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
NPHP4	261734	broad.mit.edu	37	1	5926507	5926507	+	Silent	SNP	T	C	C	rs555164	by1000genomes	TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr1:5926507T>C	uc001alq.1	-	26	3836	c.3570A>G	c.(3568-3570)GAA>GAG	p.E1190E	NPHP4_uc001alr.1_Silent_p.E132E	NM_015102	NP_055917	O75161	NPHP4_HUMAN	nephroretinin	1190					actin cytoskeleton organization|cell-cell adhesion|signal transduction|visual behavior	cell-cell junction|centrosome|cilium|microtubule basal body	protein binding|structural molecule activity			pancreas(1)	1	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		TGTCCCGTGGTTCCCCGGGGC	0.562													5	4	---	---	---	---	PASS
FAM131C	348487	broad.mit.edu	37	1	16361925	16361925	+	Silent	SNP	G	A	A	rs146790110		TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr1:16361925G>A	uc010obz.1	-	7	781	c.591C>T	c.(589-591)AGC>AGT	p.S197S	CLCNKB_uc001axw.3_Intron	NM_182623	NP_872429	Q96AQ9	F131C_HUMAN	hypothetical protein LOC348487	197											0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		CGCTGGGAAGGCTGTCCTGAA	0.647													2	3	---	---	---	---	PASS
FAM131C	348487	broad.mit.edu	37	1	16385178	16385178	+	Silent	SNP	G	A	A	rs80297394		TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr1:16385178G>A	uc001axz.3	-	7	787	c.597C>T	c.(595-597)CCC>CCT	p.P199P	FAM131C_uc010obz.1_Intron	NM_182623	NP_872429	Q96AQ9	F131C_HUMAN	hypothetical protein LOC348487	199											0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGGCCGCTGGGAAGGCTGT	0.647													5	8	---	---	---	---	PASS
ESPNP	284729	broad.mit.edu	37	1	17026504	17026504	+	Silent	SNP	G	A	A	rs146166916	by1000genomes	TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr1:17026504G>A	uc001azn.1	-	7	1182	c.1068C>T	c.(1066-1068)TGC>TGT	p.C356C		NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						CGTGGCCGTCGCAGGAGCTCG	0.711													5	7	---	---	---	---	PASS
JAK1	3716	broad.mit.edu	37	1	65310466	65310466	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr1:65310466C>T	uc001dbu.1	-	16	2471	c.2222G>A	c.(2221-2223)GGC>GAC	p.G741D	JAK1_uc009wam.1_Missense_Mutation_p.G729D|JAK1_uc009wal.1_5'UTR	NM_002227	NP_002218	P23458	JAK1_HUMAN	janus kinase 1	741	Protein kinase 1.				interferon-gamma-mediated signaling pathway|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|response to antibiotic|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|endomembrane system|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity			haematopoietic_and_lymphoid_tissue(34)|prostate(7)|soft_tissue(6)|lung(4)|breast(3)|central_nervous_system(2)|liver(2)|large_intestine(1)|stomach(1)|ovary(1)	61				BRCA - Breast invasive adenocarcinoma(111;0.0485)		AATGGGGATGCCGGGGTCACT	0.587			Mis		ALL								23	41	---	---	---	---	PASS
SPTA1	6708	broad.mit.edu	37	1	158585065	158585065	+	Silent	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr1:158585065G>A	uc001fst.1	-	48	6928	c.6729C>T	c.(6727-6729)GAC>GAT	p.D2243D		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2243	Spectrin 21.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)					GGTAGAGCTGGTCCCACTGCT	0.542													87	233	---	---	---	---	PASS
CCDC121	79635	broad.mit.edu	37	2	27850383	27850383	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr2:27850383T>C	uc002rle.2	-	2	465	c.284A>G	c.(283-285)AAT>AGT	p.N95S	ZNF512_uc010yly.1_Intron|CCDC121_uc010eze.2_Missense_Mutation_p.N259S|CCDC121_uc002rld.2_Missense_Mutation_p.N257S|GPN1_uc010ezf.2_5'Flank|GPN1_uc010yma.1_5'Flank|GPN1_uc010ymb.1_5'Flank|GPN1_uc010ymc.1_5'Flank|GPN1_uc010ymd.1_5'Flank|GPN1_uc010yme.1_5'Flank|GPN1_uc010ezg.1_5'Flank	NM_024584	NP_078860	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121 isoform 3	95											0	Acute lymphoblastic leukemia(172;0.155)					GGATTGGATATTTTCCTTTTG	0.393													158	322	---	---	---	---	PASS
RGPD5	84220	broad.mit.edu	37	2	113127775	113127775	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr2:113127775G>C	uc002ths.1	-	23	5355	c.5278C>G	c.(5278-5280)CCT>GCT	p.P1760A	RGPD8_uc010fkk.1_Missense_Mutation_p.P1620A	NM_005054	NP_005045	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5 isoform	1760					intracellular transport	cytoplasm	binding				0						GAACGGGAAGGATTTTCTTCC	0.308													4	51	---	---	---	---	PASS
