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
PEX10	5192	broad.mit.edu	37	1	2340172	2340172	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:2340172C>G	uc001ajh.2	-	3	388	c.319G>C	c.(319-321)GAC>CAC	p.D107H	PEX10_uc001ajg.2_Missense_Mutation_p.D107H	NM_002617	NP_002608	O60683	PEX10_HUMAN	peroxisome biogenesis factor 10 isoform 2	107					protein import into peroxisome matrix|protein import into peroxisome matrix	integral to peroxisomal membrane|peroxisomal membrane	protein binding|protein C-terminus binding|zinc ion binding|zinc ion binding			central_nervous_system(1)	1	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)		AGGGCCTTGTCCAGCAGGTAG	0.687													7	22	---	---	---	---	PASS
PRAMEF2	65122	broad.mit.edu	37	1	12921252	12921252	+	Missense_Mutation	SNP	C	A	A	rs150748226	by1000genomes	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:12921252C>A	uc001aum.1	+	4	1130	c.1043C>A	c.(1042-1044)GCT>GAT	p.A348D		NM_023014	NP_075390	O60811	PRAM2_HUMAN	PRAME family member 2	348	LRR 2.										0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GAGAAAATTGCTGCCTCTCTC	0.557													45	107	---	---	---	---	PASS
PRAMEF4	400735	broad.mit.edu	37	1	12942116	12942116	+	Missense_Mutation	SNP	C	T	T	rs145911043	byFrequency	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:12942116C>T	uc001aun.2	-	3	505	c.434G>A	c.(433-435)GGA>GAA	p.G145E		NM_001009611	NP_001009611	O60810	PRAM4_HUMAN	PRAME family member 4	145										ovary(1)	1	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGGCTGCCGTCCTCTCATCCT	0.502													61	205	---	---	---	---	PASS
DNAJC16	23341	broad.mit.edu	37	1	15894409	15894409	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:15894409G>T	uc001aws.2	+	15	2206	c.2086G>T	c.(2086-2088)GGT>TGT	p.G696C	DNAJC16_uc001awt.2_Missense_Mutation_p.G384C|DNAJC16_uc001awu.2_RNA	NM_015291	NP_056106	Q9Y2G8	DJC16_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 16	696	Extracellular (Potential).				cell redox homeostasis|protein folding	integral to membrane	heat shock protein binding|unfolded protein binding			urinary_tract(1)|lung(1)|kidney(1)	3		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00173)|all_lung(284;0.00459)|Lung NSC(340;0.00499)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		TGACTACACTGGTTATGTACT	0.443													8	175	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19403254	19403254	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:19403254G>A	uc001bbi.2	-	105	15471	c.15467C>T	c.(15466-15468)TCA>TTA	p.S5156L	UBR4_uc001bbe.1_5'Flank|UBR4_uc001bbf.2_Missense_Mutation_p.S51L|UBR4_uc010ocv.1_Missense_Mutation_p.S679L|UBR4_uc009vph.2_Missense_Mutation_p.S811L|UBR4_uc010ocw.1_Missense_Mutation_p.S820L|UBR4_uc001bbg.2_Missense_Mutation_p.S867L|UBR4_uc001bbh.2_Missense_Mutation_p.S865L	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	5156					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GAGGAACTCTGAGAAGGTCTC	0.527													98	237	---	---	---	---	PASS
UBR4	23352	broad.mit.edu	37	1	19492186	19492186	+	Missense_Mutation	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:19492186T>A	uc001bbi.2	-	30	4179	c.4175A>T	c.(4174-4176)CAG>CTG	p.Q1392L	UBR4_uc001bbm.1_Missense_Mutation_p.Q603L	NM_020765	NP_065816	Q5T4S7	UBR4_HUMAN	retinoblastoma-associated factor 600	1392					interspecies interaction between organisms	cytoplasm|cytoskeleton|integral to membrane|nucleus	calmodulin binding|ubiquitin-protein ligase activity|zinc ion binding			kidney(10)|ovary(7)|breast(4)|pancreas(2)|skin(2)	25		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TTTACGAGCCTGGCTACTTTC	0.433													15	46	---	---	---	---	PASS
MATN1	4146	broad.mit.edu	37	1	31188829	31188829	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:31188829C>A	uc001brz.2	-	5	1168	c.1134G>T	c.(1132-1134)AAG>AAT	p.K378N	uc001bsb.1_5'Flank|MATN1_uc001bsa.1_Missense_Mutation_p.K296N	NM_002379	NP_002370	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein precursor	378	VWFA 2.				protein complex assembly	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding			central_nervous_system(1)	1		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		CAATGCCCACCTTCTGGGCCC	0.562													22	48	---	---	---	---	PASS
ZSCAN20	7579	broad.mit.edu	37	1	33960553	33960553	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:33960553C>A	uc001bxj.3	+	8	2776	c.2609C>A	c.(2608-2610)TCA>TAA	p.S870*	ZSCAN20_uc009vui.2_Nonsense_Mutation_p.S869*	NM_145238	NP_660281	P17040	ZSC20_HUMAN	zinc finger protein 31	870					viral reproduction	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AGCACAAACTCAGGGGAGAAA	0.438													8	265	---	---	---	---	PASS
EIF2C3	192669	broad.mit.edu	37	1	36506013	36506013	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:36506013C>A	uc001bzp.2	+	16	2399	c.2143C>A	c.(2143-2145)CGA>AGA	p.R715R	EIF2C3_uc001bzq.2_Silent_p.R481R	NM_024852	NP_079128	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	715	Piwi.				mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				ACATCACACTCGATTATTTTG	0.368													4	68	---	---	---	---	PASS
INPP5B	3633	broad.mit.edu	37	1	38338764	38338764	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:38338764G>C	uc001ccg.1	-	19	2119	c.2025C>G	c.(2023-2025)GAC>GAG	p.D675E	INPP5B_uc009vvk.1_Missense_Mutation_p.D616E|INPP5B_uc001ccf.1_Missense_Mutation_p.D511E	NM_005540	NP_005531	P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	755					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|integral to membrane|microtubule cytoskeleton	GTPase activator activity|inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity|protein binding			urinary_tract(1)	1	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CCTCAATTTTGTCTTCACCCG	0.418													40	61	---	---	---	---	PASS
HIVEP3	59269	broad.mit.edu	37	1	41976621	41976621	+	Missense_Mutation	SNP	C	T	T	rs147749727		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:41976621C>T	uc001cgz.3	-	9	7935	c.6722G>A	c.(6721-6723)CGA>CAA	p.R2241Q	HIVEP3_uc001cha.3_Missense_Mutation_p.R2240Q|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	2241					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)				CCAGCGGCCTCGCTCCTGGGC	0.692													15	14	---	---	---	---	PASS
HIVEP3	59269	broad.mit.edu	37	1	42045798	42045798	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:42045798C>T	uc001cgz.3	-	4	5884	c.4671G>A	c.(4669-4671)AAG>AAA	p.K1557K	HIVEP3_uc001cha.3_Silent_p.K1557K|HIVEP3_uc001cgy.2_RNA	NM_024503	NP_078779	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer	1557					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)				CAGGTTGTTCCTTGGAATCTT	0.542													23	54	---	---	---	---	PASS
KIAA0467	23334	broad.mit.edu	37	1	43914311	43914311	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:43914311G>T	uc001cjk.1	+	55	7763	c.7301G>T	c.(7300-7302)TGG>TTG	p.W2434L	KIAA0467_uc001cjl.1_Missense_Mutation_p.W422L	NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	3333						peroxisome					0	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				ACGGTCTCCTGGTACCAGAGC	0.572													10	206	---	---	---	---	PASS
PTPRF	5792	broad.mit.edu	37	1	44056897	44056897	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:44056897G>A	uc001cjr.2	+	9	1544	c.1204G>A	c.(1204-1206)GAG>AAG	p.E402K	PTPRF_uc001cjs.2_Missense_Mutation_p.E402K|PTPRF_uc001cju.2_5'UTR|PTPRF_uc009vwt.2_5'UTR|PTPRF_uc001cjv.2_5'UTR	NM_002840	NP_002831	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	402	Extracellular (Potential).|Fibronectin type-III 1.				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|skin(3)|lung(1)|kidney(1)|central_nervous_system(1)	10	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCCGCCCAGCGAGGCAGTGCG	0.697													8	7	---	---	---	---	PASS
TESK2	10420	broad.mit.edu	37	1	45821049	45821049	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:45821049G>C	uc001cns.1	-	5	869	c.466C>G	c.(466-468)CTG>GTG	p.L156V	TESK2_uc009vxr.1_Missense_Mutation_p.L156V|TESK2_uc010olo.1_Missense_Mutation_p.L73V|TESK2_uc009vxs.1_5'UTR	NM_007170	NP_009101	Q96S53	TESK2_HUMAN	testis-specific protein kinase 2	156	Protein kinase.				actin cytoskeleton organization|focal adhesion assembly|spermatogenesis	nucleus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(2)|breast(2)|pancreas(1)	5	Acute lymphoblastic leukemia(166;0.155)					TCATAGGCCAGTTTTACCCTC	0.468													8	26	---	---	---	---	PASS
TTC39A	22996	broad.mit.edu	37	1	51753897	51753897	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:51753897C>A	uc001csl.2	-	18	1879	c.1774G>T	c.(1774-1776)GCC>TCC	p.A592S	TTC39A_uc001csk.2_Missense_Mutation_p.A557S|TTC39A_uc010ond.1_Missense_Mutation_p.A529S|TTC39A_uc010one.1_Missense_Mutation_p.A556S|TTC39A_uc010onf.1_Missense_Mutation_p.A560S|TTC39A_uc001csj.2_Missense_Mutation_p.A193S	NM_001080494	NP_001073963	Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A isoform 2	592							binding			skin(1)	1						TGGAGTGTGGCTGCCTGGATT	0.512													5	86	---	---	---	---	PASS
SLC1A7	6512	broad.mit.edu	37	1	53554564	53554564	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:53554564C>A	uc001cuy.2	-	10	1617	c.1449G>T	c.(1447-1449)CGG>CGT	p.R483R	SLC1A7_uc001cux.2_Silent_p.R136R	NM_006671	NP_006662	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter),	483						integral to membrane|plasma membrane	high-affinity glutamate transmembrane transporter activity|sodium:dicarboxylate symporter activity			ovary(2)|large_intestine(1)	3				Colorectal(1306;0.234)	L-Glutamic Acid(DB00142)	TGCCTGTGTCCCGGGCAAAAT	0.547													17	38	---	---	---	---	PASS
FGGY	55277	broad.mit.edu	37	1	59844452	59844452	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:59844452G>A	uc001czi.3	+	5	709	c.497G>A	c.(496-498)GGA>GAA	p.G166E	FGGY_uc001czg.2_Missense_Mutation_p.G54E|FGGY_uc001czh.2_RNA|FGGY_uc009wac.2_Missense_Mutation_p.G166E|FGGY_uc001czj.3_Missense_Mutation_p.G166E|FGGY_uc001czk.3_Missense_Mutation_p.G54E|FGGY_uc001czl.3_Missense_Mutation_p.G78E	NM_018291	NP_060761	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing	166					carbohydrate metabolic process|cell death|neuron homeostasis		kinase activity|phosphotransferase activity, alcohol group as acceptor			ovary(1)	1	all_cancers(7;7.36e-05)					GATAAGGCGGGACATTTCTTT	0.393													12	14	---	---	---	---	PASS
HFM1	164045	broad.mit.edu	37	1	91778938	91778938	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:91778938G>A	uc001doa.3	-	30	3459	c.3359C>T	c.(3358-3360)TCA>TTA	p.S1120L	HFM1_uc009wdb.2_RNA|HFM1_uc010osu.1_Missense_Mutation_p.S799L|HFM1_uc001dob.3_Missense_Mutation_p.S308L|HFM1_uc010osv.1_Missense_Mutation_p.S804L	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein	1120							ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AGATATGTCTGAATGTTTAGA	0.328													7	19	---	---	---	---	PASS
CNN3	1266	broad.mit.edu	37	1	95368960	95368960	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:95368960C>A	uc010otw.1	-	3	260	c.178G>T	c.(178-180)GAA>TAA	p.E60*	CNN3_uc010otv.1_Nonsense_Mutation_p.E19*|CNN3_uc001dqz.3_Nonsense_Mutation_p.E60*|CNN3_uc010otx.1_Nonsense_Mutation_p.E60*	NM_001839	NP_001830	Q15417	CNN3_HUMAN	calponin 3	60	CH.				actomyosin structure organization|smooth muscle contraction		actin binding|calmodulin binding|tropomyosin binding|troponin C binding				0		all_lung(203;0.00206)|Lung NSC(277;0.00948)		all cancers(265;0.0325)|Epithelial(280;0.0861)		GTAACTCACTCGCAGAGGATG	0.507													5	56	---	---	---	---	PASS
FNDC7	163479	broad.mit.edu	37	1	109271508	109271508	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:109271508G>T	uc001dvx.2	+	8	1624	c.1624G>T	c.(1624-1626)GTG>TTG	p.V542L	FNDC7_uc010ova.1_Missense_Mutation_p.V309L	NM_001144937	NP_001138409	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	543						extracellular region				ovary(1)|skin(1)	2		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		CCTGGAAACAGGTATGTAGCA	0.532													9	16	---	---	---	---	PASS
GSTM4	2948	broad.mit.edu	37	1	110201701	110201701	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:110201701C>A	uc001dyf.2	+	7	850	c.536C>A	c.(535-537)CCA>CAA	p.P179Q	GSTM4_uc001dyg.2_Missense_Mutation_p.P75Q|GSTM4_uc009wfj.2_Missense_Mutation_p.P118Q|GSTM4_uc001dyh.2_Missense_Mutation_p.P179Q|GSTM2_uc001dyi.2_Intron	NM_000850	NP_000841	Q03013	GSTM4_HUMAN	glutathione S-transferase mu 4 isoform 1	179	GST C-terminal.				xenobiotic metabolic process	endoplasmic reticulum membrane	glutathione transferase activity				0		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0123)|Colorectal(144;0.0129)|Epithelial(280;0.0147)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.0471)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	GACGCCTTTCCAAATCTGAAG	0.498													9	367	---	---	---	---	PASS
CSF1	1435	broad.mit.edu	37	1	110460061	110460061	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:110460061C>A	uc001dyu.2	+	4	785	c.372C>A	c.(370-372)ACC>ACA	p.T124T	CSF1_uc001dyt.2_Silent_p.T124T|CSF1_uc001dyv.3_Silent_p.T124T|CSF1_uc001dyw.3_Silent_p.T124T	NM_172212	NP_757351	P09603	CSF1_HUMAN	colony stimulating factor 1 isoform a precursor	124	Lumenal (Potential).				cell proliferation|developmental process involved in reproduction|macrophage differentiation|monocyte activation|osteoclast differentiation|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of cellular protein metabolic process|positive regulation of gene expression|positive regulation of macrophage derived foam cell differentiation|positive regulation of macrophage differentiation|positive regulation of monocyte differentiation|positive regulation of mononuclear cell proliferation|positive regulation of protein kinase activity	extracellular space|integral to membrane|perinuclear region of cytoplasm|plasma membrane|receptor complex	cytokine activity|growth factor activity|macrophage colony-stimulating factor receptor binding|protein homodimerization activity			ovary(1)	1		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		GCTGCTTCACCAAGGATTATG	0.557													8	261	---	---	---	---	PASS
CD101	9398	broad.mit.edu	37	1	117556285	117556285	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:117556285C>G	uc010oxb.1	+	4	1157	c.1099C>G	c.(1099-1101)CTG>GTG	p.L367V	CD101_uc009whd.2_Missense_Mutation_p.L367V|CD101_uc010oxc.1_Missense_Mutation_p.L367V|CD101_uc010oxd.1_Missense_Mutation_p.L305V	NM_004258	NP_004249	Q93033	IGSF2_HUMAN	immunoglobulin superfamily, member 2 precursor	367	Ig-like C2-type 3.|Extracellular (Potential).				cell surface receptor linked signaling pathway	integral to membrane|plasma membrane	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides			skin(2)|upper_aerodigestive_tract(1)|ovary(1)	4						GATCTTCTCTCTGGGCCCAGA	0.517													14	42	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144873931	144873931	+	Missense_Mutation	SNP	T	C	C	rs137931320	byFrequency	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:144873931T>C	uc001elw.3	-	31	5317	c.5026A>G	c.(5026-5028)ATC>GTC	p.I1676V	NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Missense_Mutation_p.I1632V|PDE4DIP_uc001elv.3_Missense_Mutation_p.I683V	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform	1676					cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GGCAAGCTGATGGGGTTGCTG	0.517			T	PDGFRB	MPD								31	248	---	---	---	---	PASS
ITGA10	8515	broad.mit.edu	37	1	145531022	145531022	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:145531022G>T	uc001eoa.2	+	7	830	c.754G>T	c.(754-756)GCC>TCC	p.A252S	NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Missense_Mutation_p.A121S|ITGA10_uc009wiw.2_Missense_Mutation_p.A109S|ITGA10_uc010oyw.1_Missense_Mutation_p.A197S	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	252	VWFA.|Extracellular (Potential).				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AATAATGGTGGCCTGGTGAGG	0.458													8	21	---	---	---	---	PASS
ACP6	51205	broad.mit.edu	37	1	147126410	147126410	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:147126410C>A	uc001epr.2	-	6	1143	c.679G>T	c.(679-681)GGA>TGA	p.G227*	ACP6_uc009wjj.1_Nonsense_Mutation_p.G184*	NM_016361	NP_057445	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic precursor	227					lipid metabolic process	extracellular region|mitochondrion	acid phosphatase activity|protein binding			ovary(4)	4	all_hematologic(923;0.0276)					TCTGAGATTCCTGGCTGTAAA	0.353													6	57	---	---	---	---	PASS
FCGR1A	2209	broad.mit.edu	37	1	149761656	149761656	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:149761656C>T	uc001esp.3	+	5	656	c.606C>T	c.(604-606)CTC>CTT	p.L202L	HIST2H2BF_uc010pbj.1_Intron|FCGR1A_uc009wlg.2_Intron	NM_000566	NP_000557	P12314	FCGR1_HUMAN	Fc fragment of IgG, high affinity Ia, receptor	202	Extracellular (Potential).|Ig-like C2-type 3.				interferon-gamma-mediated signaling pathway|phagocytosis, engulfment	integral to membrane|plasma membrane	IgG binding|receptor activity|receptor signaling protein activity			ovary(1)	1	Breast(34;0.0124)|all_hematologic(923;0.127)				Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Methyl aminolevulinate(DB00992)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Porfimer(DB00707)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CATCCCCACTCCTGGAGGGGA	0.512													9	21	---	---	---	---	PASS
MTMR11	10903	broad.mit.edu	37	1	149905510	149905510	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:149905510C>G	uc001etl.3	-	9	1104	c.853G>C	c.(853-855)GAT>CAT	p.D285H	MTMR11_uc001etm.1_Missense_Mutation_p.D213H|MTMR11_uc010pbm.1_Missense_Mutation_p.D257H|MTMR11_uc010pbn.1_Missense_Mutation_p.D127H	NM_001145862	NP_001139334	A4FU01	MTMRB_HUMAN	myotubularin related protein 11 isoform a	285	Myotubularin phosphatase.						phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			CACCTGATATCCTCCTTGTTA	0.542													21	46	---	---	---	---	PASS
HRNR	388697	broad.mit.edu	37	1	152190884	152190884	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:152190884G>T	uc001ezt.1	-	3	3297	c.3221C>A	c.(3220-3222)TCT>TAT	p.S1074Y		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	1074	12.				keratinization		calcium ion binding|protein binding			skin(2)|ovary(1)	3	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCATGGGTAGAGGAATGACC	0.562													10	360	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152285051	152285051	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:152285051G>T	uc001ezu.1	-	3	2347	c.2311C>A	c.(2311-2313)CAT>AAT	p.H771N	uc001ezv.2_5'Flank	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	771	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)			CTCTGCTGATGGTGACCAGCC	0.562									Ichthyosis				9	305	---	---	---	---	PASS
KPRP	448834	broad.mit.edu	37	1	152732412	152732412	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:152732412G>T	uc001fal.1	+	2	406	c.348G>T	c.(346-348)GAG>GAT	p.E116D		NM_001025231	NP_001020402	Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	116	Gln-rich.					cytoplasm				ovary(4)|pancreas(1)	5	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCAATCTGAGGTGTCCTACG	0.502													10	395	---	---	---	---	PASS
PGLYRP4	57115	broad.mit.edu	37	1	153318633	153318633	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:153318633C>A	uc001fbo.2	-	3	149	c.84G>T	c.(82-84)CAG>CAT	p.Q28H	PGLYRP4_uc001fbp.2_Missense_Mutation_p.Q28H	NM_020393	NP_065126	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein-I-beta	28					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(3)|skin(1)	4	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTCTGATACCTGTTTAGCTT	0.488													7	190	---	---	---	---	PASS
CLK2	1196	broad.mit.edu	37	1	155239429	155239429	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:155239429G>T	uc001fjy.2	-	3	539	c.249C>A	c.(247-249)AGC>AGA	p.S83R	RAG1AP1_uc010pey.1_Intron|CLK2_uc001fjw.2_Missense_Mutation_p.S83R|CLK2_uc001fjx.2_5'UTR|CLK2_uc009wqm.2_Missense_Mutation_p.S83R	NM_003993	NP_003984	P49760	CLK2_HUMAN	CDC-like kinase 2	83						nucleus	ATP binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CCCGATCCCGGCTATAATCGT	0.527								Other_conserved_DNA_damage_response_genes					23	108	---	---	---	---	PASS
ARHGEF11	9826	broad.mit.edu	37	1	156954202	156954202	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:156954202T>C	uc001fqo.2	-	3	1192	c.152A>G	c.(151-153)CAA>CGA	p.Q51R	ARHGEF11_uc001fqn.2_Missense_Mutation_p.Q51R	NM_014784	NP_055599	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	51	PDZ.				actin cytoskeleton organization|apoptosis|axon guidance|cellular component movement|cytokinesis|establishment of cell polarity|G-protein coupled receptor protein signaling pathway|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of cell growth|regulation of Rho protein signal transduction|Rho protein signal transduction|striated muscle contraction	cytosol|Golgi apparatus|plasma membrane	G-protein-coupled receptor binding|GTPase activator activity|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			ovary(3)|skin(2)|pleura(1)|lung(1)|kidney(1)|pancreas(1)	9	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CTGGTCCTTTTGGATAATGAC	0.557													3	5	---	---	---	---	PASS
FCRL5	83416	broad.mit.edu	37	1	157504490	157504490	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:157504490G>A	uc001fqu.2	-	8	1753	c.1595C>T	c.(1594-1596)ACT>ATT	p.T532I	FCRL5_uc009wsm.2_Missense_Mutation_p.T532I|FCRL5_uc010phv.1_Missense_Mutation_p.T532I|FCRL5_uc010phw.1_Missense_Mutation_p.T447I|FCRL5_uc001fqv.1_Missense_Mutation_p.T532I|FCRL5_uc010phx.1_Missense_Mutation_p.T283I	NM_031281	NP_112571	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	532	Extracellular (Potential).|Ig-like C2-type 5.					integral to membrane|plasma membrane	receptor activity			ovary(3)|breast(2)|central_nervous_system(1)	6	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				ATGTCCTTCAGTCAGAGAGAA	0.507													6	15	---	---	---	---	PASS
PYHIN1	149628	broad.mit.edu	37	1	158914791	158914791	+	Nonsense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:158914791C>T	uc001ftb.2	+	7	1563	c.1318C>T	c.(1318-1320)CAG>TAG	p.Q440*	PYHIN1_uc001ftc.2_Nonsense_Mutation_p.Q431*|PYHIN1_uc001ftd.2_Nonsense_Mutation_p.Q440*|PYHIN1_uc001fte.2_Nonsense_Mutation_p.Q431*	NM_152501	NP_689714	Q6K0P9	IFIX_HUMAN	pyrin and HIN domain family, member 1 alpha 1	440					cell cycle	nuclear speck				ovary(3)|pancreas(1)	4	all_hematologic(112;0.0378)					CAAGACTCCTCAGATGCCACC	0.488													10	30	---	---	---	---	PASS
OLFML2B	25903	broad.mit.edu	37	1	161967615	161967615	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:161967615C>A	uc001gbu.2	-	6	1898	c.1474G>T	c.(1474-1476)GGA>TGA	p.G492*	OLFML2B_uc010pkq.1_Nonsense_Mutation_p.G493*	NM_015441	NP_056256	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B precursor	492										skin(1)	1	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			ATGAACTTACCTATGACATTC	0.542													9	304	---	---	---	---	PASS
ILDR2	387597	broad.mit.edu	37	1	166908752	166908752	+	Silent	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:166908752T>A	uc001gdx.1	-	4	611	c.555A>T	c.(553-555)CCA>CCT	p.P185P		NM_199351	NP_955383	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor	185	Extracellular (Potential).					integral to membrane				ovary(1)	1						ACCGAATACCTGGCATAATCT	0.413													12	30	---	---	---	---	PASS
SMG7	9887	broad.mit.edu	37	1	183511607	183511607	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:183511607G>T	uc001gqg.2	+	14	1934	c.1812G>T	c.(1810-1812)CAG>CAT	p.Q604H	SMG7_uc010pob.1_Intron|SMG7_uc001gqf.2_Intron|SMG7_uc001gqh.2_Intron|SMG7_uc001gqi.2_Intron|SMG7_uc010poc.1_Missense_Mutation_p.Q562H	NM_173156	NP_775179	Q92540	SMG7_HUMAN	SMG-7 homolog isoform 1	604					mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of dephosphorylation	cytoplasm|intermediate filament cytoskeleton|nucleus	protein phosphatase 2A binding			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3						AAAAGTTACAGGAAACAGGAA	0.383													6	72	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186294905	186294905	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:186294905G>C	uc001grv.2	-	42	6400	c.6103C>G	c.(6103-6105)CAA>GAA	p.Q2035E		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	2035					carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CCACTGTTTTGAGAATCAGCA	0.338			T	NTRK1	papillary thyroid								6	18	---	---	---	---	PASS
TPR	7175	broad.mit.edu	37	1	186324872	186324872	+	Silent	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:186324872T>C	uc001grv.2	-	16	2214	c.1917A>G	c.(1915-1917)GCA>GCG	p.A639A		NM_003292	NP_003283	P12270	TPR_HUMAN	nuclear pore complex-associated protein TPR	639					carbohydrate metabolic process|glucose transport|mitotic cell cycle spindle assembly checkpoint|mRNA transport|protein import into nucleus|regulation of glucose transport|seryl-tRNA aminoacylation|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytoplasm|nuclear membrane|nuclear pore|nucleoplasm	ATP binding|protein binding|serine-tRNA ligase activity			ovary(2)|lung(2)|urinary_tract(1)|central_nervous_system(1)|skin(1)	7		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TTGGAGTTGATGCAAGAGAAA	0.393			T	NTRK1	papillary thyroid								22	31	---	---	---	---	PASS
CFHR4	10877	broad.mit.edu	37	1	196882045	196882045	+	Silent	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:196882045T>A	uc001gto.2	+	3	501	c.432T>A	c.(430-432)ATT>ATA	p.I144I	CFHR4_uc009wyy.2_Silent_p.I390I|CFHR4_uc001gtp.2_Silent_p.I391I	NM_006684	NP_006675	Q92496	FHR4_HUMAN	complement factor H-related 4 precursor	144	Sushi 2.					extracellular region	lipid transporter activity			ovary(1)|pancreas(1)|skin(1)	3						CACAACCAATTTGCATTAGTA	0.308													13	23	---	---	---	---	PASS
SHISA4	149345	broad.mit.edu	37	1	201859588	201859588	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:201859588G>A	uc001gxa.2	+	3	343	c.252G>A	c.(250-252)AAG>AAA	p.K84K		NM_198149	NP_937792	Q96DD7	SHSA4_HUMAN	shisa homolog 4 precursor	84	Extracellular (Potential).					integral to membrane					0						AAAGCCCCAAGACCATAGCAG	0.562													37	110	---	---	---	---	PASS
SYT2	127833	broad.mit.edu	37	1	202571625	202571625	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:202571625C>A	uc001gye.2	-	5	707	c.514G>T	c.(514-516)GGA>TGA	p.G172*	SYT2_uc010pqb.1_Nonsense_Mutation_p.G172*|SYT2_uc009xaf.2_Nonsense_Mutation_p.G2*	NM_001136504	NP_001129976	Q8N9I0	SYT2_HUMAN	synaptotagmin II	172	Phospholipid binding (By similarity).|C2 1.|Cytoplasmic (Potential).				neurotransmitter secretion	cell junction|chromaffin granule membrane|endocytic vesicle membrane|integral to membrane|synaptic vesicle membrane	protein binding|transporter activity			ovary(2)|skin(1)	3			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	GAGGTGCCTCCCATGTCCAGG	0.537													6	86	---	---	---	---	PASS
PPFIA4	8497	broad.mit.edu	37	1	203036822	203036822	+	Splice_Site	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:203036822G>C	uc001gyz.2	+	13	2126	c.1533_splice	c.e13-1	p.R511_splice	PPFIA4_uc009xaj.2_Splice_Site_p.R1142_splice|PPFIA4_uc010pqf.1_Splice_Site_p.R724_splice|PPFIA4_uc001gza.2_Splice_Site_p.R502_splice|PPFIA4_uc001gzb.1_Splice_Site_p.R197_splice|PPFIA4_uc001gzc.1_Splice_Site_p.R53_splice	NM_015053	NP_055868	O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f						cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5						TGTGCCTGCAGAACCAGTCTT	0.562													19	34	---	---	---	---	PASS
TMEM206	55248	broad.mit.edu	37	1	212558649	212558649	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:212558649G>A	uc001hjc.3	-	4	630	c.462C>T	c.(460-462)ATC>ATT	p.I154I	TMEM206_uc010pte.1_Silent_p.I215I	NM_018252	NP_060722	Q9H813	TM206_HUMAN	transmembrane protein 206	154	Extracellular (Potential).					integral to membrane				breast(1)	1				all cancers(67;0.012)|OV - Ovarian serous cystadenocarcinoma(81;0.0121)|GBM - Glioblastoma multiforme(131;0.0377)|Epithelial(68;0.148)		CCGTGTAGTTGATCCTCTGGG	0.577													10	68	---	---	---	---	PASS
USH2A	7399	broad.mit.edu	37	1	216052233	216052233	+	Missense_Mutation	SNP	G	A	A	rs111033529		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:216052233G>A	uc001hku.1	-	42	8818	c.8431C>T	c.(8431-8433)CCT>TCT	p.P2811S		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	2811	Fibronectin type-III 14.|Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|upper_aerodigestive_tract(2)|skin(2)|kidney(1)|central_nervous_system(1)	26				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACATAGGTAGGTAAACTCTCT	0.443										HNSCC(13;0.011)			11	18	---	---	---	---	PASS
ESRRG	2104	broad.mit.edu	37	1	216850693	216850693	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:216850693C>A	uc001hkw.1	-	2	363	c.197G>T	c.(196-198)GGG>GTG	p.G66V	ESRRG_uc001hky.1_Missense_Mutation_p.G43V|ESRRG_uc009xdp.1_Missense_Mutation_p.G43V|ESRRG_uc001hkz.1_Missense_Mutation_p.G43V|ESRRG_uc010puc.1_Missense_Mutation_p.G43V|ESRRG_uc001hla.1_Missense_Mutation_p.G43V|ESRRG_uc001hlb.1_Missense_Mutation_p.G43V|ESRRG_uc010pud.1_Intron|ESRRG_uc001hlc.1_Missense_Mutation_p.G43V|ESRRG_uc001hld.1_Missense_Mutation_p.G43V|ESRRG_uc001hkx.1_Missense_Mutation_p.G71V|ESRRG_uc009xdo.1_Missense_Mutation_p.G43V|ESRRG_uc001hle.1_Missense_Mutation_p.G43V	NM_001438	NP_001429	P62508	ERR3_HUMAN	estrogen-related receptor gamma isoform 1	66					positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	AF-2 domain binding|retinoic acid receptor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|zinc ion binding			ovary(1)|kidney(1)	2				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	ACTGTAGCTCCCACTGGCGTC	0.577													10	21	---	---	---	---	PASS
SIPA1L2	57568	broad.mit.edu	37	1	232607249	232607249	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:232607249T>C	uc001hvg.2	-	6	2269	c.2111A>G	c.(2110-2112)AAT>AGT	p.N704S		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	704	Rap-GAP.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)|skin(1)	6		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GACGATGTCATTTCCTATGTG	0.383													16	33	---	---	---	---	PASS
KIAA1383	54627	broad.mit.edu	37	1	232942333	232942333	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:232942333C>G	uc001hvh.2	+	1	1696	c.1564C>G	c.(1564-1566)CAA>GAA	p.Q522E		NM_019090	NP_061963	Q9P2G4	K1383_HUMAN	hypothetical protein LOC54627	380										ovary(1)	1		all_cancers(173;0.00528)|Prostate(94;0.122)|all_epithelial(177;0.169)				AGCAACTAATCAAACATGTCA	0.378													15	29	---	---	---	---	PASS
HEATR1	55127	broad.mit.edu	37	1	236727825	236727825	+	Silent	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:236727825G>C	uc001hyd.1	-	32	4697	c.4572C>G	c.(4570-4572)CTC>CTG	p.L1524L	HEATR1_uc009xgh.1_Silent_p.L686L	NM_018072	NP_060542	Q9H583	HEAT1_HUMAN	protein BAP28	1524					rRNA processing	nucleolus|ribonucleoprotein complex	protein binding			ovary(2)|skin(1)	3	Ovarian(103;0.0634)|Breast(184;0.133)	all_cancers(173;0.0255)|Prostate(94;0.175)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			TGGAAGACAGGAGCTGAGACA	0.358													12	32	---	---	---	---	PASS
ACTN2	88	broad.mit.edu	37	1	236917316	236917316	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:236917316C>T	uc001hyf.2	+	16	2113	c.1909C>T	c.(1909-1911)CGT>TGT	p.R637C	ACTN2_uc001hyg.2_Missense_Mutation_p.R429C|ACTN2_uc009xgi.1_Missense_Mutation_p.R637C|ACTN2_uc010pxu.1_Missense_Mutation_p.R326C|ACTN2_uc001hyh.2_Missense_Mutation_p.R325C	NM_001103	NP_001094	P35609	ACTN2_HUMAN	actinin, alpha 2	637	Spectrin 4.				focal adhesion assembly|microspike assembly|muscle filament sliding|platelet activation|platelet degranulation|protein homotetramerization|regulation of apoptosis|synaptic transmission	actin filament|cytosol|dendritic spine|extracellular region|filopodium|focal adhesion|nucleolus|platelet alpha granule lumen|pseudopodium|Z disc	actin binding|calcium ion binding|FATZ 1 binding|identical protein binding|integrin binding|protein dimerization activity|structural constituent of muscle|titin binding|titin Z domain binding|ZASP binding			ovary(4)|skin(1)	5	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TGCTAACGAGCGTCTGAGGCG	0.602													22	35	---	---	---	---	PASS
MTR	4548	broad.mit.edu	37	1	236973829	236973829	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:236973829C>G	uc001hyi.3	+	5	859	c.436C>G	c.(436-438)CTG>GTG	p.L146V	MTR_uc010pxv.1_RNA|MTR_uc010pxw.1_5'UTR|MTR_uc010pxx.1_Missense_Mutation_p.L146V|MTR_uc010pxy.1_Missense_Mutation_p.L146V|MTR_uc009xgj.1_5'UTR	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine	146	Hcy-binding.				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	GGCAGGGGCTCTGGGTCCGAC	0.373													12	27	---	---	---	---	PASS
FMN2	56776	broad.mit.edu	37	1	240341241	240341241	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:240341241G>T	uc010pyd.1	+	3	2028	c.1803G>T	c.(1801-1803)TGG>TGT	p.W601C	FMN2_uc010pye.1_Missense_Mutation_p.W601C	NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	601					actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|skin(3)|large_intestine(1)|central_nervous_system(1)	12	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TTTATACCTGGGCTGCAGTTA	0.388													14	21	---	---	---	---	PASS
KMO	8564	broad.mit.edu	37	1	241712164	241712164	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:241712164G>C	uc009xgp.2	+	2	155	c.90G>C	c.(88-90)AGG>AGC	p.R30S	KMO_uc001hyy.2_Missense_Mutation_p.R30S|KMO_uc009xgo.1_Missense_Mutation_p.R30S	NM_003679	NP_003670	O15229	KMO_HUMAN	kynurenine 3-monooxygenase	30					pyridine nucleotide biosynthetic process|response to salt stress	cytosol|integral to membrane|mitochondrial outer membrane	electron carrier activity|flavin adenine dinucleotide binding|kynurenine 3-monooxygenase activity|NAD(P)H oxidase activity			ovary(2)	2	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			TTGCAAAGAGGAATTTCCAGA	0.279													9	31	---	---	---	---	PASS
OR2T4	127074	broad.mit.edu	37	1	248525429	248525429	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:248525429C>T	uc001ieh.1	+	1	547	c.547C>T	c.(547-549)CTG>TTG	p.L183L		NM_001004696	NP_001004696	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T,	183	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CTGCTGGTTCCTGGGCTCAGT	0.542													27	77	---	---	---	---	PASS
OR2G6	391211	broad.mit.edu	37	1	248685389	248685389	+	Missense_Mutation	SNP	G	A	A	rs138151830		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr1:248685389G>A	uc001ien.1	+	1	442	c.442G>A	c.(442-444)GCA>ACA	p.A148T		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G,	148	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|skin(1)	3	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGCCGGTGGAGCATGGCTCAG	0.577													9	23	---	---	---	---	PASS
ATP6V1C2	245973	broad.mit.edu	37	2	10912726	10912726	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:10912726C>A	uc002ras.2	+	8	737	c.628C>A	c.(628-630)CGA>AGA	p.R210R	ATP6V1C2_uc002rat.2_Silent_p.R210R	NM_001039362	NP_001034451	Q8NEY4	VATC2_HUMAN	vacuolar H+ ATPase C2 isoform a	210					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		GGTGGTCCCTCGATCAACCAA	0.512													7	348	---	---	---	---	PASS
DNMT3A	1788	broad.mit.edu	37	2	25462032	25462032	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:25462032C>T	uc002rgc.2	-	20	2632	c.2375G>A	c.(2374-2376)CGC>CAC	p.R792H	DNMT3A_uc002rgd.2_Missense_Mutation_p.R792H|DNMT3A_uc010eyi.2_RNA|DNMT3A_uc002rgb.2_Missense_Mutation_p.R603H	NM_022552	NP_072046	Q9Y6K1	DNM3A_HUMAN	DNA cytosine methyltransferase 3 alpha isoform	792					regulation of gene expression by genetic imprinting	cytoplasm|euchromatin|nuclear matrix	DNA (cytosine-5-)-methyltransferase activity|DNA binding|metal ion binding|protein binding	p.R792H(1)		haematopoietic_and_lymphoid_tissue(133)|lung(4)|ovary(3)	140	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGAAGTAGCGGGCCCTGTG	0.557			Mis|F|N|S		AML								6	12	---	---	---	---	PASS
SLC4A1AP	22950	broad.mit.edu	37	2	27900188	27900188	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:27900188G>C	uc002rlk.3	+	7	1815	c.1533G>C	c.(1531-1533)AGG>AGC	p.R511S		NM_018158	NP_060628	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger),	511	Potential.					cytoplasm|nucleus	double-stranded RNA binding|protein binding				0	Acute lymphoblastic leukemia(172;0.155)					ATGCTGAAAGGGAACTTTCTG	0.259													4	23	---	---	---	---	PASS
YIPF4	84272	broad.mit.edu	37	2	32517245	32517245	+	Splice_Site	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:32517245G>T	uc002rok.2	+	3	501	c.234_splice	c.e3-1	p.L78_splice		NM_032312	NP_115688	Q9BSR8	YIPF4_HUMAN	Yip1 domain family, member 4							endoplasmic reticulum|integral to membrane	protein binding				0	Acute lymphoblastic leukemia(172;0.155)					taaaattataGGGAAGAATTG	0.284													4	9	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32738083	32738083	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:32738083C>T	uc010ezu.2	+	54	10564	c.10430C>T	c.(10429-10431)CCT>CTT	p.P3477L		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	3477					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					TACATGTGTCCTAACTCCTCA	0.433													14	31	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32740349	32740349	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:32740349G>C	uc010ezu.2	+	55	10995	c.10861G>C	c.(10861-10863)GAA>CAA	p.E3621Q		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	3621					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					TCAATCTCCTGAAGCTATTAA	0.408													11	40	---	---	---	---	PASS
