p.G2000R|MYCBP2_uc001vkg.1_Missense_Mutation_p.G59R	NM_015057	NP_055872	O75592	MYCB2_HUMAN	MYC binding protein 2	2596					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ligase activity|protein binding|zinc ion binding			ovary(4)|breast(4)|skin(3)|lung(2)|pancreas(1)	14		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		ACCCATGTCCCTTCAGAATTG	0.443													8	43	---	---	---	---	PASS
GPC5	2262	broad.mit.edu	37	13	92346109	92346109	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr13:92346109C>A	uc010tif.1	+	3	1360	c.994C>A	c.(994-996)CTC>ATC	p.L332I		NM_004466	NP_004457	P78333	GPC5_HUMAN	glypican 5 precursor	332						anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding			ovary(2)|skin(2)|upper_aerodigestive_tract(1)	5	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				ACAGGCTCACCTCAATGGACA	0.393													5	60	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	102029299	102029299	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr13:102029299G>T	uc001vox.1	-	5	673	c.484C>A	c.(484-486)CTG>ATG	p.L162M	NALCN_uc001voy.2_Translation_Start_Site|NALCN_uc001voz.2_Missense_Mutation_p.L162M|NALCN_uc001vpa.2_Missense_Mutation_p.L162M	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	162	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTCCTTGGCAGTTCAAATCGG	0.368													5	34	---	---	---	---	PASS
HECTD1	25831	broad.mit.edu	37	14	31585550	31585550	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:31585550G>C	uc001wrc.1	-	30	5999	c.5510C>G	c.(5509-5511)ACC>AGC	p.T1837S	HECTD1_uc001wra.1_5'UTR|HECTD1_uc001wrb.1_5'UTR|HECTD1_uc001wrd.1_Missense_Mutation_p.T1305S	NM_015382	NP_056197	Q9ULT8	HECD1_HUMAN	HECT domain containing 1	1837					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	intracellular	metal ion binding|protein binding|ubiquitin-protein ligase activity			ovary(3)|large_intestine(1)|lung(1)	5	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TCTGAAATTGGTGAGTGGTAA	0.408													3	41	---	---	---	---	PASS
SEC23A	10484	broad.mit.edu	37	14	39565184	39565184	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:39565184C>A	uc001wup.1	-	2	362	c.139G>T	c.(139-141)GAG>TAG	p.E47*	SEC23A_uc010tqa.1_Intron|SEC23A_uc010tqb.1_Nonsense_Mutation_p.E47*	NM_006364	NP_006355	Q15436	SC23A_HUMAN	SEC23-related protein A	47					COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|Golgi membrane|smooth endoplasmic reticulum membrane	protein binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		TCAGGTCTCTCTTTCAGTGGT	0.428													8	72	---	---	---	---	PASS
RPL10L	140801	broad.mit.edu	37	14	47120931	47120931	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:47120931G>T	uc001wwg.2	-	1	98	c.9C>A	c.(7-9)CGC>CGA	p.R3R		NM_080746	NP_542784	Q96L21	RL10L_HUMAN	ribosomal protein L10-like protein	3					spermatogenesis|translation	cytosolic large ribosomal subunit|nucleus	structural constituent of ribosome			ovary(1)	1						GAGCTGGACGGCGCCCCATGG	0.557													5	51	---	---	---	---	PASS
ATXN3	4287	broad.mit.edu	37	14	92548666	92548666	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:92548666C>A	uc001yac.3	-	8	822	c.753G>T	c.(751-753)AGG>AGT	p.R251S	ATXN3_uc010aug.2_Missense_Mutation_p.R236S|ATXN3_uc001yad.3_Missense_Mutation_p.R196S|ATXN3_uc010auh.2_Missense_Mutation_p.R185S|ATXN3_uc001yae.3_Missense_Mutation_p.R153S|ATXN3_uc010twl.1_RNA	NM_004993	NP_004984	P54252	ATX3_HUMAN	ataxin 3 reference isoform	251	UIM 2.				cell death|nervous system development|nucleotide-excision repair|regulation of transcription, DNA-dependent|synaptic transmission|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleoplasm	cysteine-type peptidase activity|protein binding				0		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		GCTGAATAGCCCTGCGGAGAT	0.413													12	49	---	---	---	---	PASS
DICER1	23405	broad.mit.edu	37	14	95560326	95560326	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:95560326G>T	uc001ydw.2	-	25	5445	c.5263C>A	c.(5263-5265)CAC>AAC	p.H1755N	DICER1_uc010avh.1_Missense_Mutation_p.H653N|DICER1_uc001ydv.2_Missense_Mutation_p.H1745N|DICER1_uc001ydx.2_Missense_Mutation_p.H1755N	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	1755	RNase III 2.				negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-miRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			skin(2)|ovary(1)|pancreas(1)|lung(1)	5		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		AAGTACTTGTGGTAGTCGTAC	0.507			Mis F|N			pleuropulmonary blastoma			DICER_1_syndrome_|Familial_Multinodular_Goiter_				6	77	---	---	---	---	PASS
CLMN	79789	broad.mit.edu	37	14	95669862	95669862	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:95669862C>A	uc001yef.2	-	9	1940	c.1824G>T	c.(1822-1824)AGG>AGT	p.R608S		NM_024734	NP_079010	Q96JQ2	CLMN_HUMAN	calmin	608						integral to membrane	actin binding				0				Epithelial(152;0.193)		ATTTAATACTCCTTTTACCTA	0.443													18	46	---	---	---	---	PASS
ATG2B	55102	broad.mit.edu	37	14	96771996	96771996	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:96771996G>T	uc001yfi.2	-	31	5028	c.4663C>A	c.(4663-4665)CTT>ATT	p.L1555I		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1555										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TGCCAGACAAGAGAGACCTCC	0.408													5	54	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106110271	106110271	+	RNA	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:106110271C>T	uc010tyt.1	-	3642		c.60980G>A			uc001yrs.2_Intron|uc001yrt.2_Intron|uc001yrw.1_Intron|uc001yrx.1_Intron|uc001yrz.1_RNA					Parts of antibodies, mostly variable regions.												0						GACTGACGGTCCTGCCACAGG	0.627													10	51	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106494206	106494206	+	RNA	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:106494206T>C	uc010tyt.1	-	1760		c.34792A>G								Parts of antibodies, mostly variable regions.												0						ACCTGGTTTTTGGAGGTGTCC	0.517													20	57	---	---	---	---	PASS
ADAM6	8755	broad.mit.edu	37	14	106494324	106494324	+	RNA	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr14:106494324G>C	uc010tyt.1	-	1760		c.34674C>G								Parts of antibodies, mostly variable regions.												0						GACGGATCCAGCCCACACCCA	0.562													5	51	---	---	---	---	PASS
TUBGCP5	114791	broad.mit.edu	37	15	22853811	22853811	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:22853811G>T	uc001yur.3	+	12	1579	c.1449G>T	c.(1447-1449)GGG>GGT	p.G483G	TUBGCP5_uc001yuq.2_Silent_p.G483G|TUBGCP5_uc010axz.1_Silent_p.G70G	NM_052903	NP_443135	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	483					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		TCGTGCACGGGCACCTGTGGG	0.602													4	18	---	---	---	---	PASS
GABRG3	2567	broad.mit.edu	37	15	27222171	27222171	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:27222171G>A	uc001zbg.1	+	2	242	c.76G>A	c.(76-78)GAA>AAA	p.E26K	GABRG3_uc001zbf.2_Missense_Mutation_p.E26K	NM_033223	NP_150092	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma	26	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway|synaptic transmission	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity				0		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)		GGAAGAGGATGAATATGAAGA	0.428													8	52	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34032134	34032134	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:34032134G>T	uc001zhi.2	+	51	7828	c.7758G>T	c.(7756-7758)TTG>TTT	p.L2586F	RYR3_uc010bar.2_Missense_Mutation_p.L2586F	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	2586	4 X approximate repeats.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CAGCCACGTTGGAGAAACAGA	0.463													10	49	---	---	---	---	PASS
TYRO3	7301	broad.mit.edu	37	15	41856430	41856430	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:41856430G>A	uc001zof.1	+	5	853	c.629G>A	c.(628-630)GGC>GAC	p.G210D		NM_006293	NP_006284	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase precursor	210	Ig-like C2-type 2.|Extracellular (Potential).					integral to plasma membrane	ATP binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			ovary(3)|lung(2)|central_nervous_system(1)	6		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		AACCTAAAAGGCCTGGCCTCT	0.597													12	62	---	---	---	---	PASS
ZFP106	64397	broad.mit.edu	37	15	42742724	42742724	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:42742724G>T	uc001zpw.2	-	2	2012	c.1677C>A	c.(1675-1677)ACC>ACA	p.T559T	ZFP106_uc001zpu.2_5'Flank|ZFP106_uc001zpv.2_Intron|ZFP106_uc001zpx.2_Intron|ZFP106_uc010udh.1_Silent_p.T342T|ZFP106_uc001zpy.1_Silent_p.T582T	NM_022473	NP_071918	Q9H2Y7	ZF106_HUMAN	zinc finger protein 106 homolog	559						nucleolus	zinc ion binding			central_nervous_system(2)|ovary(1)	3		all_cancers(109;1.63e-12)|all_epithelial(112;3.97e-11)|Lung NSC(122;2.04e-07)|all_lung(180;8.31e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.6e-07)		CATAGTTCCTGGTACTTTTAG	0.368													6	80	---	---	---	---	PASS
WDR76	79968	broad.mit.edu	37	15	44143306	44143306	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:44143306G>T	uc001zti.1	+	9	1077	c.1054G>T	c.(1054-1056)GGA>TGA	p.G352*		NM_024908	NP_079184	Q9H967	WDR76_HUMAN	WD repeat domain 76	352	WD 1.										0		all_cancers(109;3.26e-11)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.61e-06)|all_lung(180;1.5e-05)|Melanoma(134;0.0417)		all cancers(107;3.78e-21)|GBM - Glioblastoma multiforme(94;5.04e-07)		TAAAGAAGATGGAGTTTATGT	0.433													6	87	---	---	---	---	PASS
CTDSPL2	51496	broad.mit.edu	37	15	44816320	44816320	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:44816320G>T	uc001ztr.2	+	13	1765	c.1349G>T	c.(1348-1350)CGA>CTA	p.R450L	CTDSPL2_uc001zts.2_Missense_Mutation_p.R450L|CTDSPL2_uc001ztt.2_Missense_Mutation_p.R450L|CTDSPL2_uc010bdv.2_Missense_Mutation_p.R378L	NM_016396	NP_057480	Q05D32	CTSL2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II,	450							phosphoprotein phosphatase activity				0		all_cancers(109;4.36e-14)|all_epithelial(112;9.8e-12)|Lung NSC(122;1.66e-07)|all_lung(180;1.47e-06)|Melanoma(134;0.0122)		all cancers(107;1.02e-20)|GBM - Glioblastoma multiforme(94;1.49e-06)|COAD - Colon adenocarcinoma(120;0.0857)|Colorectal(105;0.0905)		GAAGATGTTCGACCACACATC	0.388													4	50	---	---	---	---	PASS