ITGA4	3676	broad.mit.edu	37	2	182376434	182376434	+	Silent	SNP	T	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr2:182376434T>C	uc002unu.2	+	17	2617	c.1854T>C	c.(1852-1854)TTT>TTC	p.F618F	ITGA4_uc010frj.1_Silent_p.F100F	NM_000885	NP_000876	P13612	ITA4_HUMAN	integrin alpha 4 precursor	618	Extracellular (Potential).				blood coagulation|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response	integrin complex	identical protein binding|receptor activity			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)	AGATAAACTTTGCAAGGTTTT	0.303													63	180	---	---	---	---	PASS
AGFG1	3267	broad.mit.edu	37	2	228389506	228389506	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr2:228389506A>C	uc002vpc.2	+	5	819	c.569A>C	c.(568-570)CAG>CCG	p.Q190P	AGFG1_uc002vpd.2_Missense_Mutation_p.Q190P|AGFG1_uc002vpe.2_Missense_Mutation_p.Q190P|AGFG1_uc002vpf.2_Missense_Mutation_p.Q190P	NM_004504	NP_004495	P52594	AGFG1_HUMAN	HIV-1 Rev binding protein isoform 2	190					cell differentiation|mRNA export from nucleus|multicellular organismal development|regulation of ARF GTPase activity|spermatogenesis	cytoplasmic membrane-bounded vesicle|Golgi apparatus|nuclear pore	ARF GTPase activator activity|DNA binding|protein binding|RNA binding|zinc ion binding			skin(2)|ovary(1)|central_nervous_system(1)	4						TCTCAAGGGCAGCAGCAGGAG	0.423													57	194	---	---	---	---	PASS
VGLL4	9686	broad.mit.edu	37	3	11744501	11744501	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr3:11744501G>A	uc003bwf.2	-	2	374	c.8C>T	c.(7-9)ACG>ATG	p.T3M	VGLL4_uc003bwg.2_Translation_Start_Site	NM_014667	NP_055482	Q14135	VGLL4_HUMAN	vestigial like 4 isoform b	3					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)	1				LUSC - Lung squamous cell carcinoma(1;0.089)|Lung(1;0.111)		ATCCAATGGCGTCTCCATTCC	0.368													11	44	---	---	---	---	PASS
AMIGO3	386724	broad.mit.edu	37	3	49755885	49755885	+	Silent	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr3:49755885G>A	uc003cxj.2	-	1	1354	c.1014C>T	c.(1012-1014)GCC>GCT	p.A338A	RNF123_uc003cxh.2_Intron|RNF123_uc003cxi.2_Intron	NM_198722	NP_942015	Q86WK7	AMGO3_HUMAN	adhesion molecule with Ig-like domain 3	338	Extracellular (Potential).|Ig-like C2-type.				heterophilic cell-cell adhesion	integral to membrane				pancreas(1)	1				BRCA - Breast invasive adenocarcinoma(193;4.47e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CGTTGCCTATGGCCAAGCTGC	0.667													9	34	---	---	---	---	PASS
SLC9A10	285335	broad.mit.edu	37	3	112005630	112005630	+	Silent	SNP	T	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr3:112005630T>C	uc003dyu.2	-	2	231	c.9A>G	c.(7-9)GGA>GGG	p.G3G	SLC9A10_uc011bhu.1_5'UTR|SLC9A10_uc010hqc.2_Silent_p.G3G	NM_183061	NP_898884	Q4G0N8	S9A10_HUMAN	sperm-specific sodium proton exchanger	3					cell differentiation|multicellular organismal development|sodium ion transport|spermatogenesis	cilium|flagellar membrane|integral to membrane	solute:hydrogen antiporter activity			ovary(3)|breast(2)	5						CCTTAAATATTCCAGCCATGT	0.353													10	30	---	---	---	---	PASS
ANKRD50	57182	broad.mit.edu	37	4	125591185	125591185	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr4:125591185G>A	uc003ifg.3	-	3	3513	c.3247C>T	c.(3247-3249)CGT>TGT	p.R1083C	ANKRD50_uc011cgo.1_Missense_Mutation_p.R904C|ANKRD50_uc010inw.2_Missense_Mutation_p.R1083C	NM_020337	NP_065070	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1083	ANK 19.									central_nervous_system(1)	1						GCTGCAACACGCATAGCAGTG	0.418													5	136	---	---	---	---	PASS
RAI14	26064	broad.mit.edu	37	5	34826505	34826505	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr5:34826505C>G	uc003jir.2	+	16	2916	c.2720C>G	c.(2719-2721)TCA>TGA	p.S907*	RAI14_uc010iur.2_Nonsense_Mutation_p.S878*|RAI14_uc011coj.1_Nonsense_Mutation_p.S907*|RAI14_uc003jis.2_Nonsense_Mutation_p.S910*|RAI14_uc003jit.2_Nonsense_Mutation_p.S907*|RAI14_uc011cok.1_Nonsense_Mutation_p.S899*	NM_015577	NP_056392	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14 isoform a	907	Potential.					cell cortex|cytoskeleton	protein binding			ovary(1)	1	all_lung(31;0.000191)					CTCTCCTACTCAACAAGCTCA	0.512													28	67	---	---	---	---	PASS
