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	pox	qox	isArtifactMode	oxoGCut
PRAMEF2	65122	broad.mit.edu	37	1	12920037	12920037	+	Silent	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr1:12920037C>T	uc001aum.1	+	3	864	c.777C>T	c.(775-777)TTC>TTT	p.F259F		NM_023014	NP_075390	O60811	PRAM2_HUMAN	PRAME family member 2	259											0	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCACCAGATTCACCTCTGTGT	0.458													10	125					0	0	0	0
MPL	4352	broad.mit.edu	37	1	43812539	43812539	+	Silent	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr1:43812539G>A	uc001ciw.2	+	8	1287	c.1242G>A	c.(1240-1242)TCG>TCA	p.S414S	MPL_uc001civ.2_Silent_p.S414S|MPL_uc009vwr.2_Silent_p.S407S	NM_005373	NP_005364	P40238	TPOR_HUMAN	myeloproliferative leukemia virus oncogene	414	Fibronectin type-III 2.|Extracellular (Potential).				cell proliferation|platelet activation	integral to plasma membrane	cytokine receptor activity			haematopoietic_and_lymphoid_tissue(361)|upper_aerodigestive_tract(1)|pancreas(1)	363	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				AGCACCCATCGTCCTGGGCAG	0.567			Mis		MPD	MPD	congenital amegakaryocytic thrombocytopenia						10	69					0	0	0	0
KIAA0494	9813	broad.mit.edu	37	1	47148983	47148983	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr1:47148983G>C	uc001cqk.3	-	10	2278	c.1301C>G	c.(1300-1302)TCT>TGT	p.S434C	KIAA0494_uc010omh.1_Missense_Mutation_p.S370C|KIAA0494_uc010omj.1_Missense_Mutation_p.S226C	NM_014774	NP_055589	O75071	K0494_HUMAN	hypothetical protein LOC9813	434	EF-hand 1.						calcium ion binding				0	Acute lymphoblastic leukemia(166;0.155)					TTCAGTGCTAGAAACTCCTGG	0.358													9	126					0	0	0	0
ARMC4	55130	broad.mit.edu	37	10	28228887	28228887	+	Missense_Mutation	SNP	A	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr10:28228887A>G	uc009xky.2	-	14	2134	c.2036T>C	c.(2035-2037)GTC>GCC	p.V679A	ARMC4_uc010qds.1_Missense_Mutation_p.V204A|ARMC4_uc010qdt.1_Missense_Mutation_p.V371A|ARMC4_uc001itz.2_Missense_Mutation_p.V679A	NM_018076	NP_060546	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	679	ARM 4.|HEAT.						binding			ovary(4)|skin(2)	6						TAGGTTCTTGACAAGGTTTTC	0.433													5	58					0	0	0	0
MTPAP	55149	broad.mit.edu	37	10	30630542	30630542	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr10:30630542C>G	uc001iva.3	-	2	248	c.185G>C	c.(184-186)AGA>ACA	p.R62T	MTPAP_uc001ivb.3_Missense_Mutation_p.R192T|MTPAP_uc001ivc.2_Missense_Mutation_p.R62T	NM_018109	NP_060579	Q9NVV4	PAPD1_HUMAN	PAP associated domain containing 1 precursor	62					cell death|histone mRNA catabolic process|mRNA polyadenylation|transcription, DNA-dependent	mitochondrion	ATP binding|magnesium ion binding|manganese ion binding|polynucleotide adenylyltransferase activity|protein homodimerization activity|RNA binding|UTP binding			ovary(1)	1						CTCAGAGAATCTCCTTTTGGG	0.348													6	82					0	0	0	0
C10orf11	83938	broad.mit.edu	37	10	77818491	77818491	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr10:77818491C>T	uc001jxi.2	+	4	597	c.382C>T	c.(382-384)CGA>TGA	p.R128*		NM_032024	NP_114413	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	128	LRRCT.										0	Prostate(51;0.0095)|all_epithelial(25;0.0221)					CAGACAAGAACGAGAGGAGGC	0.478													13	106					0	0	0	0
