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
NASP	4678	broad.mit.edu	37	1	46073803	46073803	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr1:46073803G>T	uc001coi.1	+	6	1322	c.1220G>T	c.(1219-1221)GGC>GTC	p.G407V	NASP_uc010olq.1_Missense_Mutation_p.G370V|NASP_uc001coh.1_Missense_Mutation_p.G409V|NASP_uc001coj.1_Intron|NASP_uc010olr.1_Missense_Mutation_p.G343V|NASP_uc001cok.1_Missense_Mutation_p.G290V	NM_002482	NP_002473	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein isoform 2	407	Glu-rich (acidic).				blastocyst development|cell cycle|cell proliferation|DNA replication|histone exchange|protein transport	cytoplasm|nucleus	Hsp90 protein binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					ACAAAAGATGGCTCAGGACTA	0.488													6	154	---	---	---	---	PASS
FCRL4	83417	broad.mit.edu	37	1	157551405	157551405	+	Missense_Mutation	SNP	C	T	T	rs143188744	byFrequency	TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr1:157551405C>T	uc001fqw.2	-	7	1301	c.1165G>A	c.(1165-1167)GCC>ACC	p.A389T	FCRL4_uc010phy.1_RNA	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor	389	Helical; (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				GCTCCCGCGGCGACAAGGCCA	0.572													5	44	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186147655	186147655	+	Missense_Mutation	SNP	G	A	A	rs144069476	by1000genomes	TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr1:186147655G>A	uc001grq.1	+	104	16280	c.16051G>A	c.(16051-16053)GGG>AGG	p.G5351R	HMCN1_uc001grs.1_Intron	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	5351	EGF-like 6; calcium-binding (Potential).				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						ATTAGGGGACGGGAAATCTTG	0.483													11	333	---	---	---	---	PASS
HHIPL2	79802	broad.mit.edu	37	1	222717002	222717002	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr1:222717002C>T	uc001hnh.1	-	2	909	c.851G>A	c.(850-852)CGC>CAC	p.R284H		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2 precursor	284					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1				GBM - Glioblastoma multiforme(131;0.0185)		GCGATTGTGGCGGAATTTGGG	0.483													8	236	---	---	---	---	PASS
UBR3	130507	broad.mit.edu	37	2	170930058	170930058	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr2:170930058A>G	uc010zdi.1	+	36	5140	c.5140A>G	c.(5140-5142)ATA>GTA	p.I1714V	UBR3_uc002ufr.3_RNA|UBR3_uc010fqa.2_Missense_Mutation_p.I535V|UBR3_uc002uft.3_Missense_Mutation_p.I571V|UBR3_uc010zdj.1_Missense_Mutation_p.I405V|UBR3_uc002ufu.3_Missense_Mutation_p.I220V	NM_172070	NP_742067	Q6ZT12	UBR3_HUMAN	E3 ubiquitin-protein ligase UBR3	1714					sensory perception of smell|suckling behavior|ubiquitin-dependent protein catabolic process	integral to membrane	ubiquitin-protein ligase activity|zinc ion binding				0						ATTTGATATTATAACTCAGTG	0.418													90	137	---	---	---	---	PASS
CXCR1	3577	broad.mit.edu	37	2	219028938	219028938	+	Missense_Mutation	SNP	G	A	A	rs140349292	byFrequency	TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr2:219028938G>A	uc002vhc.2	-	2	1116	c.997C>T	c.(997-999)CGT>TGT	p.R333C		NM_000634	NP_000625	P25024	CXCR1_HUMAN	interleukin 8 receptor alpha	333	Cytoplasmic (Potential).				dendritic cell chemotaxis|inflammatory response	integral to membrane|plasma membrane	interleukin-8 receptor activity			lung(2)	2						ACACGATGACGTGCCAAGAAC	0.468													8	107	---	---	---	---	PASS