HCN1	348980	broad.mit.edu	37	5	45262494	45262494	+	Silent	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr5:45262494C>T	uc003jok.2	-	8	2227	c.2202G>A	c.(2200-2202)CCG>CCA	p.P734P		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	734	Gln-rich.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1						cctgctgctgcggctgctgtt	0.443													6	13	---	---	---	---	PASS
SLCO6A1	133482	broad.mit.edu	37	5	101813486	101813486	+	Silent	SNP	G	A	A	rs145273103		TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr5:101813486G>A	uc003knn.2	-	3	868	c.696C>T	c.(694-696)TTC>TTT	p.F232F	SLCO6A1_uc003kno.2_Intron|SLCO6A1_uc003knp.2_Silent_p.F232F|SLCO6A1_uc003knq.2_Intron	NM_173488	NP_775759	Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family,	232	Helical; Name=4; (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)|skin(3)|central_nervous_system(1)	7		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		GCCCAAGGATGAAGAAAGACA	0.383													77	206	---	---	---	---	PASS
ADAMTS19	171019	broad.mit.edu	37	5	128957923	128957923	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr5:128957923A>C	uc003kvb.1	+	10	1634	c.1634A>C	c.(1633-1635)AAT>ACT	p.N545T	ADAMTS19_uc010jdh.1_RNA	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	545	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)|skin(1)	9		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		CTACAAACAAATCCGCAGAGT	0.428													28	70	---	---	---	---	PASS
GMDS	2762	broad.mit.edu	37	6	1624710	1624710	+	Silent	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr6:1624710G>A	uc003mtq.2	-	10	1243	c.1053C>T	c.(1051-1053)TTC>TTT	p.F351F		NM_001500	NP_001491	O60547	GMDS_HUMAN	GDP-mannose 4,6-dehydratase	351					'de novo' GDP-L-fucose biosynthetic process|GDP-mannose metabolic process|leukocyte cell-cell adhesion		coenzyme binding|GDP-mannose 4,6-dehydratase activity			central_nervous_system(1)	1	Ovarian(93;0.0733)	all_cancers(2;7.64e-19)|all_epithelial(2;3.05e-16)|Colorectal(2;0.00414)|all_hematologic(90;0.00997)|all_lung(73;0.0141)|Lung NSC(90;0.0802)		Epithelial(2;7.61e-06)|all cancers(2;0.000111)|STAD - Stomach adenocarcinoma(2;0.000231)|Colorectal(2;0.00445)|COAD - Colon adenocarcinoma(2;0.0125)|OV - Ovarian serous cystadenocarcinoma(45;0.0563)		TACTCACATCGAAAGCGACCC	0.667													3	24	---	---	---	---	PASS
HIST1H4K	8362	broad.mit.edu	37	6	27799301	27799301	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr6:27799301G>C	uc003njr.2	-	1	5	c.5C>G	c.(4-6)TCT>TGT	p.S2C		NM_003541	NP_003532	P62805	H4_HUMAN	histone cluster 1, H4k	2					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0						GCCGCGGCCAGACATGACGAG	0.592													16	68	---	---	---	---	PASS
HCRTR2	3062	broad.mit.edu	37	6	55147206	55147206	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr6:55147206G>A	uc003pcl.2	+	7	1604	c.1289G>A	c.(1288-1290)AGC>AAC	p.S430N	HCRTR2_uc010jzv.2_RNA	NM_001526	NP_001517	O43614	OX2R_HUMAN	orexin receptor 2	430	Cytoplasmic (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)			ACTAGCATAAGCACACTCCCA	0.408													11	25	---	---	---	---	PASS
H2AFV	94239	broad.mit.edu	37	7	44874131	44874131	+	Missense_Mutation	SNP	A	G	G	rs114398265	byFrequency	TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr7:44874131A>G	uc003tma.2	-	5	511	c.356T>C	c.(355-357)ATT>ACT	p.I119T	H2AFV_uc003tlz.2_Intron|H2AFV_uc011kca.1_5'Flank|H2AFV_uc003tmb.2_Missense_Mutation_p.I81T|H2AFV_uc003tmc.2_3'UTR|H2AFV_uc003tmd.2_Missense_Mutation_p.I93T	NM_012412	NP_036544	Q71UI9	H2AV_HUMAN	H2A histone family, member V isoform 1	119					nucleosome assembly	nucleosome|nucleus	DNA binding				0						CTTCTTTCCAATCAGAGATTT	0.368													4	112	---	---	---	---	PASS