MUC6	4588	broad.mit.edu	37	11	1018367	1018367	+	Silent	SNP	T	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr11:1018367T>A	uc001lsw.2	-	31	4485	c.4434A>T	c.(4432-4434)TCA>TCT	p.S1478S		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	1478	Pro-rich.|Thr-rich.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGTTGGCGCTGAGTGGTTGG	0.587													20	206					0	0	0	0
MOB2	81532	broad.mit.edu	37	11	1501645	1501645	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr11:1501645G>A	uc010qwz.1	-	3	533	c.343C>T	c.(343-345)CAG>TAG	p.Q115*	MOB2_uc001lto.1_5'UTR|MOB2_uc001ltp.1_5'UTR|MOB2_uc001ltq.1_Nonsense_Mutation_p.Q78*|MOB2_uc010qwy.1_5'UTR	NM_053005	NP_443731	Q70IA6	MOB2_HUMAN	HCCA2 protein	84						nucleus|perinuclear region of cytoplasm	metal ion binding				0						GCCATCGTCTGACACGTCTCT	0.587													10	82					0	0	0	0
CSRP3	8048	broad.mit.edu	37	11	19213969	19213969	+	Missense_Mutation	SNP	T	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr11:19213969T>G	uc001mpk.2	-	2	144	c.27A>C	c.(25-27)AAA>AAC	p.K9N		NM_003476	NP_003467	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3	9					cell differentiation|skeletal muscle tissue development	cytoskeleton|nucleus	protein binding|zinc ion binding				0						AGGCTCCACATTTTGCGCCTC	0.498													3	45					0	0	0	0
C11orf59	55004	broad.mit.edu	37	11	71808908	71808908	+	Missense_Mutation	SNP	T	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr11:71808908T>A	uc001ort.2	-	5	498	c.446A>T	c.(445-447)GAC>GTC	p.D149V	LRTOMT_uc010rqv.1_Intron|LRTOMT_uc010rqw.1_Intron|LRTOMT_uc001ors.3_Intron|C11orf59_uc009ytb.2_Silent_p.G73G|C11orf59_uc001oru.1_3'UTR	NM_017907	NP_060377	Q6IAA8	LTOR1_HUMAN	hypothetical protein LOC55004	149	Interaction with LAMTOR2 and LAMTOR3 (By similarity).				cell growth|cellular protein localization|cellular response to amino acid stimulus|cholesterol homeostasis|endosome localization|endosome organization|lysosome localization|lysosome organization|positive regulation of MAPKKK cascade|positive regulation of TOR signaling cascade|regulation of cholesterol efflux|regulation of cholesterol esterification|regulation of cholesterol import|regulation of receptor recycling	Golgi apparatus|lysosomal membrane|plasma membrane|Ragulator complex	protein binding				0						CTCTTTTGCGTCCACACGGAT	0.463													18	238					0	0	0	0
TMEM25	84866	broad.mit.edu	37	11	118404820	118404820	+	Missense_Mutation	SNP	A	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr11:118404820A>T	uc010rye.1	+	7	1087	c.913A>T	c.(913-915)AAT>TAT	p.N305Y	TMEM25_uc001ptk.3_Missense_Mutation_p.N305Y|TMEM25_uc001pth.2_Missense_Mutation_p.N261Y|TMEM25_uc009zad.2_Missense_Mutation_p.N261Y|TMEM25_uc001pti.2_Missense_Mutation_p.N157Y|TMEM25_uc010ryf.1_Missense_Mutation_p.N208Y|TMEM25_uc001ptl.2_Missense_Mutation_p.N305Y|TMEM25_uc001ptm.2_Missense_Mutation_p.N261Y|TMEM25_uc001ptn.2_Missense_Mutation_p.N261Y	NM_032780	NP_116169	Q86YD3	TMM25_HUMAN	transmembrane protein 25 isoform 1	305	Cytoplasmic (Potential).					extracellular region|integral to membrane|plasma membrane					0	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		CCTTCAGCTCAATGACCTCAC	0.517													7	46					0	0	0	0