BIRC6	57448	broad.mit.edu	37	2	32774431	32774431	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:32774431C>G	uc010ezu.2	+	65	13161	c.13027C>G	c.(13027-13029)CAG>GAG	p.Q4343E		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat-containing 6	4343					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			ovary(5)|skin(4)|lung(2)|central_nervous_system(1)|breast(1)|pancreas(1)	14	Acute lymphoblastic leukemia(172;0.155)					TGGAGAAGCTCAGTCATCTCA	0.418													3	41	---	---	---	---	PASS
ABCG8	64241	broad.mit.edu	37	2	44099383	44099383	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:44099383C>T	uc002rtq.2	+	8	1239	c.1149C>T	c.(1147-1149)ACC>ACT	p.T383T	ABCG8_uc010yoa.1_Silent_p.T382T	NM_022437	NP_071882	Q9H221	ABCG8_HUMAN	ATP-binding cassette sub-family G member 8	383	Cytoplasmic (Potential).				cholesterol efflux|cholesterol homeostasis|excretion|lipid metabolic process|negative regulation of intestinal cholesterol absorption|negative regulation of intestinal phytosterol absorption	apical plasma membrane|integral to membrane	ATP binding|ATPase activity|protein heterodimerization activity			skin(3)|ovary(1)	4		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CACTAGACACCAACTGCCTCC	0.592													6	21	---	---	---	---	PASS
SIX3	6496	broad.mit.edu	37	2	45169910	45169910	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:45169910G>C	uc002run.1	+	1	874	c.667G>C	c.(667-669)GAG>CAG	p.E223Q		NM_005413	NP_005404	O95343	SIX3_HUMAN	SIX homeobox 3	223	Homeobox.				visual perception	nucleus					0		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CCTGTTGCGGGAGTGGTACCT	0.607													12	21	---	---	---	---	PASS
EPCAM	4072	broad.mit.edu	37	2	47612328	47612328	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:47612328G>T	uc002rvx.2	+	8	1240	c.882G>T	c.(880-882)ATG>ATT	p.M294I	EPCAM_uc002rvw.2_Missense_Mutation_p.M322I	NM_002354	NP_002345	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule precursor	294	Cytoplasmic (Potential).				positive regulation of cell proliferation	apical plasma membrane|basolateral plasma membrane|integral to membrane|lateral plasma membrane|tight junction	protein binding			skin(1)	1						AGAAGAGAATGGCAAAGTATG	0.353									Lynch_syndrome				8	167	---	---	---	---	PASS
MSH2	4436	broad.mit.edu	37	2	47637275	47637275	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:47637275G>T	uc002rvy.1	+	3	477	c.409G>T	c.(409-411)GGT>TGT	p.G137C	MSH2_uc010yoh.1_Missense_Mutation_p.G71C|MSH2_uc002rvz.2_Missense_Mutation_p.G137C|MSH2_uc010fbg.2_5'UTR|MSH2_uc010fbf.1_Intron	NM_000251	NP_000242	P43246	MSH2_HUMAN	mutS homolog 2	137					B cell differentiation|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|double-strand break repair|intra-S DNA damage checkpoint|isotype switching|maintenance of DNA repeat elements|male gonad development|meiotic gene conversion|meiotic mismatch repair|negative regulation of neuron apoptosis|negative regulation of reciprocal meiotic recombination|positive regulation of helicase activity|postreplication repair|response to UV-B|response to X-ray|somatic hypermutation of immunoglobulin genes	MutSalpha complex|MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|guanine/thymine mispair binding|loop DNA binding|protein C-terminus binding|protein homodimerization activity|protein kinase binding|Y-form DNA binding			large_intestine(33)|haematopoietic_and_lymphoid_tissue(6)|endometrium(4)|ovary(3)|cervix(2)|central_nervous_system(2)|stomach(1)|small_intestine(1)|breast(1)|skin(1)|prostate(1)	55		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			cattctctttggtaacaatga	0.284			D|Mis|N|F|S		colorectal|endometrial|ovarian	colorectal|endometrial|ovarian		MMR	Lynch_syndrome|Muir-Torre_syndrome|Turcot_syndrome|Constitutional_Mismatch_Repair_Deficiency_Syndrome				9	247	---	---	---	---	PASS
CCDC88A	55704	broad.mit.edu	37	2	55529038	55529038	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:55529038A>T	uc002ryv.2	-	27	5481	c.4639T>A	c.(4639-4641)TTC>ATC	p.F1547I	CCDC88A_uc010yoz.1_Missense_Mutation_p.F1520I|CCDC88A_uc010ypa.1_Missense_Mutation_p.F1547I|CCDC88A_uc010fbw.2_Intron|CCDC88A_uc002ryu.2_Missense_Mutation_p.F802I|CCDC88A_uc002rys.2_Missense_Mutation_p.F505I|CCDC88A_uc002ryw.2_Missense_Mutation_p.F831I|CCDC88A_uc010fby.1_Missense_Mutation_p.F399I	NM_001135597	NP_001129069	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A isoform 1	1548					activation of protein kinase B activity|cell migration|cellular membrane organization|DNA replication|lamellipodium assembly|microtubule cytoskeleton organization|regulation of actin cytoskeleton organization|regulation of cell proliferation|regulation of DNA replication|regulation of neuron projection development|TOR signaling cascade	cytoplasmic membrane-bounded vesicle|cytosol|endoplasmic reticulum|Golgi apparatus|lamellipodium|plasma membrane	actin binding|microtubule binding|phosphatidylinositol binding|protein homodimerization activity|protein kinase B binding			ovary(2)|skin(2)	4						TTGGATCTGAAGCCTGCAGAA	0.393													24	46	---	---	---	---	PASS
CCDC104	112942	broad.mit.edu	37	2	55771501	55771501	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:55771501T>C	uc002ryy.2	+	9	1121	c.923T>C	c.(922-924)GTA>GCA	p.V308A	CCDC104_uc002ryx.2_Missense_Mutation_p.V333A	NM_080667	NP_542398	Q96G28	CC104_HUMAN	coiled-coil domain containing 104	308										ovary(1)	1			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ACTGGGGAGGTAGAGGTATGG	0.378													7	19	---	---	---	---	PASS
C2orf86	51057	broad.mit.edu	37	2	63631216	63631216	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:63631216T>C	uc002sch.2	-	10	1848	c.1402A>G	c.(1402-1404)AGA>GGA	p.R468G	C2orf86_uc002sce.2_RNA|C2orf86_uc002scf.2_Missense_Mutation_p.R309G|C2orf86_uc010ypu.1_RNA|C2orf86_uc002scg.2_Missense_Mutation_p.R276G|C2orf86_uc002sci.1_Missense_Mutation_p.R444G|C2orf86_uc010fcr.1_Missense_Mutation_p.R358G	NM_015910	NP_056994	O95876	FRITZ_HUMAN	hypothetical protein LOC51057 isoform 2	468					cilium morphogenesis|regulation of embryonic cell shape|regulation of protein localization|septin cytoskeleton organization	cilium axoneme|cytoplasm|cytoskeleton|plasma membrane					0						AAAGGTCCTCTTTCAAACCTG	0.388													12	32	---	---	---	---	PASS
ALMS1	7840	broad.mit.edu	37	2	73717530	73717530	+	Nonsense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:73717530C>G	uc002sje.1	+	12	8558	c.8447C>G	c.(8446-8448)TCA>TGA	p.S2816*	ALMS1_uc002sjf.1_Nonsense_Mutation_p.S2772*|ALMS1_uc002sjg.2_Nonsense_Mutation_p.S2202*|ALMS1_uc002sjh.1_Nonsense_Mutation_p.S2202*	NM_015120	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2814					G2/M transition of mitotic cell cycle	centrosome|cilium|cytosol|microtubule basal body|spindle pole				skin(3)|ovary(2)|breast(2)|pancreas(1)|lung(1)	9						TTAGAAAGATCAGATTTTACA	0.378													7	40	---	---	---	---	PASS
MFSD9	84804	broad.mit.edu	37	2	103353166	103353166	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:103353166G>T	uc002tcb.2	-	1	172	c.104C>A	c.(103-105)GCC>GAC	p.A35D	TMEM182_uc002tcc.3_5'Flank|TMEM182_uc002tcd.3_5'Flank|MFSD9_uc010fja.2_RNA	NM_032718	NP_116107	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing	35					transmembrane transport	integral to membrane|plasma membrane	transporter activity			ovary(2)|breast(2)	4						ACCGGAGTCGGCAGCCTCCGC	0.657													7	12	---	---	---	---	PASS
NPHP1	4867	broad.mit.edu	37	2	110926116	110926116	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:110926116G>T	uc002tfn.3	-	6	631	c.537C>A	c.(535-537)CTC>CTA	p.L179L	NPHP1_uc002tfm.3_Silent_p.L179L|NPHP1_uc002tfl.3_Silent_p.L179L|NPHP1_uc002tfo.3_Silent_p.L117L|NPHP1_uc010ywx.1_Silent_p.L179L|NPHP1_uc010fjv.1_Silent_p.L179L	NM_207181	NP_997064	O15259	NPHP1_HUMAN	nephrocystin 1 isoform 2	179	SH3.				actin cytoskeleton organization|cell projection organization|cell-cell adhesion|excretion|retina development in camera-type eye|signal transduction|spermatid differentiation|visual behavior	adherens junction|cell-cell junction|cilium axoneme|cytoplasm|cytoskeleton|motile cilium|photoreceptor connecting cilium	protein binding|structural molecule activity			ovary(2)	2						CAATTACAAGGAGAATTTCCC	0.338													5	29	---	---	---	---	PASS
NCKAP5	344148	broad.mit.edu	37	2	133618158	133618158	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:133618158C>G	uc002ttp.2	-	11	1088	c.714G>C	c.(712-714)TTG>TTC	p.L238F	NCKAP5_uc002ttq.2_Missense_Mutation_p.L238F	NM_207363	NP_997246	O14513	NCKP5_HUMAN	Nck-associated protein 5 isoform 1	238	Potential.						protein binding				0						CTCTTGTTTTCAACTTCACAC	0.393													4	4	---	---	---	---	PASS
STAM2	10254	broad.mit.edu	37	2	152977291	152977291	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:152977291G>C	uc002tyc.3	-	14	1725	c.1375C>G	c.(1375-1377)CCT>GCT	p.P459A		NM_005843	NP_005834	O75886	STAM2_HUMAN	signal transducing adaptor molecule 2	459					cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway	cytosol|early endosome membrane	protein binding			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.22)		ATATAAGTAGGATTGGAAACA	0.353													3	30	---	---	---	---	PASS
KCNJ3	3760	broad.mit.edu	37	2	155555379	155555379	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:155555379A>T	uc002tyv.1	+	1	287	c.92A>T	c.(91-93)CAG>CTG	p.Q31L	KCNJ3_uc010zce.1_Missense_Mutation_p.Q31L	NM_002239	NP_002230	P48549	IRK3_HUMAN	potassium inwardly-rectifying channel J3	31	Cytoplasmic (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			upper_aerodigestive_tract(1)|pancreas(1)	2					Halothane(DB01159)	GGGCCAGGCCAGGACCCTCAG	0.597													5	21	---	---	---	---	PASS
ACVR1	90	broad.mit.edu	37	2	158622653	158622653	+	Silent	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:158622653A>G	uc002tzm.3	-	9	1185	c.846T>C	c.(844-846)ATT>ATC	p.I282I	ACVR1_uc002tzn.3_Silent_p.I282I|ACVR1_uc010fog.2_Silent_p.I282I	NM_001111067	NP_001104537	Q04771	ACVR1_HUMAN	activin A receptor, type I precursor	282	Cytoplasmic (Potential).|Protein kinase.				BMP signaling pathway|G1/S transition of mitotic cell cycle|negative regulation of activin receptor signaling pathway|negative regulation of apoptosis|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of transcription, DNA-dependent|transforming growth factor beta receptor signaling pathway	activin receptor complex	activin binding|ATP binding|follistatin binding|metal ion binding|protein homodimerization activity|SMAD binding|transforming growth factor beta binding			ovary(2)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	GATAATGTGTAATTAACCACA	0.408													10	38	---	---	---	---	PASS
MYO3B	140469	broad.mit.edu	37	2	171073828	171073828	+	Splice_Site	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:171073828G>T	uc002ufy.2	+	6	670	c.527_splice	c.e6-1	p.G176_splice	MYO3B_uc002ufv.2_Splice_Site_p.G163_splice|MYO3B_uc010fqb.1_Splice_Site_p.G163_splice|MYO3B_uc002ufz.2_Splice_Site_p.G176_splice|MYO3B_uc002ufw.2_Splice_Site|MYO3B_uc002ufx.2_Splice_Site|MYO3B_uc002uga.2_Splice_Site_p.G163_splice	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2						response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(6)|skin(4)|central_nervous_system(1)	19						TTTCCTTATAGGTGTTTCAGC	0.348													7	133	---	---	---	---	PASS
DIRC1	116093	broad.mit.edu	37	2	189599468	189599468	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:189599468G>A	uc002uqi.1	-	2	451	c.180C>T	c.(178-180)ATC>ATT	p.I60I		NM_052952	NP_443184	Q969H9	DIRC1_HUMAN	disrupted in renal carcinoma 1	60											0			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)			TGTCTGAGATGATGGAAGGCT	0.428													7	32	---	---	---	---	PASS
RAPH1	65059	broad.mit.edu	37	2	204305807	204305807	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:204305807C>A	uc002vad.2	-	14	2331	c.2106G>T	c.(2104-2106)CTG>CTT	p.L702L		NM_213589	NP_998754	Q70E73	RAPH1_HUMAN	Ras association and pleckstrin homology domains	702					cell-matrix adhesion|signal transduction	cytoplasm|cytoskeleton|filopodium|lamellipodium|nucleus|plasma membrane				ovary(3)|breast(3)|central_nervous_system(2)|lung(1)|skin(1)	10						TGGGGGGTACCAGGATCTGAG	0.468													5	30	---	---	---	---	PASS
MAP2	4133	broad.mit.edu	37	2	210559534	210559534	+	Silent	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:210559534A>G	uc002vde.1	+	7	2888	c.2640A>G	c.(2638-2640)CCA>CCG	p.P880P	MAP2_uc002vdc.1_Silent_p.P880P|MAP2_uc002vdd.1_Intron|MAP2_uc002vdf.1_Intron|MAP2_uc002vdg.1_Intron|MAP2_uc002vdh.1_Intron|MAP2_uc002vdi.1_Silent_p.P876P	NM_002374	NP_002365	P11137	MAP2_HUMAN	microtubule-associated protein 2 isoform 1	880					central nervous system neuron development|dendrite morphogenesis|negative regulation of microtubule depolymerization	cytoplasm|microtubule|microtubule associated complex	beta-dystroglycan binding|calmodulin binding|structural molecule activity			ovary(9)|upper_aerodigestive_tract(2)|large_intestine(2)|pancreas(2)|central_nervous_system(1)|skin(1)	17		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Estramustine(DB01196)	TCCCATTGCCATCACCTGTTC	0.458													5	21	---	---	---	---	PASS
TNS1	7145	broad.mit.edu	37	2	218682908	218682908	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:218682908G>T	uc002vgt.2	-	24	4233	c.3835C>A	c.(3835-3837)CAC>AAC	p.H1279N	TNS1_uc002vgr.2_Missense_Mutation_p.H1266N|TNS1_uc002vgs.2_Missense_Mutation_p.H1258N|TNS1_uc010zjv.1_Missense_Mutation_p.H1258N	NM_022648	NP_072174	Q9HBL0	TENS1_HUMAN	tensin	1279						cytoplasm|cytoskeleton|focal adhesion	actin binding			ovary(3)|breast(1)	4		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TTGCCTTGGTGAGCCCCAGGG	0.657													6	14	---	---	---	---	PASS
PRKAG3	53632	broad.mit.edu	37	2	219688495	219688495	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:219688495A>T	uc002vjb.1	-	13	1479	c.1460T>A	c.(1459-1461)CTC>CAC	p.L487H		NM_017431	NP_059127	Q9UGI9	AAKG3_HUMAN	AMP-activated protein kinase, non-catalytic	487				ALGA -> PSGPEKI (in Ref. 1; CAB65117).	cell cycle arrest|fatty acid biosynthetic process|insulin receptor signaling pathway|intracellular protein kinase cascade|regulation of fatty acid oxidation	cytosol	AMP-activated protein kinase activity|protein kinase binding			ovary(1)|lung(1)	2		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCAGGCCCCGAGGGCATCGAT	0.602													29	77	---	---	---	---	PASS
CCDC108	255101	broad.mit.edu	37	2	219878615	219878615	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:219878615C>G	uc002vjl.1	-	22	3838	c.3754G>C	c.(3754-3756)GAG>CAG	p.E1252Q		NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	1252						integral to membrane	structural molecule activity			ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACCATCTGCTCCTGCCCAGGA	0.567													6	25	---	---	---	---	PASS
TUBA4A	7277	broad.mit.edu	37	2	220115077	220115077	+	Silent	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:220115077T>C	uc002vkt.1	-	4	1402	c.1344A>G	c.(1342-1344)GAA>GAG	p.E448E	TUBA4A_uc010zkz.1_Silent_p.E433E|TUBA4B_uc002vku.2_5'Flank|TUBA4B_uc002vkv.1_5'Flank	NM_006000	NP_005991	P68366	TBA4A_HUMAN	tubulin, alpha 4a	448					'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|platelet activation|platelet degranulation|protein polymerization	cytosol|extracellular region|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(3)	3		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCTGCTTTATTCTTCTCCCT	0.493													57	157	---	---	---	---	PASS
PAX3	5077	broad.mit.edu	37	2	223066140	223066140	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:223066140G>T	uc002vmt.1	-	9	1808	c.1442C>A	c.(1441-1443)CCA>CAA	p.P481Q	PAX3_uc002vmy.1_Missense_Mutation_p.P480Q|PAX3_uc002vmv.1_Missense_Mutation_p.P481Q|PAX3_uc002vmw.1_Missense_Mutation_p.Q399K|PAX3_uc002vmx.1_Missense_Mutation_p.Q399K	NM_181459	NP_852124	P23760	PAX3_HUMAN	paired box 3 isoform PAX3e	Error:Variant_position_missing_in_P23760_after_alignment					apoptosis|organ morphogenesis|positive regulation of transcription from RNA polymerase II promoter|sensory perception of sound|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		PAX3/FOXO1(749)|PAX3/NCOA1(8)|PAX3/NCOA2(4)	soft_tissue(761)|ovary(4)|skin(1)	766		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CGCGATATCTGGCTTGAGATA	0.453			T	FOXO1A|NCOA1	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome						16	59	---	---	---	---	PASS
KIAA1486	57624	broad.mit.edu	37	2	226446968	226446968	+	Missense_Mutation	SNP	T	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:226446968T>G	uc002voe.2	+	4	1010	c.835T>G	c.(835-837)TTG>GTG	p.L279V	KIAA1486_uc010fxa.1_Intron|KIAA1486_uc002vof.1_Missense_Mutation_p.L49V	NM_020864	NP_065915	Q9P242	K1486_HUMAN	hypothetical protein LOC57624	279										ovary(2)|central_nervous_system(1)	3		Renal(207;0.0112)|all_lung(227;0.0477)|Lung NSC(271;0.0644)|all_hematologic(139;0.101)|Esophageal squamous(248;0.129)		Epithelial(121;6.73e-10)|all cancers(144;4.32e-07)|Lung(261;0.0161)|LUSC - Lung squamous cell carcinoma(224;0.0223)		CTTTGACGACTTGGGCCAAGA	0.547													27	84	---	---	---	---	PASS
TRIP12	9320	broad.mit.edu	37	2	230678991	230678991	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:230678991C>A	uc002vpw.1	-	11	1747	c.1638G>T	c.(1636-1638)TTG>TTT	p.L546F	TRIP12_uc002vpx.1_Missense_Mutation_p.L594F|TRIP12_uc002vpy.1_Missense_Mutation_p.L249F|TRIP12_uc010zlz.1_Intron|TRIP12_uc010fxh.1_Missense_Mutation_p.L552F	NM_004238	NP_004229	Q14669	TRIPC_HUMAN	thyroid hormone receptor interactor 12	546					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	proteasome complex	thyroid hormone receptor binding|ubiquitin-protein ligase activity			ovary(4)|lung(2)|breast(1)|central_nervous_system(1)|skin(1)	9		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.126)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;4.76e-13)|all cancers(144;4.34e-10)|LUSC - Lung squamous cell carcinoma(224;0.00864)|Lung(119;0.0116)		ACAACATCTCCAAGGCAGTCA	0.393													6	61	---	---	---	---	PASS
SP100	6672	broad.mit.edu	37	2	231404037	231404037	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:231404037G>T	uc002vqu.1	+	25	2291	c.2150G>T	c.(2149-2151)TGC>TTC	p.C717F	SP100_uc010fxp.1_Missense_Mutation_p.C35F	NM_001080391	NP_001073860	P23497	SP100_HUMAN	nuclear antigen Sp100 isoform 1	Error:Variant_position_missing_in_P23497_after_alignment					DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|interspecies interaction between organisms|negative regulation of cellular component movement|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of transcription, DNA-dependent|negative regulation of viral transcription|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|response to cytokine stimulus|response to retinoic acid|response to type I interferon	cytoplasm|nuclear periphery|nucleolus|PML body	chromo shadow domain binding|DNA binding|identical protein binding|kinase binding|protein homodimerization activity|transcription coactivator activity|transcription corepressor activity|transcription factor binding			ovary(4)|central_nervous_system(1)	5		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CTGTTCTGCTGCGACACTTGT	0.507													16	49	---	---	---	---	PASS
DGKD	8527	broad.mit.edu	37	2	234356821	234356821	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:234356821C>A	uc002vui.1	+	13	1520	c.1508C>A	c.(1507-1509)TCG>TAG	p.S503*	DGKD_uc002vuj.1_Nonsense_Mutation_p.S459*|DGKD_uc010fyh.1_Nonsense_Mutation_p.S370*|DGKD_uc010fyi.1_RNA	NM_152879	NP_690618	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa isoform 2	503					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell growth|diacylglycerol metabolic process|endocytosis|epidermal growth factor receptor signaling pathway|multicellular organismal development|platelet activation|protein homooligomerization|protein transport|response to organic substance|second-messenger-mediated signaling	cytoplasm|cytoplasmic membrane-bounded vesicle|plasma membrane|plasma membrane	ATP binding|diacylglycerol binding|diacylglycerol kinase activity|metal ion binding|protein heterodimerization activity|protein homodimerization activity			central_nervous_system(2)|pancreas(1)|lung(1)|skin(1)	5		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	GTCATCTCCTCGGCCAAGTGA	0.582													4	56	---	---	---	---	PASS
ASB18	401036	broad.mit.edu	37	2	237172907	237172907	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:237172907C>G	uc010znh.1	-	1	82	c.82G>C	c.(82-84)GAT>CAT	p.D28H		NM_212556	NP_997721	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box-containing 18	28					intracellular signal transduction					ovary(1)	1		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		CTCTCCTCATCTTTGGCATCC	0.488													24	47	---	---	---	---	PASS
GADL1	339896	broad.mit.edu	37	3	30842474	30842474	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:30842474C>T	uc003cep.2	-	12	1204	c.1157G>A	c.(1156-1158)AGA>AAA	p.R386K	GADL1_uc003ceq.1_Missense_Mutation_p.R386K	NM_207359	NP_997242	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	386					carboxylic acid metabolic process		carboxy-lyase activity|pyridoxal phosphate binding				0					Pyridoxal Phosphate(DB00114)	ATCTGGTCTTCTGCTACACTG	0.438													12	14	---	---	---	---	PASS
DYNC1LI1	51143	broad.mit.edu	37	3	32574570	32574570	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:32574570C>G	uc003cfb.3	-	8	1076	c.988G>C	c.(988-990)GAT>CAT	p.D330H	DYNC1LI1_uc011axh.1_Missense_Mutation_p.D214H	NM_016141	NP_057225	Q9Y6G9	DC1L1_HUMAN	dynein, cytoplasmic 1, light intermediate chain	330					cell division|interspecies interaction between organisms|mitosis|positive regulation of mitotic cell cycle spindle assembly checkpoint|transport	centrosome|condensed chromosome kinetochore|cytoplasmic dynein complex|microtubule|plasma membrane|spindle pole	ATP binding|motor activity			ovary(1)	1						ATTTTCTTATCATTATCCCAC	0.303													9	25	---	---	---	---	PASS
CX3CR1	1524	broad.mit.edu	37	3	39306949	39306949	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:39306949G>A	uc003cjl.2	-	2	1144	c.1052C>T	c.(1051-1053)GCA>GTA	p.A351V		NM_001337	NP_001328	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	351	Cytoplasmic (Potential).				cell adhesion|cellular defense response|chemotaxis|interspecies interaction between organisms|response to wounding	integral to plasma membrane	chemokine receptor activity			lung(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		AAGGAGCAATGCATCTCCATC	0.458													71	86	---	---	---	---	PASS
DOCK3	1795	broad.mit.edu	37	3	51400047	51400047	+	Silent	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:51400047G>C	uc011bds.1	+	49	5258	c.5235G>C	c.(5233-5235)CTG>CTC	p.L1745L		NM_004947	NP_004938	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1745	Ser-rich.					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity|SH3 domain binding				0				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		CCTCCAGCCTGAGTTCCACTC	0.572													13	20	---	---	---	---	PASS
WDR52	55779	broad.mit.edu	37	3	113135375	113135375	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:113135375G>T	uc003eae.1	-	6	716	c.670C>A	c.(670-672)CGA>AGA	p.R224R		NM_018338	NP_060808	Q96MT7	WDR52_HUMAN	WD repeat domain 52 isoform 2	224										central_nervous_system(1)	1						GACTCACCTCGAAGGACTCTG	0.313													3	11	---	---	---	---	PASS
ZNF80	7634	broad.mit.edu	37	3	113955552	113955552	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:113955552G>C	uc010hqo.2	-	1	874	c.370C>G	c.(370-372)CGC>GGC	p.R124G	ZNF80_uc003ebf.2_RNA	NM_007136	NP_009067	P51504	ZNF80_HUMAN	zinc finger protein 80	124	C2H2-type 3; atypical.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(201;0.0233)|all_neural(597;0.0837)				TGAATCTGGCGGTAGCACAGG	0.562													16	46	---	---	---	---	PASS
NR1I2	8856	broad.mit.edu	37	3	119530414	119530414	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:119530414G>C	uc003edj.2	+	4	2199	c.360G>C	c.(358-360)GAG>GAC	p.E120D	NR1I2_uc003edi.2_Missense_Mutation_p.E120D|NR1I2_uc003edk.2_Missense_Mutation_p.E159D|NR1I2_uc003edl.2_Missense_Mutation_p.E8D	NM_003889	NP_003880	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	120	Hinge.				drug export|exogenous drug catabolic process|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|steroid metabolic process|xenobiotic metabolic process|xenobiotic transport	nucleoplasm	drug binding|protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding			ovary(2)	2				GBM - Glioblastoma multiforme(114;0.175)	Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Rifampin(DB01045)|Vitamin E(DB00163)	CCGTGGAGGAGAGGCGGGCCT	0.632													8	22	---	---	---	---	PASS
STXBP5L	9515	broad.mit.edu	37	3	120876471	120876471	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:120876471C>G	uc003eec.3	+	9	1014	c.874C>G	c.(874-876)CAT>GAT	p.H292D	STXBP5L_uc011bji.1_Missense_Mutation_p.H292D	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	292					exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane				ovary(7)|skin(2)	9				GBM - Glioblastoma multiforme(114;0.0694)		CACAATTCCACATGGTAAGAT	0.413													4	27	---	---	---	---	PASS
PARP14	54625	broad.mit.edu	37	3	122447289	122447289	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:122447289G>T	uc003efq.3	+	17	5310	c.5251G>T	c.(5251-5253)GGA>TGA	p.G1751*	PARP14_uc010hrk.2_RNA|PARP14_uc003efr.2_Nonsense_Mutation_p.G1468*	NM_017554	NP_060024	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1751	PARP catalytic.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus|plasma membrane	NAD+ ADP-ribosyltransferase activity			ovary(2)|breast(2)|lung(1)|pancreas(1)	6				GBM - Glioblastoma multiforme(114;0.0531)		CTATACACATGGAAATCATTC	0.393													8	117	---	---	---	---	PASS
PIK3R4	30849	broad.mit.edu	37	3	130463401	130463401	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:130463401G>A	uc003enj.2	-	2	1243	c.662C>T	c.(661-663)CCG>CTG	p.P221L		NM_014602	NP_055417	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	221	Protein kinase.				fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	cytosol	ATP binding|protein binding|protein serine/threonine kinase activity			ovary(3)|lung(2)|breast(2)|skin(2)|stomach(1)|central_nervous_system(1)|kidney(1)	12						GTCTACAAGCGGAGTTGAAGG	0.428													22	73	---	---	---	---	PASS
MRPL3	11222	broad.mit.edu	37	3	131220414	131220414	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:131220414G>T	uc003eoh.2	-	2	402	c.238C>A	c.(238-240)CTG>ATG	p.L80M	MRPL3_uc011blo.1_Translation_Start_Site|MRPL3_uc011blp.1_Missense_Mutation_p.L107M	NM_007208	NP_009139	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	80					translation	mitochondrial large ribosomal subunit	RNA binding|structural constituent of ribosome				0						TCATCTTTCAGAGGACACAGT	0.398													8	205	---	---	---	---	PASS
DNAJC13	23317	broad.mit.edu	37	3	132185186	132185186	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:132185186C>A	uc003eor.2	+	19	2077	c.2012C>A	c.(2011-2013)CCT>CAT	p.P671H	DNAJC13_uc010htq.1_Missense_Mutation_p.P671H	NM_015268	NP_056083	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	671							heat shock protein binding			ovary(1)|breast(1)	2						GATCTCGTACCTGAGAAGGAT	0.393													6	54	---	---	---	---	PASS
TF	7018	broad.mit.edu	37	3	133478162	133478162	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:133478162G>T	uc003epu.1	+	14	2920	c.1192G>T	c.(1192-1194)GCC>TCC	p.A398S	TF_uc011blt.1_Missense_Mutation_p.A271S|TF_uc003epw.1_Intron|TF_uc003epv.1_Missense_Mutation_p.A398S	NM_001063	NP_001054	P02787	TRFE_HUMAN	transferrin precursor	398	Transferrin-like 2.				cellular iron ion homeostasis|platelet activation|platelet degranulation|transferrin transport|transmembrane transport	apical plasma membrane|basal plasma membrane|coated pit|early endosome|endocytic vesicle|endosome membrane|extracellular region|late endosome|perinuclear region of cytoplasm|recycling endosome|stored secretory granule	ferric iron binding			ovary(1)|skin(1)	2					Aluminium(DB01370)|Bismuth(DB01402)|Iron Dextran(DB00893)	AGACTGCATCGCCAAGATCAT	0.547													53	64	---	---	---	---	PASS
SLCO2A1	6578	broad.mit.edu	37	3	133666218	133666218	+	Missense_Mutation	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:133666218A>G	uc003eqa.3	-	9	1451	c.1177T>C	c.(1177-1179)TCT>CCT	p.S393P	SLCO2A1_uc003eqb.3_Missense_Mutation_p.S317P|SLCO2A1_uc011blv.1_Missense_Mutation_p.S212P	NM_005630	NP_005621	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family,	393	Helical; Name=9; (Potential).				sodium-independent organic anion transport	integral to plasma membrane|membrane fraction	prostaglandin transmembrane transporter activity|protein binding			central_nervous_system(1)	1						GCTTGTAGAGAGAAAACAAAG	0.507													13	51	---	---	---	---	PASS
MSL2	55167	broad.mit.edu	37	3	135870092	135870092	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:135870092C>A	uc003eqx.1	-	2	2364	c.1631G>T	c.(1630-1632)AGT>ATT	p.S544I	MSL2_uc011bmb.1_Missense_Mutation_p.S470I	NM_018133	NP_060603	Q9HCI7	MSL2_HUMAN	ring finger protein 184 isoform 1	544					histone H4-K16 acetylation	MSL complex	zinc ion binding			central_nervous_system(1)	1						ATTTATTACACTGGTGCTGGT	0.473													11	56	---	---	---	---	PASS
A4GNT	51146	broad.mit.edu	37	3	137843236	137843236	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:137843236C>T	uc003ers.2	-	3	1095	c.893G>A	c.(892-894)CGG>CAG	p.R298Q		NM_016161	NP_057245	Q9UNA3	A4GCT_HUMAN	alpha-1,4-N-acetylglucosaminyltransferase	298	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	acetylglucosaminyltransferase activity|galactosyltransferase activity			central_nervous_system(1)	1						AATCACAGCCCGCCCCTCCTG	0.517													16	66	---	---	---	---	PASS
ESYT3	83850	broad.mit.edu	37	3	138183263	138183263	+	Nonsense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:138183263C>G	uc003esk.2	+	9	1218	c.992C>G	c.(991-993)TCA>TGA	p.S331*	ESYT3_uc010hug.2_RNA	NM_031913	NP_114119	A0FGR9	ESYT3_HUMAN	family with sequence similarity 62 (C2 domain	331	C2 1.					integral to membrane|plasma membrane					0						CGAGGCAAGTCAGATCCCTAC	0.572													20	37	---	---	---	---	PASS
ZBTB38	253461	broad.mit.edu	37	3	141163129	141163129	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:141163129G>T	uc003etw.2	+	8	2881	c.1899G>T	c.(1897-1899)TTG>TTT	p.L633F	ZBTB38_uc010hun.2_Missense_Mutation_p.L630F|ZBTB38_uc010huo.2_Missense_Mutation_p.L633F|ZBTB38_uc003ety.2_Missense_Mutation_p.L633F|ZBTB38_uc010hup.2_Missense_Mutation_p.L634F	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	633					positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						CCATCCCATTGGAAACATCTG	0.448													7	114	---	---	---	---	PASS
XRN1	54464	broad.mit.edu	37	3	142116193	142116193	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:142116193C>G	uc003eus.2	-	20	2384	c.2317G>C	c.(2317-2319)GAA>CAA	p.E773Q	XRN1_uc010huu.2_Missense_Mutation_p.E239Q|XRN1_uc003eut.2_Missense_Mutation_p.E773Q|XRN1_uc003euu.2_Missense_Mutation_p.E773Q|XRN1_uc003euv.1_Missense_Mutation_p.E634Q	NM_019001	NP_061874	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1 isoform a	773					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear mRNA surveillance|rRNA catabolic process	cytosol|Golgi apparatus|intermediate filament cytoskeleton|plasma membrane	5'-3' exonuclease activity|DNA binding|protein binding|RNA binding			ovary(3)	3						CCTTGTACTTCTTTTGCCCAG	0.358													5	21	---	---	---	---	PASS
TNIK	23043	broad.mit.edu	37	3	170811686	170811686	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:170811686G>T	uc003fhh.2	-	23	3008	c.2663C>A	c.(2662-2664)TCT>TAT	p.S888Y	TNIK_uc003fhi.2_Missense_Mutation_p.S833Y|TNIK_uc003fhj.2_Missense_Mutation_p.S859Y|TNIK_uc003fhk.2_Missense_Mutation_p.S880Y|TNIK_uc003fhl.2_Missense_Mutation_p.S804Y|TNIK_uc003fhm.2_Missense_Mutation_p.S825Y|TNIK_uc003fhn.2_Missense_Mutation_p.S851Y|TNIK_uc003fho.2_Missense_Mutation_p.S796Y|TNIK_uc003fhg.2_Missense_Mutation_p.S66Y	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	TRAF2 and NCK interacting kinase isoform 1	888	Mediates interaction with NEDD4.				actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(4)|large_intestine(1)	5	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			GTCCGCATGAGAGGTCTCCAG	0.478													7	88	---	---	---	---	PASS
MRPL47	57129	broad.mit.edu	37	3	179316559	179316559	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:179316559C>A	uc003fjz.2	-	4	328	c.306G>T	c.(304-306)TGG>TGT	p.W102C	MRPL47_uc003fka.2_5'UTR|MRPL47_uc003fkb.2_Missense_Mutation_p.W82C	NM_020409	NP_065142	Q9HD33	RM47_HUMAN	mitochondrial ribosomal protein L47 isoform a	102					translation	mitochondrial ribosome	structural constituent of ribosome				0	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			GTAAGACATACCTATACAAAA	0.383													10	62	---	---	---	---	PASS
ABCF3	55324	broad.mit.edu	37	3	183905548	183905548	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:183905548C>A	uc003fmz.2	+	5	578	c.445C>A	c.(445-447)CTA>ATA	p.L149I	ABCF3_uc003fna.2_Missense_Mutation_p.L143I|ABCF3_uc003fnb.2_5'Flank	NM_018358	NP_060828	Q9NUQ8	ABCF3_HUMAN	ATP-binding cassette, sub-family F (GCN20),	149							ATP binding|ATPase activity			ovary(3)|lung(1)	4	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.35e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CAGCAACCCTCTGTGAGTGGG	0.522													6	116	---	---	---	---	PASS
TMEM207	131920	broad.mit.edu	37	3	190165606	190165606	+	Nonsense_Mutation	SNP	G	T	T	rs138370145		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:190165606G>T	uc003fsj.2	-	2	153	c.86C>A	c.(85-87)TCG>TAG	p.S29*		NM_207316	NP_997199	Q6UWW9	TM207_HUMAN	transmembrane protein 207 precursor	29						integral to membrane					0	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.0176)		TGGTAGGTCCGAGAGCACCAA	0.353													5	96	---	---	---	---	PASS
FGF12	2257	broad.mit.edu	37	3	191888416	191888416	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:191888416C>A	uc003fsx.2	-	4	1270	c.444G>T	c.(442-444)AAG>AAT	p.K148N	FGF12_uc003fsy.2_Missense_Mutation_p.K86N	NM_021032	NP_066360	P61328	FGF12_HUMAN	fibroblast growth factor 12 isoform 1	148					cell-cell signaling|heart development|JNK cascade|nervous system development|signal transduction	extracellular space|nucleus	growth factor activity|heparin binding			ovary(1)|skin(1)|lung(1)|pancreas(1)	4	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		ACACAGATTCCTTGAATTTGC	0.373													7	152	---	---	---	---	PASS
FYTTD1	84248	broad.mit.edu	37	3	197501077	197501077	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:197501077C>A	uc003fyi.2	+	6	871	c.652C>A	c.(652-654)CGT>AGT	p.R218S	FYTTD1_uc011bui.1_Missense_Mutation_p.R192S|FYTTD1_uc011buj.1_RNA|FYTTD1_uc011buk.1_Missense_Mutation_p.R151S	NM_032288	NP_115664	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1 isoform 1	218					mRNA export from nucleus	nuclear speck	mRNA binding|protein binding				0	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		AAAGAGAACTCGTCAGTAAGT	0.383													6	200	---	---	---	---	PASS
EVC	2121	broad.mit.edu	37	4	5733382	5733382	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:5733382G>A	uc003gil.1	+	4	799	c.615G>A	c.(613-615)GAG>GAA	p.E205E	EVC_uc003gim.1_RNA	NM_153717	NP_714928	P57679	EVC_HUMAN	Ellis van Creveld syndrome protein	205					muscle organ development	integral to membrane				ovary(1)|skin(1)	2		Myeloproliferative disorder(84;0.117)				TGGCCTGCGAGAGGTAAGGAG	0.517													7	10	---	---	---	---	PASS
SH3TC1	54436	broad.mit.edu	37	4	8226901	8226901	+	Splice_Site	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:8226901G>A	uc003gkv.3	+	11	1345	c.1244_splice	c.e11-1	p.D415_splice	SH3TC1_uc003gkw.3_Splice_Site_p.D339_splice|SH3TC1_uc003gkx.3_Splice_Site	NM_018986	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1								binding			large_intestine(2)|pancreas(1)	3						TCCCTTGCCAGACTCAGTAGA	0.562													6	8	---	---	---	---	PASS
CLRN2	645104	broad.mit.edu	37	4	17517142	17517142	+	Missense_Mutation	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:17517142A>G	uc003gpg.1	+	1	355	c.253A>G	c.(253-255)ATC>GTC	p.I85V		NM_001079827	NP_001073296	A0PK11	CLRN2_HUMAN	clarin 2	85						integral to membrane					0						CCAATTCACGAGTGAGTATAT	0.488													5	15	---	---	---	---	PASS
PCDH7	5099	broad.mit.edu	37	4	30723409	30723409	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:30723409G>T	uc003gsk.1	+	1	1373	c.365G>T	c.(364-366)AGC>ATC	p.S122I	PCDH7_uc011bxw.1_Missense_Mutation_p.S122I|PCDH7_uc011bxx.1_Missense_Mutation_p.S122I	NM_002589	NP_002580	O60245	PCDH7_HUMAN	protocadherin 7 isoform a precursor	122	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			upper_aerodigestive_tract(1)|ovary(1)|liver(1)|skin(1)	4						CCCTCGCAGAGCTGGGTGGAC	0.612													7	5	---	---	---	---	PASS