COPS6	10980	broad.mit.edu	37	7	99686977	99686977	+	Silent	SNP	C	G	G			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr7:99686977C>G	uc003usu.2	+	2	172	c.141C>G	c.(139-141)GTC>GTG	p.V47V	COPS6_uc011kjf.1_Silent_p.V47V	NM_006833	NP_006824	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	47	MPN.				cullin deneddylation|interspecies interaction between organisms	cytoplasm|signalosome	protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			ATCCCCTTGTCATTCTCAACA	0.592													75	191	---	---	---	---	PASS
LRCH4	4034	broad.mit.edu	37	7	100172836	100172836	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr7:100172836G>A	uc003uvj.2	-	18	1999	c.1946C>T	c.(1945-1947)GCC>GTC	p.A649V	uc003uvh.2_5'Flank|LRCH4_uc010lgz.2_RNA|LRCH4_uc003uvi.2_RNA|LRCH4_uc011kjw.1_3'UTR	NM_002319	NP_002310	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH)	649	CH.				nervous system development	PML body	protein binding			large_intestine(1)|ovary(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGGCGGTAGGGCCTTGCCCCC	0.697													5	13	---	---	---	---	PASS
NKX3-1	4824	broad.mit.edu	37	8	23538909	23538909	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr8:23538909T>C	uc011kzx.1	-	2	578	c.530A>G	c.(529-531)TAT>TGT	p.Y177C	NKX3-1_uc003xdv.1_Intron	NM_006167	NP_006158	Q99801	NKX31_HUMAN	NK3 homeobox 1	177	Homeobox.				negative regulation of estrogen receptor binding|negative regulation of transcription, DNA-dependent|positive regulation of cell division|positive regulation of mitotic cell cycle|positive regulation of transcription from RNA polymerase II promoter	nucleus	estrogen receptor activity|estrogen receptor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region sequence-specific DNA binding				0		Prostate(55;0.114)		Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)|BRCA - Breast invasive adenocarcinoma(99;0.0708)		CTTAGTCTTATAGCGTCTGTT	0.582													80	250	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413981	68413981	+	RNA	SNP	G	T	T	rs71184958		TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr9:68413981G>T	uc004aex.2	+	1		c.536G>T								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		GGATGGGAGAGCCCCAGTTTC	0.652													2	1	---	---	---	---	PASS
ALDOB	229	broad.mit.edu	37	9	104192139	104192139	+	Silent	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr9:104192139G>A	uc004bbk.2	-	3	304	c.222C>T	c.(220-222)ATC>ATT	p.I74I		NM_000035	NP_000026	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	74			I -> T (in HFI; affects proper folding).		fructose 1,6-bisphosphate metabolic process|fructose catabolic process|gluconeogenesis|glycolysis|NADH oxidation|positive regulation of ATPase activity|vacuolar proton-transporting V-type ATPase complex assembly	centriolar satellite|cytosol	ATPase binding|cytoskeletal protein binding|fructose binding|fructose-bisphosphate aldolase activity|identical protein binding			skin(1)	1		Acute lymphoblastic leukemia(62;0.0559)				TCACACCCCCGATGCTCTGGT	0.532													94	247	---	---	---	---	PASS
FIBCD1	84929	broad.mit.edu	37	9	133799131	133799131	+	Silent	SNP	C	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr9:133799131C>A	uc004bzz.2	-	4	1094	c.849G>T	c.(847-849)ACG>ACT	p.T283T	FIBCD1_uc011mcc.1_Silent_p.T283T	NM_032843	NP_116232	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	283	Fibrinogen C-terminal.|Extracellular (Potential).				signal transduction	extracellular space|integral to membrane	chitin binding|metal ion binding|receptor binding				0	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		GGACACTCACCGTCCAGCCGC	0.682													9	16	---	---	---	---	PASS
TUBB8	347688	broad.mit.edu	37	10	93555	93555	+	Silent	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr10:93555C>T	uc001ifi.2	-	4	777	c.777G>A	c.(775-777)CCG>CCA	p.P259P	TUBB8_uc009xhe.2_Silent_p.P222P|TUBB8_uc010pzs.1_Silent_p.P187P	NM_177987	NP_817124	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 isoform 1	259					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		GCCGGGGAAACGGGACCATGT	0.637													3	37	---	---	---	---	PASS