DUOX2	50506	broad.mit.edu	37	15	45402882	45402882	+	Silent	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:45402882G>A	uc010bea.2	-	8	1112	c.909C>T	c.(907-909)CCC>CCT	p.P303P	DUOX2_uc001zun.2_Silent_p.P303P	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	303	Extracellular (Potential).|Peroxidase-like; mediates peroxidase activity (By similarity).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|skin(2)|pancreas(1)	5		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		GCAGGAAGCTGGGCAGCCACT	0.612													6	21	---	---	---	---	PASS
UNC13C	440279	broad.mit.edu	37	15	54306924	54306924	+	Silent	SNP	A	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:54306924A>C	uc002ack.2	+	1	1824	c.1824A>C	c.(1822-1824)GGA>GGC	p.G608G		NM_001080534	NP_001074003	Q8NB66	UN13C_HUMAN	unc-13 homolog C	608					exocytosis|intracellular signal transduction	cell junction|cytoplasm|presynaptic membrane	metal ion binding			ovary(5)|pancreas(2)	7				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ATTTGAATGGAGGTGTTCAGG	0.512													15	63	---	---	---	---	PASS
TLN2	83660	broad.mit.edu	37	15	63014652	63014652	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:63014652C>T	uc002alb.3	+	23	3092	c.3092C>T	c.(3091-3093)ACC>ATC	p.T1031I		NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1031	Ala-rich.				cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						AACCTGGCCACCAGCTTGGCG	0.627													7	25	---	---	---	---	PASS
TLN2	83660	broad.mit.edu	37	15	63045984	63045984	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:63045984G>T	uc002alb.3	+	33	4345	c.4345G>T	c.(4345-4347)GTT>TTT	p.V1449F	TLN2_uc002alc.3_5'UTR	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1449					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(5)|upper_aerodigestive_tract(2)|lung(2)|breast(2)	11						TGCATACTTGGTTGGCATCTC	0.577													6	52	---	---	---	---	PASS
PML	5371	broad.mit.edu	37	15	74326832	74326832	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:74326832G>T	uc002awv.2	+	7	1811	c.1671G>T	c.(1669-1671)GTG>GTT	p.V557V	PML_uc002awm.2_Silent_p.V557V|PML_uc002awl.2_Missense_Mutation_p.W423L|PML_uc002awj.1_3'UTR|PML_uc002awk.2_Silent_p.V557V|PML_uc002awn.2_Missense_Mutation_p.W560L|PML_uc002awo.2_Silent_p.V509V|PML_uc002awp.2_Intron|PML_uc002awq.2_Missense_Mutation_p.W560L|PML_uc002awr.2_Silent_p.V557V|PML_uc002aws.2_Silent_p.V509V|PML_uc002awt.2_Missense_Mutation_p.W423L|PML_uc002awu.2_Silent_p.V509V|PML_uc010ule.1_Silent_p.V118V|PML_uc002awx.2_Missense_Mutation_p.W270L|PML_uc002awy.2_5'UTR	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1	557	Interaction with SUMO1 and sumoylated proteins.			VVVI->AAAS: Abolishes SUMO1 binding.	cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)|breast(1)	5						AACGCGTTGTGGTGATCAGCA	0.582			T	RARA|PAX5	APL|ALL								8	145	---	---	---	---	PASS
TMED3	23423	broad.mit.edu	37	15	79606180	79606180	+	Nonsense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:79606180C>T	uc002beu.2	+	2	351	c.250C>T	c.(250-252)CAG>TAG	p.Q84*	TMED3_uc010unj.1_Nonsense_Mutation_p.Q84*|TMED3_uc002bev.2_RNA	NM_007364	NP_031390	Q9Y3Q3	TMED3_HUMAN	transmembrane emp24 domain containing 3	84	Lumenal (Potential).|GOLD.				protein transport	ER-Golgi intermediate compartment membrane|Golgi apparatus|integral to membrane				ovary(1)|skin(1)	2						AACGAAGAAGCAGTACGACAG	0.473													20	74	---	---	---	---	PASS
ARNT2	9915	broad.mit.edu	37	15	80872871	80872871	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:80872871G>T	uc002bfr.2	+	16	1899	c.1733G>T	c.(1732-1734)CGT>CTT	p.R578L	ARNT2_uc010unm.1_Missense_Mutation_p.R567L|ARNT2_uc002bfs.2_Missense_Mutation_p.R567L	NM_014862	NP_055677	Q9HBZ2	ARNT2_HUMAN	aryl hydrocarbon receptor nuclear translocator	578					central nervous system development|in utero embryonic development|response to hypoxia		aryl hydrocarbon receptor binding|DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(3)|ovary(1)|pancreas(1)	5			BRCA - Breast invasive adenocarcinoma(143;0.134)			ACAGGGAGTCGTCCGCCCTTT	0.562													7	38	---	---	---	---	PASS
ISG20	3669	broad.mit.edu	37	15	89182735	89182735	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:89182735G>C	uc002bmv.1	+	2	431	c.138G>C	c.(136-138)GAG>GAC	p.E46D	ISG20_uc002bmu.1_Intron|ISG20_uc002bmw.1_RNA|ISG20_uc010upn.1_RNA	NM_002201	NP_002192	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease	46					cell proliferation|DNA catabolic process, exonucleolytic|response to virus|RNA catabolic process|type I interferon-mediated signaling pathway	PML body	3'-5'-exoribonuclease activity|exoribonuclease II activity|metal ion binding|RNA binding|single-stranded DNA specific 3'-5' exodeoxyribonuclease activity				0	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			TCCGGCCTGAGGGAGAGATCA	0.637													7	46	---	---	---	---	PASS
C15orf51	196968	broad.mit.edu	37	15	100339997	100339997	+	RNA	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:100339997G>C	uc010urx.1	-	4		c.930C>G			C15orf51_uc010ury.1_RNA|uc002bvp.2_5'Flank|C15orf51_uc010urz.1_RNA|uc002bvq.2_RNA|uc002bvt.1_5'Flank	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						GTGTCTTCTCGTTCCCACGCG	0.612													4	43	---	---	---	---	PASS
LRRK1	79705	broad.mit.edu	37	15	101528851	101528851	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:101528851C>A	uc002bwr.2	+	5	765	c.446C>A	c.(445-447)CCC>CAC	p.P149H	LRRK1_uc010usb.1_RNA|LRRK1_uc010usc.1_RNA|LRRK1_uc002bwq.1_Missense_Mutation_p.P149H	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	149					small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CCCTGCAGTCCCCAGCGGCTT	0.607													7	130	---	---	---	---	PASS
PKD1	5310	broad.mit.edu	37	16	2160565	2160565	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr16:2160565G>A	uc002cos.1	-	15	4812	c.4603C>T	c.(4603-4605)CGC>TGC	p.R1535C	PKD1_uc002cot.1_Missense_Mutation_p.R1535C	NM_001009944	NP_001009944	P98161	PKD1_HUMAN	polycystin 1 isoform 1 precursor	1535	Extracellular (Potential).|PKD 10.				calcium-independent cell-matrix adhesion|homophilic cell adhesion|neuropeptide signaling pathway	basolateral plasma membrane|integral to plasma membrane	protein domain specific binding|sugar binding			central_nervous_system(2)|skin(1)	3						GCCTCGCTGCGGCTCACCTCA	0.657													12	18	---	---	---	---	PASS
TMC5	79838	broad.mit.edu	37	16	19481080	19481080	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr16:19481080G>C	uc002dgc.3	+	10	2464	c.1715G>C	c.(1714-1716)TGG>TCG	p.W572S	TMC5_uc010vaq.1_Missense_Mutation_p.W572S|TMC5_uc002dgb.3_Missense_Mutation_p.W572S|TMC5_uc010var.1_Missense_Mutation_p.W572S|TMC5_uc002dgd.1_Missense_Mutation_p.W326S|TMC5_uc002dge.3_Missense_Mutation_p.W326S|TMC5_uc002dgf.3_Missense_Mutation_p.W255S|TMC5_uc002dgg.3_Missense_Mutation_p.W213S	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	572	Cytoplasmic (Potential).					integral to membrane				skin(1)	1						ATCTTTTGCTGGGACTTCACT	0.448													11	67	---	---	---	---	PASS
TMC5	79838	broad.mit.edu	37	16	19481081	19481081	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr16:19481081G>T	uc002dgc.3	+	10	2465	c.1716G>T	c.(1714-1716)TGG>TGT	p.W572C	TMC5_uc010vaq.1_Missense_Mutation_p.W572C|TMC5_uc002dgb.3_Missense_Mutation_p.W572C|TMC5_uc010var.1_Missense_Mutation_p.W572C|TMC5_uc002dgd.1_Missense_Mutation_p.W326C|TMC5_uc002dge.3_Missense_Mutation_p.W326C|TMC5_uc002dgf.3_Missense_Mutation_p.W255C|TMC5_uc002dgg.3_Missense_Mutation_p.W213C	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	572	Cytoplasmic (Potential).					integral to membrane				skin(1)	1						TCTTTTGCTGGGACTTCACTG	0.448													13	67	---	---	---	---	PASS
ATXN2L	11273	broad.mit.edu	37	16	28841356	28841356	+	Silent	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr16:28841356G>C	uc002drc.2	+	8	1179	c.1011G>C	c.(1009-1011)CGG>CGC	p.R337R	uc010vct.1_Intron|ATXN2L_uc010byl.1_Silent_p.R337R|ATXN2L_uc002drb.2_Silent_p.R337R|ATXN2L_uc002dqy.2_Silent_p.R337R|ATXN2L_uc002dra.2_Silent_p.R337R|ATXN2L_uc002dqz.2_Silent_p.R337R|ATXN2L_uc010vdb.1_Silent_p.R337R|ATXN2L_uc002dre.2_Silent_p.R337R|ATXN2L_uc002drf.2_5'UTR	NM_007245	NP_009176	Q8WWM7	ATX2L_HUMAN	ataxin 2 related protein isoform A	337				R -> RG (in Ref. 6; AAB19201).		membrane				upper_aerodigestive_tract(1)|ovary(1)	2						GCTCAGGGCGGGAGAGCCCCA	0.612													4	16	---	---	---	---	PASS
STX1B	112755	broad.mit.edu	37	16	31012876	31012876	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr16:31012876G>T	uc010cad.2	-	2	191	c.79C>A	c.(79-81)CAC>AAC	p.H27N	STX1B_uc010vfd.1_Missense_Mutation_p.H27N	NM_052874	NP_443106	P61266	STX1B_HUMAN	syntaxin 1B	27	Cytoplasmic (Potential).				intracellular protein transport|neurotransmitter transport|synaptic transmission	integral to plasma membrane	extracellular-glutamate-gated ion channel activity|SNAP receptor activity				0						TCCATGAAGTGGTCCCGATCC	0.408													6	36	---	---	---	---	PASS
ATP2A3	489	broad.mit.edu	37	17	3850763	3850763	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:3850763C>A	uc002fxb.1	-	8	1168	c.1017G>T	c.(1015-1017)GTG>GTT	p.V339V	ATP2A3_uc002fwx.1_Silent_p.V339V|ATP2A3_uc002fwy.1_Silent_p.V339V|ATP2A3_uc002fwz.1_Silent_p.V339V|ATP2A3_uc002fxa.1_Silent_p.V339V|ATP2A3_uc002fxc.1_Silent_p.V339V|ATP2A3_uc002fxd.1_Silent_p.V339V	NM_174955	NP_777615	Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous isoform b	339	Cytoplasmic (By similarity).				ATP biosynthetic process|platelet activation	integral to membrane|nuclear membrane|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			ovary(3)|breast(1)|central_nervous_system(1)	5				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		CCAGGGTCTCCACGGACGGCA	0.652													5	59	---	---	---	---	PASS