DCP1B	196513	broad.mit.edu	37	12	2107117	2107117	+	Missense_Mutation	SNP	A	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr12:2107117A>T	uc001qjx.1	-	2	255	c.175T>A	c.(175-177)TTA>ATA	p.L59I	DCP1B_uc010sdy.1_5'UTR|DCP1B_uc010sdz.1_Missense_Mutation_p.L59I	NM_152640	NP_689853	Q8IZD4	DCP1B_HUMAN	decapping enzyme Dcp1b	59					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	hydrolase activity|protein binding			skin(1)	1			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			TAAACAAATAAGGTTCCTTCC	0.308													7	81					0	0	0	0
A2M	2	broad.mit.edu	37	12	9251236	9251236	+	Silent	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr12:9251236G>A	uc001qvk.1	-	15	1931	c.1818C>T	c.(1816-1818)CTC>CTT	p.L606L	A2M_uc009zgk.1_Silent_p.L456L	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	606					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	CAGGCTTCATGAGCAGCACGC	0.617													3	17					0	0	0	0
DDX12	440081	broad.mit.edu	37	12	9583286	9583286	+	Silent	SNP	A	G	G	rs2429895	by1000genomes	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr12:9583286A>G	uc010sgs.1	-	10	1335	c.1140T>C	c.(1138-1140)GCT>GCC	p.A380A		NM_004400	NP_004391			DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 12												0						GGATGCCCGCAGCCTGCCGAG	0.672													4	13					0	0	0	0
CAPRIN2	65981	broad.mit.edu	37	12	30869532	30869532	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr12:30869532G>C	uc001rji.1	-	14	3125	c.2374C>G	c.(2374-2376)CAA>GAA	p.Q792E	CAPRIN2_uc001rjf.1_Missense_Mutation_p.Q589E|CAPRIN2_uc001rjg.1_Missense_Mutation_p.Q459E|CAPRIN2_uc001rjh.1_Missense_Mutation_p.Q743E|CAPRIN2_uc001rjj.1_Missense_Mutation_p.Q459E|CAPRIN2_uc001rjk.3_Missense_Mutation_p.Q792E|CAPRIN2_uc001rjl.3_Missense_Mutation_p.Q757E|CAPRIN2_uc001rjm.1_Missense_Mutation_p.Q424E	NM_001002259	NP_001002259	Q6IMN6	CAPR2_HUMAN	C1q domain containing 1 isoform 1	792					negative regulation of cell growth|negative regulation of translation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of dendrite morphogenesis|positive regulation of dendritic spine morphogenesis|positive regulation of peptidyl-serine phosphorylation|positive regulation of protein binding|positive regulation of transcription from RNA polymerase II promoter	mitochondrion|receptor complex	receptor binding|RNA binding			ovary(1)|central_nervous_system(1)	2	all_lung(12;1.13e-09)|Lung NSC(12;7.98e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0355)|Lung SC(12;0.0905)|Esophageal squamous(101;0.233)					GTAAAACTTTGATTGTAGCCA	0.408													14	190					0	0	0	0
ANO6	196527	broad.mit.edu	37	12	45782051	45782051	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr12:45782051C>G	uc001roo.2	+	11	1608	c.1273C>G	c.(1273-1275)CGA>GGA	p.R425G	ANO6_uc010sld.1_Missense_Mutation_p.R425G|ANO6_uc010sle.1_Missense_Mutation_p.R425G|ANO6_uc010slf.1_Missense_Mutation_p.R446G|ANO6_uc010slg.1_Missense_Mutation_p.R407G	NM_001025356	NP_001020527	Q4KMQ2	ANO6_HUMAN	anoctamin 6 isoform a	425	Cytoplasmic (Potential).				activation of blood coagulation via clotting cascade|phosphatidylserine exposure on blood platelet	chloride channel complex|plasma membrane	chloride channel activity			ovary(1)|kidney(1)	2						ATACGAAGCACGATGTACTCA	0.393													10	120					0	0	0	0