N4BP2	55728	broad.mit.edu	37	4	40123493	40123493	+	Silent	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:40123493A>G	uc003guy.3	+	9	4100	c.3762A>G	c.(3760-3762)CTA>CTG	p.L1254L	N4BP2_uc010ifq.2_Silent_p.L1174L|N4BP2_uc010ifr.2_Silent_p.L1174L	NM_018177	NP_060647	Q86UW6	N4BP2_HUMAN	Nedd4 binding protein 2	1254						cytoplasm	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|endonuclease activity|protein binding			lung(3)|breast(2)|kidney(2)|ovary(1)	8						CAGGTATTCTAAAAGCTACTA	0.373													17	15	---	---	---	---	PASS
GABRB1	2560	broad.mit.edu	37	4	47408751	47408751	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:47408751C>A	uc003gxh.2	+	8	1262	c.888C>A	c.(886-888)ACC>ACA	p.T296T	GABRB1_uc011bze.1_Silent_p.T226T	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	296					synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)	TCAGGGAGACCCTGCCAAAGA	0.438													6	14	---	---	---	---	PASS
CORIN	10699	broad.mit.edu	37	4	47765446	47765446	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:47765446C>A	uc003gxm.2	-	4	660	c.567G>T	c.(565-567)CTG>CTT	p.L189L	CORIN_uc011bzf.1_Silent_p.L50L|CORIN_uc011bzg.1_Silent_p.L122L|CORIN_uc011bzh.1_Silent_p.L189L|CORIN_uc011bzi.1_Silent_p.L189L|CORIN_uc003gxn.3_Silent_p.L189L	NM_006587	NP_006578	Q9Y5Q5	CORIN_HUMAN	corin	189	Extracellular (Potential).|FZ 1.				peptide hormone processing|regulation of systemic arterial blood pressure by atrial natriuretic peptide	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity|serine-type exopeptidase activity			ovary(1)|central_nervous_system(1)	2						TACAGCCAAACAGCATGATAT	0.438													4	7	---	---	---	---	PASS
UGT2B28	54490	broad.mit.edu	37	4	70156481	70156481	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:70156481C>T	uc003hej.2	+	5	1264	c.1262C>T	c.(1261-1263)TCG>TTG	p.S421L	UGT2B28_uc010ihr.2_Intron	NM_053039	NP_444267	Q9BY64	UDB28_HUMAN	UDP glucuronosyltransferase 2 family,	421					xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			skin(1)	1					Flunitrazepam(DB01544)	CACACAATGTCGAGTACAGAC	0.423													7	19	---	---	---	---	PASS
UTP3	57050	broad.mit.edu	37	4	71555257	71555257	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:71555257G>T	uc003hfo.2	+	1	1062	c.863G>T	c.(862-864)AGG>ATG	p.R288M		NM_020368	NP_065101	Q9NQZ2	SAS10_HUMAN	UTP3, small subunit processome component	288					brain development|chromatin modification|gene silencing	nucleolus					0			Lung(101;0.235)			CTGAAAGCTAGGAGAGTCCCA	0.433													10	364	---	---	---	---	PASS
MTHFD2L	441024	broad.mit.edu	37	4	75040299	75040299	+	Missense_Mutation	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:75040299T>A	uc003hhn.1	+	5	564	c.46T>A	c.(46-48)TGG>AGG	p.W16R	MTHFD2L_uc011cbj.1_Missense_Mutation_p.W16R|MTHFD2L_uc011cbk.1_Missense_Mutation_p.W74R|MTHFD2L_uc003hho.2_RNA|MTHFD2L_uc003hhs.2_RNA	NM_001144978	NP_001138450	Q9H903	MTD2L_HUMAN	methylenetetrahydrofolate dehydrogenase 2-like	16					folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process		binding|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NAD+) activity			ovary(1)|central_nervous_system(1)	2			all cancers(17;0.0101)|Lung(101;0.196)			TGTGGAATCATGGGTTTCCCT	0.408													23	9	---	---	---	---	PASS
MTHFD2L	441024	broad.mit.edu	37	4	75040300	75040300	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:75040300G>T	uc003hhn.1	+	5	565	c.47G>T	c.(46-48)TGG>TTG	p.W16L	MTHFD2L_uc011cbj.1_Missense_Mutation_p.W16L|MTHFD2L_uc011cbk.1_Missense_Mutation_p.W74L|MTHFD2L_uc003hho.2_RNA|MTHFD2L_uc003hhs.2_RNA	NM_001144978	NP_001138450	Q9H903	MTD2L_HUMAN	methylenetetrahydrofolate dehydrogenase 2-like	16					folic acid-containing compound biosynthetic process|histidine biosynthetic process|methionine biosynthetic process|one-carbon metabolic process|purine nucleotide biosynthetic process		binding|methenyltetrahydrofolate cyclohydrolase activity|methylenetetrahydrofolate dehydrogenase (NAD+) activity			ovary(1)|central_nervous_system(1)	2			all cancers(17;0.0101)|Lung(101;0.196)			GTGGAATCATGGGTTTCCCTT	0.408													24	8	---	---	---	---	PASS
BTC	685	broad.mit.edu	37	4	75675877	75675877	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:75675877G>T	uc003hig.2	-	4	681	c.334C>A	c.(334-336)CTA>ATA	p.L112I		NM_001729	NP_001720	P35070	BTC_HUMAN	betacellulin precursor	112	Extracellular (Potential).				positive regulation of cell division|positive regulation of cell proliferation	extracellular space|integral to membrane|plasma membrane|soluble fraction	epidermal growth factor receptor binding|growth factor activity			central_nervous_system(1)|skin(1)	2			Lung(101;0.219)			TCTCCTCTTAGGTAAAACAAG	0.398													8	273	---	---	---	---	PASS
G3BP2	9908	broad.mit.edu	37	4	76582779	76582779	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:76582779C>G	uc003hir.2	-	4	478	c.313G>C	c.(313-315)GAA>CAA	p.E105Q	G3BP2_uc003his.2_Missense_Mutation_p.E105Q|G3BP2_uc003hit.2_Missense_Mutation_p.E105Q	NM_012297	NP_036429	Q9UN86	G3BP2_HUMAN	Ras-GTPase activating protein SH3 domain-binding	105	NTF2.				cytoplasmic sequestering of NF-kappaB|mRNA transport|Ras protein signal transduction|regulation of small GTPase mediated signal transduction	cytosol	GTPase activator activity|nucleotide binding|receptor signaling complex scaffold activity|RNA binding			breast(2)|central_nervous_system(1)	3			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			AACTTTCTTTCTGGTTGTCCA	0.398													33	390	---	---	---	---	PASS
PPEF2	5470	broad.mit.edu	37	4	76782018	76782018	+	Missense_Mutation	SNP	C	A	A	rs148045586		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:76782018C>A	uc003hix.2	-	17	2421	c.2064G>T	c.(2062-2064)ATG>ATT	p.M688I	PPEF2_uc003hiy.2_RNA	NM_006239	NP_006230	O14830	PPE2_HUMAN	serine/threonine protein phosphatase with	688					detection of stimulus involved in sensory perception|negative regulation of MAPKKK cascade|negative regulation of peptidyl-threonine phosphorylation|protein dephosphorylation|visual perception	cytoplasm|photoreceptor inner segment|photoreceptor outer segment	calcium ion binding|Hsp70 protein binding|Hsp90 protein binding|iron ion binding|manganese ion binding|mitogen-activated protein kinase kinase kinase binding|protein serine/threonine phosphatase activity			ovary(2)|lung(1)|central_nervous_system(1)	4			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			TGTCGATATTCATGTGAGAGC	0.453													23	284	---	---	---	---	PASS
SHROOM3	57619	broad.mit.edu	37	4	77661234	77661234	+	Silent	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:77661234C>G	uc011cbx.1	+	5	2861	c.1908C>G	c.(1906-1908)GCC>GCG	p.A636A	SHROOM3_uc011cbz.1_Silent_p.A460A|SHROOM3_uc003hkf.1_Silent_p.A511A|SHROOM3_uc003hkg.2_Silent_p.A414A	NM_020859	NP_065910	Q8TF72	SHRM3_HUMAN	shroom family member 3 protein	636					apical protein localization|cell morphogenesis|cellular pigment accumulation|pattern specification process|regulation of cell shape	adherens junction|apical junction complex|apical plasma membrane|cytoplasm|microtubule	actin binding			skin(2)|ovary(1)	3			Lung(101;0.0903)			ACCACAATGCCAACCTCTGGA	0.567													8	445	---	---	---	---	PASS
AFF1	4299	broad.mit.edu	37	4	88035792	88035792	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:88035792C>G	uc003hqj.3	+	11	2193	c.1786C>G	c.(1786-1788)CAA>GAA	p.Q596E	AFF1_uc011ccz.1_Missense_Mutation_p.Q603E|AFF1_uc003hqk.3_Missense_Mutation_p.Q596E|AFF1_uc011cda.1_Missense_Mutation_p.Q234E	NM_005935	NP_005926	P51825	AFF1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	596						nucleus	sequence-specific DNA binding transcription factor activity			breast(1)	1		Acute lymphoblastic leukemia(40;0.0935)|all_hematologic(202;0.111)|Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000233)		GGAGCCCCCACAAAGGCAAAC	0.637													16	27	---	---	---	---	PASS
SPP1	6696	broad.mit.edu	37	4	88903701	88903701	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:88903701G>A	uc003hra.2	+	7	763	c.598G>A	c.(598-600)GGT>AGT	p.G200S	SPP1_uc003hrb.2_Missense_Mutation_p.G173S|SPP1_uc003hrc.2_Missense_Mutation_p.G186S|SPP1_uc011cde.1_Missense_Mutation_p.G213S|SPP1_uc003hrd.2_Missense_Mutation_p.G159S	NM_001040058	NP_001035147	P10451	OSTP_HUMAN	secreted phosphoprotein 1 isoform a	200					biomineral tissue development|cell adhesion|decidualization|embryo implantation|ossification|response to vitamin D	extracellular space	cytokine activity			ovary(1)	1		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		GGAGTTGAATGGTGCATACAA	0.507													17	37	---	---	---	---	PASS
SMARCAD1	56916	broad.mit.edu	37	4	95204388	95204388	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:95204388A>T	uc003htc.3	+	22	3098	c.2843A>T	c.(2842-2844)GAT>GTT	p.D948V	SMARCAD1_uc003htb.3_Missense_Mutation_p.D950V|SMARCAD1_uc003htd.3_Missense_Mutation_p.D950V|SMARCAD1_uc010ila.2_Missense_Mutation_p.D813V|SMARCAD1_uc011cdw.1_Missense_Mutation_p.D518V	NM_020159	NP_064544	Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated	948	Helicase C-terminal.				chromatin modification|nucleotide metabolic process|positive regulation of transcription, DNA-dependent|protein homooligomerization|regulation of DNA recombination	nuclear matrix	ATP binding|DNA binding|helicase activity			skin(2)|ovary(1)|breast(1)	4				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		ATACTTCACGATATTGACTGT	0.333													33	58	---	---	---	---	PASS
ANK2	287	broad.mit.edu	37	4	114280136	114280136	+	Missense_Mutation	SNP	G	T	T	rs55726422		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:114280136G>T	uc003ibe.3	+	38	10462	c.10362G>T	c.(10360-10362)AGG>AGT	p.R3454S	ANK2_uc003ibd.3_Intron|ANK2_uc003ibf.3_Intron|ANK2_uc011cgc.1_Intron|ANK2_uc003ibg.3_Intron|ANK2_uc003ibh.3_Intron|ANK2_uc011cgd.1_Missense_Mutation_p.R756S|ANK2_uc011cgb.1_Missense_Mutation_p.R3469S	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	3421					axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)|skin(1)	14		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTTCCTGCAGGGGGGGCACGA	0.448													12	29	---	---	---	---	PASS
UGT8	7368	broad.mit.edu	37	4	115544119	115544119	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:115544119C>A	uc003ibs.2	+	2	605	c.83C>A	c.(82-84)CCA>CAA	p.P28Q	UGT8_uc003ibt.2_Missense_Mutation_p.P28Q|UGT8_uc011cge.1_RNA	NM_001128174	NP_001121646	Q16880	CGT_HUMAN	UDP-galactose-ceramide galactosyltransferase 8	28					central nervous system development|peripheral nervous system development	integral to membrane	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity			ovary(1)|skin(1)	2		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		ATCGTGCCGCCAATTATGTTT	0.468													5	17	---	---	---	---	PASS
TBC1D9	23158	broad.mit.edu	37	4	141578722	141578722	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:141578722C>G	uc010ioj.2	-	12	2438	c.2166G>C	c.(2164-2166)TTG>TTC	p.L722F		NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	722						intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				CCTTGCAGTTCAACAGTTTGT	0.438													38	110	---	---	---	---	PASS
LRBA	987	broad.mit.edu	37	4	151604779	151604779	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:151604779T>C	uc010ipj.2	-	37	6319	c.5845A>G	c.(5845-5847)ACA>GCA	p.T1949A	LRBA_uc003ilt.3_Missense_Mutation_p.T608A|LRBA_uc003ilu.3_Missense_Mutation_p.T1949A	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1949						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)|skin(1)	7	all_hematologic(180;0.151)					TGAGTTGCTGTCACGTGGTCA	0.428													10	28	---	---	---	---	PASS
WWC2	80014	broad.mit.edu	37	4	184233499	184233499	+	Silent	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:184233499A>G	uc010irx.2	+	22	3572	c.3390A>G	c.(3388-3390)GAA>GAG	p.E1130E	WWC2_uc003ivk.3_Silent_p.E925E|WWC2_uc003ivl.3_RNA|WWC2_uc010iry.2_Silent_p.E812E|WWC2_uc003ivn.3_Silent_p.E645E|WWC2_uc010irz.2_Silent_p.E471E|WWC2_uc003ivo.3_Silent_p.E258E	NM_024949	NP_079225	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	1130	Potential.									ovary(2)|lung(1)	3		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TCCAGGCTGAACAGTCCAAAG	0.458													61	74	---	---	---	---	PASS
TRIML1	339976	broad.mit.edu	37	4	189068016	189068016	+	Silent	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr4:189068016C>G	uc003izm.1	+	6	1012	c.897C>G	c.(895-897)CTC>CTG	p.L299L	TRIML1_uc003izn.1_Silent_p.L23L	NM_178556	NP_848651	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	299	B30.2/SPRY.				multicellular organismal development		ligase activity|zinc ion binding			ovary(1)|pancreas(1)|breast(1)|skin(1)	4		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		ATGCCTATCTCGTGTTGTCGG	0.512													52	83	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13766275	13766275	+	Missense_Mutation	SNP	G	A	A	rs139821753		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:13766275G>A	uc003jfd.2	-	59	9953	c.9911C>T	c.(9910-9912)TCG>TTG	p.S3304L	DNAH5_uc003jfc.2_5'UTR	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3304	Stalk (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)					GGCGATGTCCGAAGGCCTGAT	0.527									Kartagener_syndrome				11	28	---	---	---	---	PASS
DNAH5	1767	broad.mit.edu	37	5	13919404	13919404	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:13919404C>T	uc003jfd.2	-	7	898	c.856G>A	c.(856-858)GAG>AAG	p.E286K	DNAH5_uc003jfe.1_RNA	NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	286	Potential.|Stem (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)					TGCTCCAGCTCCGCTCGTGGC	0.537									Kartagener_syndrome				36	119	---	---	---	---	PASS
CDH18	1016	broad.mit.edu	37	5	19483619	19483619	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:19483619C>A	uc003jgc.2	-	11	2050	c.1673G>T	c.(1672-1674)CGA>CTA	p.R558L	CDH18_uc003jgd.2_Missense_Mutation_p.R558L|CDH18_uc011cnm.1_Intron	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	558	Extracellular (Potential).|Cadherin 5.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)|skin(1)	7	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CTGAACAGTTCGACTAAATCT	0.458													6	20	---	---	---	---	PASS
C5orf34	375444	broad.mit.edu	37	5	43487154	43487154	+	Missense_Mutation	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:43487154A>G	uc003jnz.1	-	14	2097	c.1780T>C	c.(1780-1782)TCT>CCT	p.S594P		NM_198566	NP_940968	Q96MH7	CE034_HUMAN	hypothetical protein LOC375444	594										breast(1)	1	Lung NSC(6;2.07e-05)					TGATCAAAAGACTGTTGTTCA	0.333													9	12	---	---	---	---	PASS
C5orf34	375444	broad.mit.edu	37	5	43506193	43506193	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:43506193C>T	uc003jnz.1	-	5	906	c.589G>A	c.(589-591)GAG>AAG	p.E197K	C5orf34_uc011cpx.1_Missense_Mutation_p.E83K	NM_198566	NP_940968	Q96MH7	CE034_HUMAN	hypothetical protein LOC375444	197										breast(1)	1	Lung NSC(6;2.07e-05)					CAATGAAACTCATTTTCTTTA	0.363													23	41	---	---	---	---	PASS
PARP8	79668	broad.mit.edu	37	5	50123778	50123778	+	Nonsense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:50123778C>T	uc003jon.3	+	21	2160	c.1978C>T	c.(1978-1980)CAA>TAA	p.Q660*	PARP8_uc011cpz.1_Nonsense_Mutation_p.Q552*|PARP8_uc003joo.2_Nonsense_Mutation_p.Q660*|PARP8_uc003jop.2_Nonsense_Mutation_p.Q618*	NM_024615	NP_078891	Q8N3A8	PARP8_HUMAN	poly (ADP-ribose) polymerase family, member 8	660	PARP catalytic.					intracellular	NAD+ ADP-ribosyltransferase activity			lung(3)|large_intestine(1)|ovary(1)	5		Lung NSC(810;0.0305)|Breast(144;0.222)				TAAATGGCAGCAATTGAAGTT	0.338													6	12	---	---	---	---	PASS
ITGA2	3673	broad.mit.edu	37	5	52358679	52358679	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:52358679G>T	uc003joy.2	+	13	1665	c.1522G>T	c.(1522-1524)GTG>TTG	p.V508L	ITGA2_uc011cqa.1_RNA|ITGA2_uc011cqb.1_RNA|ITGA2_uc011cqc.1_Missense_Mutation_p.V432L|ITGA2_uc011cqd.1_RNA|ITGA2_uc011cqe.1_RNA	NM_002203	NP_002194	P17301	ITA2_HUMAN	integrin alpha 2 precursor	508	FG-GAP 5.|Extracellular (Potential).				axon guidance|blood coagulation|cell-matrix adhesion|integrin-mediated signaling pathway|interspecies interaction between organisms|organ morphogenesis	integrin complex	collagen binding|identical protein binding|receptor activity			lung(1)	1		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				CATTACAGACGTGCTCTTGGT	0.368													13	22	---	---	---	---	PASS
UTP15	84135	broad.mit.edu	37	5	72872776	72872776	+	Splice_Site	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:72872776G>T	uc003kcw.1	+	8	1033	c.810_splice	c.e8-1	p.R270_splice	UTP15_uc011cso.1_Splice_Site_p.R251_splice|UTP15_uc011csp.1_Splice_Site_p.R80_splice|UTP15_uc010ize.1_Splice_Site_p.R270_splice	NM_032175	NP_115551	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein,						rRNA processing	cytoplasm|nucleolus					0		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		CTTTTTATTAGGAAGGTGAAA	0.323													6	95	---	---	---	---	PASS
YTHDC2	64848	broad.mit.edu	37	5	112870077	112870077	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:112870077G>A	uc003kqn.2	+	6	1101	c.918G>A	c.(916-918)ACG>ACA	p.T306T	YTHDC2_uc010jce.1_Silent_p.T306T|YTHDC2_uc010jcf.1_Silent_p.T6T	NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	306	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		GAGATAGTACGTTGTCGACTG	0.348													18	34	---	---	---	---	PASS
SEC24A	10802	broad.mit.edu	37	5	134002525	134002525	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:134002525C>A	uc003kzs.2	+	3	866	c.578C>A	c.(577-579)CCT>CAT	p.P193H	SEC24A_uc011cxu.1_5'UTR	NM_021982	NP_068817	O95486	SC24A_HUMAN	SEC24 related gene family, member A	193	Pro-rich.				COPII vesicle coating|intracellular protein transport|post-translational protein modification|protein N-linked glycosylation via asparagine	COPII vesicle coat|cytosol|endoplasmic reticulum membrane|Golgi membrane|perinuclear region of cytoplasm	zinc ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCTTCTGTACCTCCCTTAGTG	0.522													6	100	---	---	---	---	PASS
FAM13B	51306	broad.mit.edu	37	5	137347574	137347574	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:137347574G>T	uc003lbz.2	-	5	965	c.431C>A	c.(430-432)CCT>CAT	p.P144H	FAM13B_uc003lcb.2_Missense_Mutation_p.P26H|FAM13B_uc003lca.2_Missense_Mutation_p.P144H	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN	hypothetical protein LOC51306 isoform 1	144	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0						ATAATTAACAGGTGGAAGCTG	0.313													7	69	---	---	---	---	PASS
KIF20A	10112	broad.mit.edu	37	5	137520077	137520077	+	Nonsense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:137520077C>G	uc003lcj.2	+	12	1998	c.1502C>G	c.(1501-1503)TCA>TGA	p.S501*	KIF20A_uc011cyo.1_Nonsense_Mutation_p.S483*	NM_005733	NP_005724	O95235	KI20A_HUMAN	kinesin family member 20A	501					cytokinesis|M phase of mitotic cell cycle|microtubule-based movement|protein transport|vesicle-mediated transport	Golgi apparatus|microtubule|nucleoplasm	ATP binding|microtubule motor activity|protein binding|transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GCCAAGTTCTCAGCCATTGCT	0.488													39	119	---	---	---	---	PASS
HARS	3035	broad.mit.edu	37	5	140056260	140056260	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:140056260G>T	uc003lgv.2	-	10	1255	c.1173C>A	c.(1171-1173)TCC>TCA	p.S391S	HARS_uc003lgu.2_Silent_p.S322S|HARS_uc011czm.1_Silent_p.S351S|HARS_uc003lgw.2_Silent_p.S371S|HARS_uc011czn.1_Silent_p.S331S|HARS_uc010jfu.2_Silent_p.S391S|HARS_uc011czo.1_Silent_p.S317S|HARS_uc011czp.1_Silent_p.S277S|HARS_uc011czq.1_Silent_p.S281S	NM_002109	NP_002100	P12081	SYHC_HUMAN	histidyl-tRNA synthetase	391					histidyl-tRNA aminoacylation	cytosol	ATP binding|histidine-tRNA ligase activity			ovary(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		L-Histidine(DB00117)	GTTCCACGATGGAGAAAATCC	0.557													8	184	---	---	---	---	PASS
PCDHB2	56133	broad.mit.edu	37	5	140476341	140476341	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:140476341C>A	uc003lil.2	+	1	2105	c.1967C>A	c.(1966-1968)GCC>GAC	p.A656D	PCDHB2_uc003lim.1_Missense_Mutation_p.A317D	NM_018936	NP_061759	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2 precursor	656	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			ovary(3)|upper_aerodigestive_tract(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCGCGCTCGGCCACCGCCACG	0.711													13	15	---	---	---	---	PASS
PCDHB13	56123	broad.mit.edu	37	5	140596022	140596022	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:140596022C>A	uc003lja.1	+	1	2514	c.2327C>A	c.(2326-2328)CCC>CAC	p.P776H		NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13 precursor	776	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			skin(2)|ovary(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AACTTCCCTCCCCAGTGCCCT	0.468													39	65	---	---	---	---	PASS
PCDHGA5	56110	broad.mit.edu	37	5	140746176	140746176	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:140746176C>G	uc003lju.1	+	1	2279	c.2279C>G	c.(2278-2280)ACC>AGC	p.T760S	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc011das.1_Missense_Mutation_p.T760S	NM_018918	NP_061741	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5 isoform 1	760	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCTCCCTCACCGCGGACTCG	0.597													56	130	---	---	---	---	PASS
NDST1	3340	broad.mit.edu	37	5	149925029	149925029	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:149925029G>A	uc003lsk.3	+	11	2628	c.2126G>A	c.(2125-2127)CGG>CAG	p.R709Q	NDST1_uc011dcj.1_Missense_Mutation_p.R709Q	NM_001543	NP_001534	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan	709	Heparan sulfate N-sulfotransferase 1.|Lumenal (Potential).				heparan sulfate proteoglycan biosynthetic process|inflammatory response	Golgi membrane|integral to membrane	[heparan sulfate]-glucosamine N-sulfotransferase activity|hydrolase activity			breast(1)|skin(1)	2		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCGCGGACCGGGCCTATTCC	0.557													33	92	---	---	---	---	PASS
ANXA6	309	broad.mit.edu	37	5	150496742	150496742	+	Splice_Site	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:150496742C>A	uc003ltl.1	-	20	1671	c.1519_splice	c.e20-1	p.G507_splice	ANXA6_uc011dcp.1_Splice_Site_p.G475_splice|ANXA6_uc003ltm.1_Splice_Site_p.G507_splice|ANXA6_uc003ltn.1_Splice_Site_p.G300_splice|ANXA6_uc003lto.1_Splice_Site_p.G94_splice	NM_001155	NP_001146	P08133	ANXA6_HUMAN	annexin VI isoform 1							melanosome	calcium ion binding|calcium-dependent phospholipid binding|protein binding				0		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CACGATGCCCCTGCAGCAGGA	0.537													16	39	---	---	---	---	PASS
SLIT3	6586	broad.mit.edu	37	5	168199840	168199840	+	Nonsense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:168199840G>A	uc003mab.2	-	14	1825	c.1405C>T	c.(1405-1407)CGA>TGA	p.R469*	SLIT3_uc010jjg.2_Nonsense_Mutation_p.R469*|SLIT3_uc010jji.2_Nonsense_Mutation_p.R469*|SLIT3_uc003mac.1_Nonsense_Mutation_p.R266*	NM_003062	NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 precursor	469	LRRCT 2.				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding			ovary(3)|skin(1)	4	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTGGCGAGTCGGCGCGGGCTG	0.602													9	26	---	---	---	---	PASS
CNOT6	57472	broad.mit.edu	37	5	179991578	179991578	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr5:179991578G>T	uc003mlx.2	+	5	824	c.475G>T	c.(475-477)GGT>TGT	p.G159C	CNOT6_uc010jld.2_Missense_Mutation_p.G159C|CNOT6_uc010jle.2_Missense_Mutation_p.V159F	NM_015455	NP_056270	Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	159					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	exonuclease activity|metal ion binding|protein binding|RNA binding				0	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		TAATTTGTCAGGTACTGCAAA	0.338													6	85	---	---	---	---	PASS
HIVEP1	3096	broad.mit.edu	37	6	12121781	12121781	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:12121781C>T	uc003nac.2	+	4	1932	c.1753C>T	c.(1753-1755)CCT>TCT	p.P585S	HIVEP1_uc011diq.1_RNA	NM_002114	NP_002105	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer	585					transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(3)|large_intestine(1)|central_nervous_system(1)|skin(1)	6	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				GGATCCCAAGCCTGAACTTTC	0.507													42	25	---	---	---	---	PASS
DCDC2	51473	broad.mit.edu	37	6	24178827	24178827	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:24178827C>A	uc003ndx.2	-	9	1359	c.1057G>T	c.(1057-1059)GGA>TGA	p.G353*	DCDC2_uc003ndy.2_Nonsense_Mutation_p.G353*|DCDC2_uc003ndw.2_Nonsense_Mutation_p.G104*	NM_016356	NP_057440	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	353					cellular defense response|intracellular signal transduction|neuron migration					ovary(1)	1		Ovarian(999;0.101)				GCCTTCTCTCCATCTTCTTCC	0.433													33	23	---	---	---	---	PASS
ZNF391	346157	broad.mit.edu	37	6	27368847	27368847	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:27368847G>A	uc003njf.1	+	3	1216	c.698G>A	c.(697-699)CGT>CAT	p.R233H		NM_001076781	NP_001070249	Q9UJN7	ZN391_HUMAN	zinc finger protein 391	233	C2H2-type 5.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(2)|skin(1)	3						TTCGGTGACCGTTCAACCATA	0.423													17	8	---	---	---	---	PASS
HIST1H3H	8357	broad.mit.edu	37	6	27778110	27778110	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:27778110A>T	uc003njm.2	+	1	269	c.259A>T	c.(259-261)AGC>TGC	p.S87C	HIST1H2BL_uc003njl.2_5'Flank	NM_003536	NP_003527	P68431	H31_HUMAN	histone cluster 1, H3h	87					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1						GCGCTTCCAGAGCTCCGCGGT	0.607													38	34	---	---	---	---	PASS
HLA-DRB5	3127	broad.mit.edu	37	6	32487330	32487330	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:32487330C>T	uc003obj.2	-	3	474	c.469G>A	c.(469-471)GAA>AAA	p.E157K	HLA-DRB1_uc011dqa.1_Intron|HLA-DRB5_uc003obk.3_Missense_Mutation_p.E157K	NM_002125	NP_002116	Q30154	DRB5_HUMAN	major histocompatibility complex, class II, DR	157	Ig-like C1-type.|Beta-2.|Extracellular (Potential).				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0						CACCTGACTTCAATGCTGCCT	0.552													8	22	---	---	---	---	PASS
HLA-DRB1	3123	broad.mit.edu	37	6	32549517	32549517	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:32549517C>T	uc003obp.3	-	3	512	c.469G>A	c.(469-471)GAA>AAA	p.E157K	HLA-DRB1_uc011dqa.1_5'UTR|HLA-DRB5_uc003obk.3_Intron|HLA-DRB6_uc003obo.1_Intron|HLA-DRB1_uc011dqb.1_5'UTR|HLA-DRB1_uc011dqc.1_5'UTR	NM_002124	NP_002115	P01911	2B1F_HUMAN	major histocompatibility complex, class II, DR	157	Ig-like C1-type.|Beta-2.|Extracellular (Potential).				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex				skin(1)	1						CACCTGACTTCAATGCTGCCT	0.547									Rheumatoid_Arthritis|Sj_gren_syndrome	Multiple Myeloma(14;0.17)			14	67	---	---	---	---	PASS
COL11A2	1302	broad.mit.edu	37	6	33139299	33139299	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:33139299A>T	uc003ocx.1	-	43	3431	c.3203T>A	c.(3202-3204)GTG>GAG	p.V1068E	COL11A2_uc010jul.1_Intron|COL11A2_uc003ocy.1_Missense_Mutation_p.V982E|COL11A2_uc003ocz.1_Missense_Mutation_p.V961E	NM_080680	NP_542411	P13942	COBA2_HUMAN	collagen, type XI, alpha 2 isoform 1	1068	Triple-helical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			ovary(3)|skin(2)	5						AGGAAGCCCCACAGGACCCTG	0.632													8	22	---	---	---	---	PASS
ZBTB9	221504	broad.mit.edu	37	6	33422975	33422975	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:33422975C>G	uc003oeq.2	+	2	366	c.98C>G	c.(97-99)TCT>TGT	p.S33C		NM_152735	NP_689948	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	33					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CATAGCTCGTCTCTGCTGGAA	0.582													37	56	---	---	---	---	PASS
PEX6	5190	broad.mit.edu	37	6	42932076	42932076	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:42932076G>T	uc003otf.2	-	17	3033	c.2940C>A	c.(2938-2940)TGC>TGA	p.C980*	uc003ote.1_5'Flank|PEX6_uc010jya.2_RNA	NM_000287	NP_000278	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	980					protein import into peroxisome matrix, translocation|protein stabilization	cytosol|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)	1			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			GGGGCTCCTAGCAGGCAGCAA	0.637													6	31	---	---	---	---	PASS
AARS2	57505	broad.mit.edu	37	6	44279966	44279966	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:44279966C>T	uc010jza.1	-	2	281	c.278G>A	c.(277-279)CGA>CAA	p.R93Q	SPATS1_uc003oxg.2_Intron	NM_020745	NP_065796	Q5JTZ9	SYAM_HUMAN	alanyl-tRNA synthetase 2, mitochondrial	93					alanyl-tRNA aminoacylation	mitochondrion	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			ovary(1)	1	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)		L-Alanine(DB00160)	CATCTCGCTTCGTGGATCCAC	0.542													24	46	---	---	---	---	PASS
CYP39A1	51302	broad.mit.edu	37	6	46620210	46620210	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:46620210G>T	uc003oyf.1	-	1	314	c.110C>A	c.(109-111)CCT>CAT	p.P37H	CYP39A1_uc011dwa.1_Missense_Mutation_p.P37H|CYP39A1_uc010jzd.1_5'UTR|SLC25A27_uc011dwb.1_5'Flank|SLC25A27_uc003oyg.2_5'Flank|SLC25A27_uc003oyh.2_5'Flank|SLC25A27_uc011dwc.1_5'Flank	NM_016593	NP_057677	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A,	37					bile acid biosynthetic process|bile acid catabolic process|digestion|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	24-hydroxycholesterol 7alpha-hydroxylase activity|electron carrier activity|heme binding|oxysterol 7-alpha-hydroxylase activity			ovary(1)	1						TCCAATCCAAGGAATCCAGCC	0.483													10	381	---	---	---	---	PASS
RHAG	6005	broad.mit.edu	37	6	49587042	49587042	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:49587042C>G	uc003ozk.3	-	2	253	c.191G>C	c.(190-192)GGG>GCG	p.G64A	RHAG_uc010jzl.2_Missense_Mutation_p.G64A|RHAG_uc010jzm.2_Missense_Mutation_p.G64A	NM_000324	NP_000315	Q02094	RHAG_HUMAN	Rh-associated glycoprotein	64	Helical; (Potential).				carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)|skin(1)	2	Lung NSC(77;0.0255)					GAAGCCAAACCCAACAAATAT	0.418													14	12	---	---	---	---	PASS
PKHD1	5314	broad.mit.edu	37	6	51890331	51890331	+	Nonsense_Mutation	SNP	G	T	T	rs149167975		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:51890331G>T	uc003pah.1	-	32	4553	c.4277C>A	c.(4276-4278)TCG>TAG	p.S1426*	PKHD1_uc003pai.2_Nonsense_Mutation_p.S1426*	NM_138694	NP_619639	P08F94	PKHD1_HUMAN	fibrocystin isoform 1	1426	IPT/TIG 9.|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)					AAAAGGACCCGAGAGGTCAAC	0.542													6	187	---	---	---	---	PASS
HCRTR2	3062	broad.mit.edu	37	6	55128539	55128539	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:55128539C>G	uc003pcl.2	+	4	996	c.681C>G	c.(679-681)TTC>TTG	p.F227L	HCRTR2_uc010jzv.2_RNA|HCRTR2_uc010jzw.1_Missense_Mutation_p.F162L	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2	227	Helical; Name=5; (Potential).				feeding behavior	integral to plasma membrane	neuropeptide receptor activity			ovary(2)|lung(2)|upper_aerodigestive_tract(1)|breast(1)	6	Lung NSC(77;0.107)|Renal(3;0.122)		LUSC - Lung squamous cell carcinoma(124;0.23)			ACATCTGTTTCTTTCTGGTGA	0.363													5	5	---	---	---	---	PASS
PHF3	23469	broad.mit.edu	37	6	64408187	64408187	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:64408187G>T	uc003pep.1	+	6	2781	c.2755G>T	c.(2755-2757)GCT>TCT	p.A919S	PHF3_uc010kag.1_Missense_Mutation_p.A831S|PHF3_uc010kah.1_Missense_Mutation_p.A733S|PHF3_uc003pen.2_Missense_Mutation_p.A831S|PHF3_uc011dxs.1_Missense_Mutation_p.A188S	NM_015153	NP_055968	Q92576	PHF3_HUMAN	PHD finger protein 3	919					multicellular organismal development|transcription, DNA-dependent	nucleus	zinc ion binding			ovary(3)|lung(1)|skin(1)	5	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			TGCTGCTTCTGCTTCCAAGCC	0.348													12	71	---	---	---	---	PASS
COL12A1	1303	broad.mit.edu	37	6	75848583	75848583	+	Silent	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:75848583G>C	uc003phs.2	-	28	5218	c.5052C>G	c.(5050-5052)CTC>CTG	p.L1684L	COL12A1_uc003pht.2_Silent_p.L520L	NM_004370	NP_004361	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1 long isoform	1684	Fibronectin type-III 12.				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength			ovary(6)|large_intestine(1)|breast(1)|skin(1)	9						TTATTCTGTAGAGAGACACAT	0.423													6	24	---	---	---	---	PASS
HTR1B	3351	broad.mit.edu	37	6	78172386	78172386	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:78172386G>T	uc003pil.1	-	1	735	c.735C>A	c.(733-735)AAC>AAA	p.N245K		NM_000863	NP_000854	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B	245	Cytoplasmic (By similarity).				G-protein signaling, coupled to cyclic nucleotide second messenger|negative regulation of cAMP biosynthetic process|synaptic transmission	integral to plasma membrane	protein binding|serotonin receptor activity				0		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Dexfenfluramine(DB01191)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Naratriptan(DB00952)|Pindolol(DB00960)|Propranolol(DB00571)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Venlafaxine(DB00285)|Zolmitriptan(DB00315)	TGCCGGTCCTGTTGGGCGTCT	0.622													21	28	---	---	---	---	PASS
SLC35A1	10559	broad.mit.edu	37	6	88221170	88221170	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:88221170G>T	uc011dzj.1	+	8	1019	c.940G>T	c.(940-942)GGA>TGA	p.G314*	SLC35A1_uc003plx.2_RNA|SLC35A1_uc010kbw.2_Nonsense_Mutation_p.G162*|SLC35A1_uc003plz.2_RNA|SLC35A1_uc011dzi.1_Nonsense_Mutation_p.G180*|SLC35A1_uc003ply.2_RNA|SLC35A1_uc010kbx.2_Nonsense_Mutation_p.G255*|SLC35A1_uc010kby.2_RNA	NM_006416	NP_006407	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid	314	Helical; (Potential).				carbohydrate metabolic process|protein modification process	Golgi membrane|integral to plasma membrane	CMP-N-acetylneuraminate transmembrane transporter activity|sugar:hydrogen symporter activity				0		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		ATATCTCTATGGATTACCCAG	0.383													5	58	---	---	---	---	PASS
MCHR2	84539	broad.mit.edu	37	6	100403965	100403965	+	Nonsense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:100403965C>T	uc003pqh.1	-	2	374	c.59G>A	c.(58-60)TGG>TAG	p.W20*	MCHR2_uc003pqi.1_Nonsense_Mutation_p.W20*	NM_001040179	NP_001035269	Q969V1	MCHR2_HUMAN	melanin-concentrating hormone receptor 2	20	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(3)|ovary(2)|breast(1)|central_nervous_system(1)|skin(1)	8		all_cancers(76;4.87e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0309)|Colorectal(196;0.069)		BRCA - Breast invasive adenocarcinoma(108;0.0429)		CTCTTTATTCCAGGATTTGTT	0.423													20	41	---	---	---	---	PASS
POPDC3	64208	broad.mit.edu	37	6	105609460	105609460	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:105609460G>T	uc003prb.2	-	2	727	c.325C>A	c.(325-327)CAA>AAA	p.Q109K	uc003pqz.2_Intron|POPDC3_uc003pra.2_Intron	NM_022361	NP_071756	Q9HBV1	POPD3_HUMAN	popeye protein 3	109						integral to membrane				skin(3)|ovary(2)	5		all_cancers(87;4.87e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0157)|Colorectal(196;0.202)|Lung NSC(302;0.238)				TACAACACTTGGAATTCTCGG	0.423													9	249	---	---	---	---	PASS
FOXO3	2309	broad.mit.edu	37	6	108985287	108985287	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:108985287C>A	uc003psk.2	+	3	1567	c.1251C>A	c.(1249-1251)ACC>ACA	p.T417T	FOXO3_uc003psn.2_Intron|FOXO3_uc003psm.2_Silent_p.T417T|FOXO3_uc011ean.1_Silent_p.T197T|FOXO3_uc010kdj.1_Silent_p.T197T	NM_201559	NP_963853	O43524	FOXO3_HUMAN	forkhead box O3A	417					antral ovarian follicle growth|apoptosis|embryo development|glucose homeostasis|induction of apoptosis|initiation of primordial ovarian follicle growth|insulin receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|oocyte maturation|ovulation from ovarian follicle|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of erythrocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding			central_nervous_system(4)|lung(2)	6		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		TCCCGTATACCACCAAGGGCT	0.597													6	84	---	---	---	---	PASS
NCOA7	135112	broad.mit.edu	37	6	126206390	126206390	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:126206390G>T	uc010kes.2	+	10	1234	c.785G>T	c.(784-786)GGG>GTG	p.G262V	NCOA7_uc003qae.3_Missense_Mutation_p.G262V|NCOA7_uc003qah.2_Missense_Mutation_p.G262V|NCOA7_uc003qai.2_Missense_Mutation_p.G262V|NCOA7_uc010ket.2_Missense_Mutation_p.G158V|NCOA7_uc003qag.2_Missense_Mutation_p.G262V	NM_181782	NP_861447	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7 isoform 1	262					cell wall macromolecule catabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			lung(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		ATTGAAAATGGGTGTGAGGAG	0.453													6	87	---	---	---	---	PASS
MOXD1	26002	broad.mit.edu	37	6	132643820	132643820	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:132643820G>T	uc003qdf.2	-	8	1402	c.1303C>A	c.(1303-1305)CCA>ACA	p.P435T	MOXD1_uc003qde.2_Missense_Mutation_p.P367T	NM_015529	NP_056344	Q6UVY6	MOXD1_HUMAN	monooxygenase, DBH-like 1 isoform 2	435	Lumenal (Potential).				catecholamine metabolic process	endoplasmic reticulum membrane|integral to membrane	copper ion binding|dopamine beta-monooxygenase activity			ovary(1)	1	Breast(56;0.0495)			OV - Ovarian serous cystadenocarcinoma(155;0.0132)|GBM - Glioblastoma multiforme(226;0.0191)		ATGCATACTGGTAAGATTGTT	0.333													8	16	---	---	---	---	PASS