CTNNB1	1499	broad.mit.edu	37	3	41266098	41266098	+	Missense_Mutation	SNP	A	T	T	rs121913396		TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr3:41266098A>T	uc010hia.1	+	4	251	c.95A>T	c.(94-96)GAC>GTC	p.D32V	CTNNB1_uc003ckp.2_Missense_Mutation_p.D32V|CTNNB1_uc003ckq.2_Missense_Mutation_p.D32V|CTNNB1_uc003ckr.2_Missense_Mutation_p.D32V|CTNNB1_uc011azf.1_Missense_Mutation_p.D25V|CTNNB1_uc011azg.1_Intron|uc010hib.1_RNA	NM_001904	NP_001895	P35222	CTNB1_HUMAN	beta-catenin	32			Missing (in hepatocellular carcinoma).|D -> A (in hepatocellular carcinoma).|D -> G (in PTR and hepatocellular carcinoma).		adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens	alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding	p.D32Y(110)|p.A5_A80del(63)|p.D32N(58)|p.D32G(53)|p.D32H(37)|p.D32V(20)|p.D32A(12)|p.H24_S47del(9)|p.A5_A80>D(7)|p.A5_Q143del(7)|p.WQQQSYLD25?(5)|p.Q28_H134del(5)|p.W25_D32del(4)|p.W25_I140del(4)|p.S23_S33del(3)|p.V22_G38del(3)|p.T3_A126del(2)|p.M5_N141>D(2)|p.D32E(2)|p.D32_S47del(2)|p.W25_H36del(2)|p.Y30_S33del(2)|p.V22_S33del(2)|p.V22_L139>V(2)|p.A5_Y142>D(2)|p.A5fs*7(2)|p.?(2)|p.L10_N141del(2)|p.D6_A43del(1)|p.E9_S47del(1)|p.Q28_Q61del(1)|p.A20_R151del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S29_H36del(1)|p.Y30_A97del(1)|p.A20_A80del(1)|p.Q28_A43del(1)|p.E15_I140>V(1)|p.D17_P128del(1)|p.H24_M131del(1)|p.L7_I140del(1)|p.K19_Y142>V(1)|p.A20_L148del(1)|p.V22_A80del(1)|p.W25_I35del(1)|p.V22_G80>NNNNN(1)|p.A5_I35del(1)|p.A20_Q143del(1)|p.A13_R151del(1)|p.D32del(1)|p.S23_I140del(1)|p.M1_A87del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.S23_A39del(1)|p.A21_A80del(1)|p.D6_I140del(1)|p.Q28_I140del(1)|p.E9_A80del(1)|p.M14_S45del(1)|p.M8_G50del(1)|p.A5_G80>(1)|p.D32_H36>D(1)|p.P16_K133del(1)|p.A5_T59del(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.A5_R90del(1)|p.V22_Y64del(1)|p.M8_A80del(1)|p.E9_I140del(1)|p.D32_S33insS(1)|p.Y30_T40del(1)|p.M1_T42del(1)|p.A5_Q143>E(1)|p.A5_Q72del(1)|p.Q28_D32>H(1)|p.Y30_A80del(1)|p.D32fs*9(1)|p.D6_K133del(1)|p.A5_T42del(1)|p.A5_D144>D(1)|p.A5_T40del(1)|p.D17_A126del(1)|p.A5_E54del(1)|p.S23_I35del(1)|p.V22_S71>A(1)|p.W25_A80del(1)|p.A20_Q72del(1)|p.A20_S111del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	liver(806)|soft_tissue(609)|large_intestine(243)|endometrium(222)|kidney(172)|stomach(157)|central_nervous_system(139)|ovary(104)|skin(97)|pancreas(91)|adrenal_gland(85)|pituitary(81)|salivary_gland(62)|haematopoietic_and_lymphoid_tissue(57)|thyroid(55)|biliary_tract(41)|lung(38)|prostate(24)|bone(20)|small_intestine(17)|cervix(9)|parathyroid(9)|urinary_tract(8)|breast(7)|oesophagus(5)|NS(3)|pleura(2)|upper_aerodigestive_tract(2)|eye(1)	3166				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)	Lithium(DB01356)	TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	H|Mis|T	PLAG1	colorectal|cvarian| hepatoblastoma|others|pleomorphic salivary adenoma				Pilomatrixoma_Familial_Clustering_of				5	52	---	---	---	---	PASS
FHIT	2272	broad.mit.edu	37	3	59999869	59999869	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr3:59999869A>G	uc003dkx.3	-	6	484	c.113T>C	c.(112-114)GTG>GCG	p.V38A	FHIT_uc003dky.2_Missense_Mutation_p.V38A|FHIT_uc010hnn.1_Missense_Mutation_p.V38A	NM_002012	NP_002003	P49789	FHIT_HUMAN	fragile histidine triad gene	38	HIT.				nucleotide metabolic process		bis(5'-adenosyl)-triphosphatase activity|protein binding				0		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		CAGCGGGCACACAAGGACATC	0.542			T	HMGA2	pleomorphic salivary gland adenoma				Renal_Cell_Cancer_associated_with_constitutional_translocation_of_chromosome_3				6	84	---	---	---	---	PASS
LIMCH1	22998	broad.mit.edu	37	4	41621299	41621299	+	Silent	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr4:41621299G>A	uc003gvu.3	+	8	831	c.777G>A	c.(775-777)GAG>GAA	p.E259E	LIMCH1_uc003gvt.1_Silent_p.E100E|LIMCH1_uc003gvv.3_Silent_p.E259E|LIMCH1_uc003gvw.3_Silent_p.E259E|LIMCH1_uc003gvx.3_Silent_p.E259E|LIMCH1_uc003gwe.3_Silent_p.E259E|LIMCH1_uc003gvy.3_Silent_p.E100E|LIMCH1_uc003gwa.3_Silent_p.E100E|LIMCH1_uc003gvz.3_Silent_p.E100E|LIMCH1_uc011byu.1_Silent_p.E105E|LIMCH1_uc003gwc.3_Silent_p.E105E|LIMCH1_uc003gwd.3_Silent_p.E105E|LIMCH1_uc011byv.1_Silent_p.E10E|LIMCH1_uc003gwb.1_Silent_p.E107E	NM_014988	NP_055803	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1 isoform a	259					actomyosin structure organization		actin binding|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4						CCCATGGTGAGCCGAAATCAG	0.547													18	261	---	---	---	---	PASS