CRY1	1407	broad.mit.edu	37	12	107393445	107393445	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr12:107393445C>G	uc001tmi.3	-	7	1880	c.1021G>C	c.(1021-1023)GAT>CAT	p.D341H		NM_004075	NP_004066	Q16526	CRY1_HUMAN	cryptochrome 1 (photolyase-like)	341	FAD-binding.				DNA repair|protein-chromophore linkage|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	blue light photoreceptor activity|DNA photolyase activity|double-stranded DNA binding|nucleotide binding|protein binding			ovary(3)	3						ATGATGGCATCAATCCATGGA	0.493													4	61					0	0	0	0
RNF34	80196	broad.mit.edu	37	12	121867998	121867998	+	Missense_Mutation	SNP	G	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr12:121867998G>T	uc001uam.1	+	7	1339	c.1225G>T	c.(1225-1227)GTC>TTC	p.V409F	KDM2B_uc001uaq.2_Intron|KDM2B_uc010szy.1_3'UTR|KDM2B_uc001uar.2_Intron|KDM2B_uc001uas.2_Intron|KDM2B_uc001uat.2_3'UTR|KDM2B_uc001uau.2_3'UTR|KDM2B_uc001uao.2_Intron|KDM2B_uc010szx.1_3'UTR|KDM2B_uc001uap.2_Intron	NM_025126	NP_079402	Q969K3	RNF34_HUMAN	ring finger protein 34 isoform 2	Error:Variant_position_missing_in_Q969K3_after_alignment					apoptosis	endomembrane system|membrane|nuclear speck	ligase activity|zinc ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		GTGGTCTGTTGTCCCACGTTC	0.473													8	79					0.000157383	0.000171219	1	0
NBEA	26960	broad.mit.edu	37	13	36229804	36229804	+	Silent	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr13:36229804C>T	uc001uvb.2	+	54	8423	c.8217C>T	c.(8215-8217)ATC>ATT	p.I2739I	NBEA_uc010abi.2_Silent_p.I1395I|NBEA_uc010tef.1_Silent_p.I532I|NBEA_uc001uvd.2_Silent_p.I317I	NM_015678	NP_056493	Q8NFP9	NBEA_HUMAN	neurobeachin	2739	WD 2.					cytosol|endomembrane system|plasma membrane|trans-Golgi network	protein binding			ovary(9)|large_intestine(2)	11		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		ACTGCTACATCGTGTCCGGAT	0.512													5	126					0	0	0	0
HEATR5A	25938	broad.mit.edu	37	14	31774252	31774252	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr14:31774252G>A	uc001wrf.3	-	26	4296	c.4219C>T	c.(4219-4221)CTC>TTC	p.L1407F	HEATR5A_uc010ami.2_Missense_Mutation_p.L1305F	NM_015473	NP_056288	Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	1694							binding			ovary(1)	1	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		AATTCTGGGAGCTGTCTAACT	0.448													16	108					0	0	0	0
CCDC88C	440193	broad.mit.edu	37	14	91780018	91780018	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr14:91780018C>G	uc010aty.2	-	15	2241	c.2142G>C	c.(2140-2142)GAG>GAC	p.E714D		NM_001080414	NP_001073883	Q9P219	DAPLE_HUMAN	DVL-binding protein DAPLE	714	Potential.				microtubule cytoskeleton organization|protein destabilization|protein homooligomerization|regulation of protein phosphorylation|Wnt receptor signaling pathway	cytoplasm|insoluble fraction	microtubule binding|PDZ domain binding|protein self-association			ovary(3)	3		all_cancers(154;0.0468)				AGCGCATGGTCTCCACCAGCC	0.602													6	75					0	0	0	0
VRK1	7443	broad.mit.edu	37	14	97321591	97321591	+	Missense_Mutation	SNP	C	T	T	rs144600646	by1000genomes	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr14:97321591C>T	uc001yft.2	+	8	713	c.607C>T	c.(607-609)CGG>TGG	p.R203W		NM_003384	NP_003375	Q99986	VRK1_HUMAN	vaccinia related kinase 1	203	Protein kinase.					cytoplasm|nucleolus	ATP binding|protein binding|protein serine/threonine kinase activity			large_intestine(1)|stomach(1)	2		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		CCTTGCTTATCGGTACTGCCC	0.408													7	103					0	0	0	0