PLD2	5338	broad.mit.edu	37	17	4712418	4712418	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:4712418C>T	uc002fzc.2	+	5	508	c.407C>T	c.(406-408)GCC>GTC	p.A136V	PLD2_uc010vsj.1_5'UTR|PLD2_uc002fzd.2_Missense_Mutation_p.A136V	NM_002663	NP_002654	O14939	PLD2_HUMAN	phospholipase D2	136	PX.				cell communication|cytoskeleton organization|small GTPase mediated signal transduction		NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5					Choline(DB00122)	TATTCTCCAGCCCGAGATGCA	0.582													29	76	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7577534	7577534	+	Missense_Mutation	SNP	C	A	A	rs28934571		TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:7577534C>A	uc002gim.2	-	7	941	c.747G>T	c.(745-747)AGG>AGT	p.R249S	TP53_uc002gig.1_Missense_Mutation_p.R249S|TP53_uc002gih.2_Missense_Mutation_p.R249S|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R117S|TP53_uc010cng.1_Missense_Mutation_p.R117S|TP53_uc002gii.1_Missense_Mutation_p.R117S|TP53_uc010cnh.1_Missense_Mutation_p.R249S|TP53_uc010cni.1_Missense_Mutation_p.R249S|TP53_uc002gij.2_Missense_Mutation_p.R249S|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R156S|TP53_uc002gio.2_Missense_Mutation_p.R117S	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	249	|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).|R -> T (in sporadic cancers; somatic mutation).|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> I (in a sporadic cancer; somatic mutation).|R -> M (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R249S(303)|p.R249M(25)|p.R249G(24)|p.R249W(23)|p.R249T(16)|p.R249K(14)|p.0?(7)|p.R249R(6)|p.R249fs*96(6)|p.M246_P250delMNRRP(2)|p.R249fs*14(2)|p.N247_P250delNRRP(1)|p.R249fs*19(1)|p.R249fs*15(1)|p.R249_I251delRPI(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.R249_T256delRPILTIIT(1)|p.R249_P250>SS(1)|p.P250fs*14(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		TGAGGATGGGCCTCCGGTTCA	0.572		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			15	30	---	---	---	---	PASS
CHD3	1107	broad.mit.edu	37	17	7806032	7806032	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:7806032C>A	uc002gje.2	+	21	3507	c.3357C>A	c.(3355-3357)ATC>ATA	p.I1119I	CHD3_uc002gjd.2_Silent_p.I1178I|CHD3_uc002gjf.2_Silent_p.I1119I|CHD3_uc002gjh.2_5'Flank	NM_001005273	NP_001005273	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1119	Helicase C-terminal.				chromatin modification|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	microtubule organizing center|NuRD complex	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|zinc ion binding			breast(1)	1		Prostate(122;0.202)				AGGAGGCCATCGATCGGTTTA	0.547													4	53	---	---	---	---	PASS
MYH8	4626	broad.mit.edu	37	17	10298626	10298626	+	Missense_Mutation	SNP	C	G	G	rs61730807	byFrequency	TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:10298626C>G	uc002gmm.2	-	34	4881	c.4786G>C	c.(4786-4788)GTC>CTC	p.V1596L	uc002gml.1_Intron	NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1596	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			skin(6)|ovary(3)|breast(2)	11						GTCTCCACGACTCTAGTGTGG	0.428									Trismus-Pseudocamptodactyly_Syndrome_with_Cardiac_Myxoma_and_Freckling				11	43	---	---	---	---	PASS
DNAH9	1770	broad.mit.edu	37	17	11514974	11514974	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:11514974G>T	uc002gne.2	+	4	849	c.781G>T	c.(781-783)GAT>TAT	p.D261Y	DNAH9_uc002gnd.1_Missense_Mutation_p.D261Y	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	261	Stem (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			skin(10)|ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	20		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CAGGTATGAAGATCTGAAATA	0.458													12	45	---	---	---	---	PASS
FLII	2314	broad.mit.edu	37	17	18149711	18149711	+	Silent	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:18149711G>A	uc002gsr.1	-	24	3168	c.3117C>T	c.(3115-3117)ATC>ATT	p.I1039I	FLII_uc002gsq.1_Silent_p.I910I|FLII_uc010cpy.1_Silent_p.I1028I|FLII_uc010vxn.1_Silent_p.I1008I|FLII_uc010vxo.1_Silent_p.I984I	NM_002018	NP_002009	Q13045	FLII_HUMAN	flightless I homolog	1039					multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(1)|skin(1)	2	all_neural(463;0.228)					CCCGGTGGATGATGAACTTCC	0.632													15	106	---	---	---	---	PASS
FBXW10	10517	broad.mit.edu	37	17	18682490	18682490	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:18682490T>C	uc002guk.2	+	14	3270	c.3038T>C	c.(3037-3039)GTT>GCT	p.V1013A	FBXW10_uc002guj.2_Missense_Mutation_p.V1012A|FBXW10_uc002gul.2_Missense_Mutation_p.V1022A|FBXW10_uc010cqh.1_Missense_Mutation_p.V960A|FAM18B_uc002gum.2_5'Flank	NM_031456	NP_113644	Q5XX13	FBW10_HUMAN	F-box and WD-40 domain protein 10	1013										ovary(1)	1						ACTGGAGTGGTTGATCCAGGA	0.502													9	40	---	---	---	---	PASS
RAB34	83871	broad.mit.edu	37	17	27042864	27042864	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:27042864C>A	uc002hce.2	-	4	892	c.268G>T	c.(268-270)GAG>TAG	p.E90*	RAB34_uc002hcg.2_Nonsense_Mutation_p.E90*|RAB34_uc002hcf.2_Nonsense_Mutation_p.E91*|RAB34_uc010was.1_Nonsense_Mutation_p.E147*|RAB34_uc010wat.1_Nonsense_Mutation_p.E147*|RAB34_uc002hch.2_Nonsense_Mutation_p.E90*|RAB34_uc010wau.1_Nonsense_Mutation_p.E68*|RAB34_uc010wav.1_Nonsense_Mutation_p.E148*	NM_031934	NP_114140	Q9BZG1	RAB34_HUMAN	Ras-related protein RAB34 isoform 1	90					protein transport|small GTPase mediated signal transduction	Golgi apparatus	GTP binding				0	Lung NSC(42;0.00431)					CGTTCCATCTCGAAGTCCACT	0.547													5	115	---	---	---	---	PASS
SLFN5	162394	broad.mit.edu	37	17	33592328	33592328	+	Silent	SNP	C	T	T	rs149671075	by1000genomes	TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:33592328C>T	uc002hjf.3	+	5	2214	c.2097C>T	c.(2095-2097)CCC>CCT	p.P699P	SLFN5_uc010wcg.1_3'UTR	NM_144975	NP_659412	Q08AF3	SLFN5_HUMAN	schlafen family member 5	699					cell differentiation		ATP binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		TCCCCCCTCCCTCAGACCAGT	0.493													16	63	---	---	---	---	PASS
TUBG2	27175	broad.mit.edu	37	17	40812318	40812318	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:40812318C>A	uc010wgr.1	+	3	570	c.314C>A	c.(313-315)GCC>GAC	p.A105D	TUBG2_uc002iaq.2_5'UTR|TUBG2_uc002iar.2_5'UTR|TUBG2_uc002ias.2_5'UTR|TUBG2_uc002iap.2_5'UTR	NM_016437	NP_057521	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	105					G2/M transition of mitotic cell cycle|microtubule-based process|protein polymerization	cytosol	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		AACAACTGGGCCAGCGGATTC	0.542													4	44	---	---	---	---	PASS
C17orf57	124989	broad.mit.edu	37	17	45507265	45507265	+	Missense_Mutation	SNP	A	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:45507265A>G	uc002iln.2	+	24	2987	c.2576A>G	c.(2575-2577)GAC>GGC	p.D859G	C17orf57_uc002ilm.2_Missense_Mutation_p.D763G	NM_152347	NP_689560	Q8IY85	CQ057_HUMAN	hypothetical protein LOC124989	859							calcium ion binding			breast(1)|central_nervous_system(1)|skin(1)	3						TTATTGATGGACAAGGACCTT	0.383													3	45	---	---	---	---	PASS
HOXB3	3213	broad.mit.edu	37	17	46629716	46629716	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:46629716T>C	uc002inn.2	-	1	521	c.121A>G	c.(121-123)ACG>GCG	p.T41A	HOXB3_uc010wlm.1_5'UTR|HOXB3_uc010dbf.2_Missense_Mutation_p.T41A|HOXB3_uc010dbg.2_Missense_Mutation_p.T41A|HOXB3_uc002ino.2_Missense_Mutation_p.T41A|HOXB3_uc010wlk.1_Intron|HOXB3_uc010wll.1_5'UTR	NM_002146	NP_002137	P14651	HXB3_HUMAN	homeobox B3	41					angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TCCAGGTGCGTGGCGGCCTGA	0.647													3	25	---	---	---	---	PASS
CA10	56934	broad.mit.edu	37	17	50008357	50008357	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:50008357C>A	uc002itw.3	-	3	1258	c.272G>T	c.(271-273)GGC>GTC	p.G91V	CA10_uc002itv.3_Missense_Mutation_p.G97V|CA10_uc002itx.3_Missense_Mutation_p.G91V|CA10_uc002ity.3_Missense_Mutation_p.G91V|CA10_uc002itz.2_Missense_Mutation_p.G91V	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	91					brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			TACCTTCCTGCCCCCCGTGTT	0.493													20	117	---	---	---	---	PASS
MED13	9969	broad.mit.edu	37	17	60042580	60042580	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:60042580G>T	uc002izo.2	-	20	4708	c.4631C>A	c.(4630-4632)TCC>TAC	p.S1544Y		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1544	Ser-rich.				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						ATTCAAGTTGGAGGATGATGA	0.418													6	72	---	---	---	---	PASS
SCN4A	6329	broad.mit.edu	37	17	62036742	62036742	+	Silent	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:62036742G>A	uc002jds.1	-	12	1979	c.1902C>T	c.(1900-1902)CCC>CCT	p.P634P		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	634	II.				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)	AATACTCGTAGGGGTCCATGG	0.572													8	38	---	---	---	---	PASS
ST6GALNAC1	55808	broad.mit.edu	37	17	74622817	74622817	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr17:74622817G>T	uc002jsh.2	-	5	1401	c.1227C>A	c.(1225-1227)TCC>TCA	p.S409S	ST6GALNAC1_uc002jsi.2_Silent_p.S277S|ST6GALNAC1_uc002jsj.2_RNA	NM_018414	NP_060884	Q9NSC7	SIA7A_HUMAN	sialyltransferase 7A	409	Lumenal (Potential).				protein glycosylation	integral to Golgi membrane	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity				0						AGCCGTAGAAGGATGTCCGAG	0.532													11	323	---	---	---	---	PASS
EMILIN2	84034	broad.mit.edu	37	18	2892094	2892094	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr18:2892094C>A	uc002kln.2	+	4	2128	c.1969C>A	c.(1969-1971)CCG>ACG	p.P657T		NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2 precursor	657					cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			skin(2)|ovary(1)	3				READ - Rectum adenocarcinoma(2;0.1)		GGACACCCTGCCGTCCCCCCA	0.552													6	46	---	---	---	---	PASS
CEP192	55125	broad.mit.edu	37	18	13073110	13073110	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr18:13073110C>A	uc010xac.1	+	30	5622	c.5542C>A	c.(5542-5544)CGA>AGA	p.R1848R	CEP192_uc010dlf.1_RNA|CEP192_uc010xad.1_Silent_p.R1373R|CEP192_uc002kru.2_RNA|CEP192_uc002krv.2_Silent_p.R270R|CEP192_uc002krw.2_5'UTR|CEP192_uc002krx.2_5'UTR	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa	1848										ovary(4)|pancreas(1)	5						TGCACCTACTCGATTATCTTG	0.383													6	87	---	---	---	---	PASS