LRRC66	339977	broad.mit.edu	37	4	52861922	52861922	+	Silent	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr4:52861922G>A	uc003gzi.2	-	4	1279	c.1266C>T	c.(1264-1266)AAC>AAT	p.N422N		NM_001024611	NP_001019782	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	422						integral to membrane				ovary(1)|central_nervous_system(1)|skin(1)	3						AGAAGCCCTCGTTTGAATACG	0.537													11	168	---	---	---	---	PASS
PCDHA4	56144	broad.mit.edu	37	5	140188929	140188929	+	Silent	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr5:140188929C>T	uc003lhi.2	+	1	2258	c.2157C>T	c.(2155-2157)ACC>ACT	p.T719T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.T719T|PCDHA4_uc011daa.1_Silent_p.T719T	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	719	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGTACACCGCGCTGCGGT	0.657													6	93	---	---	---	---	PASS
PCDHB7	56129	broad.mit.edu	37	5	140554610	140554610	+	Nonsense_Mutation	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr5:140554610C>T	uc003lit.2	+	1	2368	c.2194C>T	c.(2194-2196)CGA>TGA	p.R732*	PCDHB8_uc011dai.1_5'Flank	NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	732	Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	p.R732*(1)		ovary(4)|central_nervous_system(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCCTTTCCACGACATCTGGT	0.637													21	525	---	---	---	---	PASS
TFAP2D	83741	broad.mit.edu	37	6	50740477	50740477	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr6:50740477C>T	uc003paf.2	+	8	1771	c.1259C>T	c.(1258-1260)GCG>GTG	p.A420V	TFAP2D_uc011dwt.1_RNA	NM_172238	NP_758438	Q7Z6R9	AP2D_HUMAN	transcription factor AP-2 beta-like 1	420							DNA binding|sequence-specific DNA binding transcription factor activity			ovary(6)|breast(1)	7	Lung NSC(77;0.0334)					AACGGCGGAGCGGCGGATTCT	0.507													12	73	---	---	---	---	PASS
TBX18	9096	broad.mit.edu	37	6	85446536	85446536	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr6:85446536G>A	uc003pkl.1	-	8	1691	c.1691C>T	c.(1690-1692)ACG>ATG	p.T564M	TBX18_uc010kbq.1_Intron	NM_001080508	NP_001073977	O95935	TBX18_HUMAN	T-box 18	564					multicellular organismal development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)|pancreas(2)|lung(1)	5		all_cancers(76;0.000283)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0858)		BRCA - Breast invasive adenocarcinoma(108;0.0267)		CTGCCGATCCGTCATGGTCCC	0.527													10	102	---	---	---	---	PASS
CDK19	23097	broad.mit.edu	37	6	110948346	110948346	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr6:110948346T>C	uc003puh.1	-	7	722	c.649A>G	c.(649-651)ATA>GTA	p.I217V	CDK19_uc003pui.1_Missense_Mutation_p.I157V|CDK19_uc011eax.1_Missense_Mutation_p.I93V	NM_015076	NP_055891	Q9BWU1	CDK19_HUMAN	cell division cycle 2-like 6 (CDK8-like)	217	Protein kinase.						ATP binding|cyclin-dependent protein kinase activity|protein binding			ovary(2)|central_nervous_system(1)|skin(1)	4						ATTGCCCATATATCTGGGAAG	0.318													45	80	---	---	---	---	PASS
NEUROD6	63974	broad.mit.edu	37	7	31378446	31378446	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr7:31378446A>G	uc003tch.2	-	2	790	c.437T>C	c.(436-438)CTT>CCT	p.L146P		NM_022728	NP_073565	Q96NK8	NDF6_HUMAN	neurogenic differentiation 6	146	Helix-loop-helix motif.				cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(2)	2						AATTTCAGAAAGTGCCCAGAT	0.443													42	94	---	---	---	---	PASS