HIVEP2	3097	broad.mit.edu	37	6	143081135	143081135	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:143081135C>G	uc003qjd.2	-	9	7033	c.6290G>C	c.(6289-6291)AGA>ACA	p.R2097T		NM_006734	NP_006725	P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer	2097	10 X 4 AA tandem repeats of S-P-[RGMKC]- [RK].|Arg-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)|skin(2)|central_nervous_system(1)	6				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CATCTCTCTTCTCAATGCAGC	0.458													10	16	---	---	---	---	PASS
SASH1	23328	broad.mit.edu	37	6	148869683	148869683	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:148869683G>C	uc003qme.1	+	20	4208	c.3733G>C	c.(3733-3735)GAG>CAG	p.E1245Q	SASH1_uc003qmf.1_Missense_Mutation_p.E655Q	NM_015278	NP_056093	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	1245							protein binding			central_nervous_system(1)	1		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		GCCAGGCCCTGAGGCCATGTA	0.552													15	43	---	---	---	---	PASS
AKAP12	9590	broad.mit.edu	37	6	151671465	151671465	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:151671465G>T	uc011eep.1	+	4	2179	c.1939G>T	c.(1939-1941)GAG>TAG	p.E647*	AKAP12_uc003qoe.2_Nonsense_Mutation_p.E647*|AKAP12_uc003qof.2_Nonsense_Mutation_p.E549*|AKAP12_uc010kim.2_Intron|AKAP12_uc003qog.2_Nonsense_Mutation_p.E542*	NM_005100	NP_005091	Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12 isoform 1	647					G-protein coupled receptor protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of protein kinase A signaling cascade|protein targeting	cell cortex|cytoskeleton|plasma membrane	adenylate cyclase binding|protein kinase A binding			large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	8		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GTCTTCCACCGAGAGCACAGC	0.502													5	89	---	---	---	---	PASS
CNKSR3	154043	broad.mit.edu	37	6	154744078	154744078	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:154744078C>T	uc003qpy.2	-	8	1274	c.769G>A	c.(769-771)GAA>AAA	p.E257K		NM_173515	NP_775786	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	257	PDZ.				negative regulation of ERK1 and ERK2 cascade|negative regulation of peptidyl-serine phosphorylation|positive regulation of sodium ion transport	cytoplasm|membrane				ovary(2)|breast(1)|skin(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		TGAATGACTTCGTCACCAGCA	0.328													7	31	---	---	---	---	PASS
TFB1M	51106	broad.mit.edu	37	6	155579120	155579120	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:155579120G>C	uc003qqj.3	-	7	955	c.891C>G	c.(889-891)ATC>ATG	p.I297M	TFB1M_uc003qqk.2_Intron|uc003qqi.1_5'Flank	NM_016020	NP_057104	Q8WVM0	TFB1M_HUMAN	transcription factor B1, mitochondrial	297					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial nucleoid	DNA binding|protein binding|rRNA (adenine-N6,N6-)-dimethyltransferase activity			skin(1)	1		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;1.48e-12)|BRCA - Breast invasive adenocarcinoma(81;0.0131)		TAAAGTGTGAGATGGAGAGCT	0.463													27	63	---	---	---	---	PASS
TMEM181	57583	broad.mit.edu	37	6	158957791	158957791	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:158957791G>C	uc003qrm.3	+	1	324	c.313G>C	c.(313-315)GAG>CAG	p.E105Q	TMEM181_uc010kjr.1_5'UTR	NM_020823	NP_065874	Q9P2C4	TM181_HUMAN	G protein-coupled receptor 178	105					pathogenesis	integral to membrane	toxin binding			ovary(2)|central_nervous_system(1)	3		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;8.15e-18)|BRCA - Breast invasive adenocarcinoma(81;1.38e-05)		CCCTGCCTTTGAGCCCCCGCT	0.697													3	3	---	---	---	---	PASS
LPA	4018	broad.mit.edu	37	6	160953575	160953575	+	Silent	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:160953575A>G	uc003qtl.2	-	39	6069	c.5949T>C	c.(5947-5949)ACT>ACC	p.T1983T		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	4491	Peptidase S1.				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GGCAACTGTCAGTGCCTCTGG	0.463													11	27	---	---	---	---	PASS
MAP3K4	4216	broad.mit.edu	37	6	161514085	161514085	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:161514085C>A	uc003qtn.2	+	14	3487	c.3345C>A	c.(3343-3345)TTC>TTA	p.F1115L	MAP3K4_uc010kkc.1_Missense_Mutation_p.F1115L|MAP3K4_uc003qto.2_Missense_Mutation_p.F1115L|MAP3K4_uc011efz.1_RNA|MAP3K4_uc011ega.1_Missense_Mutation_p.F568L|MAP3K4_uc003qtp.2_Missense_Mutation_p.F105L	NM_005922	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1115					activation of MAPKK activity|JNK cascade|positive regulation of JUN kinase activity	perinuclear region of cytoplasm	ATP binding|MAP kinase kinase kinase activity|metal ion binding|protein binding			ovary(3)|lung(3)|skin(2)|stomach(1)	9		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AAGATGACTTCTTGGTATGGA	0.323													4	20	---	---	---	---	PASS
AGPAT4	56895	broad.mit.edu	37	6	161653130	161653130	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:161653130C>A	uc003qtr.1	-	2	343	c.116G>T	c.(115-117)TGG>TTG	p.W39L	AGPAT4_uc003qts.1_5'UTR|AGPAT4_uc011egb.1_Missense_Mutation_p.W39L|AGPAT4_uc003qtt.1_RNA|AGPAT4_uc011egc.1_Missense_Mutation_p.W39L|AGPAT4_uc011egd.1_Intron|AGPAT4_uc011ege.1_Missense_Mutation_p.W39L	NM_020133	NP_064518	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	39					phospholipid biosynthetic process	integral to membrane	1-acylglycerol-3-phosphate O-acyltransferase activity|protein binding				0		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		GTTAATGGGCCAGAGGAGGAG	0.463													5	52	---	---	---	---	PASS
MLLT4	4301	broad.mit.edu	37	6	168352586	168352586	+	Silent	SNP	C	T	T	rs141139097		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:168352586C>T	uc003qwd.2	+	29	4670	c.4528C>T	c.(4528-4530)CTG>TTG	p.L1510L	MLLT4_uc003qwb.1_Silent_p.L1495L|MLLT4_uc003qwc.1_Silent_p.L1511L|MLLT4_uc003qwg.1_Silent_p.L820L	NM_001040001	NP_001035090	P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia	1511					adherens junction organization|cell adhesion|cell junction assembly|cell-cell signaling|signal transduction	adherens junction|cell-cell junction|cytosol|nucleus	protein C-terminus binding			ovary(2)|lung(1)|kidney(1)|central_nervous_system(1)	5		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		GGGGGACAGTCTGTCCCCCGA	0.602			T	MLL	AL								14	26	---	---	---	---	PASS
SNX8	29886	broad.mit.edu	37	7	2297430	2297430	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:2297430C>A	uc003slw.2	-	8	967	c.924G>T	c.(922-924)CAG>CAT	p.Q308H		NM_013321	NP_037453	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	308					cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		CGTTCTCTTCCTGCTTACCCT	0.612													9	346	---	---	---	---	PASS
MMD2	221938	broad.mit.edu	37	7	4959907	4959907	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:4959907T>C	uc003sno.3	-	3	381	c.185A>G	c.(184-186)GAT>GGT	p.D62G	MMD2_uc003snl.1_RNA|MMD2_uc003snn.3_Missense_Mutation_p.D62G|MMD2_uc010ksq.2_Missense_Mutation_p.D62G	NM_001100600	NP_001094070	Q8IY49	PAQRA_HUMAN	monocyte to macrophage	62	Extracellular (Potential).					integral to membrane	receptor activity			central_nervous_system(1)	1		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.097)|OV - Ovarian serous cystadenocarcinoma(56;3.4e-14)		CTCCCAGTCATCGTCCGACAG	0.617													15	5	---	---	---	---	PASS
ZDHHC4	55146	broad.mit.edu	37	7	6628525	6628525	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:6628525G>T	uc003sqi.2	+	9	1377	c.1019G>T	c.(1018-1020)AGG>ATG	p.R340M	ZDHHC4_uc003sql.2_Missense_Mutation_p.R340M|ZDHHC4_uc003sqh.2_Missense_Mutation_p.R340M|ZDHHC4_uc003sqj.2_Missense_Mutation_p.R340M|ZDHHC4_uc003sqk.2_Missense_Mutation_p.R340M|ZDHHC4_uc003sqm.2_Missense_Mutation_p.R340M|uc011jwy.1_5'Flank|C7orf26_uc003sqo.1_5'Flank|C7orf26_uc003sqp.1_5'Flank|C7orf26_uc003sqq.1_5'Flank	NM_001134388	NP_001127860	Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	340						integral to membrane	acyltransferase activity|zinc ion binding			breast(1)|pancreas(1)	2		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		TGTCATGAGAGGAAGAAACAA	0.473													10	250	---	---	---	---	PASS
AHR	196	broad.mit.edu	37	7	17378616	17378616	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:17378616G>T	uc011jxz.1	+	10	1780	c.1167G>T	c.(1165-1167)GAG>GAT	p.E389D	AHR_uc003stt.3_RNA	NM_001621	NP_001612	P35869	AHR_HUMAN	aryl hydrocarbon receptor precursor	389					apoptosis|blood vessel development|cell cycle|regulation of B cell proliferation|response to stress|transcription from RNA polymerase II promoter|xenobiotic metabolic process	cytosolic aryl hydrocarbon receptor complex|transcription factor complex	Hsp90 protein binding|ligand-dependent nuclear receptor activity|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding			urinary_tract(1)|kidney(1)|pancreas(1)	3	Lung NSC(10;0.0392)|all_lung(11;0.0754)					TTAGAGATGAGGAAGGAACAG	0.303													6	113	---	---	---	---	PASS
HOXA11	3207	broad.mit.edu	37	7	27224653	27224653	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:27224653G>T	uc003syx.2	-	1	183	c.111C>A	c.(109-111)ACC>ACA	p.T37T	HOXA11_uc003syy.2_Intron|HOXA11AS_uc003syz.1_5'Flank	NM_005523	NP_005514	P31270	HXA11_HUMAN	homeobox A11	37					branching involved in ureteric bud morphogenesis|cartilage development involved in endochondral bone morphogenesis|developmental growth|dorsal/ventral pattern formation|mesodermal cell fate specification|positive regulation of cell development|positive regulation of chondrocyte differentiation	protein-DNA complex|transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			lung(1)|breast(1)	2						GCGAAGACGGGGTCTGGGGCA	0.562			T	NUP98	CML						OREG0003747	type=REGULATORY REGION|Gene=BC025338|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	49	44	---	---	---	---	PASS
MYO1G	64005	broad.mit.edu	37	7	45016187	45016187	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:45016187G>T	uc003tmh.2	-	3	518	c.374C>A	c.(373-375)CCA>CAA	p.P125Q	MYO1G_uc003tmg.2_5'Flank|MYO1G_uc010kym.2_Missense_Mutation_p.P10Q|MYO1G_uc003tmi.1_Missense_Mutation_p.P37Q|MYO1G_uc003tmj.2_5'UTR	NM_033054	NP_149043	B0I1T2	MYO1G_HUMAN	myosin IG	125	Myosin head-like.					myosin complex|plasma membrane	actin binding|ATP binding|calmodulin binding|motor activity			breast(2)|ovary(1)|pancreas(1)	4						CCTCTGGCTTGGATTGGTGAC	0.597													5	61	---	---	---	---	PASS
SEC61G	23480	broad.mit.edu	37	7	54823496	54823496	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:54823496T>C	uc003tqf.2	-	3	264	c.173A>G	c.(172-174)CAT>CGT	p.H58R	SEC61G_uc003tqg.2_Missense_Mutation_p.H58R	NM_001012456	NP_001012474	P60059	SC61G_HUMAN	Sec61 gamma subunit	58	Helical; (Potential).				protein targeting to ER	endoplasmic reticulum membrane|integral to membrane	P-P-bond-hydrolysis-driven protein transmembrane transporter activity			lung(1)	1	Esophageal squamous(2;7.55e-08)|Breast(14;0.0654)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)			AATAGGAATATGGATCAATTT	0.323													12	113	---	---	---	---	PASS
LANCL2	55915	broad.mit.edu	37	7	55493093	55493093	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:55493093G>T	uc003tqp.2	+	7	1733	c.1155G>T	c.(1153-1155)CAG>CAT	p.Q385H		NM_018697	NP_061167	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2	385					negative regulation of transcription, DNA-dependent|positive regulation of abscisic acid mediated signaling pathway	cortical actin cytoskeleton|cytosol|nucleus|plasma membrane	ATP binding|catalytic activity|GTP binding|phosphatidylinositol-3-phosphate binding|phosphatidylinositol-4-phosphate binding|phosphatidylinositol-5-phosphate binding			ovary(1)|skin(1)	2	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GTCTCACGCAGGATAAGAAGT	0.537													10	327	---	---	---	---	PASS
SEPT14	346288	broad.mit.edu	37	7	55863741	55863741	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:55863741C>G	uc003tqz.2	-	10	1281	c.1164G>C	c.(1162-1164)GAG>GAC	p.E388D		NM_207366	NP_997249	Q6ZU15	SEP14_HUMAN	septin 14	388	Potential.				cell cycle|cell division	septin complex	GTP binding|protein binding				0	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GCTTCCTTATCTCCTCCTGTT	0.438													62	24	---	---	---	---	PASS
DBF4	10926	broad.mit.edu	37	7	87526637	87526637	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:87526637G>T	uc003ujf.1	+	8	1167	c.663G>T	c.(661-663)AAG>AAT	p.K221N	DBF4_uc003ujh.1_Translation_Start_Site|DBF4_uc003ujg.1_Translation_Start_Site|DBF4_uc011khf.1_Intron	NM_006716	NP_006707	Q9UBU7	DBF4A_HUMAN	activator of S phase kinase	221					cell cycle checkpoint|DNA replication|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle	nucleoplasm	enzyme activator activity|nucleic acid binding|protein binding|zinc ion binding			lung(2)	2	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				CTTTTGTAAAGGTGGAAGATA	0.313													9	245	---	---	---	---	PASS
AKAP9	10142	broad.mit.edu	37	7	91726596	91726596	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:91726596G>T	uc003ulg.2	+	41	10548	c.10323G>T	c.(10321-10323)CAG>CAT	p.Q3441H	AKAP9_uc003ulf.2_Missense_Mutation_p.Q3433H|AKAP9_uc003uli.2_Missense_Mutation_p.Q3064H|AKAP9_uc003ulj.2_Missense_Mutation_p.Q1211H|AKAP9_uc003ull.2_Missense_Mutation_p.Q337H	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	3445	Potential.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAATCATGCAGGAATTCCAGA	0.393			T	BRAF	papillary thyroid								7	104	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98508832	98508832	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:98508832G>T	uc003upp.2	+	17	2154	c.1945G>T	c.(1945-1947)GAA>TAA	p.E649*	TRRAP_uc011kis.1_Nonsense_Mutation_p.E649*|TRRAP_uc003upr.2_Nonsense_Mutation_p.E341*	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	649					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			AACGTTCAAAGAAATCTTCCA	0.403													10	106	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98588092	98588092	+	Missense_Mutation	SNP	G	C	C	rs77396759		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:98588092G>C	uc003upp.2	+	63	9827	c.9618G>C	c.(9616-9618)TTG>TTC	p.L3206F	TRRAP_uc011kis.1_Missense_Mutation_p.L3177F|TRRAP_uc003upr.2_Missense_Mutation_p.L2894F	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3206	FAT.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TGTGGCTTTTGAGTTTTGATG	0.473													14	222	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98601931	98601931	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:98601931G>T	uc003upp.2	+	67	10595	c.10386G>T	c.(10384-10386)GAG>GAT	p.E3462D	TRRAP_uc011kis.1_Missense_Mutation_p.E3433D|TRRAP_uc003upr.2_Missense_Mutation_p.E3168D	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	3462					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TCCTCATAGAGGAAAAGTGCC	0.428													15	588	---	---	---	---	PASS
EPHB4	2050	broad.mit.edu	37	7	100404041	100404041	+	Splice_Site	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:100404041C>T	uc003uwn.1	-	14	2975	c.2484_splice	c.e14+1	p.D828_splice	EPHB4_uc003uwm.1_Splice_Site_p.D735_splice|EPHB4_uc010lhj.1_Splice_Site_p.D828_splice	NM_004444	NP_004435	P54760	EPHB4_HUMAN	EPH receptor B4 precursor						cell proliferation|organ morphogenesis|regulation of angiogenesis	cell surface|integral to plasma membrane	ATP binding|ephrin receptor activity			lung(4)|stomach(3)|skin(3)|central_nervous_system(2)|ovary(2)|breast(1)	15	Lung NSC(181;0.041)|all_lung(186;0.0581)					GGGACACTTACGTCCTGATTG	0.542													23	25	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100679392	100679392	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:100679392C>A	uc003uxp.1	+	3	4748	c.4695C>A	c.(4693-4695)ACC>ACA	p.T1565T	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1565	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|24.					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)					GCATGCAAACCTCAACTTATA	0.488													8	189	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100683654	100683654	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:100683654G>A	uc003uxp.1	+	3	9010	c.8957G>A	c.(8956-8958)AGA>AAA	p.R2986K	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	2986	Extracellular (Potential).|Ser-rich.|48.|59 X approximate tandem repeats.					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)					GGCGAAAGAAGAACTCCATTA	0.517													101	107	---	---	---	---	PASS
IQUB	154865	broad.mit.edu	37	7	123104992	123104992	+	Silent	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:123104992T>C	uc003vkn.2	-	10	2230	c.1653A>G	c.(1651-1653)GGA>GGG	p.G551G	IQUB_uc003vko.2_Silent_p.G551G|IQUB_uc010lkt.2_RNA|IQUB_uc003vkp.1_Silent_p.G551G	NM_178827	NP_849149	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	551										ovary(3)|large_intestine(1)	4						GATGTTTGACTCCTCTCATCA	0.323													4	13	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131853105	131853105	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:131853105T>C	uc003vra.3	-	22	4473	c.4244A>G	c.(4243-4245)AAG>AGG	p.K1415R		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	1415	Cytoplasmic (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						CTCCAGGTTCTTGTCAATGAG	0.607													6	15	---	---	---	---	PASS
PLXNA4	91584	broad.mit.edu	37	7	131872233	131872233	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:131872233T>C	uc003vra.3	-	15	3219	c.2990A>G	c.(2989-2991)CAC>CGC	p.H997R		NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN	plexin A4 isoform 1	997	IPT/TIG 2.|Extracellular (Potential).					integral to membrane|intracellular|plasma membrane				ovary(1)	1						GAGTTACCTGTGGAAGAGACA	0.532													75	106	---	---	---	---	PASS
SLC13A4	26266	broad.mit.edu	37	7	135387595	135387595	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:135387595C>A	uc003vta.2	-	6	1317	c.628G>T	c.(628-630)GAG>TAG	p.E210*	SLC13A4_uc003vtb.2_Nonsense_Mutation_p.E211*	NM_012450	NP_036582	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate	210						integral to plasma membrane	sodium:sulfate symporter activity				0						GGCCATACCTCGTTGTGCATC	0.522													5	95	---	---	---	---	PASS
DENND2A	27147	broad.mit.edu	37	7	140301337	140301337	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:140301337G>T	uc010lnj.2	-	1	1006	c.861C>A	c.(859-861)ATC>ATA	p.I287I	DENND2A_uc011kre.1_RNA|DENND2A_uc010lnk.2_Silent_p.I287I|DENND2A_uc003vvw.2_Silent_p.I287I|DENND2A_uc003vvx.2_Silent_p.I287I	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	287										ovary(3)|breast(1)	4	Melanoma(164;0.00956)					TCCTGAAGCCGATGCCAGGCT	0.378													4	50	---	---	---	---	PASS
EZH2	2146	broad.mit.edu	37	7	148512011	148512011	+	Nonsense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:148512011G>C	uc003wfd.1	-	14	1818	c.1652C>G	c.(1651-1653)TCA>TGA	p.S551*	EZH2_uc011kug.1_Intron|EZH2_uc003wfb.1_Nonsense_Mutation_p.S556*|EZH2_uc003wfc.1_Nonsense_Mutation_p.S512*|EZH2_uc011kuh.1_Nonsense_Mutation_p.S542*	NM_004456	NP_004447	Q15910	EZH2_HUMAN	enhancer of zeste 2 isoform a	551	Cys-rich.				negative regulation of retinoic acid receptor signaling pathway|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex	DNA binding|histone-lysine N-methyltransferase activity|protein binding			haematopoietic_and_lymphoid_tissue(180)|skin(2)|large_intestine(1)	183	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			CTTACACTCTGAACTACATTG	0.373			Mis		DLBCL								8	11	---	---	---	---	PASS
ZNF425	155054	broad.mit.edu	37	7	148801651	148801651	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:148801651C>T	uc003wfj.2	-	4	1385	c.1312G>A	c.(1312-1314)GGG>AGG	p.G438R		NM_001001661	NP_001001661	Q6IV72	ZN425_HUMAN	zinc finger protein 425	438					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding			breast(2)|ovary(1)	3	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GGCCGCTTCCCAATGTGCTGC	0.607													28	26	---	---	---	---	PASS
SMARCD3	6604	broad.mit.edu	37	7	150939642	150939642	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr7:150939642C>A	uc003wjs.2	-	5	605	c.504G>T	c.(502-504)GCG>GCT	p.A168A	SMARCD3_uc003wjt.2_Silent_p.A155A|SMARCD3_uc003wju.2_Silent_p.A155A|SMARCD3_uc011kvh.1_Silent_p.A168A|SMARCD3_uc010lqa.1_Silent_p.A168A	NM_001003801	NP_001003801	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin	168					cellular lipid metabolic process|chromatin modification|nervous system development|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex	nuclear hormone receptor binding|protein binding|transcription coactivator activity|transcription factor binding			ovary(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CATCAGGCTTCGCAGGGTTAA	0.577													5	94	---	---	---	---	PASS
SGCZ	137868	broad.mit.edu	37	8	14412436	14412436	+	Splice_Site	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:14412436C>T	uc003wwq.2	-	2	700	c.40_splice	c.e2-1	p.M14_splice	SGCZ_uc010lss.2_Splice_Site_p.M1_splice	NM_139167	NP_631906	Q96LD1	SGCZ_HUMAN	sarcoglycan zeta						cytoskeleton organization	cytoplasm|cytoskeleton|integral to membrane|sarcolemma				ovary(2)|central_nervous_system(1)	3				all cancers(2;0.000643)|Colorectal(111;0.00674)|COAD - Colon adenocarcinoma(73;0.0193)|GBM - Glioblastoma multiforme(2;0.026)		CTCGTGTCATCTGaaaaagaa	0.289													6	12	---	---	---	---	PASS
XPO7	23039	broad.mit.edu	37	8	21848343	21848343	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:21848343G>T	uc003xaa.3	+	18	2056	c.1954G>T	c.(1954-1956)GGT>TGT	p.G652C	XPO7_uc010lti.2_Missense_Mutation_p.G661C|XPO7_uc010ltk.2_Missense_Mutation_p.G653C	NM_015024	NP_055839	Q9UIA9	XPO7_HUMAN	exportin 7 isoform b	652					mRNA transport|protein export from nucleus|transmembrane transport	cytoplasm|nuclear pore	nuclear export signal receptor activity|protein transporter activity			ovary(1)|kidney(1)|breast(1)|central_nervous_system(1)|pancreas(1)	5				Colorectal(74;0.0187)|COAD - Colon adenocarcinoma(73;0.0724)		TTCATTTTTGGGTATTAACAA	0.408													6	99	---	---	---	---	PASS
CHMP7	91782	broad.mit.edu	37	8	23114092	23114092	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:23114092C>A	uc003xdc.2	+	5	1425	c.777C>A	c.(775-777)TCC>TCA	p.S259S	CHMP7_uc011kzs.1_RNA|CHMP7_uc003xdd.2_Silent_p.S149S|CHMP7_uc003xde.2_Silent_p.S117S	NM_152272	NP_689485	Q8WUX9	CHMP7_HUMAN	CHMP family, member 7	259	Potential.				cellular membrane organization|late endosome to vacuole transport	cytosol|ESCRT III complex	protein transporter activity				0		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		AGTCCTTATCCCAGGAAGCAG	0.512													8	144	---	---	---	---	PASS
NRG1	3084	broad.mit.edu	37	8	32617716	32617716	+	Splice_Site	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:32617716A>T	uc003xiv.2	+	11	1579	c.1062_splice	c.e11-2	p.S354_splice	NRG1_uc011lbf.1_Splice_Site_p.S351_splice|NRG1_uc010lvo.2_Splice_Site_p.S351_splice|NRG1_uc003xiu.2_Splice_Site_p.S359_splice|NRG1_uc003xiw.2_Splice_Site_p.S351_splice|NRG1_uc003xit.2_Splice_Site_p.S354_splice|NRG1_uc010lvr.2_Splice_Site_p.S96_splice|NRG1_uc010lvs.2_Splice_Site_p.S96_splice|NRG1_uc010lvp.2_Splice_Site_p.S308_splice|NRG1_uc010lvq.2_Splice_Site_p.S291_splice|NRG1_uc011lbg.1_Splice_Site_p.S200_splice|NRG1_uc011lbh.1_Splice_Site_p.S197_splice|NRG1_uc003xja.2_Splice_Site_p.S165_splice	NM_013964	NP_039258	Q02297	NRG1_HUMAN	neuregulin 1 isoform HRG-alpha						activation of transmembrane receptor protein tyrosine kinase activity|anti-apoptosis|cardiac muscle cell differentiation|cell communication|cell proliferation|cellular protein complex disassembly|embryo development|mammary gland development|negative regulation of cardiac muscle cell apoptosis|negative regulation of secretion|negative regulation of transcription, DNA-dependent|nervous system development|neural crest cell development|Notch signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of cell adhesion|positive regulation of cell growth|positive regulation of striated muscle cell differentiation|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|transmembrane receptor protein tyrosine kinase signaling pathway|ventricular cardiac muscle cell differentiation|wound healing|wound healing	apical plasma membrane|extracellular region|extracellular space|integral to membrane|nucleus|plasma membrane	cytokine activity|ErbB-3 class receptor binding|growth factor activity|growth factor activity|protein binding|protein tyrosine kinase activator activity|receptor tyrosine kinase binding|transcription cofactor activity|transmembrane receptor protein tyrosine kinase activator activity				0		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TTTCCTCCGCAGCTGGAGCAA	0.433													14	24	---	---	---	---	PASS
FUT10	84750	broad.mit.edu	37	8	33246586	33246586	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:33246586C>A	uc003xje.2	-	4	1463	c.1107G>T	c.(1105-1107)AGG>AGT	p.R369S	FUT10_uc003xjc.2_Missense_Mutation_p.R376S|FUT10_uc003xjd.2_Missense_Mutation_p.R341S|FUT10_uc011lbi.1_Missense_Mutation_p.R419S|FUT10_uc003xjf.2_Missense_Mutation_p.R307S|FUT10_uc003xjg.2_Missense_Mutation_p.R341S|FUT10_uc003xjh.2_Missense_Mutation_p.R369S	NM_032664	NP_116053	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10	369	Lumenal (Potential).				embryo development|fertilization|hemopoiesis|L-fucose catabolic process|nervous system development|protein folding|protein glycosylation|protein targeting|wound healing	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity			ovary(1)|pancreas(1)	2				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		ATTTCCGTTCCCTGAGAGCTG	0.483													7	67	---	---	---	---	PASS
BAG4	9530	broad.mit.edu	37	8	38067632	38067632	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:38067632C>A	uc003xky.1	+	5	1277	c.995C>A	c.(994-996)TCA>TAA	p.S332*	BAG4_uc003xkz.1_Nonsense_Mutation_p.S296*	NM_004874	NP_004865	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	332					anti-apoptosis|apoptosis|protein folding	cytoplasm|nucleus	receptor signaling protein activity			ovary(1)	1	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				AATGATGATTCAGATCTTTTG	0.458													28	43	---	---	---	---	PASS
AGPAT6	137964	broad.mit.edu	37	8	41467233	41467233	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:41467233G>T	uc003xnz.2	+	4	1234	c.295G>T	c.(295-297)GGT>TGT	p.G99C		NM_178819	NP_848934	Q86UL3	GPAT4_HUMAN	lysophosphatidic acid acyltransferase zeta	99					acyl-CoA metabolic process|lactation|phosphatidylcholine biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane|membrane fraction	glycerol-3-phosphate O-acyltransferase activity				0	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			TCGTCGAAGTGGTAGTAGTAA	0.468													11	219	---	---	---	---	PASS
ANK1	286	broad.mit.edu	37	8	41615563	41615563	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:41615563G>T	uc003xok.2	-	2	204	c.120C>A	c.(118-120)ACC>ACA	p.T40T	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoi.2_Silent_p.T40T|ANK1_uc003xoj.2_Silent_p.T40T|ANK1_uc003xol.2_Silent_p.T40T|ANK1_uc003xom.2_Silent_p.T73T	NM_020476	NP_065209	P16157	ANK1_HUMAN	ankyrin 1 isoform 1	40	89 kDa domain.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(3)|lung(2)|breast(1)	9	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CCTGGTTACAGGTGTTAATAT	0.498													11	533	---	---	---	---	PASS
KIAA0146	23514	broad.mit.edu	37	8	48614343	48614343	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:48614343G>T	uc003xqd.2	+	13	1843	c.1834G>T	c.(1834-1836)GGA>TGA	p.G612*	KIAA0146_uc011ldb.1_Nonsense_Mutation_p.G612*|KIAA0146_uc010lxs.2_Nonsense_Mutation_p.G87*|KIAA0146_uc011ldc.1_Nonsense_Mutation_p.G542*|KIAA0146_uc011ldd.1_Nonsense_Mutation_p.G552*|KIAA0146_uc003xqe.2_Nonsense_Mutation_p.G87*|KIAA0146_uc003xqf.2_RNA|KIAA0146_uc011lde.1_Nonsense_Mutation_p.G301*|KIAA0146_uc010lxt.2_Nonsense_Mutation_p.G301*|KIAA0146_uc011ldf.1_Nonsense_Mutation_p.G117*|KIAA0146_uc011ldg.1_Nonsense_Mutation_p.G102*|KIAA0146_uc010lxv.1_Nonsense_Mutation_p.G106*	NM_001080394	NP_001073863	Q14159	K0146_HUMAN	hypothetical protein LOC23514	612											0		Lung NSC(58;0.175)				TCCAAATCTGGGACAAATTGA	0.403													8	187	---	---	---	---	PASS
RP1	6101	broad.mit.edu	37	8	55533754	55533754	+	Silent	SNP	C	A	A	rs142600056	byFrequency	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:55533754C>A	uc003xsd.1	+	2	376	c.228C>A	c.(226-228)CTC>CTA	p.L76L	RP1_uc011ldy.1_Silent_p.L76L	NM_006269	NP_006260	P56715	RP1_HUMAN	retinitis pigmentosa RP1 protein	76	Doublecortin 1.				axoneme assembly|intracellular signal transduction|photoreceptor cell maintenance|photoreceptor cell outer segment organization|phototransduction, visible light|retinal cone cell development|retinal rod cell development	cilium axoneme|cytoplasm|microtubule|microtubule associated complex|photoreceptor connecting cilium|photoreceptor inner segment|photoreceptor outer segment	microtubule binding			skin(7)|ovary(4)|pancreas(1)	12		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AGGTGCCCCTCCCTTTTGGAG	0.612													31	94	---	---	---	---	PASS
KCNB2	9312	broad.mit.edu	37	8	73848373	73848373	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:73848373C>G	uc003xzb.2	+	3	1371	c.783C>G	c.(781-783)TTC>TTG	p.F261L		NM_004770	NP_004761	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related	261	Cytoplasmic (Potential).				regulation of smooth muscle contraction	voltage-gated potassium channel complex	delayed rectifier potassium channel activity|protein binding			skin(3)|large_intestine(1)|pancreas(1)|ovary(1)|central_nervous_system(1)	7	Breast(64;0.137)		Epithelial(68;0.105)			AATGGAAGTTCTTCAAAGGCC	0.453													6	96	---	---	---	---	PASS
LRRCC1	85444	broad.mit.edu	37	8	86050478	86050478	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:86050478G>T	uc003ycw.2	+	16	2856	c.2702G>T	c.(2701-2703)AGT>ATT	p.S901I	LRRCC1_uc010maa.1_3'UTR|LRRCC1_uc003ycx.2_Missense_Mutation_p.S808I|LRRCC1_uc003ycy.2_Missense_Mutation_p.S881I	NM_033402	NP_208325	Q9C099	LRCC1_HUMAN	sodium channel associated protein 2 isoform a	901					cell division|mitosis	centriole|nucleus					0						AAAGCTTACAGGTATTATATA	0.289													6	27	---	---	---	---	PASS
RPL30	6156	broad.mit.edu	37	8	99057209	99057209	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:99057209C>A	uc003yif.2	-	3	199	c.129G>T	c.(127-129)GCG>GCT	p.A43A	RPL30_uc010mbk.1_Silent_p.A43A|SNORA72_uc003yig.1_5'Flank	NM_000989	NP_000980	P62888	RL30_HUMAN	ribosomal protein L30	43					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.192)			TGACCAATTTCGCTTTGCCTT	0.488													7	303	---	---	---	---	PASS
DCAF13	25879	broad.mit.edu	37	8	104427350	104427350	+	Silent	SNP	G	C	C	rs140179211	byFrequency	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:104427350G>C	uc003yln.2	+	1	409	c.132G>C	c.(130-132)ACG>ACC	p.T44T	SLC25A32_uc003yll.2_5'UTR|SLC25A32_uc011lhr.1_5'UTR|DCAF13_uc003ylm.1_5'UTR|DCAF13_uc003ylo.2_5'UTR	NM_015420	NP_056235	Q9NV06	DCA13_HUMAN	WD repeats and SOF1 domain containing	Error:Variant_position_missing_in_Q9NV06_after_alignment					rRNA processing	CUL4 RING ubiquitin ligase complex|nucleolus|ribonucleoprotein complex				breast(1)	1						GGGCAAGAACGGGGCACAGAC	0.657													23	34	---	---	---	---	PASS
KCNV1	27012	broad.mit.edu	37	8	110984530	110984530	+	Silent	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:110984530C>G	uc003ynr.3	-	2	1290	c.948G>C	c.(946-948)CTG>CTC	p.L316L	KCNV1_uc010mcw.2_Silent_p.L316L	NM_014379	NP_055194	Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	316	Helical; Voltage-sensor; Name=Segment S4; (Potential).					voltage-gated potassium channel complex	ion channel inhibitor activity|potassium channel regulator activity|voltage-gated potassium channel activity			lung(1)|kidney(1)	2	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			GAGCCCTGAGCAGCCTCAACA	0.507													8	40	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113249469	113249469	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:113249469C>A	uc003ynu.2	-	67	10736	c.10577G>T	c.(10576-10578)GGG>GTG	p.G3526V	CSMD3_uc003yns.2_Missense_Mutation_p.G2728V|CSMD3_uc003ynt.2_Missense_Mutation_p.G3486V|CSMD3_uc011lhx.1_Missense_Mutation_p.G3357V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3526	Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						GTTAACTCTCCCAGTGGAAGC	0.378										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			9	34	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113301647	113301647	+	Nonsense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:113301647G>C	uc003ynu.2	-	57	9254	c.9095C>G	c.(9094-9096)TCA>TGA	p.S3032*	CSMD3_uc003yns.2_Nonsense_Mutation_p.S2234*|CSMD3_uc003ynt.2_Nonsense_Mutation_p.S2992*|CSMD3_uc011lhx.1_Nonsense_Mutation_p.S2863*	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	3032	Sushi 21.|Extracellular (Potential).					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						GCAGGTTCTTGATGACTGGCC	0.443										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			12	15	---	---	---	---	PASS
CSMD3	114788	broad.mit.edu	37	8	113332130	113332130	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:113332130C>A	uc003ynu.2	-	46	7405	c.7246G>T	c.(7246-7248)GGT>TGT	p.G2416C	CSMD3_uc003yns.2_Missense_Mutation_p.G1618C|CSMD3_uc003ynt.2_Missense_Mutation_p.G2376C|CSMD3_uc011lhx.1_Missense_Mutation_p.G2312C|CSMD3_uc003ynw.1_Missense_Mutation_p.G127C	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2416	Extracellular (Potential).|Sushi 13.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ACAGCTTTACCTATTTCAAAT	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			8	30	---	---	---	---	PASS
TRPS1	7227	broad.mit.edu	37	8	116631517	116631517	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:116631517C>T	uc003ynz.2	-	2	1228	c.769G>A	c.(769-771)GAT>AAT	p.D257N	TRPS1_uc011lhy.1_Missense_Mutation_p.D261N|TRPS1_uc003yny.2_Missense_Mutation_p.D270N|TRPS1_uc010mcy.2_Missense_Mutation_p.D257N	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	257					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			AGCTCAGCATCTTGCCTGGTG	0.468									Langer-Giedion_syndrome				13	33	---	---	---	---	PASS
SLC45A4	57210	broad.mit.edu	37	8	142228416	142228416	+	Silent	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr8:142228416C>G	uc003ywd.1	-	4	1478	c.1170G>C	c.(1168-1170)CGG>CGC	p.R390R	SLC45A4_uc003ywc.1_Silent_p.R390R|SLC45A4_uc010meq.1_Silent_p.R388R	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	441					transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			CGTTGGCGCGCCGGTAGCGGT	0.687													18	18	---	---	---	---	PASS
PTPRD	5789	broad.mit.edu	37	9	8436665	8436665	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:8436665G>T	uc003zkk.2	-	34	4724	c.4013C>A	c.(4012-4014)CCC>CAC	p.P1338H	PTPRD_uc003zkp.2_Missense_Mutation_p.P932H|PTPRD_uc003zkq.2_Missense_Mutation_p.P931H|PTPRD_uc003zkr.2_Missense_Mutation_p.P922H|PTPRD_uc003zks.2_Missense_Mutation_p.P931H|PTPRD_uc003zkl.2_Missense_Mutation_p.P1329H|PTPRD_uc003zkm.2_Missense_Mutation_p.P1325H|PTPRD_uc003zkn.2_Missense_Mutation_p.P927H|PTPRD_uc003zko.2_Missense_Mutation_p.P928H	NM_002839	NP_002830	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1338	Cytoplasmic (Potential).				transmembrane receptor protein tyrosine phosphatase signaling pathway	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(14)|large_intestine(3)|ovary(2)|breast(2)|urinary_tract(1)	22		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TTCCAAGATGGGTATTGGAGG	0.338										TSP Lung(15;0.13)			4	12	---	---	---	---	PASS
TYRP1	7306	broad.mit.edu	37	9	12695714	12695714	+	Silent	SNP	A	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:12695714A>C	uc003zkv.3	+	3	763	c.585A>C	c.(583-585)TCA>TCC	p.S195S		NM_000550	NP_000541	P17643	TYRP1_HUMAN	tyrosinase-related protein 1 precursor	195	Lumenal, melanosome (Potential).				melanin biosynthetic process	clathrin-coated endocytic vesicle membrane|endosome membrane|integral to membrane|melanosome membrane	copper ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen|protein heterodimerization activity|protein homodimerization activity			lung(1)	1		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		ACTATTACTCAGTCAAAAAGA	0.453									Oculocutaneous_Albinism				10	12	---	---	---	---	PASS
ELAVL2	1993	broad.mit.edu	37	9	23701421	23701421	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:23701421G>A	uc003zpu.2	-	5	944	c.669C>T	c.(667-669)AAC>AAT	p.N223N	ELAVL2_uc003zps.2_Silent_p.N223N|ELAVL2_uc003zpt.2_Silent_p.N223N|ELAVL2_uc003zpv.2_Silent_p.N223N|ELAVL2_uc003zpw.2_Silent_p.N223N	NM_004432	NP_004423	Q12926	ELAV2_HUMAN	ELAV (embryonic lethal, abnormal vision,	223					regulation of transcription, DNA-dependent		mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(2)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(1;2.18e-156)|Lung(42;2.15e-28)|LUSC - Lung squamous cell carcinoma(38;1.02e-19)		GATACCTTCTGTTTGGAGACT	0.488													39	50	---	---	---	---	PASS
HINT2	84681	broad.mit.edu	37	9	35813519	35813519	+	Nonsense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:35813519G>A	uc003zyh.2	-	3	316	c.250C>T	c.(250-252)CAG>TAG	p.Q84*	SPAG8_uc003zye.2_5'Flank|SPAG8_uc003zyf.2_5'Flank|SPAG8_uc003zyg.2_5'Flank|HINT2_uc003zyi.2_Nonsense_Mutation_p.Q80*	NM_032593	NP_115982	Q9BX68	HINT2_HUMAN	PKCI-1-related HIT protein precursor	84	HIT.				apoptosis|steroid biosynthetic process	mitochondrion	hydrolase activity				0	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)			ACAGGAGCCTGAGGGGCCACA	0.542											OREG0019179	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	25	22	---	---	---	---	PASS