GRID1	2894	broad.mit.edu	37	10	87628819	87628819	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr10:87628819C>T	uc001kdl.1	-	6	1000	c.899G>A	c.(898-900)CGC>CAC	p.R300H	GRID1_uc009xsu.1_RNA	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	300	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	GGAGGAGATGCGGTGGTTGTT	0.567										Multiple Myeloma(13;0.14)			41	55	---	---	---	---	PASS
KRTAP5-5	439915	broad.mit.edu	37	11	1651251	1651251	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr11:1651251G>A	uc001lty.2	+	1	219	c.181G>A	c.(181-183)GGC>AGC	p.G61S		NM_001001480	NP_001001480	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	61						keratin filament				lung(1)	1		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		atgtggctccggctgCTGTGT	0.303													13	37	---	---	---	---	PASS
ARFGAP2	84364	broad.mit.edu	37	11	47198145	47198145	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr11:47198145C>T	uc001ndt.2	-	2	128	c.113G>A	c.(112-114)AGC>AAC	p.S38N	ARFGAP2_uc010rha.1_5'Flank|ARFGAP2_uc010rhb.1_Missense_Mutation_p.S38N|ARFGAP2_uc001ndu.2_Missense_Mutation_p.S38N|ARFGAP2_uc010rhc.1_5'UTR|ARFGAP2_uc010rhd.1_Missense_Mutation_p.S38N|ARFGAP2_uc001ndv.1_Missense_Mutation_p.S38N	NM_032389	NP_115765	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating	38	C4-type.|Arf-GAP.				protein transport|regulation of ARF GTPase activity|vesicle-mediated transport	Golgi membrane|nucleolus|plasma membrane	ARF GTPase activator activity|zinc ion binding			ovary(1)	1						GTACGTGATGCTGGCCCAACT	0.632													3	57	---	---	---	---	PASS
IGHMBP2	3508	broad.mit.edu	37	11	68682435	68682435	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr11:68682435C>T	uc001ook.1	+	6	958	c.856C>T	c.(856-858)CGG>TGG	p.R286W	IGHMBP2_uc001ooj.1_RNA	NM_002180	NP_002171	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	286	Leu-rich.				cell death|DNA recombination|DNA repair|DNA replication|protein homooligomerization|transcription, DNA-dependent|translation	axon|growth cone|nucleus|ribonucleoprotein complex	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' RNA helicase activity|ribosome binding|single-stranded DNA binding|transcription factor binding|tRNA binding|zinc ion binding				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GGTTTTAGCGCGGAGCGACAG	0.597													37	135	---	---	---	---	PASS
WNT11	7481	broad.mit.edu	37	11	75907610	75907610	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr11:75907610G>T	uc001oxe.2	-	2	359	c.236C>A	c.(235-237)GCC>GAC	p.A79D	WNT11_uc001oxf.1_Missense_Mutation_p.A79D	NM_004626	NP_004617	O96014	WNT11_HUMAN	wingless-type MMTV integration site family,	79					adrenal gland development|anterior/posterior pattern formation|artery morphogenesis|axis specification|bone mineralization|cellular response to retinoic acid|cloacal septation|embryonic skeletal system development|endoderm development|lung-associated mesenchyme development|mesonephric duct development|negative regulation of apoptosis|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cartilage development|negative regulation of cell growth|negative regulation of cell migration|negative regulation of transcription, DNA-dependent|neuroendocrine cell differentiation|neuron differentiation|osteoblast differentiation|outflow tract morphogenesis|palate development|positive regulation of cell migration|positive regulation of protein kinase C signaling cascade|positive regulation of stress fiber assembly|positive regulation of transcription, DNA-dependent|positive regulation of transforming growth factor-beta2 production|protein localization at cell surface|protein phosphorylation|tight junction assembly|ureteric bud morphogenesis|ventricular septum morphogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|protein kinase activator activity|Ras GTPase activator activity|transcription regulatory region DNA binding			lung(1)|skin(1)	2						CCGGCGACAGGCCTTCATGAC	0.637													11	149	---	---	---	---	PASS