CA1	759	broad.mit.edu	37	8	86249177	86249177	+	Silent	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr8:86249177G>A	uc003ydh.2	-	5	551	c.351C>T	c.(349-351)GCC>GCT	p.A117A	CA13_uc003ydf.1_Intron|CA1_uc010mae.1_Silent_p.A117A|CA1_uc003ydi.2_Silent_p.A117A	NM_001738	NP_001729	P00915	CAH1_HUMAN	carbonic anhydrase I	117					one-carbon metabolic process	Golgi apparatus	carbonate dehydratase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_lung(136;4.89e-06)			Acetazolamide(DB00819)|Amlodipine(DB00381)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diazoxide(DB01119)|Dichlorphenamide(DB01144)|Ethinamate(DB01031)|Ethoxzolamide(DB00311)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Levetiracetam(DB01202)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Quinethazone(DB01325)|Trichlormethiazide(DB01021)|Verapamil(DB00661)|Zonisamide(DB00909)	ACATTACCTCGGCAGAATATT	0.413													16	196	---	---	---	---	PASS
ENPP2	5168	broad.mit.edu	37	8	120569893	120569893	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr8:120569893C>T	uc003yot.1	-	25	2546	c.2460G>A	c.(2458-2460)ATG>ATA	p.M820I	ENPP2_uc011lic.1_Missense_Mutation_p.M358I|ENPP2_uc003yor.1_Missense_Mutation_p.M455I|ENPP2_uc003yos.1_Missense_Mutation_p.M872I|ENPP2_uc010mdd.1_Missense_Mutation_p.M845I	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	autotaxin isoform 2 preproprotein	820					cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding			ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TGTGCATCTTCATGAGTTCTT	0.463													7	228	---	---	---	---	PASS
CRB2	286204	broad.mit.edu	37	9	126132707	126132707	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr9:126132707C>A	uc004bnx.1	+	7	1467	c.1375C>A	c.(1375-1377)CTG>ATG	p.L459M	CRB2_uc004bnw.1_Missense_Mutation_p.L459M	NM_173689	NP_775960	Q5IJ48	CRUM2_HUMAN	crumbs homolog 2 precursor	459	Extracellular (Potential).|Laminin G-like 1.					extracellular region|integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1						TGGTGGCCCCCTGGGTCTGGC	0.617													5	56	---	---	---	---	PASS
CRB2	286204	broad.mit.edu	37	9	126132708	126132708	+	Missense_Mutation	SNP	T	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr9:126132708T>A	uc004bnx.1	+	7	1468	c.1376T>A	c.(1375-1377)CTG>CAG	p.L459Q	CRB2_uc004bnw.1_Missense_Mutation_p.L459Q	NM_173689	NP_775960	Q5IJ48	CRUM2_HUMAN	crumbs homolog 2 precursor	459	Extracellular (Potential).|Laminin G-like 1.					extracellular region|integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1						GGTGGCCCCCTGGGTCTGGCA	0.612													5	55	---	---	---	---	PASS
SH3GLB2	56904	broad.mit.edu	37	9	131772101	131772101	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr9:131772101T>C	uc004bwv.2	-	9	934	c.788A>G	c.(787-789)TAC>TGC	p.Y263C	SH3GLB2_uc004bww.2_Missense_Mutation_p.Y267C|SH3GLB2_uc004bwx.1_Missense_Mutation_p.Y263C|SH3GLB2_uc011mbm.1_Missense_Mutation_p.Y267C	NM_020145	NP_064530	Q9NR46	SHLB2_HUMAN	SH3-domain GRB2-like endophilin B2	263	BAR.				filopodium assembly|signal transduction	cytoplasm|nucleus	cytoskeletal adaptor activity|SH3 domain binding				0						CTGTGCGTAGTAGGTTGTCTG	0.622													9	13	---	---	---	---	PASS
CUL2	8453	broad.mit.edu	37	10	35351967	35351967	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr10:35351967G>A	uc001ixv.2	-	3	353	c.143C>T	c.(142-144)GCC>GTC	p.A48V	CUL2_uc009xma.2_5'UTR|CUL2_uc010qer.1_Missense_Mutation_p.A67V|CUL2_uc001ixw.2_Missense_Mutation_p.A48V|CUL2_uc010qes.1_Missense_Mutation_p.A48V	NM_003591	NP_003582	Q13617	CUL2_HUMAN	cullin 2	48					cell cycle arrest|G1/S transition of mitotic cell cycle|induction of apoptosis by intracellular signals|interspecies interaction between organisms|negative regulation of cell proliferation|ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding			ovary(3)	3						TTCAGGATAGGCCACACATAA	0.313													11	118	---	---	---	---	PASS