ECM2	1842	broad.mit.edu	37	9	95256390	95256390	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:95256390G>A	uc004asf.3	-	10	2057	c.1907C>T	c.(1906-1908)TCA>TTA	p.S636L	CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron	NM_001393	NP_001384	O94769	ECM2_HUMAN	extracellular matrix protein 2 precursor	Error:Variant_position_missing_in_O94769_after_alignment					cell-matrix adhesion		integrin binding			ovary(1)|skin(1)	2						GGCCACATCTGATCTGTTTGT	0.423													26	60	---	---	---	---	PASS
ZNF484	83744	broad.mit.edu	37	9	95609565	95609565	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:95609565C>A	uc004asu.1	-	5	1653	c.1504G>T	c.(1504-1506)GGT>TGT	p.G502C	ANKRD19_uc004asr.3_Intron|ZNF484_uc011lub.1_Missense_Mutation_p.G504C|ZNF484_uc010mrb.1_Missense_Mutation_p.G466C|ZNF484_uc004asv.1_Missense_Mutation_p.G466C	NM_031486	NP_113674	Q5JVG2	ZN484_HUMAN	zinc finger protein 484 isoform a	502	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						AAGGCCTTACCACACACAGTA	0.378													4	29	---	---	---	---	PASS
KIAA1529	57653	broad.mit.edu	37	9	100124649	100124649	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:100124649C>G	uc011lut.1	+	40	5150	c.4377C>G	c.(4375-4377)TTC>TTG	p.F1459L	KIAA1529_uc004axe.1_Missense_Mutation_p.F1254L|KIAA1529_uc004axg.1_Missense_Mutation_p.F1320L|KIAA1529_uc004axh.1_RNA|KIAA1529_uc011luw.1_Missense_Mutation_p.F439L	NM_020893	NP_065944			hypothetical protein LOC57653											ovary(4)|large_intestine(2)|skin(1)	7		Acute lymphoblastic leukemia(62;0.154)				CCAAAGGCTTCAAGCGACATC	0.617													63	47	---	---	---	---	PASS
PPP3R2	5535	broad.mit.edu	37	9	104357046	104357046	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:104357046G>A	uc004bbr.2	-	1	238	c.167C>T	c.(166-168)CCG>CTG	p.P56L	GRIN3A_uc004bbp.1_Intron|GRIN3A_uc004bbq.1_Intron|PPP3R2_uc010mtf.1_Intron	NM_147180	NP_671709	Q96LZ3	CANB2_HUMAN	protein phosphatase 3 regulatory subunit B, beta	53	EF-hand 2.						calcium ion binding			ovary(1)|skin(1)	2		Acute lymphoblastic leukemia(62;0.0527)			Cyclosporine(DB00091)	CCGCACCAACGGGTTGTGGCG	0.562													38	28	---	---	---	---	PASS
TNC	3371	broad.mit.edu	37	9	117853072	117853072	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:117853072C>A	uc004bjj.3	-	2	588	c.226G>T	c.(226-228)GAC>TAC	p.D76Y	TNC_uc010mvf.2_Missense_Mutation_p.D76Y	NM_002160	NP_002151	P24821	TENA_HUMAN	tenascin C precursor	76					cell adhesion|response to wounding|signal transduction	extracellular space	receptor binding|syndecan binding			central_nervous_system(4)|upper_aerodigestive_tract(1)|ovary(1)|skin(1)	7						GGTGCCAGGTCTTTCTCCCCA	0.547													80	56	---	---	---	---	PASS
BAT2L1	84726	broad.mit.edu	37	9	134305587	134305587	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:134305587C>T	uc004can.3	+	1	111	c.56C>T	c.(55-57)TCG>TTG	p.S19L	BAT2L1_uc004cam.1_Missense_Mutation_p.S19L	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	19							protein binding				0						AGCAAGTACTCGACTCTCAGC	0.458													22	20	---	---	---	---	PASS
POMT1	10585	broad.mit.edu	37	9	134393924	134393924	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:134393924G>T	uc004cav.2	+	14	1633	c.1431G>T	c.(1429-1431)AAG>AAT	p.K477N	POMT1_uc004cax.2_Missense_Mutation_p.K455N|POMT1_uc011mcj.1_Missense_Mutation_p.K233N|POMT1_uc004cau.2_Missense_Mutation_p.K455N|POMT1_uc004caw.2_Missense_Mutation_p.K401N|POMT1_uc011mck.1_Missense_Mutation_p.K338N|POMT1_uc011mcl.1_Missense_Mutation_p.K303N|POMT1_uc011mcm.1_Missense_Mutation_p.K425N|POMT1_uc011mcn.1_Missense_Mutation_p.K180N	NM_007171	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1 isoform a	477	MIR 3.				multicellular organismal development|protein O-linked glycosylation	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-mannose-protein mannosyltransferase activity|metal ion binding			upper_aerodigestive_tract(1)	1		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		CTGTCTTAAAGGTAAGGACAC	0.552													9	194	---	---	---	---	PASS
SETX	23064	broad.mit.edu	37	9	135204730	135204730	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:135204730G>A	uc004cbk.2	-	10	2438	c.2255C>T	c.(2254-2256)ACT>ATT	p.T752I	SETX_uc004cbj.2_Missense_Mutation_p.T371I|SETX_uc010mzt.2_Missense_Mutation_p.T371I	NM_015046	NP_055861	Q7Z333	SETX_HUMAN	senataxin	752					cell death|double-strand break repair|RNA processing	cytoplasm|nucleolus|nucleoplasm	ATP binding|DNA helicase activity			ovary(2)|skin(1)	3		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CAAAGCATCAGTGCTAGAATC	0.373													36	21	---	---	---	---	PASS
DIP2C	22982	broad.mit.edu	37	10	372998	372998	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:372998C>T	uc001ifp.2	-	31	3962	c.3872G>A	c.(3871-3873)CGG>CAG	p.R1291Q		NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1291						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		GCTGACGGCCCGCGGGTGAAG	0.607													10	17	---	---	---	---	PASS
ITIH5	80760	broad.mit.edu	37	10	7608015	7608015	+	Silent	SNP	G	T	T	rs149503594		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:7608015G>T	uc001ijq.2	-	13	2584	c.2505C>A	c.(2503-2505)TCC>TCA	p.S835S	ITIH5_uc001ijp.2_Silent_p.S621S	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	835					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4						GGCAGTTGCTGGAAAGGCCCT	0.557													23	30	---	---	---	---	PASS
ITIH5	80760	broad.mit.edu	37	10	7679442	7679442	+	Splice_Site	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:7679442C>G	uc001ijq.2	-	5	481	c.402_splice	c.e5-1	p.G134_splice	ITIH5_uc001ijr.1_Splice_Site_p.G134_splice	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain						hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4						CCCCTTCTCTCTGTCAGGAAA	0.547													19	22	---	---	---	---	PASS
TAF3	83860	broad.mit.edu	37	10	8007024	8007024	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:8007024C>A	uc010qbd.1	+	3	1551	c.1551C>A	c.(1549-1551)TCC>TCA	p.S517S		NM_031923	NP_114129	Q5VWG9	TAF3_HUMAN	RNA polymerase II transcription factor TAFII140	517	Lys-rich.				maintenance of protein location in nucleus|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	transcription factor TFIID complex	protein binding|zinc ion binding			ovary(1)	1						AGCTGCCTTCCTCCGTGGAGG	0.338													5	35	---	---	---	---	PASS
SPAG6	9576	broad.mit.edu	37	10	22675703	22675703	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:22675703G>C	uc001iri.2	+	5	635	c.493G>C	c.(493-495)GAT>CAT	p.D165H	SPAG6_uc001irj.2_Missense_Mutation_p.D165H|SPAG6_uc010qct.1_Missense_Mutation_p.D135H|SPAG6_uc009xkh.2_Missense_Mutation_p.D143H	NM_012443	NP_036575	O75602	SPAG6_HUMAN	sperm associated antigen 6 isoform 1	165	ARM 4.				cell projection organization|spermatid development	axoneme|cilium|cytoplasm|flagellum|microtubule	binding			breast(1)	1						AGCTGTGGTGGATGCAGGAGC	0.458													6	6	---	---	---	---	PASS
NRP1	8829	broad.mit.edu	37	10	33552639	33552639	+	Nonsense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:33552639G>C	uc001iwx.3	-	4	1116	c.593C>G	c.(592-594)TCA>TGA	p.S198*	NRP1_uc001iwv.3_Nonsense_Mutation_p.S198*|NRP1_uc009xlz.2_Nonsense_Mutation_p.S198*|NRP1_uc001iww.3_Nonsense_Mutation_p.S17*|NRP1_uc001iwy.3_Nonsense_Mutation_p.S198*|NRP1_uc001iwz.2_Nonsense_Mutation_p.S198*|NRP1_uc001ixa.2_Nonsense_Mutation_p.S198*|NRP1_uc001ixb.1_Nonsense_Mutation_p.S198*|NRP1_uc001ixc.1_Nonsense_Mutation_p.S198*	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a	198	Extracellular (Potential).|CUB 2.				axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)|skin(1)	4					Palifermin(DB00039)|Pegaptanib(DB04895)	TGGAGGATTTGAGTCAGGCTC	0.463													5	32	---	---	---	---	PASS
AGAP7	653268	broad.mit.edu	37	10	51465352	51465352	+	Silent	SNP	C	A	A	rs4043643		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:51465352C>A	uc001jio.2	-	7	1230	c.1104G>T	c.(1102-1104)CCG>CCT	p.P368P	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron	NM_001077685	NP_001071153	Q5VUJ5	AGAP7_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH	368	PH.				regulation of ARF GTPase activity		ARF GTPase activator activity|zinc ion binding				0						GAGAGGGGGGCGGGTTGAGCT	0.512													83	117	---	---	---	---	PASS
TMEM26	219623	broad.mit.edu	37	10	63212763	63212763	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:63212763C>A	uc001jlo.2	-	1	446	c.77G>T	c.(76-78)CGA>CTA	p.R26L	TMEM26_uc010qij.1_RNA|TMEM26_uc001jlq.2_RNA|uc001jlr.2_RNA	NM_178505	NP_848600	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	26						integral to membrane					0	Prostate(12;0.0112)					CTCGGTCACTCGCCAGACCCC	0.632													5	71	---	---	---	---	PASS
CH25H	9023	broad.mit.edu	37	10	90966727	90966727	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:90966727G>A	uc001kfz.2	-	1	345	c.323C>T	c.(322-324)GCC>GTC	p.A108V		NM_003956	NP_003947	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	108					bile acid biosynthetic process|fatty acid biosynthetic process|sterol biosynthetic process	cytosol|endoplasmic reticulum membrane|integral to membrane	cholesterol 25-hydroxylase activity|iron ion binding				0		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		CGGGCTGCGGGCCCAATGCAG	0.627													15	6	---	---	---	---	PASS
CPEB3	22849	broad.mit.edu	37	10	93841226	93841226	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:93841226C>A	uc001khw.1	-	9	1893	c.1720G>T	c.(1720-1722)GGT>TGT	p.G574C	CPEB3_uc001khu.1_Missense_Mutation_p.G583C|CPEB3_uc001khv.1_Missense_Mutation_p.G560C|CPEB3_uc010qnn.1_Missense_Mutation_p.G560C	NM_014912	NP_055727	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding	574	RRM 2.						nucleotide binding|RNA binding				0		Colorectal(252;0.0869)				CAGACACCACCATACAAACGG	0.473													4	45	---	---	---	---	PASS
TMEM20	159371	broad.mit.edu	37	10	95661025	95661025	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:95661025G>T	uc001kjg.1	+	3	937	c.876G>T	c.(874-876)GGG>GGT	p.G292G	TMEM20_uc001kji.2_Intron|TMEM20_uc001kjf.1_Silent_p.G291G|TMEM20_uc001kjh.2_Intron|TMEM20_uc010qnw.1_Silent_p.G275G|TMEM20_uc001kjj.2_Intron	NM_001134658	NP_001128130	Q2M3R5	TMM20_HUMAN	transmembrane protein 20 isoform 1	292	DUF6 2.|Helical; (Potential).					integral to membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;3.46e-05)|Renal(717;0.018)|Ovarian(717;0.0228)|all_hematologic(284;0.189)		STAD - Stomach adenocarcinoma(243;0.00345)		TATTCATTGGGCTCTTTGGTT	0.428													12	12	---	---	---	---	PASS
SORBS1	10580	broad.mit.edu	37	10	97170424	97170424	+	Silent	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:97170424G>C	uc001kkp.2	-	8	966	c.921C>G	c.(919-921)GTC>GTG	p.V307V	SORBS1_uc001kkl.2_5'UTR|SORBS1_uc001kkn.2_Silent_p.V140V|SORBS1_uc001kkm.2_Silent_p.V163V|SORBS1_uc001kko.2_Silent_p.V307V|SORBS1_uc001kkq.2_Silent_p.V238V|SORBS1_uc001kkr.2_Silent_p.V143V|SORBS1_uc001kks.2_Silent_p.V143V|SORBS1_uc001kkt.2_RNA|SORBS1_uc001kku.2_Silent_p.V184V|SORBS1_uc001kkv.2_Silent_p.V275V|SORBS1_uc001kkw.2_Silent_p.V307V|SORBS1_uc010qoe.1_Silent_p.V152V|SORBS1_uc010qof.1_Silent_p.V505V	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	307					focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TAGTAGGATTGACAATCGTTG	0.463													12	26	---	---	---	---	PASS
SORBS1	10580	broad.mit.edu	37	10	97174525	97174525	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:97174525G>C	uc001kkp.2	-	7	581	c.536C>G	c.(535-537)CCT>CGT	p.P179R	SORBS1_uc001kkl.2_5'UTR|SORBS1_uc001kkn.2_Intron|SORBS1_uc001kkm.2_Intron|SORBS1_uc001kko.2_Missense_Mutation_p.P179R|SORBS1_uc001kkq.2_Intron|SORBS1_uc001kkr.2_Intron|SORBS1_uc001kks.2_Intron|SORBS1_uc001kkt.2_RNA|SORBS1_uc001kku.2_Intron|SORBS1_uc001kkv.2_Missense_Mutation_p.P147R|SORBS1_uc001kkw.2_Missense_Mutation_p.P179R|SORBS1_uc010qoe.1_Intron|SORBS1_uc010qof.1_Missense_Mutation_p.P377R|SORBS1_uc001kkx.1_Missense_Mutation_p.P147R	NM_001034954	NP_001030126	Q9BX66	SRBS1_HUMAN	sorbin and SH3 domain containing 1 isoform 3	179					focal adhesion assembly|glucose transport|insulin receptor signaling pathway|muscle contraction|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|stress fiber assembly	centrosome|cytosol|focal adhesion|membrane raft|nucleus|stress fiber|zonula adherens	actin binding|insulin receptor binding|SH3/SH2 adaptor activity			breast(1)	1		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		AGGTGTTGGAGGTCTGGCAGT	0.582													40	17	---	---	---	---	PASS
PDCD11	22984	broad.mit.edu	37	10	105166544	105166544	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:105166544G>A	uc001kwy.1	+	7	954	c.867G>A	c.(865-867)CAG>CAA	p.Q289Q		NM_014976	NP_055791	Q14690	RRP5_HUMAN	programmed cell death 11	289	S1 motif 3.				mRNA processing|rRNA processing	nucleolus	RNA binding|transcription factor binding			ovary(2)|breast(2)|skin(2)|central_nervous_system(1)	7		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		CTCAGGTACAGAAGGTAAGCT	0.323													6	44	---	---	---	---	PASS
ITPRIP	85450	broad.mit.edu	37	10	106074526	106074526	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:106074526G>A	uc001kye.2	-	2	1357	c.1284C>T	c.(1282-1284)CTC>CTT	p.L428L	ITPRIP_uc001kyf.2_Silent_p.L428L|ITPRIP_uc001kyg.2_Silent_p.L428L	NM_033397	NP_203755	Q8IWB1	IPRI_HUMAN	inositol 1,4,5-triphosphate receptor interacting	428						plasma membrane					0						GGTAGCTGCTGAGCCCGCTGG	0.667													9	24	---	---	---	---	PASS
NRAP	4892	broad.mit.edu	37	10	115381824	115381824	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:115381824A>T	uc001laj.2	-	24	2737	c.2573T>A	c.(2572-2574)CTG>CAG	p.L858Q	NRAP_uc009xyb.2_Intron|NRAP_uc001lak.2_Missense_Mutation_p.L823Q|NRAP_uc001lal.3_Missense_Mutation_p.L858Q	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	858	Nebulin 21.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)|upper_aerodigestive_tract(1)	10		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTTGTACTCCAGCTCACTCTG	0.517													24	19	---	---	---	---	PASS
DHX32	55760	broad.mit.edu	37	10	127555576	127555576	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:127555576G>T	uc001ljf.1	-	2	950	c.459C>A	c.(457-459)ACC>ACA	p.T153T	DHX32_uc001ljg.1_Silent_p.T153T	NM_018180	NP_060650	Q7L7V1	DHX32_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32	153	Helicase ATP-binding.					mitochondrion|nucleus	ATP binding|helicase activity			breast(2)|ovary(1)|lung(1)	4		all_lung(145;0.00751)|Lung NSC(174;0.0115)|Colorectal(57;0.0846)|all_neural(114;0.0936)				TTGTTTCGTTGGTACAGCAGT	0.502													6	108	---	---	---	---	PASS
LRRC27	80313	broad.mit.edu	37	10	134175013	134175013	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:134175013C>A	uc010quw.1	+	9	1418	c.1223C>A	c.(1222-1224)CCA>CAA	p.P408Q	LRRC27_uc001llg.2_RNA|LRRC27_uc001lli.2_Missense_Mutation_p.P408Q|LRRC27_uc001llj.2_Missense_Mutation_p.P346Q|LRRC27_uc001llk.3_Missense_Mutation_p.P281Q	NM_030626	NP_085129	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27 isoform a	408										ovary(1)	1		all_cancers(35;6.28e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;9.12e-05)|Epithelial(32;0.000116)|all cancers(32;0.000145)|BRCA - Breast invasive adenocarcinoma(275;0.218)		AGGAAAGTACCACTGAATCCG	0.433													9	227	---	---	---	---	PASS
OR51G1	79324	broad.mit.edu	37	11	4945326	4945326	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:4945326T>C	uc010qyr.1	-	1	244	c.244A>G	c.(244-246)ACT>GCT	p.T82A		NM_001005237	NP_001005237	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCCAGCACAGTGGGCAGTGTG	0.493													11	13	---	---	---	---	PASS
DCHS1	8642	broad.mit.edu	37	11	6648290	6648290	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:6648290C>A	uc001mem.1	-	14	6390	c.5980G>T	c.(5980-5982)GGT>TGT	p.G1994C		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	1994	Cadherin 19.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCATTGGCACCAGCATCACGA	0.622													5	37	---	---	---	---	PASS
NLRP10	338322	broad.mit.edu	37	11	7982058	7982058	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:7982058C>G	uc001mfv.1	-	2	1118	c.1101G>C	c.(1099-1101)CAG>CAC	p.Q367H		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	367	NACHT.						ATP binding			lung(4)|ovary(2)|pancreas(1)|kidney(1)|skin(1)	9				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CTCTCTCCATCTGCCCCTGCA	0.522													19	46	---	---	---	---	PASS
MICAL2	9645	broad.mit.edu	37	11	12280014	12280014	+	Splice_Site	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:12280014G>T	uc001mjz.2	+	25	3431	c.3143_splice	c.e25-1	p.G1048_splice	MICAL2_uc010rch.1_Splice_Site_p.G858_splice|MICAL2_uc001mka.2_Splice_Site_p.G1048_splice|MICAL2_uc010rci.1_Splice_Site_p.G1027_splice|MICAL2_uc001mkb.2_Splice_Site_p.G822_splice|MICAL2_uc001mkc.2_Splice_Site_p.G801_splice|MICAL2_uc001mkd.2_Splice_Site_p.G630_splice|MICAL2_uc010rcj.1_Splice_Site_p.G260_splice|MICAL2_uc001mkf.2_Splice_Site	NM_014632	NP_055447	O94851	MICA2_HUMAN	microtubule associated monoxygenase, calponin							cytoplasm|cytoskeleton	monooxygenase activity|zinc ion binding			upper_aerodigestive_tract(2)	2				Epithelial(150;0.00552)		TCTTTTTACAGGCAAATTTTA	0.408													6	107	---	---	---	---	PASS
C11orf58	10944	broad.mit.edu	37	11	16766187	16766187	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:16766187G>A	uc001mmk.2	+	2	281	c.103G>A	c.(103-105)GAA>AAA	p.E35K	C11orf58_uc010rct.1_5'UTR	NM_014267	NP_055082	O00193	SMAP_HUMAN	small acidic protein isoform a	35											0						CTTGGGTAATGAAGAGAGAAA	0.333													10	16	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	11	31099473	31099473	+	Splice_Site	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:31099473C>T	uc009yjk.1	-	6	651	c.582_splice	c.e6-1	p.R194_splice	uc009yjl.1_Splice_Site_p.R122_splice|DCDC1_uc001msu.1_Splice_Site_p.R365_splice					RecName: Full=Doublecortin domain-containing protein 5;																		TCCACTATGTCTGTAACGAAA	0.368													6	6	---	---	---	---	PASS
TRIM48	79097	broad.mit.edu	37	11	55032762	55032762	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:55032762C>A	uc010rid.1	+	2	517	c.431C>A	c.(430-432)CCC>CAC	p.P144H		NM_024114	NP_077019	Q8IWZ4	TRI48_HUMAN	tripartite motif-containing 48	128	B box-type.					intracellular	zinc ion binding				0						AGACACTGTCCCGCTGAGTGG	0.493													11	24	---	---	---	---	PASS
OR5D13	390142	broad.mit.edu	37	11	55541450	55541450	+	Silent	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:55541450T>C	uc010ril.1	+	1	537	c.537T>C	c.(535-537)TTT>TTC	p.F179F		NM_001001967	NP_001001967	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D,	179	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)|skin(1)	3		all_epithelial(135;0.196)				TAAATAATTTTATCTGTGACC	0.418													21	27	---	---	---	---	PASS
OR5R1	219479	broad.mit.edu	37	11	56184925	56184925	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:56184925G>C	uc010rji.1	-	1	784	c.784C>G	c.(784-786)CCC>GCC	p.P262A		NM_001004744	NP_001004744	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R,	262	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)					TTTGATTTGGGCTGTAGGTAC	0.448													23	19	---	---	---	---	PASS
OR5M1	390168	broad.mit.edu	37	11	56380709	56380709	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:56380709C>A	uc001nja.1	-	1	270	c.270G>T	c.(268-270)AAG>AAT	p.K90N		NM_001004740	NP_001004740	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M,	90	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1						AGGAGATGGTCTTCTGTTCTG	0.448													20	55	---	---	---	---	PASS
OR5AR1	219493	broad.mit.edu	37	11	56431846	56431846	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:56431846C>T	uc010rjm.1	+	1	685	c.685C>T	c.(685-687)CGT>TGT	p.R229C		NM_001004730	NP_001004730	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR,	229	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CATCAGAATGCGTTCAGCTGA	0.478													21	24	---	---	---	---	PASS
MS4A2	2206	broad.mit.edu	37	11	59857872	59857872	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:59857872G>C	uc001nop.2	+	3	352	c.250G>C	c.(250-252)GAT>CAT	p.D84H	MS4A2_uc009ymu.2_Missense_Mutation_p.D84H	NM_000139	NP_000130	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member	84	Extracellular (Potential).				cell proliferation|humoral immune response	integral to plasma membrane	calcium channel activity			ovary(1)	1		all_epithelial(135;0.245)			Omalizumab(DB00043)	CTCTGTACTTGATATTTCACA	0.323													30	38	---	---	---	---	PASS
MS4A13	503497	broad.mit.edu	37	11	60310041	60310041	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:60310041C>T	uc001nps.2	+	7	775	c.452C>T	c.(451-453)ACT>ATT	p.T151I	MS4A13_uc009ync.2_Missense_Mutation_p.T111I|MS4A13_uc009ynd.2_Missense_Mutation_p.T92I	NM_001012417	NP_001012417	Q5J8X5	M4A13_HUMAN	membrane-spanning 4-domains, subfamily A, member	151						integral to membrane					0						GCTGAGAGCACTCCTTAAAAA	0.358													3	11	---	---	---	---	PASS
CCDC88B	283234	broad.mit.edu	37	11	64124516	64124516	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:64124516G>T	uc001nzy.2	+	27	4425	c.4381G>T	c.(4381-4383)GAG>TAG	p.E1461*	CCDC88B_uc001oaa.2_Silent_p.L565L|CCDC88B_uc001oab.1_3'UTR|CCDC88B_uc001oac.2_Silent_p.L76L|RPS6KA4_uc001oad.2_5'Flank|RPS6KA4_uc001oae.2_5'Flank|RPS6KA4_uc010rnl.1_5'Flank|RPS6KA4_uc001oaf.2_5'Flank|RPS6KA4_uc009ypp.2_5'Flank	NM_032251	NP_115627	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88	1461					microtubule cytoskeleton organization	cytoplasm	microtubule binding			ovary(3)|skin(1)	4						TCTAGGCCCTGAGGTACAGGA	0.637													6	122	---	---	---	---	PASS
ATG2A	23130	broad.mit.edu	37	11	64664289	64664289	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:64664289C>T	uc001obx.2	-	38	5318	c.5203G>A	c.(5203-5205)GAC>AAC	p.D1735N	ATG2A_uc001obw.2_Missense_Mutation_p.D500N	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1735							protein binding			ovary(1)|central_nervous_system(1)	2						TTGCGGATGTCCTGCAGCCAC	0.637											OREG0004026	type=REGULATORY REGION|Gene=BC027481|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	10	22	---	---	---	---	PASS
C11orf80	79703	broad.mit.edu	37	11	66555707	66555707	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:66555707G>A	uc001ojf.2	+	5	607	c.600G>A	c.(598-600)ATG>ATA	p.M200I	C11orf80_uc001ojg.2_5'UTR|C11orf80_uc001ojh.2_Intron|C11orf80_uc001oji.2_5'UTR|C11orf80_uc010rpk.1_Missense_Mutation_p.M34I	NM_024650	NP_078926	Q8N6T0	CK080_HUMAN	hypothetical protein LOC79703	45											0						CTCAGGATATGACAGGGGTAA	0.388													10	55	---	---	---	---	PASS
PPFIA1	8500	broad.mit.edu	37	11	70171654	70171654	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:70171654G>T	uc001opo.2	+	5	778	c.580G>T	c.(580-582)GAG>TAG	p.E194*	PPFIA1_uc001opn.1_Nonsense_Mutation_p.E194*|PPFIA1_uc001opp.2_RNA|PPFIA1_uc001opq.1_5'Flank	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b	194	Potential.				cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TTTGTTAGAAGAGGAATTAGG	0.373													6	113	---	---	---	---	PASS
ATG16L2	89849	broad.mit.edu	37	11	72539821	72539821	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:72539821G>T	uc001otd.2	+	16	1710	c.1670G>T	c.(1669-1671)AGC>ATC	p.S557I	ATG16L2_uc001ote.2_Missense_Mutation_p.S451I|ATG16L2_uc009ytj.1_3'UTR|ATG16L2_uc001otf.2_Missense_Mutation_p.S312I|ATG16L2_uc001otg.2_Missense_Mutation_p.S291I|ATG16L2_uc009ytk.2_Missense_Mutation_p.S312I	NM_033388	NP_203746	Q8NAA4	A16L2_HUMAN	ATG16 autophagy related 16-like 2	557	WD 6.				autophagy|protein transport	cytoplasm	protein binding				0			BRCA - Breast invasive adenocarcinoma(5;2.73e-06)			GCTGTGTTCAGGTATGTCCGT	0.587													9	196	---	---	---	---	PASS
SLCO2B1	11309	broad.mit.edu	37	11	74880411	74880411	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:74880411C>A	uc001owb.2	+	5	1029	c.642C>A	c.(640-642)ATC>ATA	p.I214I	SLCO2B1_uc010rrq.1_Intron|SLCO2B1_uc010rrr.1_Silent_p.I70I|SLCO2B1_uc010rrs.1_Silent_p.I98I|SLCO2B1_uc001owc.2_Intron|SLCO2B1_uc001owd.2_Silent_p.I192I	NM_007256	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family,	214	Helical; Name=4; (Potential).				sodium-independent organic anion transport	integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|breast(1)	2					Ergoloid mesylate(DB01049)	TCTCCTACATCGATGACTTTG	0.602													4	59	---	---	---	---	PASS
AQP11	282679	broad.mit.edu	37	11	77301476	77301476	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:77301476C>T	uc001oyj.2	+	1	797	c.439C>T	c.(439-441)CAC>TAC	p.H147Y	AQP11_uc009yuu.2_Intron	NM_173039	NP_766627	Q8NBQ7	AQP11_HUMAN	aquaporin 11	147						cell surface|integral to membrane	transporter activity				0	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			GACCCAGTATCACGTCAGCGA	0.592													19	51	---	---	---	---	PASS
GRM5	2915	broad.mit.edu	37	11	88780767	88780767	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:88780767C>A	uc001pcq.2	-	1	474	c.274G>T	c.(274-276)GGC>TGC	p.G92C	GRM5_uc009yvm.2_Missense_Mutation_p.G92C|GRM5_uc009yvn.1_Missense_Mutation_p.G92C	NM_001143831	NP_001137303	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5 isoform a	92	Extracellular (Potential).				activation of phospholipase C activity by metabotropic glutamate receptor signaling pathway|synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity	p.G92R(1)		central_nervous_system(4)|ovary(2)|lung(2)|breast(1)	9		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)	ATCTCACAGCCCAGTGTGATG	0.522													7	16	---	---	---	---	PASS
TRPC6	7225	broad.mit.edu	37	11	101362388	101362388	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:101362388C>A	uc001pgk.3	-	3	1452	c.1027G>T	c.(1027-1029)GAG>TAG	p.E343*	TRPC6_uc009ywy.2_Intron|TRPC6_uc009ywz.1_Nonsense_Mutation_p.E343*	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	343	Cytoplasmic (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		AGAATGGCCTCGACTTCTTCA	0.408													6	167	---	---	---	---	PASS
BIRC3	330	broad.mit.edu	37	11	102201750	102201750	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:102201750G>A	uc001pgx.2	+	7	1324	c.1102G>A	c.(1102-1104)GAA>AAA	p.E368K		NM_182962	NP_892007	Q13489	BIRC3_HUMAN	baculoviral IAP repeat-containing protein 3	368					anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		TGAACCTGGAGAAGACCATTC	0.333			T	MALT1	MALT								7	45	---	---	---	---	PASS
BIRC3	330	broad.mit.edu	37	11	102201903	102201903	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:102201903G>C	uc001pgx.2	+	7	1477	c.1255G>C	c.(1255-1257)GAC>CAC	p.D419H		NM_182962	NP_892007	Q13489	BIRC3_HUMAN	baculoviral IAP repeat-containing protein 3	419					anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		TCTTGTGTTAGACTTACTCAA	0.363			T	MALT1	MALT								11	51	---	---	---	---	PASS
TMPRSS5	80975	broad.mit.edu	37	11	113568023	113568023	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:113568023C>A	uc001poc.3	-	5	568	c.446G>T	c.(445-447)TGG>TTG	p.W149L	TMPRSS5_uc009yys.2_Missense_Mutation_p.W140L|TMPRSS5_uc009yyt.2_Missense_Mutation_p.W105L|TMPRSS5_uc001pod.3_5'UTR|TMPRSS5_uc010rww.1_Missense_Mutation_p.W139L|TMPRSS5_uc009yyu.2_5'UTR|TMPRSS5_uc010rwx.1_Missense_Mutation_p.W105L	NM_030770	NP_110397	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	149	SRCR.|Extracellular (Potential).				proteolysis	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)	1		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		CCCAAGGCTCCAGCAGATCTG	0.617													6	76	---	---	---	---	PASS
TMPRSS5	80975	broad.mit.edu	37	11	113570845	113570845	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:113570845C>T	uc001poc.3	-	2	171	c.49G>A	c.(49-51)GAG>AAG	p.E17K	TMPRSS5_uc009yys.2_5'UTR|TMPRSS5_uc009yyt.2_Intron|TMPRSS5_uc001pod.3_Intron|TMPRSS5_uc010rww.1_Missense_Mutation_p.E7K|TMPRSS5_uc009yyu.2_Intron|TMPRSS5_uc010rwx.1_Intron	NM_030770	NP_110397	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	17	Cytoplasmic (Potential).				proteolysis	integral to membrane|plasma membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(1)	1		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		GGGCCCTCCTCTGCATACTGG	0.602													7	11	---	---	---	---	PASS
SIDT2	51092	broad.mit.edu	37	11	117063911	117063911	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:117063911C>A	uc001pqh.1	+	23	2189	c.2148C>A	c.(2146-2148)TCC>TCA	p.S716S	SIDT2_uc010rxe.1_Silent_p.S716S|SIDT2_uc001pqg.2_Silent_p.S737S|SIDT2_uc001pqi.1_Silent_p.S713S|SIDT2_uc001pqj.1_Silent_p.S28S	NM_001040455	NP_001035545	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2 precursor	716	Helical; (Potential).					integral to membrane|lysosomal membrane					0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		ATTTCGCTTCCTACTTGTTGG	0.552													13	621	---	---	---	---	PASS
RNF214	257160	broad.mit.edu	37	11	117153509	117153509	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:117153509C>G	uc001pqt.2	+	13	1938	c.1893C>G	c.(1891-1893)ATC>ATG	p.I631M	RNF214_uc001pqu.2_Missense_Mutation_p.I631M|RNF214_uc010rxf.1_Missense_Mutation_p.I476M	NM_207343	NP_997226	Q8ND24	RN214_HUMAN	ring finger protein 214	631							zinc ion binding				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.88e-05)|Epithelial(105;0.000397)|all cancers(92;0.00258)		TGGCCCAAATCAGTACCCCAA	0.478													11	63	---	---	---	---	PASS
VSIG2	23584	broad.mit.edu	37	11	124617436	124617436	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:124617436C>A	uc001qas.2	-	7	1055	c.979G>T	c.(979-981)GTG>TTG	p.V327L		NM_014312	NP_055127	Q96IQ7	VSIG2_HUMAN	V-set and immunoglobulin domain containing 2	327	Cytoplasmic (Potential).					integral to plasma membrane|membrane fraction				ovary(3)|central_nervous_system(1)	4	all_hematologic(175;0.215)	Breast(109;0.00663)|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;0.0215)		AGAAGTCACACGACCATAGGG	0.527													27	40	---	---	---	---	PASS
ADAMTS8	11095	broad.mit.edu	37	11	130286835	130286835	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr11:130286835C>G	uc001qgg.3	-	3	1454	c.1096G>C	c.(1096-1098)GGG>CGG	p.G366R		NM_007037	NP_008968	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1	366	Peptidase M12B.				negative regulation of cell proliferation|proteolysis	proteinaceous extracellular matrix	heparin binding|integrin binding|low affinity phosphate transmembrane transporter activity|metalloendopeptidase activity|zinc ion binding			central_nervous_system(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		CAAATCTTACCTAGTTCATGG	0.562													49	47	---	---	---	---	PASS
WNK1	65125	broad.mit.edu	37	12	1005676	1005676	+	Missense_Mutation	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:1005676A>G	uc001qio.3	+	24	6530	c.6023A>G	c.(6022-6024)AAT>AGT	p.N2008S	WNK1_uc001qip.3_Missense_Mutation_p.N1760S|WNK1_uc001qir.3_Missense_Mutation_p.N1181S	NM_018979	NP_061852	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	2008					intracellular protein kinase cascade|ion transport|neuron development	cytoplasm	ATP binding|protein binding|protein kinase inhibitor activity|protein serine/threonine kinase activity			stomach(6)|breast(6)|ovary(5)|lung(4)|large_intestine(1)|central_nervous_system(1)	23	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			TCACATCTAAATGGGCCGTCT	0.502													28	61	---	---	---	---	PASS
A2ML1	144568	broad.mit.edu	37	12	8975787	8975787	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:8975787G>T	uc001quz.3	+	2	170	c.72G>T	c.(70-72)CTG>CTT	p.L24L		NM_144670	NP_653271	A8K2U0	A2ML1_HUMAN	alpha-2-macroglobulin-like 1 precursor	Error:Variant_position_missing_in_B3KVV6_after_alignment						extracellular space	endopeptidase inhibitor activity			ovary(2)|skin(1)	3						GAAACTACCTGGTGACATTAC	0.368													5	58	---	---	---	---	PASS
TAS2R42	353164	broad.mit.edu	37	12	11339450	11339450	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:11339450A>T	uc001qzr.1	-	1	94	c.94T>A	c.(94-96)TGC>AGC	p.C32S	PRB4_uc001qzf.1_Intron	NM_181429	NP_852094	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	32	Cytoplasmic (Potential).				sensory perception of taste	integral to membrane	G-protein coupled receptor activity			ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			CCTTCAGAGCAGTTTACCAGT	0.448													14	32	---	---	---	---	PASS
PRB4	5545	broad.mit.edu	37	12	11461631	11461631	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:11461631G>C	uc001qzf.1	-	3	320	c.286C>G	c.(286-288)CCA>GCA	p.P96A	PRB4_uc001qzt.2_Missense_Mutation_p.P96A	NM_002723	NP_002714	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	117	4.|9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.		Missing (in allele M and allele S).			extracellular region				ovary(1)	1						GGCTTTCCTGGATGAGGTGGG	0.597										HNSCC(22;0.051)			16	308	---	---	---	---	PASS
CMAS	55907	broad.mit.edu	37	12	22208428	22208428	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:22208428G>A	uc001rfm.2	+	3	522	c.443G>A	c.(442-444)TGT>TAT	p.C148Y	CMAS_uc001rfn.2_RNA	NM_018686	NP_061156	Q8NFW8	NEUA_HUMAN	cytidine monophospho-N-acetylneuraminic acid	148					lipopolysaccharide biosynthetic process	nucleus	N-acylneuraminate cytidylyltransferase activity			ovary(1)|pancreas(1)|skin(1)	3						ACTTCTCCATGTTTACATCCT	0.343													8	18	---	---	---	---	PASS
PRICKLE1	144165	broad.mit.edu	37	12	42853690	42853690	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:42853690G>T	uc010skv.1	-	8	2704	c.2417C>A	c.(2416-2418)CCC>CAC	p.P806H	PRICKLE1_uc001rnl.2_Missense_Mutation_p.P806H|PRICKLE1_uc010skw.1_Missense_Mutation_p.P806H|PRICKLE1_uc001rnm.2_Missense_Mutation_p.P806H|PRICKLE1_uc001rnk.1_5'Flank	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	806					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		CTGAGGGGTGGGAAGTGCAGA	0.433													25	61	---	---	---	---	PASS
ADAMTS20	80070	broad.mit.edu	37	12	43833468	43833468	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:43833468C>A	uc010skx.1	-	18	2550	c.2550G>T	c.(2548-2550)TGG>TGT	p.W850C	ADAMTS20_uc001rno.1_Missense_Mutation_p.W4C|ADAMTS20_uc001rnp.1_Missense_Mutation_p.W4C	NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	850	TSP type-1 2.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CATAGGGGTCCCATGTGAACA	0.423													5	48	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49441761	49441761	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:49441761C>A	uc001rta.3	-	14	4223	c.4223G>T	c.(4222-4224)TGT>TTT	p.C1408F		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1408	Cys-rich.|PHD-type 3.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						GCTGTTGACACAGTAAGGGTG	0.552			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			13	24	---	---	---	---	PASS
MLL2	8085	broad.mit.edu	37	12	49443899	49443899	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:49443899C>A	uc001rta.3	-	11	3472	c.3472G>T	c.(3472-3474)GAG>TAG	p.E1158*		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	1158	Pro-rich.				chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|protein binding|transcription regulatory region DNA binding|zinc ion binding			kidney(16)|central_nervous_system(12)|lung(4)|skin(4)|ovary(3)|pancreas(2)	41						GCCAGCTCCTCGGGGTCCAGG	0.602			N|F|Mis		medulloblastoma|renal					HNSCC(34;0.089)			4	60	---	---	---	---	PASS
SCN8A	6334	broad.mit.edu	37	12	52162746	52162746	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:52162746C>A	uc001ryw.2	+	17	3177	c.2999C>A	c.(2998-3000)TCA>TAA	p.S1000*	SCN8A_uc010snl.1_Nonsense_Mutation_p.S865*	NM_014191	NP_055006	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha	1000	II.				axon guidance|myelination|peripheral nervous system development	cytoplasmic membrane-bounded vesicle|node of Ranvier	ATP binding|voltage-gated sodium channel activity			ovary(7)	7				BRCA - Breast invasive adenocarcinoma(357;0.181)	Lamotrigine(DB00555)	CTCCAGATCTCAGTGATCCGT	0.537													6	61	---	---	---	---	PASS
MIR148B	442892	broad.mit.edu	37	12	54731020	54731020	+	RNA	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:54731020G>T	hsa-mir-148b|MI0000811	+			c.21G>T			COPZ1_uc001sfs.1_Intron|COPZ1_uc001sft.2_Intron|COPZ1_uc009znm.1_Intron|COPZ1_uc010sot.1_Intron|uc010sou.1_RNA																	0						TAGCATTTGAGGTGAAGTTCT	0.398													10	142	---	---	---	---	PASS
RDH5	5959	broad.mit.edu	37	12	56115129	56115129	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:56115129G>C	uc001shk.2	+	2	344	c.161G>C	c.(160-162)CGA>CCA	p.R54P	BLOC1S1_uc001shj.3_Intron|RDH5_uc010spt.1_Missense_Mutation_p.R54P|RDH5_uc010spu.1_5'UTR|RDH5_uc001shl.2_Missense_Mutation_p.R54P	NM_002905	NP_002896	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis and 9-cis)	54	NADP (By similarity).				response to stimulus|visual perception	membrane	binding|retinol dehydrogenase activity			ovary(1)	1					NADH(DB00157)|Vitamin A(DB00162)	AGAGGCTTCCGAGTCCTGGCC	0.662											OREG0021907	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	10	29	---	---	---	---	PASS