ADAM6	8755	broad.mit.edu	37	14	106518702	106518702	+	RNA	SNP	C	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr14:106518702C>A	uc010tyt.1	-	1630		c.32735G>T								Parts of antibodies, mostly variable regions.												0						TCACACTGGACACCTGCAAAC	0.522													12	152					9.31168e-06	1.0596e-05	1	0
RNF40	9810	broad.mit.edu	37	16	30777510	30777510	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr16:30777510G>C	uc002dzq.2	+	9	1143	c.1020G>C	c.(1018-1020)GAG>GAC	p.E340D	RNF40_uc010caa.2_Missense_Mutation_p.E340D|RNF40_uc010cab.2_Intron|RNF40_uc010vfa.1_Intron|RNF40_uc002dzr.2_Missense_Mutation_p.E340D|RNF40_uc010vfb.1_Intron|RNF40_uc010vfc.1_5'Flank	NM_014771	NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40	340	Potential.				histone H2B ubiquitination|histone monoubiquitination|ubiquitin-dependent protein catabolic process	nucleus|synaptosome|ubiquitin ligase complex	protein homodimerization activity|ubiquitin protein ligase binding|zinc ion binding			central_nervous_system(1)	1			Colorectal(24;0.198)			CAGAGTTAGAGGAAAACCAGG	0.592													5	92					0	0	0	0
HPR	3250	broad.mit.edu	37	16	72108189	72108189	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr16:72108189G>A	uc002fby.2	+	3	128	c.98G>A	c.(97-99)CGC>CAC	p.R33H	TXNL4B_uc010cgl.2_Intron	NM_020995	NP_066275	P00739	HPTR_HUMAN	haptoglobin-related protein precursor	33					proteolysis	spherical high-density lipoprotein particle	hemoglobin binding|serine-type endopeptidase activity			central_nervous_system(1)	1		Ovarian(137;0.125)				GCAGATGACCGCTTCCCGAAG	0.483													12	75					0	0	0	0
DPEP1	1800	broad.mit.edu	37	16	89696859	89696859	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr16:89696859G>A	uc010cin.2	+	2	244	c.41G>A	c.(40-42)TGC>TAC	p.C14Y	DPEP1_uc002fnr.3_Missense_Mutation_p.C14Y|DPEP1_uc002fns.3_Missense_Mutation_p.C14Y	NM_001128141	NP_001121613	P16444	DPEP1_HUMAN	dipeptidase 1 precursor	14					proteolysis	anchored to membrane|apical plasma membrane|microvillus membrane	dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metalloexopeptidase activity|protein binding			large_intestine(1)	1		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	GTGGCCGTCTGCACTGCAGAC	0.632													10	72					0	0	0	0
TP53	7157	broad.mit.edu	37	17	7577098	7577098	+	Missense_Mutation	SNP	T	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr17:7577098T>G	uc002gim.2	-	8	1034	c.840A>C	c.(838-840)AGA>AGC	p.R280S	TP53_uc002gig.1_Intron|TP53_uc002gih.2_Missense_Mutation_p.R280S|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R148S|TP53_uc010cng.1_Missense_Mutation_p.R148S|TP53_uc002gii.1_Missense_Mutation_p.R148S|TP53_uc010cnh.1_Missense_Mutation_p.R280S|TP53_uc010cni.1_Missense_Mutation_p.R280S|TP53_uc002gij.2_Missense_Mutation_p.R280S	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	280	Interaction with DNA.||Interaction with E4F1.|Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> T (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> K (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in a sporadic cancer; somatic mutation).