ATP2A2	488	broad.mit.edu	37	12	110765384	110765384	+	Silent	SNP	T	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr12:110765384T>A	uc001tqk.3	+	8	1220	c.657T>A	c.(655-657)GCT>GCA	p.A219A	ATP2A2_uc001tql.3_Silent_p.A219A|ATP2A2_uc010sxy.1_Silent_p.A192A	NM_170665	NP_733765	P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, slow twitch 2 isoform	219	Cytoplasmic (By similarity).				ATP biosynthetic process|cell adhesion|epidermis development|platelet activation|sarcoplasmic reticulum calcium ion transport	integral to plasma membrane|microsome|platelet dense tubular network membrane|sarcoplasmic reticulum membrane	ATP binding|calcium-transporting ATPase activity|protein C-terminus binding|S100 alpha binding			ovary(3)|skin(1)	4						CTGGGAAAGCTATGGGAGTGG	0.468													100	239	---	---	---	---	PASS
EEF1DP3	196549	broad.mit.edu	37	13	32527029	32527029	+	RNA	SNP	C	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr13:32527029C>A	uc001utu.2	+	4		c.787C>A			EEF1DP3_uc010tdv.1_Intron|uc001utv.2_RNA					Homo sapiens similar to hypothetical protein FLJ20897, mRNA (cDNA clone IMAGE:5267252).												0						TGCCCGGCCACTGGGCCACAG	0.642													10	19	---	---	---	---	PASS
NOVA1	4857	broad.mit.edu	37	14	26917506	26917506	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr14:26917506T>A	uc001wpy.2	-	5	1501	c.1183A>T	c.(1183-1185)ACC>TCC	p.T395S	NOVA1_uc001wpz.2_Missense_Mutation_p.T371S|NOVA1_uc001wqa.2_Missense_Mutation_p.T273S	NM_002515	NP_002506	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1 isoform 1	398	Ala-rich.				locomotory behavior|RNA splicing|synaptic transmission	nucleus	RNA binding			skin(2)|upper_aerodigestive_tract(1)|breast(1)|liver(1)	5				GBM - Glioblastoma multiforme(265;0.0135)		TATCCATTGGTTGCAGCAGTA	0.522													13	36	---	---	---	---	PASS
PCNX	22990	broad.mit.edu	37	14	71485847	71485847	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr14:71485847G>A	uc001xmo.2	+	12	3564	c.3118G>A	c.(3118-3120)GTC>ATC	p.V1040I	PCNX_uc010are.1_Missense_Mutation_p.V929I|PCNX_uc010arf.1_5'UTR	NM_014982	NP_055797	Q96RV3	PCX1_HUMAN	pecanex-like 1	1040	Helical; (Potential).					integral to membrane				ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GTTCTGCCTCGTCATAGCCAG	0.423													98	210	---	---	---	---	PASS
C15orf51	196968	broad.mit.edu	37	15	100341319	100341319	+	RNA	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr15:100341319C>T	uc010urx.1	-	3		c.328G>A			C15orf51_uc010ury.1_RNA|uc002bvp.2_5'Flank|C15orf51_uc010urz.1_RNA|C15orf51_uc010bow.2_RNA	NR_003260				Homo sapiens cDNA FLJ43799 fis, clone TESTI4000288.												0						TTTCCATTTGCCGCTCCAGCT	0.582													4	68	---	---	---	---	PASS
SEH1L	81929	broad.mit.edu	37	18	12955467	12955467	+	Silent	SNP	T	C	C	rs144783239	byFrequency	TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr18:12955467T>C	uc002krr.2	+	3	306	c.168T>C	c.(166-168)CAT>CAC	p.H56H	SEH1L_uc002krq.2_Silent_p.H56H	NM_031216	NP_112493	Q96EE3	SEH1_HUMAN	sec13-like protein isoform 2	56	WD 2.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|carbohydrate metabolic process|cell division|glucose transport|mitotic metaphase plate congression|mitotic prometaphase|mRNA transport|nuclear pore organization|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|Nup107-160 complex					0						CCCAGACACATAGTGGATCTG	0.398													5	181	---	---	---	---	PASS
OLFM2	93145	broad.mit.edu	37	19	9965490	9965490	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr19:9965490C>T	uc002mmp.2	-	6	765	c.737G>A	c.(736-738)CGT>CAT	p.R246H	OLFM2_uc002mmo.2_Missense_Mutation_p.R168H	NM_058164	NP_477512	O95897	NOE2_HUMAN	olfactomedin 2 precursor	246	Olfactomedin-like.					extracellular region				large_intestine(1)|skin(1)	2						TCCCAGGGTACGGAACTCCAG	0.612													6	23	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39965233	39965233	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr19:39965233A>C	uc002olo.3	+	28	3078	c.2899A>C	c.(2899-2901)ACG>CCG	p.T967P	SUPT5H_uc002olp.3_Missense_Mutation_p.T967P|SUPT5H_uc002olq.3_Missense_Mutation_p.T963P|SUPT5H_uc002oln.3_Missense_Mutation_p.T967P|SUPT5H_uc002olr.3_Missense_Mutation_p.T967P|SUPT5H_uc002ols.1_Missense_Mutation_p.T590P	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	967	Pro-rich.				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)			CAACCCACACACGCCAGGCTC	0.607											OREG0025462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	61	---	---	---	---	PASS