DGKA	1606	broad.mit.edu	37	12	56347166	56347166	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:56347166G>T	uc001sij.2	+	23	2360	c.2096G>T	c.(2095-2097)GGA>GTA	p.G699V	DGKA_uc001sik.2_Missense_Mutation_p.G699V|DGKA_uc001sil.2_Missense_Mutation_p.G699V|DGKA_uc001sim.2_Missense_Mutation_p.G699V|DGKA_uc001sin.2_Missense_Mutation_p.G699V|DGKA_uc009zof.2_Missense_Mutation_p.G345V|DGKA_uc001sio.2_Missense_Mutation_p.G441V	NM_001345	NP_001336	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	699				G -> V (in Ref. 1; CAA44396).	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)	CAAATTGACGGAGAACCCTGG	0.468													10	338	---	---	---	---	PASS
ANKRD52	283373	broad.mit.edu	37	12	56645804	56645804	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:56645804G>A	uc001skm.3	-	15	1677	c.1587C>T	c.(1585-1587)GCC>GCT	p.A529A		NM_173595	NP_775866	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	529	ANK 15.						protein binding			ovary(2)	2						CTCACAAGAAGGCCTCCTTCC	0.562													19	30	---	---	---	---	PASS
INHBC	3626	broad.mit.edu	37	12	57843575	57843575	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:57843575A>T	uc001snv.1	+	2	956	c.829A>T	c.(829-831)ATA>TTA	p.I277L		NM_005538	NP_005529	P55103	INHBC_HUMAN	inhibin beta C chain preproprotein	277					growth	extracellular region	growth factor activity|hormone activity|transforming growth factor beta receptor binding				0						GAACTTCTGCATAGGGCAGTG	0.542													14	37	---	---	---	---	PASS
MON2	23041	broad.mit.edu	37	12	62954451	62954451	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:62954451T>C	uc001sre.2	+	26	3981	c.3590T>C	c.(3589-3591)GTT>GCT	p.V1197A	MON2_uc009zqj.2_Missense_Mutation_p.V1197A|MON2_uc010ssl.1_Missense_Mutation_p.V1125A|MON2_uc010ssm.1_Missense_Mutation_p.V1174A|MON2_uc010ssn.1_Missense_Mutation_p.V1197A|MON2_uc001srf.2_Missense_Mutation_p.V960A|MON2_uc001srg.2_Missense_Mutation_p.V72A	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	1198					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		CCTGTGCCTGTTCTTATAGGG	0.448													9	13	---	---	---	---	PASS
PTPRB	5787	broad.mit.edu	37	12	70933760	70933760	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:70933760C>A	uc001swb.3	-	22	5013	c.4983G>T	c.(4981-4983)AGG>AGT	p.R1661S	PTPRB_uc010sto.1_Missense_Mutation_p.R1571S|PTPRB_uc010stp.1_Missense_Mutation_p.R1571S|PTPRB_uc001swc.3_Missense_Mutation_p.R1879S|PTPRB_uc001swa.3_Missense_Mutation_p.R1791S	NM_002837	NP_002828	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1661	Cytoplasmic (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ATGGTCGATCCCTACGAATGC	0.408													8	17	---	---	---	---	PASS
SLC6A15	55117	broad.mit.edu	37	12	85255533	85255533	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:85255533C>A	uc001szv.2	-	12	2564	c.2071G>T	c.(2071-2073)GGT>TGT	p.G691C	SLC6A15_uc010sul.1_Missense_Mutation_p.G584C|SLC6A15_uc001szw.1_3'UTR	NM_182767	NP_877499	Q9H2J7	S6A15_HUMAN	solute carrier family 6, member 15 isoform 1	691	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|leucine transport|proline transport	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			pancreas(2)|ovary(1)	3						ATATTTTTACCAAAATTTGGA	0.443													8	16	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88449427	88449427	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:88449427G>T	uc001tar.2	-	50	7230	c.6886C>A	c.(6886-6888)CTT>ATT	p.L2296I	CEP290_uc001taq.2_Missense_Mutation_p.L1356I|uc001tas.2_Intron	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	2296	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						AGCTGTTTAAGGTCAGTAATG	0.294													4	10	---	---	---	---	PASS
CEP290	80184	broad.mit.edu	37	12	88479931	88479931	+	Nonsense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:88479931G>C	uc001tar.2	-	34	4666	c.4322C>G	c.(4321-4323)TCA>TGA	p.S1441*	CEP290_uc001taq.2_Nonsense_Mutation_p.S501*	NM_025114	NP_079390	O15078	CE290_HUMAN	centrosomal protein 290kDa	1441	Potential.				cilium assembly|eye photoreceptor cell development|G2/M transition of mitotic cell cycle|hindbrain development|otic vesicle formation|positive regulation of transcription, DNA-dependent|pronephros development|protein transport	cell surface|centrosome|cytosol|nucleus|photoreceptor connecting cilium	protein binding			ovary(5)|breast(1)|pancreas(1)	7						GTCAGGGATTGATCCTGTAGC	0.348													13	22	---	---	---	---	PASS
BTG1	694	broad.mit.edu	37	12	92539232	92539232	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:92539232C>G	uc001tby.3	-	1	442	c.80G>C	c.(79-81)CGC>CCC	p.R27P	BTG1_uc001tbv.1_5'Flank|BTG1_uc001tbw.1_5'Flank|BTG1_uc001tbx.1_5'Flank|BTG1_uc009zss.1_5'Flank|uc001tca.2_5'Flank	NM_001731	NP_001722	P62324	BTG1_HUMAN	B-cell translocation protein 1	27					cell migration|negative regulation of cell growth|negative regulation of cell proliferation|positive regulation of angiogenesis|positive regulation of endothelial cell differentiation|positive regulation of myoblast differentiation|regulation of apoptosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	kinase binding|transcription cofactor activity				0		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				CCCCTTGGTGCGGAGAAACTT	0.592			T	MYC	BCLL								9	39	---	---	---	---	PASS
ANO4	121601	broad.mit.edu	37	12	101490328	101490328	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:101490328G>C	uc010svm.1	+	19	2325	c.1753G>C	c.(1753-1755)GAG>CAG	p.E585Q	ANO4_uc001thw.2_Missense_Mutation_p.E550Q|ANO4_uc001thx.2_Missense_Mutation_p.E585Q|ANO4_uc001thy.2_Missense_Mutation_p.E105Q	NM_178826	NP_849148	Q32M45	ANO4_HUMAN	anoctamin 4	585	Extracellular (Potential).					chloride channel complex	chloride channel activity			ovary(4)|skin(2)	6						GCCTCGCACAGAGTCTGAGTG	0.478										HNSCC(74;0.22)			19	17	---	---	---	---	PASS
CIT	11113	broad.mit.edu	37	12	120139707	120139707	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:120139707G>A	uc001txi.1	-	41	5288	c.5235C>T	c.(5233-5235)CTC>CTT	p.L1745L	CIT_uc001txh.1_Silent_p.L1264L|CIT_uc001txj.1_Silent_p.L1787L	NM_007174	NP_009105	O14578	CTRO_HUMAN	citron	1745	CNH.				intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity			ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TGGTTCCAATGAGGATACTGT	0.512													39	97	---	---	---	---	PASS
MLEC	9761	broad.mit.edu	37	12	121132899	121132899	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:121132899G>T	uc001tyy.1	+	4	744	c.593G>T	c.(592-594)GGG>GTG	p.G198V		NM_014730	NP_055545	Q14165	MLEC_HUMAN	malectin precursor	198	Lumenal (Potential).				post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	carbohydrate binding			ovary(1)	1						TTTTCCTAGGGGTACTATGAC	0.493													9	193	---	---	---	---	PASS
RAN	5901	broad.mit.edu	37	12	131359125	131359125	+	Silent	SNP	G	T	T	rs1802283		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:131359125G>T	uc001uir.2	+	5	347	c.282G>T	c.(280-282)TCG>TCT	p.S94S	RAN_uc010tbk.1_Silent_p.S6S|RAN_uc010tbl.1_Silent_p.S6S|RAN_uc001uis.2_Silent_p.S114S	NM_006325	NP_006316	P62826	RAN_HUMAN	ras-related nuclear protein	94					androgen receptor signaling pathway|cell division|DNA metabolic process|mitosis|mitotic spindle organization|positive regulation of transcription, DNA-dependent|protein export from nucleus|RNA export from nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|melanosome|nuclear pore|nucleoplasm	androgen receptor binding|chromatin binding|GTP binding|GTPase activity|transcription coactivator activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	Lung NSC(355;7.46e-07)|all_epithelial(31;7.36e-06)		OV - Ovarian serous cystadenocarcinoma(86;9.18e-49)|Epithelial(86;1.42e-45)|all cancers(50;6.28e-40)		ATGTAACATCGAGAGTTACTT	0.408													4	40	---	---	---	---	PASS
ZNF10	7556	broad.mit.edu	37	12	133733275	133733275	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr12:133733275G>A	uc009zzb.2	+	5	1890	c.1443G>A	c.(1441-1443)AGG>AGA	p.R481R	ZNF268_uc010tbv.1_Intron|ZNF10_uc001ulq.2_Silent_p.R481R	NM_015394	NP_056209	P21506	ZNF10_HUMAN	zinc finger protein 10	481	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)|skin(1)	3	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TGCATCAGAGGATACACACTG	0.428													9	27	---	---	---	---	PASS
SACS	26278	broad.mit.edu	37	13	23912516	23912516	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr13:23912516G>T	uc001uon.2	-	10	6088	c.5499C>A	c.(5497-5499)TCC>TCA	p.S1833S	SACS_uc001uoo.2_Silent_p.S1686S|SACS_uc001uop.1_Intron|SACS_uc001uoq.1_Intron	NM_014363	NP_055178	Q9NZJ4	SACS_HUMAN	sacsin	1833					cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding			ovary(7)|skin(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	12		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TCTCACTCAGGGAAAACTTCA	0.478													6	56	---	---	---	---	PASS
MTMR6	9107	broad.mit.edu	37	13	25835837	25835837	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr13:25835837C>G	uc001uqf.3	-	6	1014	c.695G>C	c.(694-696)CGC>CCC	p.R232P	MTMR6_uc001uqe.1_Missense_Mutation_p.R232P	NM_004685	NP_004676	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	232	Myotubularin phosphatase.					cytoplasm|nuclear envelope	calcium-activated potassium channel activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity			ovary(2)|skin(2)	4		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.00927)|Epithelial(112;0.0474)|OV - Ovarian serous cystadenocarcinoma(117;0.164)		GTACATATAGCGATTGACTGG	0.383													13	29	---	---	---	---	PASS
FLT1	2321	broad.mit.edu	37	13	28893635	28893635	+	Missense_Mutation	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr13:28893635T>A	uc001usb.3	-	24	3496	c.3211A>T	c.(3211-3213)ATC>TTC	p.I1071F	FLT1_uc010aap.2_Missense_Mutation_p.I76F|FLT1_uc010aaq.2_Missense_Mutation_p.I196F|FLT1_uc001usa.3_Missense_Mutation_p.I289F	NM_002019	NP_002010	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1 isoform 1	1071	Cytoplasmic (Potential).|Protein kinase.				cell differentiation|female pregnancy|positive regulation of vascular endothelial growth factor receptor signaling pathway	extracellular space|Golgi apparatus|integral to plasma membrane|nucleus	ATP binding|growth factor binding|vascular endothelial growth factor receptor activity			lung(10)|central_nervous_system(5)|ovary(3)|stomach(2)|skin(2)|urinary_tract(1)|breast(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Sunitinib(DB01268)	TTGTCAAAGATAGATTCAGGA	0.468													10	34	---	---	---	---	PASS
NHLRC3	387921	broad.mit.edu	37	13	39621263	39621263	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr13:39621263C>T	uc001uxc.2	+	6	1087	c.765C>T	c.(763-765)TTC>TTT	p.F255F	NHLRC3_uc001uxd.2_Silent_p.F188F|NHLRC3_uc001uxe.2_Silent_p.F58F	NM_001012754	NP_001012772	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3 isoform a	255						extracellular region				skin(1)	1		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		ATAATTGTTTCACAGAAGAGG	0.393													23	44	---	---	---	---	PASS
LCP1	3936	broad.mit.edu	37	13	46730703	46730703	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr13:46730703C>A	uc001vaz.3	-	5	487	c.361G>T	c.(361-363)GAA>TAA	p.E121*	LCP1_uc001vba.3_Nonsense_Mutation_p.E121*	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin	121	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)		TACTTTTCTTCCTCTGCAAGT	0.373			T	BCL6	NHL 								28	92	---	---	---	---	PASS
SUCLA2	8803	broad.mit.edu	37	13	48563071	48563071	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr13:48563071C>G	uc001vbs.2	-	3	374	c.317G>C	c.(316-318)AGA>ACA	p.R106T	SUCLA2_uc010tgb.1_Missense_Mutation_p.R46T|SUCLA2_uc010tgc.1_5'UTR|SUCLA2_uc010tgd.1_Missense_Mutation_p.R46T|SUCLA2_uc001vbt.1_RNA|SUCLA2_uc001vbu.1_Missense_Mutation_p.R106T	NM_003850	NP_003841	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	106	ATP-grasp.				succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|metal ion binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)	TCCTTTTCCTCTACCACCAGC	0.373													40	81	---	---	---	---	PASS
CAB39L	81617	broad.mit.edu	37	13	49885033	49885033	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr13:49885033C>G	uc001vcw.2	-	9	1429	c.931G>C	c.(931-933)GAA>CAA	p.E311Q	CAB39L_uc001vcx.2_Missense_Mutation_p.E311Q|CAB39L_uc010adf.2_Missense_Mutation_p.E308Q	NM_030925	NP_112187	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	311					cell cycle arrest|insulin receptor signaling pathway|regulation of fatty acid oxidation	cytosol	protein binding				0		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)		TCCGTCCTTTCTTTTTGGAAG	0.473													47	125	---	---	---	---	PASS
SOX1	6656	broad.mit.edu	37	13	112722129	112722129	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr13:112722129C>T	uc001vsb.1	+	1	217	c.157C>T	c.(157-159)CGG>TGG	p.R53W		NM_005986	NP_005977	O00570	SOX1_HUMAN	SRY (sex determining region Y)-box 1	53	HMG box.				chromatin organization	nucleus	core promoter sequence-specific DNA binding|protein binding|sequence-specific DNA binding transcription factor activity				0	all_lung(23;0.000652)|Lung NSC(43;0.017)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	all_cancers(25;0.000331)|Lung NSC(25;0.0496)|all_lung(25;0.0831)|all_epithelial(44;0.0868)|Breast(118;0.231)		OV - Ovarian serous cystadenocarcinoma(48;0.132)		CCGGGTCAAACGGCCCATGAA	0.517													6	7	---	---	---	---	PASS
OR11H12	440153	broad.mit.edu	37	14	19377713	19377713	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:19377713C>A	uc010tkp.1	+	1	120	c.120C>A	c.(118-120)ATC>ATA	p.I40I		NM_001013354	NP_001013372	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H,	40	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CAATTCAGATCTTCCTCTTCT	0.428													17	15	---	---	---	---	PASS
CHD8	57680	broad.mit.edu	37	14	21884067	21884067	+	Splice_Site	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:21884067C>T	uc001was.1	-	6	974	c.880_splice	c.e6-1	p.K294_splice	CHD8_uc001war.1_Splice_Site_p.K190_splice	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8						ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|negative regulation of transcription, DNA-dependent|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	MLL1 complex	ATP binding|beta-catenin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		AGCGTCTCTTCTGTAGAGCAA	0.368													21	76	---	---	---	---	PASS
PRKD1	5587	broad.mit.edu	37	14	30105671	30105671	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:30105671C>T	uc001wqh.2	-	7	1196	c.1015G>A	c.(1015-1017)GTG>ATG	p.V339M		NM_002742	NP_002733	Q15139	KPCD1_HUMAN	protein kinase D1	339					cell proliferation|intracellular signal transduction|sphingolipid metabolic process	cytosol|integral to plasma membrane	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(3)|large_intestine(2)|ovary(2)|skin(1)	8	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		TCCATGACCACATCAGACTCT	0.458													5	26	---	---	---	---	PASS
FANCM	57697	broad.mit.edu	37	14	45658053	45658053	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:45658053G>A	uc001wwd.3	+	20	4927	c.4828G>A	c.(4828-4830)GAA>AAA	p.E1610K	FANCM_uc010anf.2_Missense_Mutation_p.E1584K|FANCM_uc001wwe.3_Missense_Mutation_p.E1146K|FANCM_uc010ang.2_Missense_Mutation_p.E824K	NM_020937	NP_065988	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1610					DNA repair	Fanconi anaemia nuclear complex	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|nuclease activity|protein binding			ovary(3)|lung(2)|breast(2)	7						TTGTGTTGATGAAGAGGAGTC	0.294								Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				7	23	---	---	---	---	PASS
MDGA2	161357	broad.mit.edu	37	14	47389363	47389363	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:47389363C>A	uc001wwj.3	-	10	2079	c.1883G>T	c.(1882-1884)GGA>GTA	p.G628V	MDGA2_uc001wwi.3_Missense_Mutation_p.G399V|MDGA2_uc010ani.2_Missense_Mutation_p.G188V	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	628					spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						ATAGGCCTTTCCTGAAAACAG	0.358													8	43	---	---	---	---	PASS
ACTR10	55860	broad.mit.edu	37	14	58678108	58678108	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:58678108G>T	uc001xdf.2	+	5	544	c.441G>T	c.(439-441)CTG>CTT	p.L147L	C14orf37_uc010tro.1_Intron|ACTR10_uc001xdg.2_5'UTR|ACTR10_uc001xdh.2_5'UTR|ACTR10_uc010trp.1_5'Flank|ACTR10_uc010apc.2_5'Flank	NM_018477	NP_060947	Q9NZ32	ARP10_HUMAN	uncharacterized hypothalamus protein HARP11	147						cytoplasm				central_nervous_system(1)	1						GGGAAAGCCTGGTGTTACCCA	0.383													6	95	---	---	---	---	PASS
SYNE2	23224	broad.mit.edu	37	14	64491954	64491954	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:64491954C>A	uc001xgm.2	+	41	6297	c.6067C>A	c.(6067-6069)CAG>AAG	p.Q2023K	SYNE2_uc001xgl.2_Missense_Mutation_p.Q2023K	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2023	Potential.|Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GGATAGATACCAGACATTACT	0.373													6	41	---	---	---	---	PASS
C14orf50	145376	broad.mit.edu	37	14	65056048	65056048	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:65056048C>A	uc001xhl.1	+	12	1357	c.1261C>A	c.(1261-1263)CCT>ACT	p.P421T	C14orf50_uc001xhm.1_Missense_Mutation_p.P151T	NM_172365	NP_758953	Q96LQ0	CN050_HUMAN	hypothetical protein LOC145376	421										skin(1)	1				OV - Ovarian serous cystadenocarcinoma(108;0.00382)|all cancers(60;0.00427)|BRCA - Breast invasive adenocarcinoma(234;0.0488)		TACATCATGCCCTAAGTAACC	0.333													16	41	---	---	---	---	PASS
C14orf45	80127	broad.mit.edu	37	14	74516689	74516689	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:74516689G>T	uc010tup.1	+	8	1200	c.1077G>T	c.(1075-1077)GTG>GTT	p.V359V	C14orf45_uc001xpm.1_RNA	NM_025057	NP_079333	Q8ND07	CN045_HUMAN	hypothetical protein LOC80127	359	Potential.										0				BRCA - Breast invasive adenocarcinoma(234;0.00351)		GAACAGAAGTGGAAAGATTCT	0.403													6	53	---	---	---	---	PASS
ATXN3	4287	broad.mit.edu	37	14	92549498	92549498	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:92549498C>A	uc001yac.3	-	7	649	c.580G>T	c.(580-582)GAA>TAA	p.E194*	ATXN3_uc010aug.2_Nonsense_Mutation_p.E179*|ATXN3_uc001yad.3_Nonsense_Mutation_p.E139*|ATXN3_uc010auh.2_Nonsense_Mutation_p.E128*|ATXN3_uc001yae.3_Nonsense_Mutation_p.E96*|ATXN3_uc010twl.1_RNA	NM_004993	NP_004984	P54252	ATX3_HUMAN	ataxin 3 reference isoform	194					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)		GCTAATTCTTCTCCAATAAGT	0.373													22	64	---	---	---	---	PASS
WDR25	79446	broad.mit.edu	37	14	100847918	100847918	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:100847918G>T	uc010avx.2	+	2	750	c.657G>T	c.(655-657)GAG>GAT	p.E219D	WDR25_uc001yhm.2_Missense_Mutation_p.E211D|WDR25_uc001yhn.2_Missense_Mutation_p.E219D|WDR25_uc010avy.2_RNA|WDR25_uc001yho.2_5'Flank	NM_001161476	NP_001154948	Q64LD2	WDR25_HUMAN	WD repeat domain 25	219											0		Melanoma(154;0.212)				GAGTGTCTGAGTTTATTCAGC	0.562													11	11	---	---	---	---	PASS
MIR495	574453	broad.mit.edu	37	14	101500125	101500125	+	RNA	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:101500125C>T	hsa-mir-495|MI0003135	+			c.34C>T																				0						ATGTTATTTTCGCTTTATATG	0.522													8	45	---	---	---	---	PASS
PPP2R5C	5527	broad.mit.edu	37	14	102276371	102276371	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:102276371G>A	uc001yko.2	+	1	232	c.92G>A	c.(91-93)CGA>CAA	p.R31Q	PPP2R5C_uc001ykj.3_Intron|PPP2R5C_uc010txr.1_Intron|PPP2R5C_uc001ykk.2_Intron|PPP2R5C_uc010txt.1_Missense_Mutation_p.R21Q|PPP2R5C_uc001ykn.2_Missense_Mutation_p.R31Q|PPP2R5C_uc001ykp.2_Missense_Mutation_p.R31Q|PPP2R5C_uc010txs.1_Missense_Mutation_p.R21Q	NM_002719	NP_002710	Q13362	2A5G_HUMAN	gamma isoform of regulatory subunit B56, protein	31					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|negative regulation of cell proliferation|proteasomal ubiquitin-dependent protein catabolic process|signal transduction	chromosome, centromeric region|nucleus|protein phosphatase type 2A complex	protein binding|protein binding|protein phosphatase type 2A regulator activity|protein phosphatase type 2A regulator activity			ovary(1)|breast(1)	2						CTCCATATTCGAGGTAAGTTA	0.468													8	26	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102467534	102467534	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:102467534G>T	uc001yks.2	+	20	4402	c.4238G>T	c.(4237-4239)TGG>TTG	p.W1413L		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	1413	Stem (By similarity).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						GACCGCCATTGGAAACAGCTC	0.423													16	581	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102493548	102493548	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:102493548G>T	uc001yks.2	+	45	8973	c.8809G>T	c.(8809-8811)GGT>TGT	p.G2937C		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	2937	AAA 4 (By similarity).|ATP (Potential).				cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						GCTTCTGATTGGTGTTAGTGG	0.463													10	351	---	---	---	---	PASS
DYNC1H1	1778	broad.mit.edu	37	14	102515002	102515002	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:102515002G>T	uc001yks.2	+	74	13532	c.13368G>T	c.(13366-13368)GTG>GTT	p.V4456V		NM_001376	NP_001367	Q14204	DYHC1_HUMAN	cytoplasmic dynein 1 heavy chain 1	4456					cytoplasmic mRNA processing body assembly|G2/M transition of mitotic cell cycle|microtubule-based movement|mitotic spindle organization|stress granule assembly|transport	centrosome|cytoplasmic dynein complex|cytosol|Golgi apparatus|microtubule	ATP binding|ATPase activity, coupled|microtubule motor activity|protein binding			ovary(7)|central_nervous_system(2)|pancreas(1)	10						ACGAGCTAGTGAAAGGTGCGT	0.607													14	39	---	---	---	---	PASS
ZNF839	55778	broad.mit.edu	37	14	102800977	102800977	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:102800977G>A	uc001ylo.2	+	4	1505	c.1155G>A	c.(1153-1155)CTG>CTA	p.L385L	ZNF839_uc010awk.1_Silent_p.L501L|ZNF839_uc001ylp.2_RNA|ZNF839_uc001ylq.1_Silent_p.L385L|ZNF839_uc001ylr.2_Silent_p.L310L|ZNF839_uc001yls.2_5'UTR|ZNF839_uc001ylt.2_5'Flank	NM_018335	NP_060805	A8K0R7	ZN839_HUMAN	zinc finger protein 839	385						intracellular	zinc ion binding			ovary(1)|central_nervous_system(1)	2						AGTTTCTTCTGATGAAGGTGA	0.398													13	27	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105410132	105410132	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:105410132G>T	uc010axc.1	-	7	11776	c.11656C>A	c.(11656-11658)CTG>ATG	p.L3886M	AHNAK2_uc001ypx.2_Missense_Mutation_p.L3786M	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3886						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACCTTGGGCAGGTGTCCTTTG	0.587													9	338	---	---	---	---	PASS
GPR132	29933	broad.mit.edu	37	14	105517538	105517538	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:105517538C>T	uc001yqd.2	-	4	1835	c.936G>A	c.(934-936)ACG>ACA	p.T312T	GPR132_uc001yqc.2_Silent_p.T124T|GPR132_uc001yqe.2_Silent_p.T303T	NM_013345	NP_037477	Q9UNW8	GP132_HUMAN	G protein-coupled receptor 132	312	Cytoplasmic (Potential).				response to stress	integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(2)|central_nervous_system(1)	3		all_cancers(154;0.0953)|Melanoma(154;0.155)|all_epithelial(191;0.219)	OV - Ovarian serous cystadenocarcinoma(23;0.00778)|all cancers(16;0.00936)|Epithelial(46;0.0227)	Epithelial(152;0.02)|all cancers(159;0.0419)|OV - Ovarian serous cystadenocarcinoma(161;0.0521)		GGGAATGGTCCGTGGCCAGCA	0.582													12	26	---	---	---	---	PASS
MTA1	9112	broad.mit.edu	37	14	105927231	105927231	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr14:105927231C>A	uc001yqx.2	+	10	1070	c.883C>A	c.(883-885)CTT>ATT	p.L295I	MTA1_uc001yqy.2_RNA|MTA1_uc001yqz.1_Missense_Mutation_p.L209I|MTA1_uc001yra.1_Missense_Mutation_p.L209I|MTA1_uc001yrb.2_Missense_Mutation_p.L56I	NM_004689	NP_004680	Q13330	MTA1_HUMAN	metastasis associated protein	295	SANT.				signal transduction	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			breast(1)|central_nervous_system(1)	2		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		AGAGGCCAACCTTTTCGAGGA	0.587													7	115	---	---	---	---	PASS
C15orf2	23742	broad.mit.edu	37	15	24923588	24923588	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:24923588G>A	uc001ywo.2	+	1	3048	c.2574G>A	c.(2572-2574)GGG>GGA	p.G858G		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	858					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	8		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)		CTGGTTCTGGGAACACACTAC	0.493													18	49	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	33833011	33833011	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:33833011G>T	uc001zhi.2	+	7	636	c.566G>T	c.(565-567)GGT>GTT	p.G189V	RYR3_uc010bar.2_Missense_Mutation_p.G189V	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	189	MIR 2.|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)		GTATCAAATGGTAACATACAA	0.428													11	23	---	---	---	---	PASS
PGBD4	161779	broad.mit.edu	37	15	34396159	34396159	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:34396159C>A	uc001zho.2	+	1	1886	c.1427C>A	c.(1426-1428)CCT>CAT	p.P476H	C15orf24_uc001zhm.2_5'Flank|C15orf24_uc001zhn.2_5'Flank	NM_152595	NP_689808	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	476											0		all_lung(180;1.76e-08)		all cancers(64;1.22e-17)|GBM - Glioblastoma multiforme(113;1.78e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0242)		AAGGATAATCCTGAGCACACG	0.433													5	52	---	---	---	---	PASS
SLC12A1	6557	broad.mit.edu	37	15	48539204	48539204	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:48539204A>T	uc001zwn.3	+	12	1767	c.1551A>T	c.(1549-1551)AAA>AAT	p.K517N	SLC12A1_uc010uew.1_Missense_Mutation_p.K323N|SLC12A1_uc010bem.2_Missense_Mutation_p.K517N|SLC12A1_uc001zwq.3_Missense_Mutation_p.K288N|SLC12A1_uc001zwr.3_Missense_Mutation_p.K244N	NM_000338	NP_000329	Q13621	S12A1_HUMAN	sodium potassium chloride cotransporter 2	517	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to membrane|membrane fraction	sodium:potassium:chloride symporter activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;0.00219)		all cancers(107;1.76e-09)|GBM - Glioblastoma multiforme(94;1.48e-06)	Bumetanide(DB00887)|Chlormerodrin(DB00534)|Chlorthalidone(DB00310)|Ethacrynic acid(DB00903)|Furosemide(DB00695)|Hydroflumethiazide(DB00774)|Methyclothiazide(DB00232)|Metolazone(DB00524)|Potassium Chloride(DB00761)|Torasemide(DB00214)|Trichlormethiazide(DB01021)	GCGCACCCAAAGTGTTCCAGG	0.498													29	87	---	---	---	---	PASS
FBN1	2200	broad.mit.edu	37	15	48782117	48782117	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:48782117C>A	uc001zwx.1	-	25	3341	c.3013G>T	c.(3013-3015)GAG>TAG	p.E1005*		NM_000138	NP_000129	P35555	FBN1_HUMAN	fibrillin 1 precursor	1005	TB 5.				heart development|negative regulation of BMP signaling pathway by extracellular sequestering of BMP|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|skeletal system development	basement membrane|extracellular space|microfibril	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(2)|large_intestine(1)	3		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CACAGCTCCTCGTACTCAGGA	0.537													4	54	---	---	---	---	PASS
C15orf33	196951	broad.mit.edu	37	15	49867260	49867260	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:49867260G>A	uc001zxl.2	-	8	887	c.593C>T	c.(592-594)TCC>TTC	p.S198F	C15orf33_uc001zxm.2_Missense_Mutation_p.S198F	NM_152647	NP_689860	Q96M60	CO033_HUMAN	hypothetical protein LOC196951	198										ovary(1)	1		all_lung(180;0.00187)		all cancers(107;3.45e-08)|GBM - Glioblastoma multiforme(94;0.000124)		AAGAGCAATGGAGGCTTCTGA	0.303													10	15	---	---	---	---	PASS
HERC1	8925	broad.mit.edu	37	15	63932475	63932475	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:63932475C>A	uc002amp.2	-	61	11925	c.11777G>T	c.(11776-11778)TGG>TTG	p.W3926L		NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	3926					protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						ACATTCTAACCAGGCCCATTC	0.498													20	45	---	---	---	---	PASS
SNX1	6642	broad.mit.edu	37	15	64418374	64418374	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:64418374C>G	uc002amv.2	+	6	643	c.607C>G	c.(607-609)CAG>GAG	p.Q203E	SNX1_uc010bgv.2_5'UTR|SNX1_uc010uio.1_Missense_Mutation_p.Q203E|SNX1_uc002amw.2_Missense_Mutation_p.Q203E|SNX1_uc002amx.2_Missense_Mutation_p.Q138E|SNX1_uc002amy.2_Missense_Mutation_p.Q132E|SNX1_uc010bgw.2_Missense_Mutation_p.Q105E	NM_003099	NP_003090	Q13596	SNX1_HUMAN	sorting nexin 1 isoform a	203	PX.				cell communication|early endosome to Golgi transport|endocytosis|intracellular protein transport	early endosome membrane|Golgi apparatus	phosphatidylinositol binding|protein binding|protein transporter activity				0						GAAGCACTCTCAGAATGGCTT	0.443													13	43	---	---	---	---	PASS
ISL2	64843	broad.mit.edu	37	15	76629258	76629258	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:76629258G>T	uc002bbw.1	+	1	112	c.34G>T	c.(34-36)GGT>TGT	p.G12C		NM_145805	NP_665804	Q96A47	ISL2_HUMAN	ISL LIM homeobox 2	12						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TCCTTTTCTGGGTGCTATGGG	0.468													9	348	---	---	---	---	PASS
IDH3A	3419	broad.mit.edu	37	15	78454050	78454050	+	Missense_Mutation	SNP	T	G	G	rs61752770	byFrequency	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:78454050T>G	uc002bdd.2	+	5	444	c.417T>G	c.(415-417)GAT>GAG	p.D139E	IDH3A_uc010umt.1_Missense_Mutation_p.D104E|IDH3A_uc010umu.1_Missense_Mutation_p.D30E|IDH3A_uc002bde.2_Missense_Mutation_p.D89E|IDH3A_uc010umv.1_Missense_Mutation_p.D89E|IDH3A_uc002bdf.2_5'UTR|IDH3A_uc002bdg.2_Missense_Mutation_p.D52E	NM_005530	NP_005521	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	139					carbohydrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NAD+) activity|magnesium ion binding|NAD binding				0					NADH(DB00157)	CTTACACCGATGTAAATATTG	0.418													41	149	---	---	---	---	PASS
TMC3	342125	broad.mit.edu	37	15	81654635	81654635	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:81654635C>T	uc002bgo.1	-	4	320	c.320G>A	c.(319-321)CGG>CAG	p.R107Q	TMC3_uc010blr.1_RNA|TMC3_uc002bgp.2_Missense_Mutation_p.R107Q	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	107	Cytoplasmic (Potential).					integral to membrane				ovary(1)|liver(1)	2						AGCAAATTTCCGCCAGAGCTA	0.468													18	22	---	---	---	---	PASS
ALPK3	57538	broad.mit.edu	37	15	85405880	85405880	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:85405880G>A	uc002ble.2	+	10	4917	c.4750G>A	c.(4750-4752)GAG>AAG	p.E1584K	ALPK3_uc010upc.1_5'Flank	NM_020778	NP_065829	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1584					heart development	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(3)|ovary(3)|lung(2)|skin(2)|central_nervous_system(1)|breast(1)	12			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGAAGAGATTGAGATGACCCC	0.572													30	47	---	---	---	---	PASS
WDR93	56964	broad.mit.edu	37	15	90260146	90260146	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:90260146C>T	uc002boj.2	+	7	862	c.761C>T	c.(760-762)TCC>TTC	p.S254F	WDR93_uc010bnr.2_Missense_Mutation_p.S254F	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	254					electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TCTCAGAACTCCCTTGGTCCC	0.338													9	58	---	---	---	---	PASS
C15orf51	196968	broad.mit.edu	37	15	100331935	100331935	+	RNA	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:100331935G>A	uc010urx.1	-	5		c.2257C>T			C15orf51_uc010ury.1_RNA	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						CCTGCCTTCTGATTTCTCTGG	0.572													7	33	---	---	---	---	PASS
PCSK6	5046	broad.mit.edu	37	15	101970216	101970216	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:101970216C>T	uc002bwy.2	-	6	1024	c.710G>A	c.(709-711)CGA>CAA	p.R237Q	PCSK6_uc010bpd.2_Missense_Mutation_p.R107Q|PCSK6_uc010bpe.2_Missense_Mutation_p.R237Q|PCSK6_uc002bxa.2_Missense_Mutation_p.R237Q|PCSK6_uc002bxb.2_Missense_Mutation_p.R237Q|PCSK6_uc002bxc.1_Missense_Mutation_p.R237Q|PCSK6_uc002bxd.1_Missense_Mutation_p.R237Q|PCSK6_uc002bxe.2_Missense_Mutation_p.R237Q|PCSK6_uc002bxg.1_Missense_Mutation_p.R237Q	NM_002570	NP_002561	P29122	PCSK6_HUMAN	paired basic amino acid cleaving system 4	237	Catalytic.				glycoprotein metabolic process|nerve growth factor processing|nerve growth factor production|nerve growth factor receptor signaling pathway|regulation of BMP signaling pathway|secretion by cell	cell surface|endomembrane system|endoplasmic reticulum|extracellular matrix|extracellular space|Golgi lumen|membrane|soluble fraction	eukaryotic cell surface binding|heparin binding|nerve growth factor binding|serine-type endopeptidase activity			pancreas(2)	2	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GGCATCATATCGTGGAGATGG	0.507													11	77	---	---	---	---	PASS
CHTF18	63922	broad.mit.edu	37	16	847697	847697	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:847697G>C	uc002cke.3	+	21	2800	c.2737G>C	c.(2737-2739)GAG>CAG	p.E913Q	CHTF18_uc002ckf.3_Missense_Mutation_p.E941Q|CHTF18_uc010brf.2_Missense_Mutation_p.E495Q|CHTF18_uc002ckg.3_Missense_Mutation_p.E431Q	NM_022092	NP_071375	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor	913					cell cycle|DNA replication	nucleus	ATP binding|DNA binding|nucleoside-triphosphatase activity			kidney(1)	1		Hepatocellular(780;0.00335)				CCATCAGCCTGAGAAGGACTT	0.612													15	39	---	---	---	---	PASS
SRRM2	23524	broad.mit.edu	37	16	2815495	2815495	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:2815495G>T	uc002crk.2	+	11	5515	c.4966G>T	c.(4966-4968)GAG>TAG	p.E1656*	SRRM2_uc002crj.1_Nonsense_Mutation_p.E1560*|SRRM2_uc002crl.1_Nonsense_Mutation_p.E1656*|SRRM2_uc010bsu.1_Nonsense_Mutation_p.E1560*	NM_016333	NP_057417	Q9UQ35	SRRM2_HUMAN	splicing coactivator subunit SRm300	1656	Ser-rich.					Cajal body|catalytic step 2 spliceosome|nuclear speck	C2H2 zinc finger domain binding|protein N-terminus binding|RNA binding			ovary(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4						CAGCAGTACCGAGTCCTCTCC	0.572													4	35	---	---	---	---	PASS
ZNF263	10127	broad.mit.edu	37	16	3339825	3339825	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:3339825G>T	uc002cuq.2	+	6	1651	c.1319G>T	c.(1318-1320)GGG>GTG	p.G440V	ZNF263_uc010uww.1_Missense_Mutation_p.G88V|ZNF263_uc002cur.2_Missense_Mutation_p.G88V	NM_005741	NP_005732	O14978	ZN263_HUMAN	zinc finger protein 263	440	C2H2-type 2.				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(3)|ovary(1)	4						CTTGAATGTGGGAAATGCTTC	0.532													7	69	---	---	---	---	PASS
BTBD12	84464	broad.mit.edu	37	16	3633448	3633448	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:3633448G>T	uc002cvp.2	-	14	5430	c.4803C>A	c.(4801-4803)TAC>TAA	p.Y1601*		NM_032444	NP_115820	Q8IY92	SLX4_HUMAN	BTB (POZ) domain containing 12	1601	Interaction with MUS81.|Interaction with PLK1 and TERF2-TERF2IP.				DNA double-strand break processing involved in repair via single-strand annealing|double-strand break repair via homologous recombination|nucleotide-excision repair	Slx1-Slx4 complex	enzyme activator activity|protein binding				0						TCTGGTGAGTGTACTGGAATA	0.597								Direct_reversal_of_damage|Homologous_recombination	Fanconi_Anemia				5	126	---	---	---	---	PASS
C16orf68	79091	broad.mit.edu	37	16	8722882	8722882	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:8722882G>T	uc002cyz.2	+	3	705	c.429G>T	c.(427-429)AAG>AAT	p.K143N	C16orf68_uc002cza.2_Intron	NM_024109	NP_077014	Q9BUU2	MET22_HUMAN	hypothetical protein LOC79091	143							methyltransferase activity				0						TGAGAGACAAGGTACATCCCA	0.537													8	220	---	---	---	---	PASS
GRIN2A	2903	broad.mit.edu	37	16	9857084	9857084	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:9857084G>T	uc002czo.3	-	13	4865	c.4317C>A	c.(4315-4317)TAC>TAA	p.Y1439*	GRIN2A_uc010uym.1_Nonsense_Mutation_p.Y1439*|GRIN2A_uc010uyn.1_3'UTR|GRIN2A_uc002czr.3_3'UTR	NM_001134407	NP_001127879	Q12879	NMDE1_HUMAN	N-methyl-D-aspartate receptor subunit 2A isoform	1439	Cytoplasmic (Potential).				response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			skin(32)|NS(5)|ovary(4)|large_intestine(1)|lung(1)|breast(1)|kidney(1)	45					Felbamate(DB00949)|Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TGGGGGTAGAGTACATATTAT	0.403													11	32	---	---	---	---	PASS
XYLT1	64131	broad.mit.edu	37	16	17292262	17292262	+	Missense_Mutation	SNP	A	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:17292262A>C	uc002dfa.2	-	5	1181	c.1096T>G	c.(1096-1098)TAC>GAC	p.Y366D		NM_022166	NP_071449	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	366	Lumenal (Potential).				glycosaminoglycan biosynthetic process	endoplasmic reticulum membrane|extracellular region|Golgi membrane|integral to membrane	acetylglucosaminyltransferase activity|protein xylosyltransferase activity			ovary(4)	4						CGATGCAGGTAATTAGAGCGC	0.587													10	28	---	---	---	---	PASS
TMC5	79838	broad.mit.edu	37	16	19475265	19475265	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:19475265C>G	uc002dgc.3	+	8	2153	c.1404C>G	c.(1402-1404)TTC>TTG	p.F468L	TMC5_uc010vaq.1_Missense_Mutation_p.F468L|TMC5_uc002dgb.3_Missense_Mutation_p.F468L|TMC5_uc010var.1_Missense_Mutation_p.F468L|TMC5_uc002dgd.1_Missense_Mutation_p.F222L|TMC5_uc002dge.3_Missense_Mutation_p.F222L|TMC5_uc002dgf.3_Missense_Mutation_p.F151L|TMC5_uc002dgg.3_Missense_Mutation_p.F109L	NM_001105248	NP_001098718	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5 isoform a	468	Helical; (Potential).					integral to membrane				skin(1)	1						TCCTGAACTTCAGCTTCATCA	0.458													16	37	---	---	---	---	PASS