OR5D16	390144	broad.mit.edu	37	11	55606581	55606581	+	Silent	SNP	G	A	A	rs139231893	byFrequency	TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr11:55606581G>A	uc010rio.1	+	1	354	c.354G>A	c.(352-354)GCG>GCA	p.A118A		NM_001005496	NP_001005496	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D,	118	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.A118V(1)		ovary(4)|skin(1)	5		all_epithelial(135;0.208)				TTCTATTTGCGGTGATGGCCT	0.423													7	305	---	---	---	---	PASS
MEN1	4221	broad.mit.edu	37	11	64572284	64572284	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr11:64572284C>T	uc001obj.2	-	10	1443	c.1370G>A	c.(1369-1371)CGG>CAG	p.R457Q	MAP4K2_uc001obh.2_5'Flank|MAP4K2_uc001obi.2_5'Flank|MAP4K2_uc010rnp.1_5'Flank|MEN1_uc001obk.2_Missense_Mutation_p.R457Q|MEN1_uc001obl.2_Missense_Mutation_p.R417Q|MEN1_uc001obm.2_Missense_Mutation_p.R452Q|MEN1_uc001obn.2_Missense_Mutation_p.R457Q|MEN1_uc001obo.2_Missense_Mutation_p.R457Q|MEN1_uc001obp.2_Missense_Mutation_p.R452Q|MEN1_uc001obq.2_Missense_Mutation_p.R457Q|MEN1_uc001obr.2_Missense_Mutation_p.R457Q	NM_130800	NP_570712	O00255	MEN1_HUMAN	menin isoform 1	457					DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent	chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction	double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding			parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1)	238						CACCTTCTGCCGCACCTGGGC	0.726			D|Mis|N|F|S		parathyroid tumors|Pancreatic neuroendocrine tumors	parathyroid adenoma|pituitary adenoma|pancreatic islet cell|carcinoid			Hyperparathyroidism_Familial_Isolated|Multiple_Endocrine_Neoplasia_type_1				21	119	---	---	---	---	PASS
KRT1	3848	broad.mit.edu	37	12	53071120	53071120	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr12:53071120C>T	uc001sau.1	-	5	1167	c.1108G>A	c.(1108-1110)GAG>AAG	p.E370K	KRT1_uc001sav.1_Missense_Mutation_p.E370K	NM_006121	NP_006112	P04264	K2C1_HUMAN	keratin 1	370	Rod.|Coil 2.				complement activation, lectin pathway|epidermis development|fibrinolysis|regulation of angiogenesis|response to oxidative stress	plasma membrane	protein binding|receptor activity|structural constituent of cytoskeleton|sugar binding			ovary(1)|skin(1)	2						TACAAGGACTCGGCCTCAGCT	0.522													9	125	---	---	---	---	PASS
CUX2	23316	broad.mit.edu	37	12	111652018	111652018	+	Silent	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr12:111652018C>T	uc001tsa.1	+	2	231	c.78C>T	c.(76-78)TCC>TCT	p.S26S	CUX2_uc001tsb.1_Silent_p.S81S	NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2	26						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						AGCTTAATTCCGTCGCTTCTG	0.318													7	130	---	---	---	---	PASS
ACADS	35	broad.mit.edu	37	12	121176678	121176678	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr12:121176678G>A	uc001tza.3	+	8	1107	c.989G>A	c.(988-990)CGC>CAC	p.R330H	ACADS_uc010szl.1_Missense_Mutation_p.R326H|ACADS_uc001tzb.3_Missense_Mutation_p.R211H	NM_000017	NP_000008	P16219	ACADS_HUMAN	short-chain acyl-CoA dehydrogenase precursor	330						mitochondrial matrix	butyryl-CoA dehydrogenase activity			central_nervous_system(2)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)	Lung NSC(355;0.163)			NADH(DB00157)	CTGACCTGGCGCGCTGCCATG	0.642													5	113	---	---	---	---	PASS
RIMBP2	23504	broad.mit.edu	37	12	130935764	130935764	+	Silent	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr12:130935764G>A	uc001uil.2	-	5	593	c.429C>T	c.(427-429)AGC>AGT	p.S143S	RIMBP2_uc001uim.2_Silent_p.S51S	NM_015347	NP_056162	O15034	RIMB2_HUMAN	RIM-binding protein 2	143						cell junction|synapse				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TGCATCTTGCGCTACCGGATC	0.637													5	80	---	---	---	---	PASS