SUPT5H	6829	broad.mit.edu	37	19	39965235	39965235	+	Silent	SNP	G	T	T	rs138311423		TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr19:39965235G>T	uc002olo.3	+	28	3080	c.2901G>T	c.(2899-2901)ACG>ACT	p.T967T	SUPT5H_uc002olp.3_Silent_p.T967T|SUPT5H_uc002olq.3_Silent_p.T963T|SUPT5H_uc002oln.3_Silent_p.T967T|SUPT5H_uc002olr.3_Silent_p.T967T|SUPT5H_uc002ols.1_Silent_p.T590T	NM_001111020	NP_001104490	O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog isoform a	967	Pro-rich.				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)			ACCCACACACGCCAGGCTCAG	0.607											OREG0025462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	61	---	---	---	---	PASS
ZNF528	84436	broad.mit.edu	37	19	52919410	52919410	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr19:52919410G>T	uc002pzh.2	+	7	1731	c.1305G>T	c.(1303-1305)AAG>AAT	p.K435N	ZNF528_uc002pzi.2_Missense_Mutation_p.K202N	NM_032423	NP_115799	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	435					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|skin(1)	2				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		CTGATGAGAAGCCTTACAAAT	0.383													37	114	---	---	---	---	PASS
C21orf81	391267	broad.mit.edu	37	21	15352131	15352131	+	RNA	SNP	G	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr21:15352131G>C	uc002yji.2	-	1		c.635C>G			C21orf81_uc002yjj.3_RNA	NR_027270				Homo sapiens C21orf81 protein (C21orf81) mRNA, complete cds.												0						CTGCAGTTCCGAGTACCGGAT	0.632													7	15	---	---	---	---	PASS
NF2	4771	broad.mit.edu	37	22	30035110	30035110	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr22:30035110C>T	uc003age.3	+	3	715	c.272C>T	c.(271-273)CCA>CTA	p.P91L	NF2_uc003afy.3_Missense_Mutation_p.P91L|NF2_uc003afz.3_Intron|NF2_uc003agf.3_Missense_Mutation_p.P91L|NF2_uc003agb.3_Missense_Mutation_p.P14L|NF2_uc003agc.3_Missense_Mutation_p.P53L|NF2_uc003agd.3_Intron|NF2_uc003agg.3_Missense_Mutation_p.P91L|NF2_uc003aga.3_Missense_Mutation_p.P49L|NF2_uc003agh.3_Intron|NF2_uc003agi.3_Intron|NF2_uc003agj.3_Missense_Mutation_p.P91L|NF2_uc003agk.3_Missense_Mutation_p.P53L	NM_000268	NP_000259	P35240	MERL_HUMAN	neurofibromin 2 isoform 1	91	FERM.				actin cytoskeleton organization|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of cell-cell adhesion|negative regulation of cell-matrix adhesion|negative regulation of DNA replication|negative regulation of tyrosine phosphorylation of Stat3 protein|negative regulation of tyrosine phosphorylation of Stat5 protein|positive regulation of stress fiber assembly|regulation of hippo signaling cascade|Schwann cell proliferation	cytoskeleton|early endosome|extrinsic to membrane|filopodium membrane|nucleolus|perinuclear region of cytoplasm|ruffle membrane	cytoskeletal protein binding|protein binding	p.H84_F100del(1)|p.V86_Q111>E(1)|p.P91fs*32(1)		meninges(372)|soft_tissue(284)|central_nervous_system(20)|kidney(10)|pleura(9)|skin(7)|large_intestine(5)|breast(5)|urinary_tract(3)|thyroid(2)|endometrium(2)|ovary(2)|lung(2)|stomach(2)|bone(2)|pituitary(1)	728						AAGGAAGAACCAGTCACCTTT	0.423			D|Mis|N|F|S|O		meningioma|acoustic neuroma|renal 	meningioma|acoustic neuroma			Neurofibromatosis_type_2				35	88	---	---	---	---	PASS
C22orf28	51493	broad.mit.edu	37	22	32794016	32794016	+	Silent	SNP	A	G	G			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr22:32794016A>G	uc003amm.2	-	7	857	c.726T>C	c.(724-726)GCT>GCC	p.A242A	C22orf28_uc011ama.1_RNA	NM_014306	NP_055121	Q9Y3I0	RTCB_HUMAN	hypothetical protein LOC51493	242					cell-matrix adhesion|substrate adhesion-dependent cell spreading|tRNA splicing, via endonucleolytic cleavage and ligation	cytoplasm|tRNA-splicing ligase complex	ATP binding|metal ion binding|RNA ligase (ATP) activity|vinculin binding				0						TTTTTTTAGCAGCATACTCAT	0.458													45	136	---	---	---	---	PASS