|R -> I (in sporadic cancers; somatic mutation).|R -> S (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R280T(53)|p.R280K(41)|p.R280G(18)|p.R280S(13)|p.R280I(12)|p.R280*(8)|p.R280fs*65(7)|p.0?(7)|p.R280R(3)|p.?(2)|p.R280_D281delRD(2)|p.A276_R283delACPGRDRR(1)|p.A276fs*64(1)|p.G279_R280delGR(1)|p.R280fs*62(1)|p.S269fs*21(1)|p.G279fs*59(1)|p.F270_D281del12(1)|p.C275_R283delCACPGRDRR(1)|p.L265_K305del41(1)|p.D281fs*24(1)|p.V272_K292del21(1)|p.C275fs*20(1)|p.D281_R282delDR(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		TGCGCCGGTCTCTCCCAGGAC	0.542		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			5	36					0	0	0	0
MYH2	4620	broad.mit.edu	37	17	10427914	10427914	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr17:10427914G>A	uc010coi.2	-	35	5172	c.5044C>T	c.(5044-5046)CGC>TGC	p.R1682C	uc002gml.1_Intron|MYH2_uc002gmp.3_Missense_Mutation_p.R1682C|MYH2_uc010coj.2_Intron	NM_001100112	NP_001093582	Q9UKX2	MYH2_HUMAN	myosin heavy chain IIa	1682	Potential.				muscle filament sliding	muscle myosin complex|myosin filament|sarcomere	actin binding|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(5)|pancreas(4)|skin(3)|lung(1)|kidney(1)	14						TTGGCTCTGCGCTCCACCATG	0.567													6	58					0	0	0	0
Unknown	0	broad.mit.edu	37	17	45128742	45128742	+	5'Flank	SNP	T	G	G	rs34655963	by1000genomes	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr17:45128742T>G	uc010wkl.1	-						uc010wkm.1_RNA					Homo sapiens cDNA FLJ38031 fis, clone CTONG2013348.																		TAATGATTTTTATTATACTTT	0.318													4	58					0	0	0	0
COL1A1	1277	broad.mit.edu	37	17	48273002	48273002	+	Nonsense_Mutation	SNP	G	A	A	rs72645366		TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr17:48273002G>A	uc002iqm.2	-	17	1207	c.1081C>T	c.(1081-1083)CGA>TGA	p.R361*		NM_000088	NP_000079	P02452	CO1A1_HUMAN	alpha 1 type I collagen preproprotein	361	Triple-helical region.				axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)	TCAGAGCCTCGGGGCCCTTGG	0.637			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta				OREG0024559	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	39					0	0	0	0
ASXL3	80816	broad.mit.edu	37	18	31326305	31326305	+	Missense_Mutation	SNP	A	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr18:31326305A>C	uc010dmg.1	+	12	6548	c.6493A>C	c.(6493-6495)AAA>CAA	p.K2165Q	ASXL3_uc002kxq.2_Missense_Mutation_p.K1872Q	NM_030632	NP_085135	Q9C0F0	ASXL3_HUMAN	additional sex combs like 3	2165					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding			ovary(2)|pancreas(1)	3						CACGAGTTTCAAAAGGGCAGC	0.468													10	140					0	0	0	0
KIAA1328	57536	broad.mit.edu	37	18	34539358	34539358	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr18:34539358C>G	uc002kzz.2	+	6	558	c.536C>G	c.(535-537)TCT>TGT	p.S179C	KIAA1328_uc002lab.2_Intron|KIAA1328_uc002lac.1_Missense_Mutation_p.S2C|KIAA1328_uc010dnc.1_RNA	NM_020776	NP_065827	Q86T90	K1328_HUMAN	hypothetical protein LOC57536	179										central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)		CTCACCATGTCTCTCTCAGAA	0.408													2	16					0	0	0	0