FOXA1	3169	broad.mit.edu	37	14	38060572	38060572	+	Nonstop_Mutation	SNP	A	C	C			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr14:38060572A>C	uc001wuf.2	-	2	1729	c.1417T>G	c.(1417-1419)TAG>GAG	p.*473E	FOXA1_uc010tpz.1_Nonstop_Mutation_p.*440E	NM_004496	NP_004487	P55317	FOXA1_HUMAN	forkhead box A1	473					chromatin remodeling|embryo development|epithelial cell maturation involved in prostate gland development|epithelial tube branching involved in lung morphogenesis|epithelial-mesenchymal signaling involved in prostate gland development|glucose homeostasis|lung epithelial cell differentiation|negative regulation of survival gene product expression|neuron fate specification|pattern specification process|positive regulation of estrogen receptor signaling pathway|positive regulation of mitotic cell cycle|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|prostate gland epithelium morphogenesis|prostate gland stromal morphogenesis|response to estradiol stimulus|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding				0	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		CCCGGGAGCTAGGAAGTGTTT	0.562													4	88	---	---	---	---	PASS
SALL1	6299	broad.mit.edu	37	16	51173899	51173899	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr16:51173899G>A	uc010vgs.1	-	2	2265	c.2234C>T	c.(2233-2235)ACG>ATG	p.T745M	SALL1_uc010vgr.1_Missense_Mutation_p.T648M|SALL1_uc010cbv.2_Intron	NM_002968	NP_002959	Q9NSC2	SALL1_HUMAN	sal-like 1 isoform a	745	C2H2-type 4.				adrenal gland development|branching involved in ureteric bud morphogenesis|embryonic digestive tract development|embryonic digit morphogenesis|gonad development|histone deacetylation|inductive cell-cell signaling|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of transcription from RNA polymerase II promoter|olfactory bulb interneuron differentiation|olfactory bulb mitral cell layer development|olfactory nerve development|outer ear morphogenesis|pituitary gland development|positive regulation of transcription from RNA polymerase II promoter|positive regulation of Wnt receptor signaling pathway|ureteric bud invasion|ventricular septum development	chromocenter|cytoplasm|heterochromatin|nucleus	beta-catenin binding|DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			skin(5)|ovary(3)	8		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ATTCCCTTTCGTGGTGAAAGC	0.547													6	97	---	---	---	---	PASS
DPH1	1801	broad.mit.edu	37	17	1939852	1939852	+	Missense_Mutation	SNP	C	T	T	rs36104739		TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr17:1939852C>T	uc002fts.2	+	5	463	c.445C>T	c.(445-447)CGG>TGG	p.R149W	DPH1_uc002ftr.1_RNA|DPH1_uc002ftt.2_Missense_Mutation_p.R144W|DPH1_uc010cjx.2_Missense_Mutation_p.R9W|DPH1_uc010vqs.1_Missense_Mutation_p.R159W|DPH1_uc002ftu.2_5'Flank|DPH1_uc002ftv.2_5'Flank	NM_001383	NP_001374	Q9BZG8	DPH1_HUMAN	diptheria toxin resistance protein required for	149					peptidyl-diphthamide biosynthetic process from peptidyl-histidine|translation	cytoplasm|nucleus				pancreas(1)	1						CCAAGACTTCCGGGTGCTGTA	0.627													11	148	---	---	---	---	PASS
RPL19	6143	broad.mit.edu	37	17	37360425	37360425	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr17:37360425G>A	uc002hrq.1	+	5	514	c.452G>A	c.(451-453)CGC>CAC	p.R151H	RPL19_uc002hrr.1_Missense_Mutation_p.R149H	NM_000981	NP_000972	P84098	RL19_HUMAN	ribosomal protein L19	151					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit	RNA binding|structural constituent of ribosome				0						GACAAGGCCCGCAAGAAGCTC	0.453													3	51	---	---	---	---	PASS
LAMA3	3909	broad.mit.edu	37	18	21426327	21426327	+	Silent	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr18:21426327C>T	uc002kuq.2	+	31	3872	c.3786C>T	c.(3784-3786)GGC>GGT	p.G1262G	LAMA3_uc002kur.2_Silent_p.G1262G	NM_198129	NP_937762	Q16787	LAMA3_HUMAN	laminin alpha 3 subunit isoform 1	1262	Domain IV 1 (domain IV B).				cell adhesion|epidermis development|hemidesmosome assembly|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|skin(2)|central_nervous_system(1)	11	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)				Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	ACCACAAGGGCGCCCTGCCTT	0.632													7	189	---	---	---	---	PASS