XRCC6	2547	broad.mit.edu	37	22	42059704	42059704	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr22:42059704C>T	uc003bao.1	+	13	1785	c.1715C>T	c.(1714-1716)ACG>ATG	p.T572M	XRCC6_uc003bap.1_Missense_Mutation_p.T531M|XRCC6_uc011apc.1_Missense_Mutation_p.T522M|XRCC6_uc003baq.1_3'UTR|XRCC6_uc003bar.1_Missense_Mutation_p.T572M|XRCC6_uc003bas.1_Missense_Mutation_p.T522M	NM_001469	NP_001460	P12956	XRCC6_HUMAN	ATP-dependent DNA helicase II, 70 kDa subunit	572					DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5						AGCAAGGGTACGCTGGGCAAG	0.562								Direct_reversal_of_damage|NHEJ					33	128	---	---	---	---	PASS
ZNF182	7569	broad.mit.edu	37	X	47837103	47837103	+	Missense_Mutation	SNP	G	T	T			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chrX:47837103G>T	uc004dir.2	-	7	729	c.383C>A	c.(382-384)ACA>AAA	p.T128K	ZNF182_uc004dis.2_Missense_Mutation_p.T109K|ZNF182_uc004dit.2_Missense_Mutation_p.T128K|ZNF182_uc011mlu.1_Missense_Mutation_p.T108K	NM_006962	NP_008893	P17025	ZN182_HUMAN	zinc finger protein 21 isoform 1	128					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)|lung(1)	3						GGTGATAATTGTTTTCTTGTC	0.388													6	63	---	---	---	---	PASS
SCHIP1	29970	broad.mit.edu	37	3	158980372	158980373	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr3:158980372_158980373insG	uc003fcq.1	+	4	296_297	c.191_192insG	c.(190-192)CAGfs	p.Q64fs	SCHIP1_uc003fcr.1_5'UTR|IQCJ_uc003fco.2_Frame_Shift_Ins_p.Q64fs|IQCJ_uc010hvy.1_Frame_Shift_Ins_p.Q37fs|IQCJ_uc003fcp.1_Frame_Shift_Ins_p.Q64fs	NM_014575	NP_055390	Q9P0W5	SCHI1_HUMAN	schwannomin interacting protein 1	Error:Variant_position_missing_in_Q9P0W5_after_alignment						cytoplasm	identical protein binding|protein binding			ovary(1)|central_nervous_system(1)	2			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			CTGCAGCGGCAGGAGCCCCTGG	0.540													250	7	---	---	---	---	
GDPD5	81544	broad.mit.edu	37	11	75152348	75152349	+	Frame_Shift_Ins	INS	-	G	G			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr11:75152348_75152349insG	uc001owo.3	-	15	1869_1870	c.1332_1333insC	c.(1330-1335)TACGCGfs	p.Y444fs	GDPD5_uc001owp.3_Frame_Shift_Ins_p.Y444fs|GDPD5_uc001own.3_Frame_Shift_Ins_p.Y199fs|GDPD5_uc009yuc.2_Frame_Shift_Ins_p.Y306fs|GDPD5_uc009yud.2_Frame_Shift_Ins_p.Y325fs	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain	444_445	Extracellular (Potential).|GDPD.				glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1						TTCCAGGACGCGTAGTCCCTGT	0.629													80	20	---	---	---	---	
FMNL3	91010	broad.mit.edu	37	12	50041517	50041519	+	In_Frame_Del	DEL	GGG	-	-			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr12:50041517_50041519delGGG	uc001ruv.1	-	23	2979_2981	c.2745_2747delCCC	c.(2743-2748)TTCCCA>TTA	p.915_916FP>L	FMNL3_uc001ruw.1_In_Frame_Del_p.864_865FP>L|FMNL3_uc001rut.1_In_Frame_Del_p.481_482FP>L|FMNL3_uc001ruu.1_In_Frame_Del_p.765_766FP>L	NM_175736	NP_783863	Q8IVF7	FMNL3_HUMAN	formin-like 3 isoform 1	915_916	FH2.				actin cytoskeleton organization		actin binding|Rho GTPase binding			breast(2)|pancreas(2)	4						GACAAATACTGGGAAGAATACAG	0.512													92	17	---	---	---	---	
LMTK3	114783	broad.mit.edu	37	19	49002387	49002389	+	In_Frame_Del	DEL	CCT	-	-			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr19:49002387_49002389delCCT	uc002pjk.2	-	12	2024_2026	c.2024_2026delAGG	c.(2023-2028)GAGGGC>GGC	p.E675del		NM_001080434	NP_001073903			lemur tyrosine kinase 3											lung(5)|central_nervous_system(1)	6		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		GGGGAGCTGCCCTCCTCCTCCTC	0.739													4	2	---	---	---	---	
NKX2-4	644524	broad.mit.edu	37	20	21377696	21377697	+	Frame_Shift_Ins	INS	-	C	C			TCGA-CH-5794-01A-11D-1576-08	TCGA-CH-5794-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	c91139ac-56d3-49cd-852b-9732dfb3e77e	f61e6c4e-baf6-48ca-aecd-0e3ca77aeeb0	g.chr20:21377696_21377697insC	uc010gcz.2	-	1	351_352	c.341_342insG	c.(340-342)GGCfs	p.G114fs		NM_033176	NP_149416	Q9H2Z4	NKX24_HUMAN	NK2 homeobox 4	114					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						TGTTGCCCAGGCCGCCGTTGCA	0.624													4	2	---	---	---	---	