ACSM2B	348158	broad.mit.edu	37	16	20548587	20548587	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:20548587G>A	uc002dhj.3	-	15	1937	c.1727C>T	c.(1726-1728)GCG>GTG	p.A576V	ACSM2B_uc002dhk.3_Missense_Mutation_p.A576V	NM_182617	NP_872423	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member	576					fatty acid metabolic process|xenobiotic metabolic process	mitochondrial matrix	ATP binding|butyrate-CoA ligase activity|CoA-ligase activity|metal ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5						GCCTCACTGCGCACGGGCTTT	0.463													36	86	---	---	---	---	PASS
DNAH3	55567	broad.mit.edu	37	16	21151983	21151983	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:21151983C>A	uc010vbe.1	-	5	570	c.570G>T	c.(568-570)GAG>GAT	p.E190D	DNAH3_uc002die.2_Missense_Mutation_p.E161D	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	190	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		ATGTCTTTACCTCCTTCTTCA	0.468													6	72	---	---	---	---	PASS
DCTN5	84516	broad.mit.edu	37	16	23677023	23677023	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:23677023C>A	uc002dly.1	+	5	482	c.425C>A	c.(424-426)CCA>CAA	p.P142Q		NM_032486	NP_115875	Q9BTE1	DCTN5_HUMAN	dynactin 5	142						centrosome	transferase activity			upper_aerodigestive_tract(1)	1				GBM - Glioblastoma multiforme(48;0.0156)		GTGGTTCCACCATTCACTGTC	0.393													5	34	---	---	---	---	PASS
PLK1	5347	broad.mit.edu	37	16	23701356	23701356	+	Missense_Mutation	SNP	C	T	T	rs34001032	byFrequency	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:23701356C>T	uc002dlz.1	+	10	1837	c.1784C>T	c.(1783-1785)TCG>TTG	p.S595L		NM_005030	NP_005021	P53350	PLK1_HUMAN	polo-like kinase 1	595					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|G2/M transition DNA damage checkpoint|G2/M transition of mitotic cell cycle|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic prophase|negative regulation of cyclin-dependent protein kinase activity|peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|protein localization to chromatin|protein ubiquitination|regulation of mitotic anaphase|regulation of protein binding	centrosome|condensed nuclear chromosome outer kinetochore|cytosol|nucleoplasm|spindle microtubule|spindle midzone|spindle pole	anaphase-promoting complex binding|ATP binding|polo kinase kinase activity|protein kinase binding			lung(1)|skin(1)	2				GBM - Glioblastoma multiforme(48;0.0156)		AGCTCACGCTCGGCCAGCAAC	0.652													5	19	---	---	---	---	PASS
CD19	930	broad.mit.edu	37	16	28943342	28943342	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:28943342C>A	uc002drs.2	+	1	83	c.21C>A	c.(19-21)CTC>CTA	p.L7L	uc010vct.1_Intron|CD19_uc010byo.1_Silent_p.L7L	NM_001770	NP_001761	P15391	CD19_HUMAN	CD19 antigen precursor	7					cellular defense response	external side of plasma membrane|integral to plasma membrane	protein binding|receptor signaling protein activity			ovary(2)|central_nervous_system(1)	3						CTCGCCTCCTCTTCTTCCTCC	0.557													6	80	---	---	---	---	PASS
ITGAD	3681	broad.mit.edu	37	16	31425870	31425870	+	Silent	SNP	C	A	A	rs149370240	by1000genomes	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:31425870C>A	uc002ebv.1	+	17	2144	c.2095C>A	c.(2095-2097)CGA>AGA	p.R699R	ITGAD_uc010cap.1_Silent_p.R700R	NM_005353	NP_005344	Q13349	ITAD_HUMAN	integrin, alpha D precursor	699	Extracellular (Potential).				cell-cell adhesion|cell-matrix adhesion|immune response|integrin-mediated signaling pathway	integrin complex	receptor activity			skin(1)	1						CACTTTGACTCGAAGAAAAAC	0.522													8	366	---	---	---	---	PASS
ABCC11	85320	broad.mit.edu	37	16	48212568	48212568	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:48212568C>A	uc002eff.1	-	23	3638	c.3288G>T	c.(3286-3288)CGG>CGT	p.R1096R	ABCC11_uc002efg.1_Silent_p.R1096R|ABCC11_uc002efh.1_Silent_p.R1096R|ABCC11_uc010cbg.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	1096	Cytoplasmic (Potential).|ABC transmembrane type-1 2.					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				CCAAGCCAATCCGGGCAGTGG	0.582									Cerumen_Type				10	22	---	---	---	---	PASS
NOD2	64127	broad.mit.edu	37	16	50759418	50759418	+	Silent	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:50759418C>G	uc002egm.1	+	10	3006	c.2901C>G	c.(2899-2901)CTC>CTG	p.L967L	NOD2_uc010vgq.1_Silent_p.L12L	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain	967	LRR 7.				activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|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	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding			ovary(3)|skin(1)	4		all_cancers(37;0.0156)				AGAACCATCTCCAGGATGAAG	0.413													22	39	---	---	---	---	PASS
SLC6A2	6530	broad.mit.edu	37	16	55719166	55719166	+	Silent	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:55719166C>G	uc002eif.2	+	5	867	c.756C>G	c.(754-756)CTC>CTG	p.L252L	SLC6A2_uc010ccd.2_Silent_p.L252L|SLC6A2_uc002eig.2_Silent_p.L252L|SLC6A2_uc002eih.2_Silent_p.L252L|SLC6A2_uc002eii.2_Silent_p.L147L|SLC6A2_uc002eij.2_Silent_p.L11L	NM_001043	NP_001034	P23975	SC6A2_HUMAN	solute carrier family 6 member 2	252	Helical; Name=4; (Potential).				synaptic transmission	integral to plasma membrane|membrane fraction	norepinephrine:sodium symporter activity			lung(4)|ovary(2)|pancreas(2)	8				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Atomoxetine(DB00289)|Bethanidine(DB00217)|Bupropion(DB01156)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Diethylpropion(DB00937)|Doxepin(DB01142)|Duloxetine(DB00476)|Ergotamine(DB00696)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Maprotiline(DB00934)|Mazindol(DB00579)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)	ATTTTAGCCTCTGGAAAGGGG	0.483													19	67	---	---	---	---	PASS
SLC6A2	6530	broad.mit.edu	37	16	55731808	55731808	+	Splice_Site	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:55731808G>T	uc002eif.2	+	10	1372	c.1261_splice	c.e10-1	p.M421_splice	SLC6A2_uc010ccd.2_Splice_Site_p.M421_splice|SLC6A2_uc002eig.2_Splice_Site_p.M421_splice|SLC6A2_uc002eih.2_Splice_Site_p.M421_splice|SLC6A2_uc002eii.2_Splice_Site_p.M316_splice|SLC6A2_uc002eij.2_Splice_Site_p.M135_splice	NM_001043	NP_001034	P23975	SC6A2_HUMAN	solute carrier family 6 member 2						synaptic transmission	integral to plasma membrane|membrane fraction	norepinephrine:sodium symporter activity			lung(4)|ovary(2)|pancreas(2)	8				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amineptine(DB04836)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Atomoxetine(DB00289)|Bethanidine(DB00217)|Bupropion(DB01156)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Diethylpropion(DB00937)|Doxepin(DB01142)|Duloxetine(DB00476)|Ergotamine(DB00696)|Guanadrel Sulfate(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Maprotiline(DB00934)|Mazindol(DB00579)|Methylphenidate(DB00422)|Milnacipran(DB04896)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Paroxetine(DB00715)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GTTCCCTCCAGATGGGAGGCA	0.597													7	19	---	---	---	---	PASS
CDH8	1006	broad.mit.edu	37	16	61858997	61858997	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:61858997G>A	uc002eog.1	-	5	1006	c.754C>T	c.(754-756)CAC>TAC	p.H252Y	CDH8_uc002eoh.2_Missense_Mutation_p.H21Y	NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein	252	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CCACCAGAGTGTCCACCCATA	0.453													13	13	---	---	---	---	PASS
TMCO7	79613	broad.mit.edu	37	16	68893908	68893908	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:68893908C>A	uc002ewi.3	+	2	228	c.216C>A	c.(214-216)CTC>CTA	p.L72L	TMCO7_uc002ewh.2_Silent_p.L72L	NM_024562	NP_078838	Q9C0B7	TMCO7_HUMAN	transmembrane and coiled-coil domains 7	72						integral to membrane	binding				0		Ovarian(137;0.0568)		OV - Ovarian serous cystadenocarcinoma(108;0.0446)|Epithelial(162;0.198)		ATCTGAAACTCCTAAGAGATG	0.408													5	48	---	---	---	---	PASS
ZNF23	7571	broad.mit.edu	37	16	71483756	71483756	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:71483756C>A	uc002faf.2	-	6	986	c.172G>T	c.(172-174)GAA>TAA	p.E58*	ZNF23_uc002fad.2_5'UTR|ZNF23_uc002fae.2_5'UTR|ZNF23_uc010vmf.1_5'UTR|ZNF23_uc002fag.2_5'UTR|ZNF23_uc002fah.2_Nonsense_Mutation_p.E58*|ZNF23_uc002fai.2_Nonsense_Mutation_p.E97*	NM_145911	NP_666016	P17027	ZNF23_HUMAN	zinc finger protein 23	58					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		TCATACATTTCCTTTGTCAAA	0.333													11	17	---	---	---	---	PASS
ZFHX3	463	broad.mit.edu	37	16	72845851	72845851	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:72845851G>C	uc002fck.2	-	6	4289	c.3616C>G	c.(3616-3618)CTC>GTC	p.L1206V	ZFHX3_uc002fcl.2_Missense_Mutation_p.L292V	NM_006885	NP_008816	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3 isoform A	1206					muscle organ development|negative regulation of myoblast differentiation|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|positive regulation of myoblast differentiation	transcription factor complex	enzyme binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|transcription regulatory region DNA binding|zinc ion binding			ovary(2)|skin(2)	4		Ovarian(137;0.13)				TTCGAAGAGAGGGGAGACTCT	0.532													48	137	---	---	---	---	PASS
CMIP	80790	broad.mit.edu	37	16	81641237	81641237	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr16:81641237G>T	uc002fgp.2	+	2	438	c.366G>T	c.(364-366)TGG>TGT	p.W122C	CMIP_uc002fgq.1_Missense_Mutation_p.W28C|CMIP_uc010vnq.1_5'Flank	NM_198390	NP_938204	Q8IY22	CMIP_HUMAN	c-Maf-inducing protein isoform C-mip	88	PH.					cytoplasm|nucleus					0						TGCTGTCCTGGGAGAATGCCC	0.458													10	122	---	---	---	---	PASS
VPS53	55275	broad.mit.edu	37	17	613825	613825	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:613825C>A	uc002frn.2	-	2	263	c.116G>T	c.(115-117)CGA>CTA	p.R39L	VPS53_uc010cjo.1_Missense_Mutation_p.R39L|VPS53_uc002frl.2_RNA|VPS53_uc002frm.2_Missense_Mutation_p.R39L|VPS53_uc002fro.2_5'UTR|VPS53_uc010cjp.1_Missense_Mutation_p.R39L	NM_018289	NP_060759	Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 isoform 2	39					protein transport	endosome membrane|Golgi apparatus					0				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		GAAATCTGCTCGATCTAGAGG	0.328													4	48	---	---	---	---	PASS
SMYD4	114826	broad.mit.edu	37	17	1703966	1703966	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:1703966G>T	uc002ftm.3	-	5	890	c.722C>A	c.(721-723)CCT>CAT	p.P241H	SMYD4_uc002ftn.1_Missense_Mutation_p.P96H	NM_052928	NP_443160	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	241							zinc ion binding			skin(3)|kidney(2)	5						ACCTTTTAAAGGATCTACGCA	0.507													6	81	---	---	---	---	PASS
GABARAP	11337	broad.mit.edu	37	17	7144663	7144663	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:7144663G>T	uc002gfb.2	-	3	390	c.286C>A	c.(286-288)CAG>AAG	p.Q96K	PHF23_uc002gfa.2_5'Flank|PHF23_uc010vtt.1_5'Flank|PHF23_uc010cma.2_5'Flank	NM_007278	NP_009209	O95166	GBRAP_HUMAN	GABA(A) receptor-associated protein	96	Interaction with GPHN (By similarity).				protein targeting|synaptic transmission	autophagic vacuole membrane|Golgi membrane|microtubule|plasma membrane	beta-tubulin binding|GABA receptor binding				0						CACCATACCTGGTACAGCTGA	0.488													10	339	---	---	---	---	PASS
EIF4A1	1973	broad.mit.edu	37	17	7481668	7481668	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:7481668G>T	uc002gho.1	+	19	2410	c.1085G>T	c.(1084-1086)CGA>CTA	p.R362L	EIF4A1_uc002ghr.1_Silent_p.S341S|EIF4A1_uc002ghq.1_Silent_p.S335S|EIF4A1_uc002ghp.1_Missense_Mutation_p.R362L|CD68_uc002ghv.2_5'Flank|CD68_uc002ghu.2_5'Flank	NM_001416	NP_001407	P60842	IF4A1_HUMAN	eukaryotic translation initiation factor 4A	362	Helicase C-terminal.				nuclear-transcribed mRNA poly(A) tail shortening	cytosol|eukaryotic translation initiation factor 4F complex	ATP binding|ATP-dependent helicase activity|mRNA binding|protein binding|RNA cap binding|translation initiation factor activity			ovary(1)	1						AGAATCGGTCGAGGTGGACGG	0.507													4	58	---	---	---	---	PASS
TP53	7157	broad.mit.edu	37	17	7579494	7579494	+	Nonsense_Mutation	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:7579494T>A	uc002gim.2	-	4	387	c.193A>T	c.(193-195)AGA>TGA	p.R65*	TP53_uc002gig.1_Nonsense_Mutation_p.R65*|TP53_uc002gih.2_Nonsense_Mutation_p.R65*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Nonsense_Mutation_p.R65*|TP53_uc010cni.1_Nonsense_Mutation_p.R65*|TP53_uc002gij.2_Nonsense_Mutation_p.R65*|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Intron|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Nonsense_Mutation_p.R26*|TP53_uc010cnk.1_Nonsense_Mutation_p.R80*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	65	Interaction with HRMT1L2.		R -> T (in a sporadic cancer; 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.R65*(8)|p.0?(7)|p.G59fs*23(3)|p.264_265insSSGNL(1)|p.D48fs*55(1)|p.R65_P71delRMPEAAP(1)|p.P13fs*18(1)|p.R65fs*38(1)|p.D57_A76del20(1)|p.S33fs*23(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)		TCTGGCATTCTGGGAGCTTCA	0.617		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)			55	75	---	---	---	---	PASS
PIK3R6	146850	broad.mit.edu	37	17	8738701	8738701	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:8738701C>T	uc002glq.1	-	8	774	c.534G>A	c.(532-534)GCG>GCA	p.A178A	PIK3R6_uc002glr.1_RNA|PIK3R6_uc002gls.1_RNA	NM_001010855	NP_001010855	Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6	178					platelet activation	cytosol					0						GCGCCTGGGCCGCCTCGATCT	0.652													8	17	---	---	---	---	PASS
MYH3	4621	broad.mit.edu	37	17	10542913	10542913	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:10542913G>T	uc002gmq.1	-	22	2966	c.2889C>A	c.(2887-2889)GCC>GCA	p.A963A		NM_002470	NP_002461	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle,	963	Potential.				muscle filament sliding|muscle organ development	cytosol|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|central_nervous_system(2)|pancreas(1)	7						TCTCAACCTTGGCCAGGGTCA	0.433													40	78	---	---	---	---	PASS
ELAC2	60528	broad.mit.edu	37	17	12897091	12897091	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:12897091C>T	uc002gnz.3	-	23	2261	c.2166G>A	c.(2164-2166)CTG>CTA	p.L722L	ELAC2_uc002gnu.3_Silent_p.L119L|ELAC2_uc002gnv.3_Silent_p.L350L|ELAC2_uc002gnw.3_Silent_p.L378L|ELAC2_uc002gnx.3_Silent_p.L482L|ELAC2_uc010vvo.1_Silent_p.L520L|ELAC2_uc010vvp.1_Silent_p.L703L|ELAC2_uc010vvq.1_Silent_p.L721L|ELAC2_uc010vvr.1_Silent_p.L682L	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2 isoform 1	722					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0						TGAAGTGGTTCAGCATAATGA	0.547									Hereditary_Prostate_Cancer				18	24	---	---	---	---	PASS
FLCN	201163	broad.mit.edu	37	17	17127237	17127237	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:17127237T>C	uc002gra.3	-	6	1121	c.617A>G	c.(616-618)AAG>AGG	p.K206R	PLD6_uc010cpn.2_Intron|FLCN_uc002grb.3_Missense_Mutation_p.K206R	NM_144997	NP_659434	Q8NFG4	FLCN_HUMAN	folliculin isoform 1	206					regulation of protein phosphorylation	cytoplasm|nucleus|plasma membrane	protein binding			thyroid(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)	3						TGAATTCACCTTGAGCGCCTT	0.622									Birt-Hogg-Dub__syndrome|Familial_Non-VHL_Clear_Cell_Renal_Cancer				8	5	---	---	---	---	PASS
SHMT1	6470	broad.mit.edu	37	17	18250933	18250933	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:18250933C>A	uc002gta.2	-	5	586	c.396G>T	c.(394-396)GTG>GTT	p.V132V	SHMT1_uc002gtb.2_Silent_p.V132V|SHMT1_uc010cqb.2_Silent_p.V132V|SHMT1_uc010vxt.1_5'UTR|SHMT1_uc002gtd.1_Silent_p.V132V|SHMT1_uc010vxu.1_Silent_p.V132V	NM_004169	NP_004160	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	132					carnitine biosynthetic process|folic acid metabolic process|L-serine catabolic process|one-carbon metabolic process|purine base biosynthetic process	cytosol|nucleus	glycine hydroxymethyltransferase activity|protein homodimerization activity|pyridoxal phosphate binding			ovary(1)	1					Glycine(DB00145)|Mimosine(DB01055)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	CATGGGGTTCCACCAGGGCAG	0.552													31	22	---	---	---	---	PASS
NEK8	284086	broad.mit.edu	37	17	27064326	27064326	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:27064326C>G	uc002hcp.2	+	5	621	c.621C>G	c.(619-621)AAC>AAG	p.N207K		NM_178170	NP_835464	Q86SG6	NEK8_HUMAN	NIMA-related kinase 8	207	Protein kinase.					cytoplasm|primary cilium	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			stomach(2)|ovary(1)|pancreas(1)|liver(1)|skin(1)	6	Lung NSC(42;0.0158)					CTTCACAGAACTTGCCAGCAC	0.547													4	6	---	---	---	---	PASS
AMAC1	146861	broad.mit.edu	37	17	33520358	33520358	+	Silent	SNP	A	G	G	rs74740601	by1000genomes	TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:33520358A>G	uc002hjd.2	-	1	1055	c.969T>C	c.(967-969)ATT>ATC	p.I323I		NM_152462	NP_689675	Q8N808	AMAC1_HUMAN	acyl-malonyl condensing enzyme 1	323	DUF6 2.|Helical; (Potential).					integral to membrane					0				BRCA - Breast invasive adenocarcinoma(366;0.0917)		TCTGGGCTGTAATGATGGCAA	0.547													3	72	---	---	---	---	PASS
SRCIN1	80725	broad.mit.edu	37	17	36734771	36734771	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:36734771C>A	uc002hqd.2	-	2	521	c.296G>T	c.(295-297)CGA>CTA	p.R99L	SRCIN1_uc002hqh.1_Missense_Mutation_p.R133L	NM_025248	NP_079524	Q9C0H9	SRCN1_HUMAN	SNAP25-interacting protein	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					exocytosis|negative regulation of protein tyrosine kinase activity|positive regulation of protein tyrosine kinase activity|regulation of cell migration|regulation of dendritic spine morphogenesis|substrate adhesion-dependent cell spreading	actin cytoskeleton|axon|cell junction|cytoplasm|dendrite|postsynaptic density|postsynaptic membrane	protein kinase binding				0						CTGCTGGCCTCGCAGGGCCAG	0.706													11	11	---	---	---	---	PASS
KPNB1	3837	broad.mit.edu	37	17	45755688	45755688	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:45755688G>T	uc002ilt.1	+	19	2598	c.2262G>T	c.(2260-2262)ATG>ATT	p.M754I	KPNB1_uc010wkw.1_Missense_Mutation_p.M609I|KPNB1_uc010wkx.1_Missense_Mutation_p.M538I	NM_002265	NP_002256	Q14974	IMB1_HUMAN	karyopherin beta 1	754					DNA fragmentation involved in apoptotic nuclear change|NLS-bearing substrate import into nucleus|protein import into nucleus, translocation|ribosomal protein import into nucleus|viral genome transport in host cell|viral infectious cycle	cytosol|nuclear pore|nucleoplasm	nuclear localization sequence binding|protein domain specific binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3						ACTATGACATGGTGGATTATC	0.438													6	54	---	---	---	---	PASS
COL1A1	1277	broad.mit.edu	37	17	48278790	48278790	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:48278790C>T	uc002iqm.2	-	1	211	c.85G>A	c.(85-87)GAG>AAG	p.E29K		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	29					axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)	TCTTGGCCCTCGACTTGGCCT	0.587			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						8	22	---	---	---	---	PASS
CA10	56934	broad.mit.edu	37	17	50008392	50008392	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:50008392G>T	uc002itw.3	-	3	1223	c.237C>A	c.(235-237)GAC>GAA	p.D79E	CA10_uc002itv.3_Missense_Mutation_p.D85E|CA10_uc002itx.3_Missense_Mutation_p.D79E|CA10_uc002ity.3_Missense_Mutation_p.D79E|CA10_uc002itz.2_Missense_Mutation_p.D79E	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	79					brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			TCAGAAAGGGGTCGAAGATCA	0.498													32	72	---	---	---	---	PASS
HLF	3131	broad.mit.edu	37	17	53392768	53392768	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:53392768T>C	uc002iug.1	+	3	1157	c.632T>C	c.(631-633)ATC>ACC	p.I211T	HLF_uc010dce.1_Missense_Mutation_p.I126T|HLF_uc002iuh.2_Missense_Mutation_p.I126T|HLF_uc010wni.1_Missense_Mutation_p.I158T	NM_002126	NP_002117	Q16534	HLF_HUMAN	hepatic leukemia factor	211					multicellular organismal development|rhythmic process|transcription from RNA polymerase II promoter	nucleus	double-stranded DNA binding|protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2						CAGCCCATGATCAAGAAAGCT	0.493			T	TCF3	ALL								4	41	---	---	---	---	PASS
APPBP2	10513	broad.mit.edu	37	17	58538126	58538126	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:58538126G>A	uc002iys.1	-	9	1247	c.959C>T	c.(958-960)TCA>TTA	p.S320L	APPBP2_uc010ddl.1_Missense_Mutation_p.S249L	NM_006380	NP_006371	Q92624	APBP2_HUMAN	amyloid beta precursor protein-binding protein	320	TPR 4.				intracellular protein transport	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|nucleus	microtubule motor activity|protein binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			ACCAAACACTGACTGTCTAAT	0.358													8	47	---	---	---	---	PASS
GPRC5C	55890	broad.mit.edu	37	17	72443069	72443069	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:72443069G>T	uc002jks.2	+	3	1267	c.1228G>T	c.(1228-1230)GCT>TCT	p.A410S	GPRC5C_uc002jkp.2_Missense_Mutation_p.A455S|GPRC5C_uc002jkq.2_3'UTR|GPRC5C_uc002jkr.2_Missense_Mutation_p.A422S|GPRC5C_uc002jkt.2_Missense_Mutation_p.A410S|GPRC5C_uc002jku.2_Missense_Mutation_p.A165S	NM_018653	NP_061123	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor family C, group 5,	410	Cytoplasmic (Potential).					cytoplasmic vesicle membrane|integral to plasma membrane	G-protein coupled receptor activity|protein binding			ovary(2)|prostate(1)|central_nervous_system(1)|pancreas(1)	5						GACCCTGCGGGCTGAAGACAT	0.607													8	45	---	---	---	---	PASS
GRIN2C	2905	broad.mit.edu	37	17	72840421	72840421	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:72840421G>A	uc002jlt.1	-	12	2733	c.2577C>T	c.(2575-2577)TTC>TTT	p.F859F	GRIN2C_uc010wrh.1_RNA|GRIN2C_uc002jlu.1_Silent_p.F859F	NM_000835	NP_000826	Q14957	NMDE3_HUMAN	N-methyl-D-aspartate receptor subunit 2C	859	Cytoplasmic (Potential).				glutamate signaling pathway	cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|N-methyl-D-aspartate selective glutamate receptor activity			ovary(2)|breast(2)	4	all_lung(278;0.172)|Lung NSC(278;0.207)				Glycine(DB00145)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)	CCACCCTGCTGAAAGCCAGCA	0.617													10	40	---	---	---	---	PASS
UBE2O	63893	broad.mit.edu	37	17	74394450	74394450	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:74394450C>A	uc002jrm.3	-	12	1976	c.1911G>T	c.(1909-1911)GAG>GAT	p.E637D	UBE2O_uc002jrn.3_Missense_Mutation_p.E637D|UBE2O_uc002jrl.3_Missense_Mutation_p.E240D	NM_022066	NP_071349	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	637							ATP binding|ubiquitin-protein ligase activity			breast(2)|skin(2)|lung(1)	5						TCACATCTTCCTCTTCTCCAA	0.547											OREG0024751	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	420	---	---	---	---	PASS
ENGASE	64772	broad.mit.edu	37	17	77077136	77077136	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:77077136G>A	uc002jwv.2	+	6	861	c.853G>A	c.(853-855)GAA>AAA	p.E285K	ENGASE_uc002jwu.1_Missense_Mutation_p.E285K|ENGASE_uc010wtz.1_Missense_Mutation_p.E99K|ENGASE_uc002jww.2_5'UTR	NM_001042573	NP_001036038	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	285						cytosol	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity			skin(1)	1						ATGGCAAGACGAACTCAACCA	0.652													5	11	---	---	---	---	PASS
ENPP7	339221	broad.mit.edu	37	17	77707323	77707323	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:77707323C>G	uc002jxa.2	+	2	291	c.271C>G	c.(271-273)CAC>GAC	p.H91D		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase	91					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			central_nervous_system(2)|ovary(1)	3			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TATCGAGAACCACGGGGTGGT	0.617													33	98	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	78282825	78282825	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr17:78282825G>T	uc002jyf.2	+	14	2652	c.2509G>T	c.(2509-2511)GAG>TAG	p.E837*	uc002jyg.1_Nonsense_Mutation_p.E568*	NM_020954	NP_066005			hypothetical protein LOC57714																		CAGGATTCCCGAGGAGGCCTT	0.478													7	94	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3129295	3129295	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:3129295G>T	uc002klp.2	-	18	3063	c.2729C>A	c.(2728-2730)CCA>CAA	p.P910Q	MYOM1_uc002klq.2_Intron	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	910						striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						TTTCTGTGGTGGCGGGGTAAG	0.488											OREG0024838	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	91	---	---	---	---	PASS
MYOM1	8736	broad.mit.edu	37	18	3187488	3187488	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:3187488G>T	uc002klp.2	-	5	1253	c.919C>A	c.(919-921)CGT>AGT	p.R307S	MYOM1_uc002klq.2_Missense_Mutation_p.R307S	NM_003803	NP_003794	P52179	MYOM1_HUMAN	myomesin 1 isoform a	307	Ig-like C2-type 1.					striated muscle myosin thick filament	structural constituent of muscle			ovary(3)|central_nervous_system(1)|pancreas(1)	5						CACGTGACACGAGGTTCTGGC	0.438													8	247	---	---	---	---	PASS
AFG3L2	10939	broad.mit.edu	37	18	12358705	12358705	+	Silent	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:12358705T>A	uc002kqz.1	-	8	1103	c.990A>T	c.(988-990)CCA>CCT	p.P330P		NM_006796	NP_006787	Q9Y4W6	AFG32_HUMAN	AFG3 ATPase family gene 3-like 2	330					cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)	GATACTGCTTTGGGTTTTTCA	0.353													6	55	---	---	---	---	PASS
PSMA8	143471	broad.mit.edu	37	18	23731821	23731821	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:23731821G>T	uc002kvq.2	+	3	361	c.247G>T	c.(247-249)GGA>TGA	p.G83*	PSMA8_uc002kvo.2_Splice_Site_p.G39_splice|PSMA8_uc002kvp.2_Splice_Site_p.G77_splice|PSMA8_uc002kvr.2_Splice_Site_p.G51_splice	NM_144662	NP_653263	Q8TAA3	PSA7L_HUMAN	proteasome alpha 8 subunit isoform 1	83					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|M/G1 transition of mitotic cell cycle|mRNA metabolic process|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|regulation of apoptosis|regulation of cellular amino acid metabolic process|S phase of mitotic cell cycle|viral reproduction	cytoplasm|nucleus|proteasome core complex, alpha-subunit complex	threonine-type endopeptidase activity			skin(1)	1	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			AATTTTTATAGGACTTACTGC	0.353													7	147	---	---	---	---	PASS
CHST9	83539	broad.mit.edu	37	18	24722673	24722673	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:24722673C>A	uc002kwd.2	-	1	299	c.101G>T	c.(100-102)TGG>TTG	p.W34L	C18orf16_uc010xbm.1_Intron|CHST9_uc002kwe.2_Missense_Mutation_p.W34L	NM_031422	NP_113610	Q7L1S5	CHST9_HUMAN	GalNAc-4-sulfotransferase 2	34	Lumenal (Potential).				carbohydrate biosynthetic process|glycosaminoglycan metabolic process|hormone biosynthetic process|proteoglycan biosynthetic process|sulfur compound metabolic process	extracellular region|Golgi membrane|integral to membrane	N-acetylgalactosamine 4-O-sulfotransferase activity			ovary(2)|skin(1)	3	all_lung(6;0.0145)|Ovarian(20;0.124)					TTCTTCAATCCAGACTTGCAA	0.348													7	120	---	---	---	---	PASS
TCEB3C	162699	broad.mit.edu	37	18	44555132	44555132	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:44555132G>T	uc010xdb.1	-	1	1318	c.1082C>A	c.(1081-1083)TCG>TAG	p.S361*	KATNAL2_uc010dnq.1_Intron|KATNAL2_uc002lco.2_Intron|KATNAL2_uc002lcp.3_Intron	NM_145653	NP_663628	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide	361	Activation domain (By similarity).				regulation of transcription, DNA-dependent|transcription, DNA-dependent	integral to membrane|nucleus	DNA binding				0						TTCAAGAACCGAGTAGGGGAC	0.627													10	453	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56202524	56202524	+	Missense_Mutation	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:56202524A>G	uc002lhj.3	-	5	5109	c.4895T>C	c.(4894-4896)ATA>ACA	p.I1632T	ALPK2_uc002lhk.1_Missense_Mutation_p.I963T	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	1632							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						AAGCACCTCTATTTTAGGTTC	0.448													9	29	---	---	---	---	PASS
PHLPP1	23239	broad.mit.edu	37	18	60563036	60563036	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:60563036G>T	uc002lis.2	+	7	878	c.700G>T	c.(700-702)GGA>TGA	p.G234*		NM_194449	NP_919431	O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein	746	LRR 5.				apoptosis|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling	cytosol|membrane|nucleus	metal ion binding|protein serine/threonine phosphatase activity				0						TTTGTTGGATGGAAACTTTCT	0.328													5	63	---	---	---	---	PASS
GALR1	2587	broad.mit.edu	37	18	74962936	74962936	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:74962936C>A	uc002lms.3	+	1	929	c.432C>A	c.(430-432)TCC>TCA	p.S144S		NM_001480	NP_001471	P47211	GALR1_HUMAN	galanin receptor 1	144	Cytoplasmic (Potential).				digestion|negative regulation of adenylate cyclase activity	integral to membrane|plasma membrane	galanin receptor activity			lung(1)	1		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		GGCGCTCCTCCTCCCTCAGGG	0.667													12	18	---	---	---	---	PASS
SALL3	27164	broad.mit.edu	37	18	76753968	76753968	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr18:76753968G>A	uc002lmt.2	+	2	1977	c.1977G>A	c.(1975-1977)TCG>TCA	p.S659S	SALL3_uc010dra.2_Silent_p.S266S	NM_171999	NP_741996	Q9BXA9	SALL3_HUMAN	sal-like 3	659					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|large_intestine(1)|central_nervous_system(1)	4		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		TGCAAACGTCGGAAACCTCGA	0.647													11	11	---	---	---	---	PASS
CIRBP	1153	broad.mit.edu	37	19	1271623	1271623	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:1271623C>A	uc002lrr.3	+	5	572	c.423C>A	c.(421-423)TAC>TAA	p.Y141*	C19orf23_uc010xgk.1_5'Flank|CIRBP_uc010dsg.1_Nonsense_Mutation_p.Y130*|CIRBP_uc002lrt.2_Nonsense_Mutation_p.Y141*|CIRBP_uc010xgl.1_Nonsense_Mutation_p.Y107*|CIRBP_uc002lrv.3_Nonsense_Mutation_p.Y141*|CIRBP_uc002lru.2_RNA	NM_001280	NP_001271	Q14011	CIRBP_HUMAN	cold inducible RNA binding protein	141	Gly-rich.				mRNA stabilization|positive regulation of translation|response to cold|response to UV|stress granule assembly	nucleoplasm|stress granule	mRNA 3'-UTR binding|nucleotide binding|protein binding|SSU rRNA binding|translation repressor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000332)|all_lung(49;0.000498)|Breast(49;0.0014)		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)		CCAGAGACTACTATAGCAGGT	0.642													3	8	---	---	---	---	PASS
TJP3	27134	broad.mit.edu	37	19	3738570	3738570	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:3738570C>G	uc010xhv.1	+	11	1401	c.1401C>G	c.(1399-1401)TTC>TTG	p.F467L	TJP3_uc010xhs.1_Missense_Mutation_p.F434L|TJP3_uc010xht.1_Missense_Mutation_p.F398L|TJP3_uc010xhu.1_Missense_Mutation_p.F443L|TJP3_uc010xhw.1_Missense_Mutation_p.F453L	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	448	PDZ 3.					tight junction	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGTGCCATTCCAGAACCTGA	0.577													28	47	---	---	---	---	PASS
TJP3	27134	broad.mit.edu	37	19	3738989	3738989	+	Silent	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:3738989C>T	uc010xhv.1	+	12	1587	c.1587C>T	c.(1585-1587)TTC>TTT	p.F529F	TJP3_uc010xhs.1_Silent_p.F496F|TJP3_uc010xht.1_Silent_p.F460F|TJP3_uc010xhu.1_Silent_p.F505F|TJP3_uc010xhw.1_Silent_p.F515F	NM_014428	NP_055243	O95049	ZO3_HUMAN	tight junction protein 3	510	SH3.					tight junction	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCTGGGCTTCACCCGTGGCG	0.662													18	16	---	---	---	---	PASS
KIAA1543	57662	broad.mit.edu	37	19	7675643	7675643	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:7675643G>T	uc002mgv.3	+	7	1059	c.958G>T	c.(958-960)GAC>TAC	p.D320Y	KIAA1543_uc002mgu.3_Missense_Mutation_p.D347Y	NM_020902	NP_065953	Q9P1Y5	CAMP3_HUMAN	NEZHA isoform 2	320					epithelial cell-cell adhesion|microtubule anchoring|regulation of microtubule cytoskeleton organization|zonula adherens maintenance	cytoplasm|microtubule|zonula adherens	microtubule minus-end binding			pancreas(1)	1						GCTCAAGCCCGACTTTGTGCA	0.667													6	87	---	---	---	---	PASS
ZNF559	84527	broad.mit.edu	37	19	9449884	9449884	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:9449884G>C	uc002mlg.2	+	5	696	c.49G>C	c.(49-51)GAG>CAG	p.E17Q	ZNF559_uc002mlf.2_5'UTR|ZNF559_uc010dwl.1_5'UTR|ZNF559_uc010xkn.1_Intron|ZNF559_uc010dwm.1_Missense_Mutation_p.E17Q|ZNF559_uc002mle.3_Missense_Mutation_p.E81Q|ZNF559_uc010dwk.1_5'UTR|ZNF559_uc002mld.2_Missense_Mutation_p.E81Q|ZNF559_uc010dwo.1_Missense_Mutation_p.E45Q|ZNF559_uc002mlh.1_RNA|ZNF177_uc002mli.2_Intron|ZNF177_uc002mlj.2_Intron	NM_032497	NP_115886	Q9BR84	ZN559_HUMAN	zinc finger protein 559	17	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AGTGACCTTTGAGGATGTGGC	0.478													4	59	---	---	---	---	PASS
ZSWIM4	65249	broad.mit.edu	37	19	13941475	13941475	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:13941475G>T	uc002mxh.1	+	13	2770	c.2581G>T	c.(2581-2583)GAG>TAG	p.E861*	ZSWIM4_uc010xng.1_Nonsense_Mutation_p.E784*	NM_023072	NP_075560	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	861							zinc ion binding			central_nervous_system(2)	2			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			GGGCCGGCACGAGCTCTCTGC	0.657													5	118	---	---	---	---	PASS
RLN3	117579	broad.mit.edu	37	19	14141522	14141522	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:14141522G>T	uc002mxw.1	+	2	191	c.191G>T	c.(190-192)GGA>GTA	p.G64V	IL27RA_uc002mxx.2_5'Flank|RLN3_uc010dzj.1_Missense_Mutation_p.E101D	NM_080864	NP_543140	Q8WXF3	REL3_HUMAN	relaxin 3 preproprotein	64						extracellular region	hormone activity				0						TCTTTTGCAGGAGATACCTTC	0.567													6	81	---	---	---	---	PASS
BRD4	23476	broad.mit.edu	37	19	15349944	15349944	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:15349944C>A	uc002nar.2	-	18	3930	c.3708G>T	c.(3706-3708)GAG>GAT	p.E1236D		NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long	1236					interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			CCTTCTCACGCTCCTCTTTCT	0.662			T	NUT|C15orf55	lethal midline carcinoma of young people								5	13	---	---	---	---	PASS
TMEM38A	79041	broad.mit.edu	37	19	16791207	16791207	+	Splice_Site	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:16791207G>T	uc002nes.2	+	3	373	c.282_splice	c.e3-1	p.W94_splice		NM_024074	NP_076979	Q9H6F2	TM38A_HUMAN	transmembrane protein 38A							integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			central_nervous_system(2)|ovary(1)	3						CTCCCCAAAAGGTACTTGATT	0.547													10	330	---	---	---	---	PASS
ZNF85	7639	broad.mit.edu	37	19	21132556	21132556	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:21132556C>A	uc002npg.3	+	4	1363	c.1236C>A	c.(1234-1236)ACC>ACA	p.T412T	ZNF85_uc010ecn.2_Silent_p.T347T|ZNF85_uc010eco.2_Silent_p.T360T|ZNF85_uc002npi.2_Silent_p.T353T	NM_003429	NP_003420	Q03923	ZNF85_HUMAN	zinc finger protein 85	412	C2H2-type 10.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			central_nervous_system(1)	1						ACTCTTCAACCCTTACTAAAC	0.308													5	13	---	---	---	---	PASS
ZNF43	7594	broad.mit.edu	37	19	21990893	21990893	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:21990893G>C	uc002nqj.2	-	4	2076	c.1946C>G	c.(1945-1947)CCC>CGC	p.P649R	ZNF43_uc010ecv.2_Missense_Mutation_p.P643R|ZNF43_uc002nql.2_Missense_Mutation_p.P643R|ZNF43_uc002nqm.2_Missense_Mutation_p.P643R|ZNF43_uc002nqk.2_Missense_Mutation_p.P579R	NM_003423	NP_003414	P17038	ZNF43_HUMAN	zinc finger protein 43	649					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(1)|ovary(1)	2		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		ACATTTGTAGGGTTTCTCCTC	0.373													4	19	---	---	---	---	PASS
ZNF675	171392	broad.mit.edu	37	19	23836935	23836935	+	Missense_Mutation	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:23836935T>A	uc002nri.2	-	4	982	c.800A>T	c.(799-801)CAG>CTG	p.Q267L		NM_138330	NP_612203	Q8TD23	ZN675_HUMAN	zinc finger protein 675	267	C2H2-type 5.				bone resorption|cytokine-mediated signaling pathway|hemopoiesis|I-kappaB kinase/NF-kappaB cascade|negative regulation of JNK cascade|negative regulation of osteoclast differentiation|negative regulation of protein kinase activity|negative regulation of transcription, DNA-dependent|regulation of ossification|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding|zinc ion binding			ovary(1)|kidney(1)	2		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GTGTGAGGACTGGTTAAAGGC	0.358													6	28	---	---	---	---	PASS
ZNF681	148213	broad.mit.edu	37	19	23927658	23927658	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:23927658C>A	uc002nrk.3	-	4	836	c.694G>T	c.(694-696)GGC>TGC	p.G232C	ZNF681_uc002nrl.3_Missense_Mutation_p.G163C|ZNF681_uc002nrj.3_Missense_Mutation_p.G163C	NM_138286	NP_612143	Q96N22	ZN681_HUMAN	zinc finger protein 681	232	C2H2-type 3; degenerate.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				CAGGCTTTGCCACATTCTTCA	0.343													5	12	---	---	---	---	PASS