DSG3	1830	broad.mit.edu	37	18	29045295	29045295	+	Missense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr18:29045295G>A	uc002kws.2	+	10	1395	c.1286G>A	c.(1285-1287)CGT>CAT	p.R429H		NM_001944	NP_001935	P32926	DSG3_HUMAN	desmoglein 3 preproprotein	429	Cadherin 4.|Extracellular (Potential).				cellular component disassembly involved in apoptosis|homophilic cell adhesion	cytosol|desmosome|integral to membrane	calcium ion binding			skin(4)|ovary(3)|lung(1)|central_nervous_system(1)	9			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GTCATGGGACGTAACGATGGT	0.269													9	48	---	---	---	---	PASS
CNDP1	84735	broad.mit.edu	37	18	72245452	72245452	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr18:72245452G>T	uc002llq.2	+	9	1268	c.1057G>T	c.(1057-1059)GAG>TAG	p.E353*	CNDP1_uc002lls.2_Nonsense_Mutation_p.E156*	NM_032649	NP_116038	Q96KN2	CNDP1_HUMAN	carnosinase 1 precursor	353					proteolysis	extracellular region	carboxypeptidase activity|dipeptidase activity|metal ion binding|metallopeptidase activity|tripeptidase activity				0		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		TCATGGGATCGAGGGCGCGTT	0.423													4	58	---	---	---	---	PASS
AP3D1	8943	broad.mit.edu	37	19	2121290	2121290	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:2121290C>A	uc002luz.2	-	13	1345	c.1122G>T	c.(1120-1122)ATG>ATT	p.M374I	AP3D1_uc002luy.2_Missense_Mutation_p.M283I|AP3D1_uc002lva.2_Missense_Mutation_p.M374I	NM_003938	NP_003929	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1	374					eye pigment biosynthetic process|intracellular protein transport|regulation of sequestering of zinc ion|vesicle-mediated transport	endosome membrane|Golgi membrane|membrane coat	binding|protein transporter activity				0		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)		TCACGATCTCCATCAGGTTCT	0.562													6	83	---	---	---	---	PASS
PLIN4	729359	broad.mit.edu	37	19	4511796	4511796	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:4511796G>T	uc002mar.1	-	3	2134	c.2134C>A	c.(2134-2136)CTA>ATA	p.L712I	PLIN4_uc010dub.1_5'Flank	NM_001080400	NP_001073869	Q96Q06	PLIN4_HUMAN	plasma membrane associated protein, S3-12	712	19.|27 X 33 AA approximate tandem repeat.					lipid particle|plasma membrane					0						GTACCAGTTAGGACAGTCTTG	0.592													10	344	---	---	---	---	PASS
ARRDC5	645432	broad.mit.edu	37	19	4891523	4891523	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:4891523G>T	uc002mbm.2	-	3	564	c.564C>A	c.(562-564)GTC>GTA	p.V188V		NM_001080523	NP_001073992	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	188					signal transduction						0				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		TTTGCAAACAGACAGTGCCCT	0.537													6	32	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9048368	9048368	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:9048368G>T	uc002mkp.2	-	5	33467	c.33263C>A	c.(33262-33264)CCA>CAA	p.P11088Q		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	11090	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TGAAACAGTTGGAGTTGGAAC	0.483													5	70	---	---	---	---	PASS
ELAVL3	1995	broad.mit.edu	37	19	11565633	11565633	+	Missense_Mutation	SNP	G	T	T	rs144639070		TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:11565633G>T	uc002mry.1	-	7	1192	c.812C>A	c.(811-813)GCG>GAG	p.A271E	ELAVL3_uc002mrx.1_Missense_Mutation_p.A264E	NM_001420	NP_001411	Q14576	ELAV3_HUMAN	ELAV-like protein 3 isoform 1	271					cell differentiation|nervous system development		AU-rich element binding|nucleotide binding			ovary(1)|breast(1)|skin(1)	3						GCCCACGCCCGCCAGGCCGCT	0.577													20	58	---	---	---	---	PASS
ZNF491	126069	broad.mit.edu	37	19	11917126	11917126	+	Nonsense_Mutation	SNP	A	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:11917126A>T	uc002mso.1	+	3	643	c.358A>T	c.(358-360)AGA>TGA	p.R120*		NM_152356	NP_689569	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	120	C2H2-type 2; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						AAGCATTCGAAGATATATGGT	0.398													16	58	---	---	---	---	PASS
ZNF20	7568	broad.mit.edu	37	19	12244153	12244153	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:12244153T>C	uc002mtf.1	-	4	991	c.848A>G	c.(847-849)TAT>TGT	p.Y283C	ZNF20_uc002mte.1_Missense_Mutation_p.Y248C|ZNF20_uc002mtg.1_Missense_Mutation_p.Y283C	NM_021143	NP_066966	P17024	ZNF20_HUMAN	zinc finger protein 20	283	C2H2-type 7.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CTTACACTCATAGGGTTTTTC	0.393													4	54	---	---	---	---	PASS
CASP14	23581	broad.mit.edu	37	19	15164418	15164418	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:15164418C>A	uc010dzv.1	+	3	461	c.153C>A	c.(151-153)ACC>ACA	p.T51T	CASP14_uc002naf.2_Silent_p.T51T	NM_012114	NP_036246	P31944	CASPE_HUMAN	caspase 14 precursor	51					apoptosis|cell differentiation|epidermis development|proteolysis	cytoplasm|nucleus	cysteine-type endopeptidase activity			skin(2)|ovary(1)|lung(1)	4						TCGAAAGCACCATGAAAAGAG	0.552													7	135	---	---	---	---	PASS
CYP4F12	66002	broad.mit.edu	37	19	15794350	15794350	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:15794350T>A	uc002nbl.2	+	7	756	c.695T>A	c.(694-696)GTA>GAA	p.V232E		NM_023944	NP_076433			cytochrome P450, family 4, subfamily F,											skin(3)|ovary(2)|central_nervous_system(2)	7	Acute lymphoblastic leukemia(2;0.0367)					AGTGCCCTTGTAGAGAAAAGA	0.547													15	63	---	---	---	---	PASS
OR10H2	26538	broad.mit.edu	37	19	15839195	15839195	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:15839195G>T	uc002nbm.2	+	1	362	c.342G>T	c.(340-342)CTG>CTT	p.L114L		NM_013939	NP_039227	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H,	114	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					ACTCCTTCCTGCTCACCGTCA	0.647													5	24	---	---	---	---	PASS
NCAN	1463	broad.mit.edu	37	19	19338255	19338255	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:19338255C>A	uc002nlz.2	+	8	1925	c.1826C>A	c.(1825-1827)GCC>GAC	p.A609D	NCAN_uc010ecc.1_Missense_Mutation_p.A173D	NM_004386	NP_004377	O14594	NCAN_HUMAN	chondroitin sulfate proteoglycan 3 precursor	609					axon guidance|cell adhesion	extracellular region	calcium ion binding|hyaluronic acid binding|sugar binding			ovary(4)	4			Epithelial(12;0.00544)			CCCTTGGAGGCCACTGTCTCA	0.652													5	23	---	---	---	---	PASS
ZNF430	80264	broad.mit.edu	37	19	21205610	21205610	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:21205610G>T	uc002npj.2	+	2	129	c.19G>T	c.(19-21)GGA>TGA	p.G7*	ZNF430_uc002npk.2_Nonsense_Mutation_p.G7*	NM_025189	NP_079465	Q9H8G1	ZN430_HUMAN	zinc finger protein 430	7					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2						CCTGAAGTCTGGAGTGTATCC	0.443													5	66	---	---	---	---	PASS
ZNF254	9534	broad.mit.edu	37	19	24309473	24309473	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:24309473C>T	uc002nru.2	+	4	805	c.671C>T	c.(670-672)ACC>ATC	p.T224I	ZNF254_uc010xrk.1_Missense_Mutation_p.T139I	NM_203282	NP_975011	O75437	ZN254_HUMAN	zinc finger protein 254	224	C2H2-type 1; degenerate.				negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				TGGTCCTCAACCCTTACTAAT	0.328													5	33	---	---	---	---	PASS
DPY19L3	147991	broad.mit.edu	37	19	32923703	32923703	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:32923703C>T	uc002ntg.2	+	4	495	c.319C>T	c.(319-321)CTC>TTC	p.L107F	DPY19L3_uc002nth.1_Missense_Mutation_p.L107F	NM_207325	NP_997208	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3	107						integral to membrane				ovary(4)	4	Esophageal squamous(110;0.162)					GGCTCCAACCCTCGTGCAAGG	0.413													5	34	---	---	---	---	PASS
LGALS13	29124	broad.mit.edu	37	19	40097949	40097949	+	Silent	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:40097949C>T	uc002omb.2	+	4	430	c.390C>T	c.(388-390)ATC>ATT	p.I130I		NM_013268	NP_037400	Q9UHV8	PP13_HUMAN	galectin-13	130	Galectin.				lipid catabolic process|phospholipid metabolic process		carboxylesterase activity|lysophospholipase activity|sugar binding			ovary(1)	1	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			CGAGAGATATCTCCCTGACCT	0.468													5	41	---	---	---	---	PASS
ATP1A3	478	broad.mit.edu	37	19	42485885	42485885	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:42485885G>T	uc002osg.2	-	10	1445	c.1291C>A	c.(1291-1293)CCT>ACT	p.P431T	ATP1A3_uc010xwf.1_Missense_Mutation_p.P442T|ATP1A3_uc010xwg.1_Missense_Mutation_p.P401T|ATP1A3_uc010xwh.1_Missense_Mutation_p.P444T|ATP1A3_uc002osh.2_Missense_Mutation_p.P431T	NM_152296	NP_689509	P13637	AT1A3_HUMAN	Na+/K+ -ATPase alpha 3 subunit	431	Cytoplasmic (Potential).				ATP biosynthetic process	endoplasmic reticulum|Golgi apparatus	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(1)|pancreas(1)	2						TTGAGCACAGGGATGTTGTCC	0.592													7	33	---	---	---	---	PASS
ZNF284	342909	broad.mit.edu	37	19	44590805	44590805	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:44590805G>T	uc002oyg.1	+	5	1390	c.1174G>T	c.(1174-1176)GTC>TTC	p.V392F	ZNF284_uc010ejd.2_RNA	NM_001037813	NP_001032902	Q2VY69	ZN284_HUMAN	zinc finger protein 284	392	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.0435)				ACATCAGCGGGTCCACAATGG	0.433													33	94	---	---	---	---	PASS
SYT3	84258	broad.mit.edu	37	19	51133130	51133130	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:51133130C>A	uc002pst.2	-	3	1607	c.973G>T	c.(973-975)GAC>TAC	p.D325Y	SYT3_uc002psv.2_Missense_Mutation_p.D325Y|SYT3_uc010ycd.1_Missense_Mutation_p.D325Y	NM_032298	NP_115674	Q9BQG1	SYT3_HUMAN	synaptotagmin III	325	C2 1.|Cytoplasmic (Potential).					cell junction|endosome|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|breast(1)	3		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GCAGGGAGGTCCAGGGCCTGC	0.587													11	57	---	---	---	---	PASS
LILRB4	11006	broad.mit.edu	37	19	55179385	55179385	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:55179385G>T	uc002qgp.2	+	12	1624	c.1262G>T	c.(1261-1263)AGA>ATA	p.R421I	LILRB4_uc002qgq.2_Missense_Mutation_p.R420I|LILRB4_uc002qgr.2_Missense_Mutation_p.R463I|LILRB4_uc010ert.2_Missense_Mutation_p.R462I|LILRB4_uc010eru.2_Missense_Mutation_p.R451I	NM_006847	NP_006838	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor,	421	Cytoplasmic (Potential).					integral to membrane|plasma membrane	antigen binding|receptor activity			ovary(3)	3				GBM - Glioblastoma multiforme(193;0.035)		TTTACCCTCAGACAGAAGGCA	0.622													9	77	---	---	---	---	PASS