CACNA1A	773	broad.mit.edu	37	19	13423526	13423526	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr19:13423526G>A	uc010dze.2	-	12	1864	c.1628C>T	c.(1627-1629)ACG>ATG	p.T543M	CACNA1A_uc010dzc.2_Missense_Mutation_p.T68M|CACNA1A_uc002mwy.3_Missense_Mutation_p.T542M|CACNA1A_uc010xne.1_Missense_Mutation_p.T68M	NM_001127221	NP_001120693	O00555	CAC1A_HUMAN	calcium channel, alpha 1A subunit isoform 3	543	Cytoplasmic (Potential).|II.				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)	GTAAGGCCGCGTCCCAAGCCC	0.438													8	93	---	---	---	---	PASS
SIPA1L3	23094	broad.mit.edu	37	19	38572930	38572930	+	Missense_Mutation	SNP	T	C	C			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr19:38572930T>C	uc002ohk.2	+	3	1234	c.725T>C	c.(724-726)CTC>CCC	p.L242P		NM_015073	NP_055888	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like	242					regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(1)|central_nervous_system(1)	2			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			ACCGAGCTCCTCCGGGCAGAT	0.701													3	58	---	---	---	---	PASS
DHX34	9704	broad.mit.edu	37	19	47878858	47878858	+	Missense_Mutation	SNP	C	T	T	rs61751860	byFrequency	TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr19:47878858C>T	uc010xyn.1	+	10	2541	c.2200C>T	c.(2200-2202)CGC>TGC	p.R734C	DHX34_uc010xyo.1_5'Flank	NM_014681	NP_055496	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	734						intracellular	ATP binding|ATP-dependent helicase activity|RNA binding|zinc ion binding			ovary(4)|upper_aerodigestive_tract(1)	5		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		GGGCGCGGGGCGCAGGCGCAA	0.736													2	1	---	---	---	---	PASS
FAM83C	128876	broad.mit.edu	37	20	33875234	33875234	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr20:33875234G>A	uc010zux.1	-	4	1466	c.1348C>T	c.(1348-1350)CGG>TGG	p.R450W	EIF6_uc002xbv.1_5'Flank|EIF6_uc002xbx.1_5'Flank|EIF6_uc002xbz.1_5'Flank|EIF6_uc002xby.1_5'Flank|FAM83C_uc002xcb.1_Missense_Mutation_p.R105W	NM_178468	NP_848563	Q9BQN1	FA83C_HUMAN	hypothetical protein LOC128876	450										ovary(2)	2			BRCA - Breast invasive adenocarcinoma(18;0.00252)			AGGAGGGGCCGGGAGCGAGGA	0.647													5	60	---	---	---	---	PASS
CEP250	11190	broad.mit.edu	37	20	34091637	34091637	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr20:34091637C>G	uc002xcm.2	+	31	6111	c.5440C>G	c.(5440-5442)CAG>GAG	p.Q1814E	CEP250_uc010zve.1_Missense_Mutation_p.Q1182E	NM_007186	NP_009117	Q9BV73	CP250_HUMAN	centrosomal protein 2	1814	Gln/Glu-rich.|Potential.				centriole-centriole cohesion|G2/M transition of mitotic cell cycle|protein localization|regulation of centriole-centriole cohesion	centriole|cilium|cytosol|microtubule basal body|perinuclear region of cytoplasm|protein complex	protein C-terminus binding|protein kinase binding			ovary(4)|central_nervous_system(1)	5	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AGCCCTAGCCCAGAGGGACCA	0.607													5	100	---	---	---	---	PASS
MXRA5	25878	broad.mit.edu	37	X	3242966	3242966	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chrX:3242966C>A	uc004crg.3	-	5	917	c.760G>T	c.(760-762)GCA>TCA	p.A254S		NM_015419	NP_056234	Q9NR99	MXRA5_HUMAN	adlican precursor	254	LRRCT.					extracellular region				ovary(5)|lung(1)|central_nervous_system(1)|skin(1)	8		all_lung(23;0.00031)|Lung NSC(23;0.000946)				AAGCACATTGCACACAACTGA	0.408													9	46	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	X	51150821	51150821	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chrX:51150821C>T	uc004dpj.2	+	1	1055	c.953C>T	c.(952-954)GCG>GTG	p.A318V		NM_203407	NP_981952			hypothetical protein LOC340602																		CGCGATTCTGCGCCAGGCCCT	0.736													9	4	---	---	---	---	PASS