KIAA0355	9710	broad.mit.edu	37	19	34818703	34818703	+	Nonsense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:34818703G>T	uc002nvd.3	+	5	1733	c.874G>T	c.(874-876)GGA>TGA	p.G292*		NM_014686	NP_055501	O15063	K0355_HUMAN	hypothetical protein LOC9710	292										ovary(1)	1	Esophageal squamous(110;0.162)					GGAAAGCTTAGGACACTGTGA	0.383													6	85	---	---	---	---	PASS
SCGBL	284402	broad.mit.edu	37	19	35085114	35085114	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:35085114G>T	uc002nvn.2	-	2	234	c.212C>A	c.(211-213)TCC>TAC	p.S71Y		NM_001025591	NP_001020762	Q4G0G5	SCGBL_HUMAN	secretoglobin-like precursor	71						extracellular region	binding				0						TTCTGTCACGGAGACATTGGC	0.547													6	104	---	---	---	---	PASS
LIN37	55957	broad.mit.edu	37	19	36245203	36245203	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:36245203G>C	uc002obm.2	+	9	756	c.642G>C	c.(640-642)TGG>TGC	p.W214C	uc002obl.2_5'Flank	NM_019104	NP_061977	Q96GY3	LIN37_HUMAN	lin-37 homolog	214							protein binding				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TGCAGCGCTGGAAACGCATCC	0.637													23	103	---	---	---	---	PASS
NPHS1	4868	broad.mit.edu	37	19	36335228	36335228	+	Silent	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:36335228G>C	uc002oby.2	-	15	2064	c.2064C>G	c.(2062-2064)CTC>CTG	p.L688L		NM_004646	NP_004637	O60500	NPHN_HUMAN	nephrin precursor	688	Extracellular (Potential).				cell adhesion|excretion|muscle organ development	integral to plasma membrane				ovary(4)|skin(1)	5	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CACCTGGACTGAGGCGATAGC	0.697													6	18	---	---	---	---	PASS
ZFP14	57677	broad.mit.edu	37	19	36832139	36832139	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:36832139C>T	uc002odx.1	-	4	682	c.589G>A	c.(589-591)GAG>AAG	p.E197K	ZFP14_uc010xtd.1_Missense_Mutation_p.E198K|ZFP14_uc010eex.1_Missense_Mutation_p.E197K	NM_020917	NP_065968	Q9HCL3	ZFP14_HUMAN	zinc finger protein 14-like	197					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Esophageal squamous(110;0.162)					TAAGGTTTCTCACCAGTATGA	0.428													23	78	---	---	---	---	PASS
ZNF420	147923	broad.mit.edu	37	19	37619911	37619911	+	Missense_Mutation	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:37619911A>G	uc002ofl.2	+	5	2233	c.2018A>G	c.(2017-2019)TAT>TGT	p.Y673C		NM_144689	NP_653290	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	673					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCTTTTGAATATAAGGAATGT	0.378													11	36	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39950220	39950220	+	Silent	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:39950220C>G	uc002olo.3	+	9	725	c.546C>G	c.(544-546)GTC>GTG	p.V182V	SUPT5H_uc002olp.3_Silent_p.V182V|SUPT5H_uc002olq.3_Silent_p.V178V|SUPT5H_uc002oln.3_Silent_p.V182V|SUPT5H_uc002olr.3_Silent_p.V182V	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	182	Interaction with SUPT4H1.				cell cycle|chromatin remodeling|mRNA capping|negative regulation of transcription elongation, DNA-dependent|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription elongation from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|response to organic substance|retroviral genome replication|transcription elongation from RNA polymerase II promoter	nucleoplasm	enzyme binding|protein heterodimerization activity			ovary(3)|pancreas(1)	4	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TGTGGACTGTCAAATGTAAGG	0.557													37	81	---	---	---	---	PASS
TEX101	83639	broad.mit.edu	37	19	43922125	43922125	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:43922125C>A	uc010xwo.1	+	5	682	c.487C>A	c.(487-489)CGA>AGA	p.R163R	TEX101_uc002owk.2_Silent_p.R181R	NM_001130011	NP_001123483	Q9BY14	TX101_HUMAN	testis expressed 101 isoform 2	163						anchored to membrane|plasma membrane				ovary(1)	1		Prostate(69;0.0199)				TGGTACAACTCGATGCTATCA	0.473													5	83	---	---	---	---	PASS
TEX101	83639	broad.mit.edu	37	19	43922432	43922432	+	Missense_Mutation	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:43922432T>A	uc010xwo.1	+	6	828	c.633T>A	c.(631-633)CAT>CAA	p.H211Q	TEX101_uc002owk.2_Missense_Mutation_p.H229Q	NM_001130011	NP_001123483	Q9BY14	TX101_HUMAN	testis expressed 101 isoform 2	211						anchored to membrane|plasma membrane				ovary(1)	1		Prostate(69;0.0199)				CGTGCCCACATCAGCTGCTCA	0.532													29	64	---	---	---	---	PASS
ZNF45	7596	broad.mit.edu	37	19	44418134	44418134	+	Nonsense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:44418134G>C	uc002oxu.1	-	4	1553	c.1454C>G	c.(1453-1455)TCA>TGA	p.S485*	ZNF45_uc002oxw.1_Nonsense_Mutation_p.S485*|ZNF45_uc002oxv.1_Nonsense_Mutation_p.S485*	NM_003425	NP_003416	Q02386	ZNF45_HUMAN	zinc finger protein 45	485	C2H2-type 12.				multicellular organismal development	nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1						ATTAAGATCTGAGCTCCGACT	0.502													11	36	---	---	---	---	PASS
ZNF229	7772	broad.mit.edu	37	19	44934257	44934257	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:44934257G>A	uc002oze.1	-	6	1133	c.699C>T	c.(697-699)TTC>TTT	p.F233F	ZNF229_uc010ejk.1_5'UTR|ZNF229_uc010ejl.1_Silent_p.F227F	NM_014518	NP_055333	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	233					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)|pancreas(1)	4		Prostate(69;0.0352)				CTATTTCAGGGAATCTGTGAT	0.378													18	47	---	---	---	---	PASS
PPP1R13L	10848	broad.mit.edu	37	19	45885827	45885827	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:45885827C>A	uc002pbn.2	-	12	2483	c.2406G>T	c.(2404-2406)GCG>GCT	p.A802A	PPP1R13L_uc002pbm.2_Silent_p.A381A|PPP1R13L_uc002pbo.2_Silent_p.A802A	NM_006663	NP_006654	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13	802	SH3.				apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	transcription corepressor activity|transcription factor binding			skin(1)	1		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)		GGCCGTGCAGCGCGGCCCACC	0.697													11	28	---	---	---	---	PASS
LIG1	3978	broad.mit.edu	37	19	48631193	48631193	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:48631193G>T	uc002pia.1	-	20	2026	c.1906C>A	c.(1906-1908)CAA>AAA	p.Q636K	LIG1_uc010xze.1_Missense_Mutation_p.Q329K|LIG1_uc002phz.1_RNA|LIG1_uc002pib.1_RNA|LIG1_uc010xzf.1_Missense_Mutation_p.Q568K|LIG1_uc010xzg.1_Missense_Mutation_p.Q605K	NM_000234	NP_000225	P18858	DNLI1_HUMAN	DNA ligase I	636					anatomical structure morphogenesis|base-excision repair|cell division|DNA ligation involved in DNA repair|DNA strand elongation involved in DNA replication|double-strand break repair via homologous recombination|nucleotide-excision repair, DNA gap filling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	nucleoplasm	ATP binding|DNA binding|DNA ligase (ATP) activity|metal ion binding			large_intestine(2)|lung(1)	3		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	GTGAGCACTTGGAATGGCTGG	0.572								NER					8	181	---	---	---	---	PASS
HRC	3270	broad.mit.edu	37	19	49657014	49657014	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:49657014G>C	uc002pmv.2	-	1	1668	c.1481C>G	c.(1480-1482)TCC>TGC	p.S494C		NM_002152	NP_002143	P23327	SRCH_HUMAN	histidine rich calcium binding protein	494					muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			ovary(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		TTCCTCATGGGAGCCGGGGTC	0.547													8	53	---	---	---	---	PASS
ETFB	2109	broad.mit.edu	37	19	51857558	51857558	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:51857558C>A	uc002pwh.2	-	2	154	c.62G>T	c.(61-63)CGA>CTA	p.R21L	ETFB_uc002pwg.2_Missense_Mutation_p.R112L	NM_001985	NP_001976	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	21					respiratory electron transport chain|transport	mitochondrial matrix	electron carrier activity				0		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		AGGCTTCACTCGGATCTGCCC	0.532													4	58	---	---	---	---	PASS
ZNF28	7576	broad.mit.edu	37	19	53302992	53302992	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:53302992C>A	uc002qad.2	-	4	2226	c.2106G>T	c.(2104-2106)CAG>CAT	p.Q702H	ZNF28_uc002qac.2_Missense_Mutation_p.Q649H|ZNF28_uc010eqe.2_Missense_Mutation_p.Q648H	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	702	C2H2-type 18.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		GGTTTGACATCTGACTGAAGG	0.413													18	40	---	---	---	---	PASS
KIR3DX1	90011	broad.mit.edu	37	19	55045040	55045040	+	RNA	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:55045040C>T	uc010yfa.1	+	3		c.266C>T			KIR3DX1_uc010yfb.1_RNA|KIR3DX1_uc010yfc.1_RNA|KIR3DX1_uc010yfd.1_RNA	NR_026716				Homo sapiens mRNA for FLJ00060 protein, partial cds.											ovary(1)	1				GBM - Glioblastoma multiforme(193;0.099)		TTCCCATCTTCGGTTTGTCAT	0.537													7	53	---	---	---	---	PASS
KIR2DS4	3809	broad.mit.edu	37	19	55349259	55349259	+	Missense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:55349259G>A	uc002qhm.1	+	3	345	c.299G>A	c.(298-300)TGC>TAC	p.C100Y	KIR2DS4_uc010yfj.1_Missense_Mutation_p.C93Y|KIR2DS4_uc010yfk.1_RNA|KIR3DL1_uc002qhl.3_Intron|KIR2DS4_uc010esg.1_Missense_Mutation_p.C100Y|KIR2DS4_uc002qhn.1_Missense_Mutation_p.C47Y	NM_012314	NP_036446	P43632	KI2S4_HUMAN	killer cell immunoglobulin-like receptor, two	100	Extracellular (Potential).|Ig-like C2-type 1.					integral to plasma membrane	receptor activity				0				GBM - Glioblastoma multiforme(193;0.0192)		ACCTACAGATGCTACGGTTCT	0.507													73	252	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56370258	56370258	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:56370258G>T	uc002qmd.3	+	3	1921	c.1499G>T	c.(1498-1500)GGG>GTG	p.G500V	NLRP4_uc002qmf.2_Missense_Mutation_p.G425V|NLRP4_uc010etf.2_Missense_Mutation_p.G331V	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	500							ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		ATTTTTTTGGGGTGTTTTCTA	0.408													48	75	---	---	---	---	PASS
NLRP4	147945	broad.mit.edu	37	19	56390162	56390162	+	Missense_Mutation	SNP	T	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:56390162T>G	uc002qmd.3	+	9	3121	c.2699T>G	c.(2698-2700)TTG>TGG	p.L900W	NLRP4_uc002qmf.2_Missense_Mutation_p.L825W|NLRP4_uc010etf.2_Missense_Mutation_p.L675W	NM_134444	NP_604393	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	900							ATP binding			ovary(5)|skin(4)|lung(3)|upper_aerodigestive_tract(1)|kidney(1)|pancreas(1)	15		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TATTGCAGGTTGGAAGAATGT	0.532													9	18	---	---	---	---	PASS
ESF1	51575	broad.mit.edu	37	20	13756704	13756704	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:13756704C>A	uc002woj.2	-	3	958	c.850G>T	c.(850-852)GAG>TAG	p.E284*	ESF1_uc002wok.1_Nonsense_Mutation_p.E284*	NM_016649	NP_057733	Q9H501	ESF1_HUMAN	ABT1-associated protein	284	Asp-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus|nucleoplasm				ovary(1)	1						tcttcatcctcctcttcatct	0.229													13	30	---	---	---	---	PASS
PCSK2	5126	broad.mit.edu	37	20	17208026	17208026	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:17208026G>C	uc002wpm.2	+	1	396	c.76G>C	c.(76-78)GAG>CAG	p.E26Q	PCSK2_uc002wpl.2_Missense_Mutation_p.E7Q|PCSK2_uc010zrm.1_Missense_Mutation_p.E26Q	NM_002594	NP_002585	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2	26					enkephalin processing|insulin processing|islet amyloid polypeptide processing	extracellular space|membrane|soluble fraction|transport vesicle	serine-type endopeptidase activity			ovary(3)|central_nervous_system(2)|large_intestine(1)|pancreas(1)	7					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	TGCATCTGCTGAGCGACCGGT	0.527													17	64	---	---	---	---	PASS
SUN5	140732	broad.mit.edu	37	20	31577469	31577469	+	Missense_Mutation	SNP	G	T	T	rs150666576		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:31577469G>T	uc002wyi.2	-	9	663	c.570C>A	c.(568-570)CAC>CAA	p.H190Q		NM_080675	NP_542406	Q8TC36	SUN5_HUMAN	sperm associated antigen 4-like	190					spermatogenesis					skin(1)	1						TGTAATCTCCGTGTATCATCT	0.488													14	43	---	---	---	---	PASS
CDK5RAP1	51654	broad.mit.edu	37	20	31967387	31967387	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:31967387G>T	uc010gek.2	-	9	1153	c.1029C>A	c.(1027-1029)ACC>ACA	p.T343T	CDK5RAP1_uc002wyy.2_Silent_p.T239T|CDK5RAP1_uc002wyz.2_Silent_p.T329T|CDK5RAP1_uc002wza.2_Silent_p.T329T|CDK5RAP1_uc010gel.2_Silent_p.T238T|CDK5RAP1_uc010gem.2_Intron|CDK5RAP1_uc002wzc.1_Silent_p.T329T	NM_016408	NP_057492	Q96SZ6	CK5P1_HUMAN	CDK5 regulatory subunit associated protein 1	343					brain development|negative regulation of cyclin-dependent protein kinase activity|regulation of neuron differentiation|tRNA modification	cytoplasm	4 iron, 4 sulfur cluster binding|metal ion binding|neuronal Cdc2-like kinase binding|transferase activity			ovary(2)|skin(2)|lung(1)	5						TTTTATAGTTGGTGGTAAAGC	0.463													5	46	---	---	---	---	PASS
PHF20	51230	broad.mit.edu	37	20	34459591	34459591	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:34459591G>T	uc002xek.1	+	9	1233	c.1122G>T	c.(1120-1122)TTG>TTT	p.L374F	PHF20_uc002xei.1_Missense_Mutation_p.L374F|PHF20_uc010gfo.1_Missense_Mutation_p.L374F|PHF20_uc002xej.1_Missense_Mutation_p.L258F	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	374					regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)					AGTCTGCTTTGGAAGCTGGCC	0.448													6	107	---	---	---	---	PASS
C20orf24	55969	broad.mit.edu	37	20	35240420	35240420	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:35240420G>T	uc002xfq.2	+	4	544	c.356G>T	c.(355-357)TGG>TTG	p.W119L	C20orf24_uc002xfo.2_Missense_Mutation_p.W145L|C20orf24_uc002xfp.2_3'UTR|C20orf24_uc002xft.2_RNA|C20orf24_uc002xfr.2_Nonsense_Mutation_p.G76*|C20orf24_uc002xfs.2_Missense_Mutation_p.L128F	NM_018840	NP_061328	Q9BUV8	CT024_HUMAN	RAB5-interacting protein isoform a	119				LFMVCVADSFTTGHLDHLLHCHPL -> IVHGHLLLLFTSH PYSMMVSDSK (in Ref. 6; AAB50849).			protein binding				0	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				TAGGTCATTTGGATCATCTTT	0.463													8	209	---	---	---	---	PASS
C20orf117	140710	broad.mit.edu	37	20	35443568	35443568	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:35443568C>A	uc002xgd.1	-	5	1890	c.1563G>T	c.(1561-1563)AAG>AAT	p.K521N	C20orf117_uc002xge.1_RNA	NM_199181	NP_954650	O94964	K0889_HUMAN	hypothetical protein LOC140710 isoform 2	521											0		Myeloproliferative disorder(115;0.00874)				GAAGAATCTCCTTAGAGAGCC	0.463													8	150	---	---	---	---	PASS
SEMG2	6407	broad.mit.edu	37	20	43851673	43851673	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:43851673C>A	uc010ggz.2	+	2	1457	c.1400C>A	c.(1399-1401)TCA>TAA	p.S467*	SEMG2_uc002xnk.2_Nonsense_Mutation_p.S467*|SEMG2_uc002xnl.2_Intron	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor	467	Repeat-rich region.|4 X 60 AA tandem repeats, type I.				sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(1)	1		Myeloproliferative disorder(115;0.0122)				AATAAAATGTCATACCAATCT	0.368													24	37	---	---	---	---	PASS
ZSWIM3	140831	broad.mit.edu	37	20	44505923	44505923	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:44505923G>T	uc002xqd.2	+	2	929	c.726G>T	c.(724-726)AAG>AAT	p.K242N	ZSWIM3_uc010zxg.1_Missense_Mutation_p.K236N	NM_080752	NP_542790	Q96MP5	ZSWM3_HUMAN	zinc finger, SWIM domain containing 3	242							zinc ion binding			ovary(2)	2		Myeloproliferative disorder(115;0.0122)				TGGAGAACAAGGAACGAGAAA	0.527													6	70	---	---	---	---	PASS
ZNF335	63925	broad.mit.edu	37	20	44586512	44586512	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:44586512G>C	uc002xqw.2	-	16	2432	c.2309C>G	c.(2308-2310)TCT>TGT	p.S770C	ZNF335_uc010zxk.1_Missense_Mutation_p.S615C	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	770					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)				CAGGGTGTCAGAACAGAGCAA	0.597													22	63	---	---	---	---	PASS
SLC13A3	64849	broad.mit.edu	37	20	45192078	45192078	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:45192078G>T	uc002xsf.1	-	12	1645	c.1607C>A	c.(1606-1608)TCT>TAT	p.S536Y	SLC13A3_uc010ghn.1_Missense_Mutation_p.S505Y|SLC13A3_uc010zxw.1_Missense_Mutation_p.S486Y|SLC13A3_uc002xsg.1_Missense_Mutation_p.S489Y|SLC13A3_uc010gho.1_Missense_Mutation_p.S454Y|SLC13A3_uc010zxx.1_Missense_Mutation_p.S438Y|SLC13A3_uc002xse.1_Missense_Mutation_p.S27Y|SLC13A3_uc010ghm.1_Missense_Mutation_p.S123Y|SLC13A3_uc010zxv.1_Missense_Mutation_p.S121Y	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a	536	Cytoplasmic (Potential).					integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CAAGTGTCCAGAGGCGAAGGC	0.622													5	38	---	---	---	---	PASS
KCNG1	3755	broad.mit.edu	37	20	49626715	49626715	+	Missense_Mutation	SNP	T	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:49626715T>A	uc002xwa.3	-	2	456	c.161A>T	c.(160-162)CAG>CTG	p.Q54L	KCNG1_uc002xwb.2_Missense_Mutation_p.Q54L	NM_002237	NP_002228	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G,	54	Cytoplasmic (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2						CTGACAGCCCTGGCGGGGCTC	0.706													7	8	---	---	---	---	PASS
RAE1	8480	broad.mit.edu	37	20	55953067	55953067	+	Splice_Site	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:55953067A>G	uc002xyg.2	+	12	1362	c.1021_splice	c.e12-2	p.G341_splice	RAE1_uc002xyh.2_Splice_Site_p.G341_splice|RAE1_uc002xyi.2_Splice_Site_p.G341_splice	NM_003610	NP_003601	P78406	RAE1L_HUMAN	RAE1 (RNA export 1, S.pombe) homolog						carbohydrate metabolic process|glucose transport|mRNA export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|cytoskeleton|nuclear outer membrane|nuclear pore	microtubule binding|RNA binding				0	Lung NSC(12;0.00263)|all_lung(29;0.00828)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;3.7e-14)|Epithelial(14;1.07e-09)|all cancers(14;1.11e-08)			TGCTCTCTTTAGGGACATGAA	0.373													11	33	---	---	---	---	PASS
PHACTR3	116154	broad.mit.edu	37	20	58322835	58322835	+	Silent	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:58322835C>A	uc002yau.2	+	3	770	c.303C>A	c.(301-303)GGC>GGA	p.G101G	PHACTR3_uc002yat.2_Silent_p.G98G|PHACTR3_uc010zzw.1_Silent_p.G60G|PHACTR3_uc002yav.2_Silent_p.G60G|PHACTR3_uc002yaw.2_Silent_p.G60G|PHACTR3_uc002yax.2_Silent_p.G60G	NM_080672	NP_542403	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3 isoform 1	101	RPEL 1.					nuclear matrix	actin binding|protein phosphatase inhibitor activity			ovary(2)|pancreas(1)	3	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;2.76e-09)			AGATGGCCGGCAGGCAAGGCC	0.607													45	61	---	---	---	---	PASS
TAF4	6874	broad.mit.edu	37	20	60582658	60582658	+	Missense_Mutation	SNP	C	A	A	rs149456775		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:60582658C>A	uc002ybs.2	-	6	1919	c.1919G>T	c.(1918-1920)AGG>ATG	p.R640M		NM_003185	NP_003176	O00268	TAF4_HUMAN	TBP-associated factor 4	640	TAFH.				interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|viral reproduction	cytoplasm|MLL1 complex|transcription factor TFIID complex|transcription factor TFTC complex	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity			ovary(2)|pancreas(1)	3	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			TCGGTATAACCTGCTTGTGAA	0.438													9	199	---	---	---	---	PASS
LIPI	149998	broad.mit.edu	37	21	15537643	15537643	+	Missense_Mutation	SNP	A	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr21:15537643A>T	uc002yjm.2	-	6	875	c.865T>A	c.(865-867)TGC>AGC	p.C289S	LIPI_uc010gkw.1_Missense_Mutation_p.C192S	NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I	268					lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		ATAAAATTGCAGTTTGTTTCT	0.353													7	13	---	---	---	---	PASS
RUNX1	861	broad.mit.edu	37	21	36252918	36252918	+	Silent	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr21:36252918G>A	uc002yuh.2	-	2	1941	c.363C>T	c.(361-363)ACC>ACT	p.T121T	RUNX1_uc002yui.2_Silent_p.T121T|RUNX1_uc010gmu.2_Silent_p.T148T|RUNX1_uc010gmv.2_Silent_p.T148T|RUNX1_uc002yuj.3_Silent_p.T16T|RUNX1_uc002yuk.3_Silent_p.T148T|RUNX1_uc002yum.1_Silent_p.T16T|RUNX1_uc010gmw.1_Silent_p.T148T|RUNX1_uc002yuo.1_Silent_p.T121T|RUNX1_uc002yur.1_Silent_p.T16T	NM_001001890	NP_001001890	Q01196	RUNX1_HUMAN	runt-related transcription factor 1 isoform	121	Runt.				myeloid cell differentiation|negative regulation of granulocyte differentiation|positive regulation of angiogenesis|positive regulation of granulocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent	nucleus|nucleus	ATP binding|calcium ion binding|DNA binding|DNA binding|protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription factor binding	p.L121fs*2(1)|p.A149fs*2(1)		haematopoietic_and_lymphoid_tissue(383)|lung(2)|ovary(1)|central_nervous_system(1)	387						TCATGGCTGCGGTAGCATTTC	0.483			T	RPL22|MDS1|EVI1|CBFA2T3|CBFA2T1|ETV6|LAF4	AML|preB- ALL|T-ALL				Platelet_disorder_associated_with_Myeloid_Malignancies				7	6	---	---	---	---	PASS
CCT8L2	150160	broad.mit.edu	37	22	17072852	17072852	+	Missense_Mutation	SNP	T	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr22:17072852T>C	uc002zlp.1	-	1	849	c.589A>G	c.(589-591)AGC>GGC	p.S197G		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	197					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				GGCTTGAAGCTGCCGTCTAGT	0.617													12	32	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	23135303	23135303	+	RNA	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr22:23135303C>A	uc011aim.1	+	251		c.11945C>A								Parts of antibodies, mostly variable regions.												0						ACTATGTCTCCTGGTACCAAC	0.552													10	331	---	---	---	---	PASS
RFPL2	10739	broad.mit.edu	37	22	32598391	32598391	+	Silent	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr22:32598391G>T	uc003amg.3	-	2	984	c.48C>A	c.(46-48)TCC>TCA	p.S16S	RFPL2_uc003amf.3_5'UTR|RFPL2_uc003amh.3_5'UTR	NM_001098527	NP_001091997	O75678	RFPL2_HUMAN	ret finger protein-like 2 isoform 2	16							zinc ion binding			skin(1)	1						gacagatcctggattgggaca	0.030													9	23	---	---	---	---	PASS
EIF3L	51386	broad.mit.edu	37	22	38247364	38247364	+	Missense_Mutation	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr22:38247364A>G	uc003auf.2	+	3	247	c.160A>G	c.(160-162)AAC>GAC	p.N54D	EIF3L_uc003aue.1_Missense_Mutation_p.N54D|EIF3L_uc011ann.1_Missense_Mutation_p.N54D|EIF3L_uc003aug.2_5'UTR	NM_016091	NP_057175	Q9Y262	EIF3L_HUMAN	eukaryotic translation initiation factor 3	54						eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)	1						GGTGATCAAAAACTTCATCCA	0.433													10	45	---	---	---	---	PASS
L3MBTL2	83746	broad.mit.edu	37	22	41613159	41613159	+	Missense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr22:41613159C>A	uc003azo.2	+	5	607	c.553C>A	c.(553-555)CTG>ATG	p.L185M	L3MBTL2_uc010gyi.1_Missense_Mutation_p.L94M|L3MBTL2_uc003azn.2_RNA|uc003azp.1_RNA	NM_031488	NP_113676	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2	185	MBT 1.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methylated histone residue binding|transcription corepressor activity|zinc ion binding			ovary(2)|central_nervous_system(1)	3						GGGGAAGTTCCTGAAGGATCA	0.637													6	83	---	---	---	---	PASS
CYP2D6	1565	broad.mit.edu	37	22	42524814	42524814	+	Missense_Mutation	SNP	A	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr22:42524814A>G	uc003bce.2	-	4	728	c.638T>C	c.(637-639)CTG>CCG	p.L213P	uc003bcd.1_Intron|CYP2D6_uc010gyu.2_5'UTR|CYP2D6_uc003bcf.2_Missense_Mutation_p.L162P	NM_000106	NP_000097	Q6NWU0	Q6NWU0_HUMAN	cytochrome P450, family 2, subfamily D,	213							electron carrier activity|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen			breast(1)|skin(1)	2						CTCCTCCTTCAGTCCCTCCTG	0.672													3	20	---	---	---	---	PASS
ZBED4	9889	broad.mit.edu	37	22	50277561	50277561	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr22:50277561G>T	uc003bix.2	+	2	721	c.251G>T	c.(250-252)GGC>GTC	p.G84V		NM_014838	NP_055653	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	84						cytoplasm|nucleus	DNA binding|metal ion binding|protein dimerization activity			ovary(2)	2		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GATGACTATGGCGCGCTGTTC	0.627													28	57	---	---	---	---	PASS
RPGR	6103	broad.mit.edu	37	X	38146439	38146439	+	Missense_Mutation	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:38146439C>G	uc004ded.1	-	15	1981	c.1813G>C	c.(1813-1815)GAG>CAG	p.E605Q	RPGR_uc004deb.2_Missense_Mutation_p.E605Q|RPGR_uc004dea.2_RNA|RPGR_uc004dec.2_Intron	NM_001034853	NP_001030025	Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator isoform C	605	Glu-rich.				intracellular protein transport|response to stimulus|visual perception	Golgi apparatus|photoreceptor outer segment	guanyl-nucleotide exchange factor activity|protein binding			ovary(1)	1						gcttctacctcttgctcctct	0.204													5	6	---	---	---	---	PASS
NHSL2	340527	broad.mit.edu	37	X	71360443	71360443	+	Silent	SNP	C	G	G			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:71360443C>G	uc011mqa.1	+	6	3045	c.3045C>G	c.(3043-3045)CTC>CTG	p.L1015L	NHSL2_uc004eak.1_Silent_p.L649L|NHSL2_uc010nli.2_Silent_p.L784L	NM_001013627	NP_001013649	Q5HYW2	NHSL2_HUMAN	NHS-like 2	1015											0	Renal(35;0.156)					ACCTGCCTCTCACTTCTCCCA	0.542													6	11	---	---	---	---	PASS
TGIF2LX	90316	broad.mit.edu	37	X	89177748	89177748	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:89177748G>T	uc004efe.2	+	2	713	c.664G>T	c.(664-666)GAT>TAT	p.D222Y		NM_138960	NP_620410	Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	222						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)|skin(1)	2						GCTGCTAGTCGATGCAGCAGT	0.507													13	12	---	---	---	---	PASS
PCDH11X	27328	broad.mit.edu	37	X	91133967	91133967	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:91133967G>T	uc004efk.1	+	2	3573	c.2728G>T	c.(2728-2730)GAT>TAT	p.D910Y	PCDH11X_uc004efl.1_Missense_Mutation_p.D910Y|PCDH11X_uc004efo.1_Missense_Mutation_p.D910Y|PCDH11X_uc010nmv.1_Missense_Mutation_p.D910Y|PCDH11X_uc004efm.1_Missense_Mutation_p.D910Y|PCDH11X_uc004efn.1_Missense_Mutation_p.D910Y|PCDH11X_uc004efh.1_Missense_Mutation_p.D910Y|PCDH11X_uc004efj.1_Missense_Mutation_p.D910Y	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	910	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						CCTTCCTATTGATCTAGAAGA	0.428													17	14	---	---	---	---	PASS
BTK	695	broad.mit.edu	37	X	100611126	100611126	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:100611126G>T	uc004ehg.2	-	15	1673	c.1480C>A	c.(1480-1482)CAG>AAG	p.Q494K	BTK_uc004ehf.2_Intron|BTK_uc010nnh.2_Intron|BTK_uc010nni.2_Intron|BTK_uc004ehe.2_Intron|BTK_uc010nnj.2_RNA|BTK_uc010nnk.2_Intron|BTK_uc010nnl.2_Intron|BTK_uc010nnm.2_Missense_Mutation_p.Q64K|BTK_uc010nnn.2_Intron|BTK_uc010nno.2_Missense_Mutation_p.Q528K|BTK_uc004ehh.1_Intron|BTK_uc004ehi.2_Missense_Mutation_p.Q494K	NM_000061	NP_000052	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	494	Protein kinase.				calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development	cytosol|membrane raft|nucleus|plasma membrane	ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding			lung(3)|central_nervous_system(2)|ovary(1)	6						TGCTGAGTCTGGAAGCGGTGG	0.547									Agammaglobulinemia_X-linked				6	41	---	---	---	---	PASS
IRS4	8471	broad.mit.edu	37	X	107977075	107977075	+	Missense_Mutation	SNP	C	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:107977075C>T	uc004eoc.2	-	1	2533	c.2500G>A	c.(2500-2502)GGA>AGA	p.G834R		NM_003604	NP_003595	O14654	IRS4_HUMAN	insulin receptor substrate 4	834						plasma membrane	insulin receptor binding|SH3/SH2 adaptor activity|signal transducer activity			ovary(4)|large_intestine(2)|lung(1)|breast(1)|skin(1)|pancreas(1)	10						AGGAACTTTCCAGGTAACATT	0.488													96	71	---	---	---	---	PASS
PAK3	5063	broad.mit.edu	37	X	110439768	110439768	+	Missense_Mutation	SNP	G	C	C			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:110439768G>C	uc004epa.2	+	13	1379	c.1352G>C	c.(1351-1353)CGA>CCA	p.R451P	PAK3_uc010npt.1_Missense_Mutation_p.R436P|PAK3_uc010npu.1_Missense_Mutation_p.R436P|PAK3_uc004eoy.1_Missense_Mutation_p.R191P|PAK3_uc004eoz.2_Missense_Mutation_p.R436P|PAK3_uc011mst.1_RNA|PAK3_uc010npv.1_Missense_Mutation_p.R472P|PAK3_uc010npw.1_Missense_Mutation_p.R457P	NM_001128173	NP_001121645	O75914	PAK3_HUMAN	p21-activated kinase 3 isoform d	451	Protein kinase.				multicellular organismal development		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding			lung(6)|ovary(3)|large_intestine(1)	10						GTGGTGACTCGAAAAGCTTAT	0.473										TSP Lung(19;0.15)			11	16	---	---	---	---	PASS
KIAA1210	57481	broad.mit.edu	37	X	118220998	118220998	+	Nonsense_Mutation	SNP	C	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:118220998C>A	uc004era.3	-	11	4195	c.4195G>T	c.(4195-4197)GGA>TGA	p.G1399*		NM_020721	NP_065772	Q9ULL0	K1210_HUMAN	hypothetical protein LOC57481	1399										ovary(4)|skin(1)	5						TCATCTCTTCCTAGGAACCAA	0.443													6	86	---	---	---	---	PASS
PHF6	84295	broad.mit.edu	37	X	133512083	133512083	+	Missense_Mutation	SNP	G	T	T			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrX:133512083G>T	uc004exj.2	+	3	389	c.187G>T	c.(187-189)GGT>TGT	p.G63C	PHF6_uc004exk.2_Missense_Mutation_p.G63C|PHF6_uc011mvk.1_Intron|PHF6_uc004exh.2_Missense_Mutation_p.G63C|PHF6_uc010nrr.2_Missense_Mutation_p.G63C|PHF6_uc004exi.2_Missense_Mutation_p.G63C	NM_001015877	NP_001015877	Q8IWS0	PHF6_HUMAN	PHD finger protein 6 isoform 1	63					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(192;0.000127)					TGAAAGTCTTGGTGGATTTTC	0.294													5	25	---	---	---	---	PASS
SRY	6736	broad.mit.edu	37	Y	2655257	2655257	+	Nonsense_Mutation	SNP	G	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chrY:2655257G>A	uc004fqg.1	-	1	536	c.388C>T	c.(388-390)CGA>TGA	p.R130*		NM_003140	NP_003131	Q05066	SRY_HUMAN	sex determining region Y	130	Sufficient for interaction with EP300.|Required for nuclear localization.|Sufficient for interaction with KPNB1.				cell differentiation|male sex determination|positive regulation of transcription, DNA-dependent|sex differentiation	cytoplasm|nuclear speck	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding				0						CGACGAGGTCGATACTTATAA	0.498									Swyer_syndrome				5	1	---	---	---	---	PASS
FER1L5	90342	broad.mit.edu	37	2	97329243	97329243	+	Frame_Shift_Del	DEL	A	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:97329243delA	uc010fia.2	+	13	1088	c.1088delA	c.(1087-1089)CAGfs	p.Q363fs		NM_001113382	NP_001106853	A0AVI2	FR1L5_HUMAN	fer-1-like 5 isoform 2	363	C2 3.					integral to membrane				ovary(1)	1						TTCCGGATTCAGGTATGGCTC	0.552													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	130725823	130725823	+	RNA	DEL	G	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr2:130725823delG	uc002tpw.1	-	6		c.802delC								Homo sapiens cDNA FLJ41458 fis, clone BRSTN2014490.																		GCAAGCTTGTGGACATCCTCA	0.458													17	9	---	---	---	---	
OXSR1	9943	broad.mit.edu	37	3	38207437	38207437	+	Frame_Shift_Del	DEL	G	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:38207437delG	uc003chy.2	+	1	412	c.70delG	c.(70-72)GGGfs	p.G24fs	OXSR1_uc010hhb.2_5'UTR|OXSR1_uc010hha.1_5'UTR	NM_005109	NP_005100	O95747	OXSR1_HUMAN	oxidative-stress responsive 1	24	Protein kinase.|ATP (By similarity).				intracellular protein kinase cascade|response to oxidative stress		ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity			skin(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GGAGGTGATCGGTGAGAGCAG	0.716													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	195427029	195427029	+	RNA	DEL	T	-	-	rs75389211		TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr3:195427029delT	uc011btd.1	+	1		c.208delT			uc003fux.1_RNA					Homo sapiens cDNA FLJ46488 fis, clone THYMU3026869.																		gcaacaggaattttttcaggc	0.015													9	4	---	---	---	---	
BAK1	578	broad.mit.edu	37	6	33541613	33541623	+	Frame_Shift_Del	DEL	GCCCAACAGAA	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr6:33541613_33541623delGCCCAACAGAA	uc003oes.2	-	6	893_903	c.593_603delTTCTGTTGGGC	c.(592-603)GTTCTGTTGGGCfs	p.V198fs	BAK1_uc003oer.2_Frame_Shift_Del_p.V128fs|BAK1_uc003oet.2_RNA|BAK1_uc010jvb.2_Frame_Shift_Del_p.V198fs|BAK1_uc003oeu.2_Frame_Shift_Del_p.V139fs	NM_001188	NP_001179	Q16611	BAK_HUMAN	BCL2-antagonist/killer 1	198_201	Helical; (Potential).				activation of pro-apoptotic gene products|cellular response to mechanical stimulus|cellular response to UV|establishment or maintenance of transmembrane electrochemical gradient|induction of apoptosis by extracellular signals|induction of apoptosis by intracellular signals|regulation of mitochondrial membrane permeability|regulation of mitochondrial membrane potential|regulation of protein heterodimerization activity|regulation of protein homodimerization activity|release of cytochrome c from mitochondria	integral to mitochondrial outer membrane|pore complex	metal ion binding|protein heterodimerization activity			ovary(1)	1						CCACAAACTGGCCCAACAGAACCACACCCAG	0.559													12	20	---	---	---	---	
GLIS3	169792	broad.mit.edu	37	9	3829318	3829318	+	Frame_Shift_Del	DEL	C	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:3829318delC	uc003zhw.1	-	9	2377	c.2183delG	c.(2182-2184)GGCfs	p.G728fs	GLIS3_uc003zhx.1_Frame_Shift_Del_p.G883fs|GLIS3_uc010mhf.1_Frame_Shift_Del_p.G277fs|GLIS3_uc003zhv.1_RNA	NM_152629	NP_689842	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3 isoform b	728					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		ACCTGTAATGCCCGAGTGAGT	0.552													16	13	---	---	---	---	
CNTNAP3	79937	broad.mit.edu	37	9	39149853	39149853	+	Frame_Shift_Del	DEL	C	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr9:39149853delC	uc004abi.2	-	10	1838	c.1599delG	c.(1597-1599)GCGfs	p.A533fs	CNTNAP3_uc004abj.2_Frame_Shift_Del_p.A533fs|CNTNAP3_uc011lqr.1_Intron|CNTNAP3_uc004abk.1_Frame_Shift_Del_p.A533fs|CNTNAP3_uc011lqs.1_Intron|CNTNAP3_uc004abl.1_Intron	NM_033655	NP_387504	Q9BZ76	CNTP3_HUMAN	cell recognition molecule CASPR3 precursor	533	Extracellular (Potential).|Laminin G-like 2.				cell adhesion|cell recognition|signal transduction	extracellular region|integral to membrane|plasma membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		AACTCCCCAGCGCCCCCTGCT	0.542													4	4	---	---	---	---	
ACBD7	414149	broad.mit.edu	37	10	15059240	15059240	+	Frame_Shift_Del	DEL	G	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr10:15059240delG	uc010qby.1	-	6	442	c.133delC	c.(133-135)CAAfs	p.Q45fs				Q8N6N7	ACBD7_HUMAN	SubName: Full=cDNA FLJ52263, highly similar to Artemis protein (EC 3.1.-.-);	Error:Variant_position_missing_in_Q8N6N7_after_alignment							fatty-acyl-CoA binding				0						CTTGGAATTTGGTAAAATCTT	0.368													31	19	---	---	---	---	
CELF6	60677	broad.mit.edu	37	15	72582506	72582507	+	Frame_Shift_Ins	INS	-	A	A			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr15:72582506_72582507insA	uc002auh.2	-	4	794_795	c.484_485insT	c.(484-486)GAGfs	p.E162fs	uc002aug.2_Intron|CELF6_uc002auk.3_RNA|CELF6_uc010biv.1_RNA|CELF6_uc010biw.2_Frame_Shift_Ins_p.E49fs|CELF6_uc010ukl.1_Frame_Shift_Ins_p.E47fs|CELF6_uc010ukm.1_Frame_Shift_Ins_p.E162fs|CELF6_uc002aui.2_Frame_Shift_Ins_p.E268fs|CELF6_uc002auj.2_Frame_Shift_Ins_p.E49fs	NM_052840	NP_443072	Q96J87	CELF6_HUMAN	bruno-like 6, RNA binding protein	162	RRM 2.				mRNA processing|regulation of alternative nuclear mRNA splicing, via spliceosome	cytoplasm|nucleus	nucleotide binding|RNA binding			large_intestine(1)|central_nervous_system(1)|skin(1)	3						GACCGTGCACTCCTCGATGTGG	0.599													36	20	---	---	---	---	
DKFZp434J0226	93429	broad.mit.edu	37	19	46716265	46716265	+	RNA	DEL	C	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:46716265delC	uc010xxw.1	+	4		c.516delC				NR_027003				Homo sapiens mRNA; cDNA DKFZp434J0226 (from clone DKFZp434J0226).												0						CCATGAGCTGCAGGTGAGTGA	0.557													4	2	---	---	---	---	
ZNF160	90338	broad.mit.edu	37	19	53571486	53571486	+	Frame_Shift_Del	DEL	C	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr19:53571486delC	uc010eqk.2	-	7	2717	c.2301delG	c.(2299-2301)GGGfs	p.G767fs	ZNF160_uc002qaq.3_Frame_Shift_Del_p.G767fs|ZNF160_uc002qar.3_Frame_Shift_Del_p.G767fs	NM_001102603	NP_001096073	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	767	C2H2-type 19.				hemopoiesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			central_nervous_system(1)	1				GBM - Glioblastoma multiforme(134;0.02)		TAAAGGCTTTCCCACACTCTG	0.433													45	23	---	---	---	---	
CHMP4B	128866	broad.mit.edu	37	20	32399279	32399279	+	Frame_Shift_Del	DEL	C	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr20:32399279delC	uc002xaa.2	+	1	161	c.5delC	c.(4-6)TCGfs	p.S2fs		NM_176812	NP_789782	Q9H444	CHM4B_HUMAN	chromatin modifying protein 4B	2					cellular membrane organization|endosome transport|protein transport	cytosol|late endosome membrane	protein binding			ovary(1)|central_nervous_system(1)	2						GCAACCATGTCGGTGTTCGGG	0.403													4	2	---	---	---	---	
KRTAP10-3	386682	broad.mit.edu	37	21	45978509	45978509	+	Frame_Shift_Del	DEL	G	-	-			TCGA-37-3789-01A-01D-0983-08	TCGA-37-3789-10A-01D-0983-08									Somatic	Phase_I	Capture				Illumina GAIIx	d732196f-ef85-43ea-aac7-7c9060bf19c5	7ad070ce-6ace-4f7a-97e5-e234783df2ec	g.chr21:45978509delG	uc002zfj.1	-	1	135	c.90delC	c.(88-90)CCCfs	p.P30fs	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198696	NP_941969	P60369	KR103_HUMAN	keratin associated protein 10-3	30	1.|18 X 5 AA repeats of C-C-X(3).					keratin filament				skin(1)	1						TGGCGCAGCAGGGGGGCTCAC	0.697													16	9	---	---	---	---	