USP29	57663	broad.mit.edu	37	19	57642748	57642748	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr19:57642748G>C	uc002qny.2	+	4	3061	c.2705G>C	c.(2704-2706)AGC>ACC	p.S902T		NM_020903	NP_065954	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	902					protein modification process|ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|protein binding|ubiquitin thiolesterase activity			lung(6)|ovary(2)|breast(2)|pancreas(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CGGCTACCTAGCACACAGGCA	0.498													11	55	---	---	---	---	PASS
RRBP1	6238	broad.mit.edu	37	20	17610501	17610501	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:17610501C>A	uc002wpv.1	-	10	1771	c.1417G>T	c.(1417-1419)GAG>TAG	p.E473*	RRBP1_uc002wpu.2_Nonsense_Mutation_p.E247*|RRBP1_uc002wpw.1_Nonsense_Mutation_p.E473*|RRBP1_uc010gcl.1_Nonsense_Mutation_p.E247*|RRBP1_uc010gcm.1_Silent_p.P58P	NM_001042576	NP_001036041	Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	906	Cytoplasmic (Potential).				protein transport|translation|transmembrane transport	integral to endoplasmic reticulum membrane|ribosome	receptor activity			ovary(1)	1						TGGGCCTTCTCGGCATCCGCC	0.711													8	10	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20505152	20505152	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:20505152C>A	uc002wrz.2	-	30	3941	c.3798G>T	c.(3796-3798)TGG>TGT	p.W1266C	RALGAPA2_uc010gcx.2_Missense_Mutation_p.W970C|RALGAPA2_uc010zsg.1_Missense_Mutation_p.W714C|RALGAPA2_uc002wsa.1_Missense_Mutation_p.W38C	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	1266					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						ATGCCATGCACCAGTCCAAGA	0.502													12	49	---	---	---	---	PASS
RALGAPA2	57186	broad.mit.edu	37	20	20505153	20505153	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:20505153C>A	uc002wrz.2	-	30	3940	c.3797G>T	c.(3796-3798)TGG>TTG	p.W1266L	RALGAPA2_uc010gcx.2_Missense_Mutation_p.W970L|RALGAPA2_uc010zsg.1_Missense_Mutation_p.W714L|RALGAPA2_uc002wsa.1_Missense_Mutation_p.W38L	NM_020343	NP_065076	Q2PPJ7	RGPA2_HUMAN	akt substrate AS250	1266					activation of Ral GTPase activity	cytosol|nucleus	protein heterodimerization activity|Ral GTPase activator activity			ovary(1)	1						TGCCATGCACCAGTCCAAGAG	0.502													12	46	---	---	---	---	PASS
ASXL1	171023	broad.mit.edu	37	20	30956834	30956834	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:30956834G>T	uc002wxs.2	+	3	586	c.160G>T	c.(160-162)GCA>TCA	p.A54S	ASXL1_uc002wxr.1_RNA|ASXL1_uc002wxt.2_RNA|ASXL1_uc010geb.2_5'UTR	NM_015338	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like 1 isoform 1	54					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	PR-DUB complex	metal ion binding|protein binding			haematopoietic_and_lymphoid_tissue(239)|large_intestine(6)|central_nervous_system(2)|ovary(1)	248						TTCCCCTCTCGCATGCCTCAA	0.438			F|N|Mis		MDS|CMML								10	49	---	---	---	---	PASS
NCOA6	23054	broad.mit.edu	37	20	33337933	33337933	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:33337933G>T	uc002xav.2	-	10	4636	c.2065C>A	c.(2065-2067)CCA>ACA	p.P689T	NCOA6_uc002xaw.2_Missense_Mutation_p.P689T	NM_014071	NP_054790	Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	689	TBP/GTF2A-binding region.|NCOA1-binding region.|Gln-rich.|CREBBP-binding region.				brain development|cellular lipid metabolic process|DNA recombination|DNA repair|DNA replication|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|heart development|myeloid cell differentiation|positive regulation of transcription from RNA polymerase II promoter|response to hormone stimulus|transcription initiation from RNA polymerase II promoter	transcription factor complex	chromatin binding|enzyme binding|estrogen receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|retinoid X receptor binding|thyroid hormone receptor binding			ovary(3)|breast(3)|central_nervous_system(1)	7						ATCATTTGTGGGCCCTGCTGG	0.547													5	56	---	---	---	---	PASS
RBM12	10137	broad.mit.edu	37	20	34241817	34241817	+	Silent	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:34241817T>C	uc002xdq.2	-	3	1660	c.1428A>G	c.(1426-1428)GTA>GTG	p.V476V	CPNE1_uc010zvj.1_5'UTR|CPNE1_uc002xde.2_Intron|CPNE1_uc002xdf.2_Intron|CPNE1_uc002xdg.2_Intron|CPNE1_uc010gfi.2_Intron|CPNE1_uc010gfj.2_Intron|CPNE1_uc002xdh.2_Intron|CPNE1_uc002xdi.2_Intron|CPNE1_uc002xdj.2_Intron|CPNE1_uc002xdk.2_Intron|CPNE1_uc002xdl.2_Intron|CPNE1_uc002xdm.2_Intron|CPNE1_uc010gfk.1_Intron|CPNE1_uc002xdn.1_Intron|CPNE1_uc002xdo.1_Intron|CPNE1_uc002xdp.1_Intron|RBM12_uc002xdr.2_Silent_p.V476V|RBM12_uc002xds.2_Silent_p.V476V	NM_152838	NP_690051	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	476	RRM 2.					nucleus	nucleotide binding|protein binding|RNA binding			ovary(3)	3	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			TTCTGAACTCTACAAAGCCTT	0.373											OREG0004044	type=REGULATORY REGION|Gene=CPNE1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	33	107	---	---	---	---	PASS
ACTR5	79913	broad.mit.edu	37	20	37384652	37384652	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:37384652C>A	uc002xjd.2	+	5	1171	c.1146C>A	c.(1144-1146)CTC>CTA	p.L382L		NM_024855	NP_079131	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog	382	Potential.				DNA recombination|double-strand break repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent|UV-damage excision repair	cytoplasm|Ino80 complex	ATP binding|protein binding				0		Myeloproliferative disorder(115;0.00878)				AAGTCAACCTCGAGGTGGATG	0.532													4	39	---	---	---	---	PASS
PTPRT	11122	broad.mit.edu	37	20	40735489	40735489	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:40735489C>A	uc002xkg.2	-	24	3511	c.3327G>T	c.(3325-3327)GTG>GTT	p.V1109V	PTPRT_uc010ggj.2_Silent_p.V1128V|PTPRT_uc010ggi.2_Silent_p.V312V	NM_007050	NP_008981	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1109	Tyrosine-protein phosphatase 1.|Cytoplasmic (Potential).				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			skin(8)|ovary(7)|lung(5)	20		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				AGATGTCCACCACCCCTTCAT	0.572													5	58	---	---	---	---	PASS
R3HDML	140902	broad.mit.edu	37	20	42965955	42965955	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:42965955G>T	uc002xls.1	+	1	330	c.158G>T	c.(157-159)CGC>CTC	p.R53L		NM_178491	NP_848586	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like precursor	53						extracellular region	peptidase inhibitor activity				0		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			CCCAGGTACCGCCGGAAGCGC	0.597													6	20	---	---	---	---	PASS
PCK1	5105	broad.mit.edu	37	20	56137948	56137948	+	Silent	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:56137948T>A	uc002xyn.3	+	4	766	c.603T>A	c.(601-603)CCT>CCA	p.P201P	PCK1_uc010zzm.1_Intron	NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1	201					gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			skin(1)	1	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GCCCTCTGCCTTTACAAAGTA	0.532													7	28	---	---	---	---	PASS
ZNF831	128611	broad.mit.edu	37	20	57769790	57769790	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:57769790G>C	uc002yan.2	+	1	3716	c.3716G>C	c.(3715-3717)GGA>GCA	p.G1239A		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1239						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					CCTGGAGAAGGAGGGCCGGCG	0.597													4	10	---	---	---	---	PASS
ZNF831	128611	broad.mit.edu	37	20	57829123	57829123	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:57829123C>A	uc002yan.2	+	5	4359	c.4359C>A	c.(4357-4359)TCC>TCA	p.S1453S		NM_178457	NP_848552	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1453						intracellular	nucleic acid binding|zinc ion binding			skin(13)|ovary(1)	14	all_lung(29;0.0085)					TGCTGGCCTCCCAGGATTCAG	0.522													6	63	---	---	---	---	PASS
C20orf11	54994	broad.mit.edu	37	20	61576136	61576136	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:61576136G>T	uc002ydy.2	+	5	736	c.559G>T	c.(559-561)GAG>TAG	p.E187*		NM_017896	NP_060366	Q9NWU2	CT011_HUMAN	chromosome 20 open reading frame 11	187						nucleus	protein binding				0	Breast(26;5.68e-08)					TGAAAATCGCGAGTCAACACC	0.418													4	71	---	---	---	---	PASS
COL20A1	57642	broad.mit.edu	37	20	61959481	61959481	+	Splice_Site	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:61959481T>A	uc011aau.1	+	33	3713	c.3613_splice	c.e33+2	p.S1205_splice	COL20A1_uc011aav.1_Nonsense_Mutation_p.C1026*	NM_020882	NP_065933	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1						cell adhesion	collagen|extracellular space	structural molecule activity			central_nervous_system(1)	1	all_cancers(38;1.39e-10)					GCCAGGCCTGTGAGTCTGCCA	0.647													3	14	---	---	---	---	PASS
ZNF512B	57473	broad.mit.edu	37	20	62595499	62595499	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr20:62595499C>G	uc002yhl.1	-	8	1459	c.1405G>C	c.(1405-1407)GCC>CCC	p.A469P		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	469					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					TTCTTCCGGGCGTCCTCAGGG	0.662													9	36	---	---	---	---	PASS
PCNT	5116	broad.mit.edu	37	21	47847543	47847543	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr21:47847543C>A	uc002zji.3	+	34	7435	c.7328C>A	c.(7327-7329)CCC>CAC	p.P2443H	PCNT_uc002zjj.2_Missense_Mutation_p.P2325H	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	2443					cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)					TAGGAAGTGCCCACCGCGTGC	0.458													6	47	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22735419	22735419	+	RNA	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:22735419C>A	uc011aim.1	+	46		c.5215C>A								Parts of antibodies, mostly variable regions.												0						GGGTCCTGGGCCCAGTCTGTG	0.577													7	53	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22735420	22735420	+	RNA	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:22735420C>A	uc011aim.1	+	46		c.5216C>A								Parts of antibodies, mostly variable regions.												0						GGTCCTGGGCCCAGTCTGTGC	0.577													6	52	---	---	---	---	PASS
ZNF280B	140883	broad.mit.edu	37	22	22843151	22843151	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:22843151C>A	uc002zwc.1	-	4	1349	c.573G>T	c.(571-573)AGG>AGT	p.R191S	LOC96610_uc011aim.1_Intron	NM_080764	NP_542942	Q86YH2	Z280B_HUMAN	zinc finger protein 280B	191					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TAATTCCATCCCTGAGTTTAG	0.383													10	68	---	---	---	---	PASS