NXF3	56000	broad.mit.edu	37	X	102337712	102337712	+	Silent	SNP	G	A	A	rs146732324		TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chrX:102337712G>A	uc004eju.2	-	8	827	c.756C>T	c.(754-756)GAC>GAT	p.D252D	NXF3_uc010noi.1_Silent_p.D102D|NXF3_uc011mrw.1_Silent_p.D252D|NXF3_uc011mrx.1_Silent_p.D163D	NM_022052	NP_071335	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	252						cytoplasm|nuclear RNA export factor complex	nucleocytoplasmic transporter activity|nucleotide binding|protein binding			ovary(1)|lung(1)|central_nervous_system(1)	3						CTTCATGGACGTCCAGGGAGG	0.478													21	159	---	---	---	---	PASS
ASH1L	55870	broad.mit.edu	37	1	155448689	155448689	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr1:155448689delA	uc009wqq.2	-	3	4452	c.3972delT	c.(3970-3972)TTTfs	p.F1324fs	ASH1L_uc001fkt.2_Frame_Shift_Del_p.F1324fs|ASH1L_uc009wqr.1_Frame_Shift_Del_p.F1324fs	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	1324					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AGAAACTATTAAAGTTGATTC	0.408													268	7	---	---	---	---	
FIP1L1	81608	broad.mit.edu	37	4	54319248	54319249	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr4:54319248_54319249delAG	uc003gzy.2	+	16	1633_1634	c.1447_1448delAG	c.(1447-1449)AGAfs	p.R483fs	PDGFRA_uc003haa.2_Intron|FIP1L1_uc011bzu.1_Frame_Shift_Del_p.R477fs|FIP1L1_uc003gzz.2_Frame_Shift_Del_p.R409fs|FIP1L1_uc003hab.2_Frame_Shift_Del_p.R448fs|FIP1L1_uc003hac.2_Frame_Shift_Del_p.R237fs|FIP1L1_uc010ign.2_RNA|FIP1L1_uc003had.2_Frame_Shift_Del_p.P67fs|FIP1L1_uc003hae.2_Frame_Shift_Del_p.P67fs	NM_030917	NP_112179	Q6UN15	FIP1_HUMAN	FIP1 like 1 isoform 1	483	Arg-rich.|Sufficient for interaction with CPSF1 and CSTF3.|Glu-rich.				mRNA processing	nucleus	RNA binding			ovary(1)|skin(1)	2			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			agaACGCACCAGAGAGAGAGAG	0.292			T	PDGFRA	idiopathic hypereosinophilic syndrome								124	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	43283606	43283606	+	RNA	DEL	A	-	-			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr11:43283606delA	uc001mxe.1	-	2		c.1330delT								Homo sapiens cDNA FLJ44864 fis, clone BRALZ2013621, moderately similar to Heterogeneous nuclear ribonucleoprotein K.																		AAGCAAATGTAAAAAAAAAAA	0.388													7	5	---	---	---	---	
FOXA1	3169	broad.mit.edu	37	14	38060721	38060721	+	Frame_Shift_Del	DEL	G	-	-			TCGA-EJ-5494-01A-01D-1576-08	TCGA-EJ-5494-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c3c8c9d3-e3d6-45ea-b448-e1143892a190	d498facd-d3ad-4e75-87a2-bea5253d9f1f	g.chr14:38060721delG	uc001wuf.2	-	2	1580	c.1268delC	c.(1267-1269)GCAfs	p.A423fs	FOXA1_uc010tpz.1_Frame_Shift_Del_p.A390fs	NM_004496	NP_004487	P55317	FOXA1_HUMAN	forkhead box A1	423					chromatin remodeling|embryo development|epithelial cell maturation involved in prostate gland development|epithelial tube branching involved in lung morphogenesis|epithelial-mesenchymal signaling involved in prostate gland development|glucose homeostasis|lung epithelial cell differentiation|negative regulation of survival gene product expression|neuron fate specification|pattern specification process|positive regulation of estrogen receptor signaling pathway|positive regulation of mitotic cell cycle|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|prostate gland epithelium morphogenesis|prostate gland stromal morphogenesis|response to estradiol stimulus|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding				0	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		GTATTGCAGTGCCTGTTCGTA	0.612													66	12	---	---	---	---	