CHCHD10	400916	broad.mit.edu	37	22	24108318	24108318	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:24108318G>T	uc002zxw.2	-	3	486	c.406C>A	c.(406-408)CAT>AAT	p.H136N		NM_213720	NP_998885	Q8WYQ3	CHC10_HUMAN	coiled-coil-helix-coiled-coil-helix domain	136						mitochondrion					0						CACTCACCATGGTAGTACTTG	0.627													5	29	---	---	---	---	PASS
RFPL1	5988	broad.mit.edu	37	22	29837623	29837623	+	Missense_Mutation	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:29837623C>T	uc003afn.2	+	2	675	c.466C>T	c.(466-468)CGG>TGG	p.R156W	RFPL1S_uc003afm.1_RNA	NM_021026	NP_066306	O75677	RFPL1_HUMAN	ret finger protein-like 1	156	B30.2/SPRY.						zinc ion binding				0						CACACAGAATCGGCAAGACCT	0.552													21	64	---	---	---	---	PASS
PATZ1	23598	broad.mit.edu	37	22	31741322	31741322	+	Silent	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:31741322G>A	uc003akq.2	-	1	928	c.267C>T	c.(265-267)GGC>GGT	p.G89G	PATZ1_uc003akp.2_Silent_p.G89G|PATZ1_uc003akr.2_Silent_p.G89G|PATZ1_uc003aks.2_Silent_p.G89G|uc003akt.2_5'Flank	NM_014323	NP_055138	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	89	BTB.				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/PATZ1(2)	soft_tissue(2)	2						CTGCCGTCGCGCCCCCTACAT	0.682													5	9	---	---	---	---	PASS
LARGE	9215	broad.mit.edu	37	22	34000433	34000433	+	Silent	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:34000433T>C	uc003and.3	-	6	1182	c.603A>G	c.(601-603)GCA>GCG	p.A201A	LARGE_uc003ane.3_Silent_p.A201A|LARGE_uc010gwp.2_Silent_p.A201A|LARGE_uc011ame.1_Silent_p.A133A|LARGE_uc011amf.1_Silent_p.A201A	NM_004737	NP_004728	O95461	LARGE_HUMAN	like-glycosyltransferase	201	Lumenal (Potential).				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(1;0.219)				TGAGCTCGTCTGCATTGTAGA	0.547													8	71	---	---	---	---	PASS
TOM1	10043	broad.mit.edu	37	22	35723368	35723368	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:35723368G>T	uc003ann.2	+	7	878	c.753G>T	c.(751-753)CTG>CTT	p.L251L	TOM1_uc011ami.1_Silent_p.L218L|TOM1_uc011amj.1_Silent_p.L94L|TOM1_uc003ans.2_Silent_p.L94L|TOM1_uc011amk.1_Silent_p.L213L|TOM1_uc003anp.2_Silent_p.L251L|TOM1_uc011aml.1_Silent_p.L206L|TOM1_uc003ano.2_RNA|TOM1_uc003anq.2_Silent_p.L245L|TOM1_uc003anr.2_Silent_p.L94L	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1	251	GAT.				endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						CCGCAGACCTGGAGCTGCTGC	0.627													9	20	---	---	---	---	PASS
MB	4151	broad.mit.edu	37	22	36003352	36003352	+	Nonsense_Mutation	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:36003352G>A	uc003anz.2	-	3	537	c.457C>T	c.(457-459)CAG>TAG	p.Q153*	MB_uc003aoa.2_Nonsense_Mutation_p.Q153*|MB_uc003aob.2_Nonsense_Mutation_p.Q153*	NM_005368	NP_005359	P02144	MYG_HUMAN	myoglobin	153							heme binding|oxygen transporter activity				0						GCCTAGCCCTGGAAGCCCAGC	0.622													6	42	---	---	---	---	PASS
CACNA1I	8911	broad.mit.edu	37	22	40045840	40045840	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:40045840C>A	uc003ayc.2	+	10	1902	c.1902C>A	c.(1900-1902)CGC>CGA	p.R634R	CACNA1I_uc003ayd.2_Silent_p.R599R|CACNA1I_uc003aye.2_Silent_p.R549R|CACNA1I_uc003ayf.2_Silent_p.R514R	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	634	II.|Cytoplasmic (Potential).				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)	CCAAGCTGCGCGGCATCGTGG	0.532													8	30	---	---	---	---	PASS
ENTHD1	150350	broad.mit.edu	37	22	40217076	40217076	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:40217076G>T	uc003ayg.2	-	5	1005	c.754C>A	c.(754-756)CTA>ATA	p.L252I		NM_152512	NP_689725	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	252										ovary(2)|skin(1)	3	Melanoma(58;0.0749)					GGTGTTGCTAGTAAAGGCAGC	0.398													5	25	---	---	---	---	PASS
RANGAP1	5905	broad.mit.edu	37	22	41647034	41647034	+	Missense_Mutation	SNP	C	A	A	rs139565299		TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:41647034C>A	uc003azs.2	-	12	2930	c.1460G>T	c.(1459-1461)AGG>ATG	p.R487M	RANGAP1_uc003azt.2_Missense_Mutation_p.R487M|RANGAP1_uc003azu.2_Missense_Mutation_p.R487M|RANGAP1_uc003azr.2_Translation_Start_Site|RANGAP1_uc010gyk.2_Translation_Start_Site|RANGAP1_uc011aoz.1_Missense_Mutation_p.R432M	NM_002883	NP_002874	P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	487					mitotic prometaphase|signal transduction	condensed chromosome kinetochore|cytosol|nuclear membrane|nuclear pore|soluble fraction|spindle pole	protein binding|Ran GTPase activator activity				0						CACTGCCATCCTCACAGTAGC	0.557													6	75	---	---	---	---	PASS
TCF20	6942	broad.mit.edu	37	22	42609031	42609031	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr22:42609031G>T	uc003bcj.1	-	1	2415	c.2281C>A	c.(2281-2283)CAC>AAC	p.H761N	TCF20_uc003bck.1_Missense_Mutation_p.H761N|TCF20_uc003bnt.2_Missense_Mutation_p.H761N	NM_005650	NP_005641	Q9UGU0	TCF20_HUMAN	transcription factor 20 isoform 1	761					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|transcription coactivator activity|zinc ion binding			ovary(4)|skin(1)	5						GGGTGGTGGTGGTAACCCTGA	0.502													5	66	---	---	---	---	PASS
GYG2	8908	broad.mit.edu	37	X	2795308	2795308	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:2795308C>A	uc004cqs.1	+	11	1586	c.1304C>A	c.(1303-1305)GCT>GAT	p.A435D	GYG2_uc004cqt.1_Missense_Mutation_p.A404D|GYG2_uc004cqu.1_Missense_Mutation_p.A403D|GYG2_uc004cqv.1_Intron|GYG2_uc004cqw.1_Missense_Mutation_p.A395D|GYG2_uc004cqx.1_Intron|GYG2_uc010ndc.1_Intron	NM_003918	NP_003909	O15488	GLYG2_HUMAN	glycogenin 2 isoform b	435					glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|soluble fraction	glycogenin glucosyltransferase activity			ovary(1)|kidney(1)	2		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				GAACTCCCTGCTGAGGCTCTC	0.547													8	56	---	---	---	---	PASS
NLGN4X	57502	broad.mit.edu	37	X	5821666	5821666	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:5821666G>T	uc010ndh.2	-	5	1554	c.1053C>A	c.(1051-1053)GAC>GAA	p.D351E	NLGN4X_uc004crp.2_Missense_Mutation_p.D371E|NLGN4X_uc004crq.2_Missense_Mutation_p.D351E|NLGN4X_uc010ndi.2_Missense_Mutation_p.D388E|NLGN4X_uc004crr.2_Missense_Mutation_p.D351E|NLGN4X_uc010ndj.2_Missense_Mutation_p.D351E	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4 precursor	351	Extracellular (Potential).				brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	chloride ion binding|neurexin binding|protein homodimerization activity|receptor activity			skin(2)|large_intestine(1)|ovary(1)	4						TCTGGGGGTCGTCTGGGATGA	0.597													11	62	---	---	---	---	PASS
NHS	4810	broad.mit.edu	37	X	17743832	17743832	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:17743832G>T	uc004cxx.2	+	6	1881	c.1543G>T	c.(1543-1545)GGT>TGT	p.G515C	NHS_uc011mix.1_Missense_Mutation_p.G536C|NHS_uc004cxy.2_Missense_Mutation_p.G359C|NHS_uc004cxz.2_Missense_Mutation_p.G338C|NHS_uc004cya.2_Missense_Mutation_p.G238C	NM_198270	NP_938011	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome protein isoform 1	515						nucleus				skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	Hepatocellular(33;0.183)					GTCTTTTGTGGGTGACCATGA	0.547													7	107	---	---	---	---	PASS
GPR64	10149	broad.mit.edu	37	X	19013118	19013118	+	Missense_Mutation	SNP	T	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:19013118T>A	uc004cyx.2	-	28	2929	c.2765A>T	c.(2764-2766)CAA>CTA	p.Q922L	GPR64_uc004cyy.2_Missense_Mutation_p.Q919L|GPR64_uc004cyz.2_Missense_Mutation_p.Q908L|GPR64_uc004czb.2_Intron|GPR64_uc004czc.2_Missense_Mutation_p.Q906L|GPR64_uc004czd.2_Missense_Mutation_p.Q898L|GPR64_uc004cze.2_Missense_Mutation_p.Q892L|GPR64_uc004czf.2_Missense_Mutation_p.Q884L|GPR64_uc004cza.2_Missense_Mutation_p.Q900L|GPR64_uc004cyw.2_Intron|GPR64_uc010nfj.2_Missense_Mutation_p.Q803L	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1	922	Cytoplasmic (Potential).				neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)					GGACACTCCTTGGTTTACAGT	0.423													15	70	---	---	---	---	PASS
GPR64	10149	broad.mit.edu	37	X	19018072	19018072	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:19018072G>T	uc004cyx.2	-	25	2401	c.2237C>A	c.(2236-2238)CCA>CAA	p.P746Q	GPR64_uc004cyy.2_Missense_Mutation_p.P743Q|GPR64_uc004cyz.2_Missense_Mutation_p.P732Q|GPR64_uc004czb.2_Missense_Mutation_p.P746Q|GPR64_uc004czc.2_Missense_Mutation_p.P730Q|GPR64_uc004czd.2_Missense_Mutation_p.P722Q|GPR64_uc004cze.2_Missense_Mutation_p.P716Q|GPR64_uc004czf.2_Missense_Mutation_p.P708Q|GPR64_uc004cza.2_Missense_Mutation_p.P724Q|GPR64_uc004cyw.2_Missense_Mutation_p.P730Q|GPR64_uc010nfj.2_Missense_Mutation_p.P627Q	NM_001079858	NP_001073327	Q8IZP9	GPR64_HUMAN	G protein-coupled receptor 64 isoform 1	746	Helical; Name=4; (Potential).				neuropeptide signaling pathway|spermatogenesis	cytoplasm|integral to plasma membrane	G-protein coupled receptor activity				0	Hepatocellular(33;0.183)					AACCACAGCTGGTACCCCTGG	0.328													20	104	---	---	---	---	PASS
PDHA1	5160	broad.mit.edu	37	X	19373469	19373469	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:19373469C>A	uc004czg.3	+	7	751	c.606C>A	c.(604-606)GGC>GGA	p.G202G	PDHA1_uc004czh.3_Silent_p.G237G|PDHA1_uc011mjc.1_Silent_p.G206G|PDHA1_uc011mjd.1_Silent_p.G168G|PDHA1_uc010nfk.2_Silent_p.G199G|PDHA1_uc010nfl.2_5'UTR	NM_000284	NP_000275	P08559	ODPA_HUMAN	pyruvate dehydrogenase E1 alpha 1 precursor	202					glycolysis|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	protein binding|pyruvate dehydrogenase (acetyl-transferring) activity			ovary(1)	1	Hepatocellular(33;0.183)				NADH(DB00157)	ACTTCCAGGGCCAGATATTCG	0.438													22	135	---	---	---	---	PASS
TAB3	257397	broad.mit.edu	37	X	30873249	30873249	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:30873249G>T	uc004dcj.2	-	6	1196	c.533C>A	c.(532-534)CCA>CAA	p.P178Q	TAB3_uc004dck.2_Missense_Mutation_p.P178Q|TAB3_uc010ngl.2_Missense_Mutation_p.P178Q	NM_152787	NP_690000	Q8N5C8	TAB3_HUMAN	mitogen-activated protein kinase kinase kinase 7	178	Pro-rich.				activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein binding|zinc ion binding			ovary(1)	1						AGGTGGCGGTGGTGGTGAAGG	0.488													19	81	---	---	---	---	PASS
USP9X	8239	broad.mit.edu	37	X	40994071	40994071	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:40994071G>T	uc004dfb.2	+	5	1049	c.416G>T	c.(415-417)GGC>GTC	p.G139V	USP9X_uc004dfc.2_Missense_Mutation_p.G139V	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN	ubiquitin specific protease 9, X-linked isoform	139					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			lung(3)|breast(2)|ovary(1)	6						GCAGTGAGTGGCTGGAAGTTT	0.393													5	59	---	---	---	---	PASS
WAS	7454	broad.mit.edu	37	X	48545326	48545326	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:48545326G>T	uc004dkm.3	+	7	773	c.716G>T	c.(715-717)GGT>GTT	p.G239V		NM_000377	NP_000368	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome protein	239	CRIB.				blood coagulation|defense response|epidermis development|immune response|T cell receptor signaling pathway	actin cytoskeleton|cytosol	identical protein binding|small GTPase regulator activity			ovary(1)	1		all_lung(315;1.27e-10)				GCTGATATTGGTGCACCCAGT	0.542			Mis|N|F|S			lymphoma			Wiskott-Aldrich_syndrome				5	23	---	---	---	---	PASS
AKAP4	8852	broad.mit.edu	37	X	49958015	49958015	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:49958015G>T	uc004dow.1	-	5	1473	c.1349C>A	c.(1348-1350)TCT>TAT	p.S450Y	AKAP4_uc004dov.1_Intron|AKAP4_uc010njp.1_Missense_Mutation_p.S272Y|AKAP4_uc004dou.1_Missense_Mutation_p.S441Y	NM_003886	NP_003877	Q5JQC9	AKAP4_HUMAN	A-kinase anchor protein 4 isoform 1	450					cell projection organization|single fertilization|sperm motility	cAMP-dependent protein kinase complex|cilium|cytoskeleton|microtubule-based flagellum	protein kinase A binding			kidney(3)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	8	Ovarian(276;0.236)					AGCTTTTAAAGATGCATATGA	0.448													19	77	---	---	---	---	PASS
HUWE1	10075	broad.mit.edu	37	X	53610791	53610791	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:53610791G>T	uc004dsp.2	-	42	5649	c.5247C>A	c.(5245-5247)GGC>GGA	p.G1749G	HUWE1_uc004dsn.2_Silent_p.G574G	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	1749					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						CTTCTGTCAAGCCCTGGATCA	0.498													11	38	---	---	---	---	PASS
KLF8	11279	broad.mit.edu	37	X	56296637	56296637	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:56296637C>A	uc004dur.2	+	5	1727	c.781C>A	c.(781-783)CAG>AAG	p.Q261K	KLF8_uc011mop.1_Intron|KLF8_uc010nkh.2_RNA	NM_007250	NP_009181	O95600	KLF8_HUMAN	Kruppel-like factor 8 isoform 1	261					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						GGCCCAAATGCAGGGAGAAGA	0.418													13	46	---	---	---	---	PASS
MSN	4478	broad.mit.edu	37	X	64957195	64957195	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:64957195C>G	uc004dwf.2	+	10	1444	c.1246C>G	c.(1246-1248)CAG>GAG	p.Q416E		NM_002444	NP_002435	P26038	MOES_HUMAN	moesin	416					leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(3)|lung(1)	10						GACTCAGGAACAGCTGGTAAA	0.517			T	ALK	ALCL								7	23	---	---	---	---	PASS
KIF4A	24137	broad.mit.edu	37	X	69510564	69510564	+	Silent	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:69510564C>G	uc004dyg.2	+	3	271	c.144C>G	c.(142-144)TCC>TCG	p.S48S	KIF4A_uc010nkw.2_Silent_p.S48S|PDZD11_uc004dyd.1_5'Flank|PDZD11_uc004dye.1_5'Flank|KIF4A_uc004dyf.1_Silent_p.S48S	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	48	Kinesin-motor.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4						CAGATAAATCCTTCACCTACG	0.453													13	55	---	---	---	---	PASS
MAGEE2	139599	broad.mit.edu	37	X	75003990	75003990	+	Silent	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:75003990C>A	uc004ecj.1	-	1	1082	c.897G>T	c.(895-897)CTG>CTT	p.L299L		NM_138703	NP_619648	Q8TD90	MAGE2_HUMAN	melanoma antigen family E, 2	299										ovary(1)|skin(1)	2						AGCCAGCAGTCAGGCTTCTTT	0.468													8	76	---	---	---	---	PASS
BRWD3	254065	broad.mit.edu	37	X	79999630	79999630	+	Silent	SNP	A	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:79999630A>G	uc004edt.2	-	8	977	c.714T>C	c.(712-714)GCT>GCC	p.A238A	BRWD3_uc004edo.2_5'UTR|BRWD3_uc004edp.2_Silent_p.A67A|BRWD3_uc004edq.2_5'UTR|BRWD3_uc010nmj.1_5'UTR|BRWD3_uc004edr.2_5'UTR|BRWD3_uc004eds.2_5'UTR|BRWD3_uc004edu.2_5'UTR|BRWD3_uc004edv.2_5'UTR|BRWD3_uc004edw.2_5'UTR|BRWD3_uc004edx.2_5'UTR|BRWD3_uc004edy.2_5'UTR|BRWD3_uc004edz.2_5'UTR|BRWD3_uc004eea.2_5'UTR|BRWD3_uc004eeb.2_Intron	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	238	WD 3.									ovary(4)	4						AGCTGCCTGCAGCAATAAGAG	0.453													8	43	---	---	---	---	PASS
ZNF711	7552	broad.mit.edu	37	X	84502603	84502603	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:84502603G>T	uc004eeo.2	+	3	372	c.25G>T	c.(25-27)GGA>TGA	p.G9*	ZNF711_uc004eep.2_Nonsense_Mutation_p.G9*|ZNF711_uc004eeq.2_Nonsense_Mutation_p.G9*	NM_021998	NP_068838	Q9Y462	ZN711_HUMAN	zinc finger protein 711	9					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|zinc ion binding			ovary(3)|skin(1)	4						TGGAAGTCTTGGATTGCACAC	0.338													6	83	---	---	---	---	PASS
CHM	1121	broad.mit.edu	37	X	85218784	85218784	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:85218784C>A	uc004eet.2	-	5	618	c.588G>T	c.(586-588)ATG>ATT	p.M196I	CHM_uc011mqz.1_Missense_Mutation_p.M48I	NM_000390	NP_000381	P24386	RAE1_HUMAN	choroideremia isoform a	196					intracellular protein transport|protein geranylgeranylation|response to stimulus|visual perception	Rab-protein geranylgeranyltransferase complex	GTPase activator activity|Rab geranylgeranyltransferase activity			ovary(1)	1		all_lung(315;5.41e-06)				CATTTTCACTCATGTCTTCTG	0.373													6	37	---	---	---	---	PASS
SYTL4	94121	broad.mit.edu	37	X	99955935	99955935	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:99955935C>A	uc004egd.3	-	7	853	c.497G>T	c.(496-498)TGG>TTG	p.W166L	SYTL4_uc010nnc.2_Missense_Mutation_p.W166L|SYTL4_uc004ege.3_Missense_Mutation_p.W166L|SYTL4_uc004egf.3_Missense_Mutation_p.W166L|SYTL4_uc004egg.3_Missense_Mutation_p.W166L	NM_080737	NP_542775	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	166					exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TCTTCCTGGCCAGATGTCACC	0.423													15	71	---	---	---	---	PASS
SERPINA7	6906	broad.mit.edu	37	X	105280734	105280734	+	Missense_Mutation	SNP	C	G	G			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:105280734C>G	uc004eme.1	-	1	332	c.316G>C	c.(316-318)GTA>CTA	p.V106L	SERPINA7_uc010npd.2_Missense_Mutation_p.V106L|SERPINA7_uc010npe.1_Missense_Mutation_p.V106L	NM_000354	NP_000345	P05543	THBG_HUMAN	serine (or cysteine) proteinase inhibitor, clade	106					regulation of proteolysis	extracellular space	serine-type endopeptidase inhibitor activity				0					Levothyroxine(DB00451)|Liothyronine(DB00279)	TGGATCTCTACCATTGGAGTG	0.478													15	51	---	---	---	---	PASS
ACSL4	2182	broad.mit.edu	37	X	108926550	108926550	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:108926550C>A	uc004eoi.2	-	4	671	c.166G>T	c.(166-168)GGA>TGA	p.G56*	ACSL4_uc004eoj.2_Nonsense_Mutation_p.G15*|ACSL4_uc004eok.2_Nonsense_Mutation_p.G15*|ACSL4_uc010npp.1_Nonsense_Mutation_p.G56*	NM_022977	NP_075266	O60488	ACSL4_HUMAN	acyl-CoA synthetase long-chain family member 4	56	Cytoplasmic (Potential).				fatty acid metabolic process|learning or memory|long-chain fatty-acyl-CoA biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|microsome|mitochondrial outer membrane|peroxisomal membrane	ATP binding|long-chain fatty acid-CoA ligase activity			large_intestine(1)|lung(1)|ovary(1)	3					Icosapent(DB00159)|Troglitazone(DB00197)	TATGGACTTCCAGGTTTGTCT	0.408													6	92	---	---	---	---	PASS
ODZ1	10178	broad.mit.edu	37	X	123554415	123554415	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:123554415G>T	uc004euj.2	-	24	4771	c.4707C>A	c.(4705-4707)ACC>ACA	p.T1569T	ODZ1_uc011muj.1_Silent_p.T1575T|ODZ1_uc010nqy.2_Silent_p.T1576T	NM_014253	NP_055068	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 3	1569	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|skin(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)	23						CAGAATTGTAGGTGAAGTTAT	0.493													9	47	---	---	---	---	PASS
OCRL	4952	broad.mit.edu	37	X	128724198	128724198	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:128724198G>C	uc004euq.2	+	24	2822	c.2657G>C	c.(2656-2658)CGT>CCT	p.R886P	OCRL_uc004eur.2_Missense_Mutation_p.R878P|OCRL_uc010nrb.2_RNA	NM_000276	NP_000267	Q01968	OCRL_HUMAN	phosphatidylinositol polyphosphate 5-phosphatase	886	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	clathrin-coated vesicle|cytosol|early endosome|Golgi stack|Golgi-associated vesicle	GTPase activator activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			lung(2)|ovary(1)|kidney(1)	4						GACCGCCAGCGTGCTATTCAG	0.502													36	161	---	---	---	---	PASS
ZDHHC9	51114	broad.mit.edu	37	X	128957775	128957775	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:128957775G>T	uc004euv.2	-	4	736	c.367C>A	c.(367-369)CCG>ACG	p.P123T	ZDHHC9_uc004euw.2_Missense_Mutation_p.P123T|ZDHHC9_uc004eux.1_Missense_Mutation_p.P123T|ZDHHC9_uc004euy.1_Missense_Mutation_p.P50T	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9	123	Cytoplasmic (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1						ATACGAGGCGGTGGTCGCTGG	0.488													12	81	---	---	---	---	PASS
RBMX	27316	broad.mit.edu	37	X	135961564	135961564	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:135961564C>A	uc004fae.1	-	2	233	c.23G>T	c.(22-24)GGA>GTA	p.G8V	RBMX_uc011mwf.1_Missense_Mutation_p.G8V|RBMX_uc004fad.1_Missense_Mutation_p.G8V|RBMX_uc011mwg.1_5'UTR|RBMX_uc004faf.1_5'UTR|RBMX_uc010nsf.1_Intron|RBMX_uc004fag.1_Intron|SNORD61_uc004fah.1_5'Flank	NM_002139	NP_002130	P38159	HNRPG_HUMAN	RNA binding motif protein, X-linked isoform 1	8	RRM.					catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					GAAGAGCTTTCCTGGGCGATC	0.408													21	112	---	---	---	---	PASS
RBMX	27316	broad.mit.edu	37	X	135961565	135961565	+	Nonsense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:135961565C>A	uc004fae.1	-	2	232	c.22G>T	c.(22-24)GGA>TGA	p.G8*	RBMX_uc011mwf.1_Nonsense_Mutation_p.G8*|RBMX_uc004fad.1_Nonsense_Mutation_p.G8*|RBMX_uc011mwg.1_Translation_Start_Site|RBMX_uc004faf.1_Translation_Start_Site|RBMX_uc010nsf.1_Intron|RBMX_uc004fag.1_Intron|SNORD61_uc004fah.1_5'Flank	NM_002139	NP_002130	P38159	HNRPG_HUMAN	RNA binding motif protein, X-linked isoform 1	8	RRM.					catalytic step 2 spliceosome|heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	nucleotide binding|protein binding|RNA binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					AAGAGCTTTCCTGGGCGATCT	0.408													21	113	---	---	---	---	PASS
MAGEC2	51438	broad.mit.edu	37	X	141291217	141291217	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:141291217C>A	uc004fbu.1	-	3	905	c.557G>T	c.(556-558)CGT>CTT	p.R186L		NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	186	MAGE.					cytoplasm|nucleus				breast(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)					CATGAACTCACGGGCTCTCTT	0.483										HNSCC(46;0.14)			30	201	---	---	---	---	PASS
AFF2	2334	broad.mit.edu	37	X	148037578	148037578	+	Missense_Mutation	SNP	G	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:148037578G>C	uc004fcp.2	+	11	2482	c.2003G>C	c.(2002-2004)AGA>ACA	p.R668T	AFF2_uc004fcq.2_Missense_Mutation_p.R658T|AFF2_uc004fcr.2_Missense_Mutation_p.R629T|AFF2_uc011mxb.1_Missense_Mutation_p.R633T|AFF2_uc004fcs.2_Missense_Mutation_p.R635T|AFF2_uc011mxc.1_Missense_Mutation_p.R309T	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2	668					brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)					GACCCACCAAGAGGCCGCAAC	0.517													34	163	---	---	---	---	PASS
MTM1	4534	broad.mit.edu	37	X	149814185	149814185	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:149814185G>T	uc004fef.3	+	9	784	c.708G>T	c.(706-708)AAG>AAT	p.K236N	MTM1_uc011mxx.1_RNA|MTM1_uc011mxy.1_Missense_Mutation_p.K199N|MTM1_uc011mxz.1_Missense_Mutation_p.K121N|MTM1_uc010nte.2_Missense_Mutation_p.K104N	NM_000252	NP_000243	Q13496	MTM1_HUMAN	myotubularin	236	Myotubularin phosphatase.				endosome to lysosome transport|intermediate filament organization|mitochondrion distribution|mitochondrion morphogenesis|phosphatidylinositol dephosphorylation|protein transport|regulation of vacuole organization	filopodium|late endosome|plasma membrane|ruffle	intermediate filament binding|phosphatidylinositol binding|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein tyrosine phosphatase activity			upper_aerodigestive_tract(1)|ovary(1)|kidney(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					CAGAAAATAAGACGGTCATTG	0.378													9	45	---	---	---	---	PASS
GPR50	9248	broad.mit.edu	37	X	150345263	150345263	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:150345263C>A	uc010ntg.1	+	1	205	c.70C>A	c.(70-72)CCA>ACA	p.P24T	uc004fes.1_Intron|GPR50_uc011myc.1_Missense_Mutation_p.P24T	NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	24	Extracellular (Potential).				cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					GCCAGAATACCCACCGGCTCT	0.522													14	70	---	---	---	---	PASS
GPR50	9248	broad.mit.edu	37	X	150349094	150349094	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:150349094C>A	uc010ntg.1	+	2	1174	c.1039C>A	c.(1039-1041)CGT>AGT	p.R347S	uc004fes.1_5'Flank|GPR50_uc011myc.1_3'UTR	NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	347	Cytoplasmic (Potential).|Pro-rich.				cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					CGACCAAGCTCGTGAACAAGA	0.592													5	85	---	---	---	---	PASS
CNGA2	1260	broad.mit.edu	37	X	150911903	150911903	+	Missense_Mutation	SNP	C	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:150911903C>A	uc004fey.1	+	7	1152	c.928C>A	c.(928-930)CCA>ACA	p.P310T		NM_005140	NP_005131	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	310	Cytoplasmic (Potential).				response to stimulus|sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					CTGGGTTTACCCAAACATCAC	0.493													8	175	---	---	---	---	PASS
CNGA2	1260	broad.mit.edu	37	X	150912080	150912080	+	Nonsense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:150912080G>T	uc004fey.1	+	7	1329	c.1105G>T	c.(1105-1107)GGA>TGA	p.G369*		NM_005140	NP_005131	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	369	Helical; Name=H5; (Potential).				response to stimulus|sensory perception of smell	intracellular cyclic nucleotide activated cation channel complex	cAMP binding|intracellular cAMP activated cation channel activity			breast(3)	3	Acute lymphoblastic leukemia(192;6.56e-05)					CACCATCGTGGGAAATGTGGG	0.512													19	103	---	---	---	---	PASS
MAGEA6	4105	broad.mit.edu	37	X	151870096	151870096	+	Silent	SNP	C	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:151870096C>T	uc004ffq.1	+	3	980	c.786C>T	c.(784-786)CCC>CCT	p.P262P	MAGEA6_uc004ffr.1_Silent_p.P262P|MAGEA2_uc010nto.2_Intron	NM_005363	NP_005354	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	262	MAGE.						protein binding				0	Acute lymphoblastic leukemia(192;6.56e-05)					GGCAGGTCCCCGGCAGTGATC	0.527													22	120	---	---	---	---	PASS
PLXNB3	5365	broad.mit.edu	37	X	153043055	153043055	+	Missense_Mutation	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:153043055G>T	uc004fii.2	+	31	5347	c.5173G>T	c.(5173-5175)GTC>TTC	p.V1725F	PLXNB3_uc010nuk.2_Missense_Mutation_p.V1748F|PLXNB3_uc011mzd.1_Missense_Mutation_p.V1364F|SRPK3_uc004fik.2_5'UTR	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3 isoform 1	1725	Cytoplasmic (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCCATCGCCGTCAAGTACCT	0.592													5	184	---	---	---	---	PASS
FLNA	2316	broad.mit.edu	37	X	153588595	153588595	+	Missense_Mutation	SNP	T	C	C			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:153588595T>C	uc004fkk.2	-	22	3817	c.3568A>G	c.(3568-3570)AGC>GGC	p.S1190G	FLNA_uc011mzn.1_5'Flank|FLNA_uc010nuu.1_Missense_Mutation_p.S1190G	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1190	Filamin 10.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					AGCTCCGCGCTGCCCGCGCTC	0.642											OREG0003593	type=REGULATORY REGION|Gene=FLNA|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	36	---	---	---	---	PASS
FLNA	2316	broad.mit.edu	37	X	153588596	153588596	+	Silent	SNP	G	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:153588596G>T	uc004fkk.2	-	22	3816	c.3567C>A	c.(3565-3567)GGC>GGA	p.G1189G	FLNA_uc011mzn.1_5'Flank|FLNA_uc010nuu.1_Silent_p.G1189G	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	1189	Filamin 10.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCTCCGCGCTGCCCGCGCTCG	0.642											OREG0003593	type=REGULATORY REGION|Gene=FLNA|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	36	---	---	---	---	PASS
PLXNA3	55558	broad.mit.edu	37	X	153689015	153689015	+	Silent	SNP	G	A	A			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chrX:153689015G>A	uc004flm.2	+	2	665	c.492G>A	c.(490-492)AAG>AAA	p.K164K		NM_017514	NP_059984	P51805	PLXA3_HUMAN	plexin A3 precursor	164	Sema.|Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity			upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGCCCAGCAAGCTGTTTGTGG	0.627													26	90	---	---	---	---	PASS
FGFRL1	53834	broad.mit.edu	37	4	1019055	1019056	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr4:1019055_1019056delCA	uc003gce.2	+	7	1596_1597	c.1435_1436delCA	c.(1435-1437)CACfs	p.H479fs	FGFRL1_uc003gcf.2_Frame_Shift_Del_p.H479fs|FGFRL1_uc003gcg.2_Frame_Shift_Del_p.H479fs|FGFRL1_uc010ibo.2_Frame_Shift_Del_p.H479fs	NM_021923	NP_068742	Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	479	His-rich.|Cytoplasmic (Potential).				regulation of cell growth	integral to membrane|plasma membrane	fibroblast growth factor receptor activity|heparin binding				0			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			cacagacatccacacacacaca	0.460													4	2	---	---	---	---	
LOC340094	340094	broad.mit.edu	37	5	5057794	5057795	+	RNA	INS	-	T	T			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr5:5057794_5057795insT	uc003jdg.2	+	3		c.428_429insT			LOC340094_uc003jdh.2_RNA	NR_026994				Homo sapiens hypothetical protein LOC340094, mRNA (cDNA clone IMAGE:5295461).												0						TCCAACACATATTTTTTTTGAA	0.361													7	7	---	---	---	---	
TDRG1	732253	broad.mit.edu	37	6	40347103	40347104	+	RNA	INS	-	C	C	rs148319526	by1000genomes	TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr6:40347103_40347104insC	uc003opg.2	+	2		c.557_558insC				NR_024015				Homo sapiens cDNA clone IMAGE:5297318.												0						GAACTGGGAAGCCCCCCCACCC	0.515													3	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	149578672	149578673	+	RNA	INS	-	G	G	rs147389970	by1000genomes	TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr7:149578672_149578673insG	uc003wgt.1	+	1		c.109_110insG								Homo sapiens cDNA clone IMAGE:40014135.																		GCTGGCTGGGCGGTGGGGCGGA	0.604													3	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	102842	102842	+	RNA	DEL	G	-	-			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr9:102842delG	uc003zfy.2	-	1		c.100delC								Homo sapiens chromosome 2 mRNA sequence.																		GTCAGCACGTGGCACTCAGCT	0.388													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	132106612	132106612	+	RNA	DEL	A	-	-			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr9:132106612delA	uc004bxu.2	+	1		c.918delA								Homo sapiens cDNA clone IMAGE:6277875, partial cds.																		AGCGGCATTGAAAAAACCCTC	0.343													4	2	---	---	---	---	
LOC84856	84856	broad.mit.edu	37	10	42990170	42990170	+	RNA	DEL	G	-	-			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr10:42990170delG	uc001izy.2	+	5		c.1691delG			LOC84856_uc009xmf.2_RNA|LOC84856_uc001izz.1_RNA	NR_026827				Homo sapiens cDNA FLJ33470 fis, clone BRAMY2002044.												0						taccacgtttggttTCAAATG	0.090													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	15	67155912	67155912	+	RNA	DEL	A	-	-			TCGA-66-2734-01A-01D-0983-08	TCGA-66-2734-11A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	9f7a24a2-10e2-4039-ad27-13d7ec28ff36	e18d5713-e75d-49ca-857e-0d974b3a0282	g.chr15:67155912delA	uc002aqh.1	+	1		c.3272delA			uc002aqi.2_5'Flank					Homo sapiens mRNA; cDNA DKFZp686F0429 (from clone DKFZp686F0429).																		agatgtggctaaaatgccacc	0.025											OREG0023212	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