ZNF236	7776	broad.mit.edu	37	18	74580734	74580734	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr18:74580734C>T	uc002lmi.2	+	4	649	c.451C>T	c.(451-453)CGG>TGG	p.R151W	ZNF236_uc002lmj.2_RNA|ZNF236_uc002lmk.1_Missense_Mutation_p.R151W	NM_007345	NP_031371	Q9UL36	ZN236_HUMAN	zinc finger protein 236	151					cellular response to glucose stimulus	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GGCTGGAACCCGGCAGCATGC	0.522													7	133					0	0	0	0
HCN2	610	broad.mit.edu	37	19	613894	613894	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr19:613894G>A	uc002lpe.2	+	7	1921	c.1868G>A	c.(1867-1869)CGG>CAG	p.R623Q		NM_001194	NP_001185	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic	623	cAMP.|Cytoplasmic (Potential).				cell-cell signaling|muscle contraction	voltage-gated potassium channel complex	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity				0		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGAGCGTGCGGGCTGACACC	0.716													4	34					0	0	0	0
ZNF486	90649	broad.mit.edu	37	19	20295277	20295277	+	Missense_Mutation	SNP	A	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr19:20295277A>C	uc002nou.2	+	2	200	c.143A>C	c.(142-144)CAC>CCC	p.H48P		NM_052852	NP_443084	Q96H40	ZN486_HUMAN	zinc finger protein 486	48	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						AACTACAGACACCTGGTCTTC	0.363													11	161					0	0	0	0
KLK12	43849	broad.mit.edu	37	19	51532606	51532606	+	Silent	SNP	A	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr19:51532606A>G	uc002pvg.1	-	5	819	c.699T>C	c.(697-699)TAT>TAC	p.Y233Y	KLK11_uc002pvd.1_5'Flank|KLK11_uc002pve.1_5'Flank|KLK11_uc002pvf.1_5'Flank|KLK11_uc002pvc.3_5'Flank|KLK11_uc010eom.2_5'Flank|KLK12_uc010ycp.1_RNA|KLK12_uc010ycq.1_Silent_p.Y123Y|KLK12_uc010ycr.1_Silent_p.Y123Y|KLK12_uc010ycs.1_Silent_p.Y123Y|KLK12_uc002pvh.1_Silent_p.Y233Y|KLK12_uc002pvi.1_Silent_p.Y233Y|KLK12_uc002pvj.1_3'UTR	NM_145894	NP_665901	Q9UKR0	KLK12_HUMAN	kallikrein 12 isoform 2	233	Peptidase S1.				proteolysis	extracellular region|soluble fraction	serine-type endopeptidase activity			ovary(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		ACTTGCAAATATAGGTGTAGA	0.587													13	113					0	0	0	0
PXDN	7837	broad.mit.edu	37	2	1652027	1652027	+	Silent	SNP	G	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr2:1652027G>C	uc002qxa.2	-	17	3589	c.3525C>G	c.(3523-3525)GTC>GTG	p.V1175V		NM_012293	NP_036425	Q92626	PXDN_HUMAN	peroxidasin precursor	1175					extracellular matrix organization|hydrogen peroxide catabolic process|immune response	endoplasmic reticulum|extracellular space|proteinaceous extracellular matrix	extracellular matrix structural constituent|heme binding|interleukin-1 receptor antagonist activity|peroxidase activity			pancreas(6)|ovary(2)	8	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GATTGCAGTAGACCCTGTAGT	0.572													16	166					0	0	0	0
GREB1	9687	broad.mit.edu	37	2	11767109	11767109	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr2:11767109C>T	uc002rbk.1	+	25	4628	c.4328C>T	c.(4327-4329)CCG>CTG	p.P1443L	GREB1_uc002rbp.1_Missense_Mutation_p.P441L	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1443						integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TCCCGGAAGCCGGAGGACCTT	0.532													4	65					0	0	0	0
Unknown	0	broad.mit.edu	37	2	89544371	89544371	+	RNA	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr2:89544371C>G	uc010ytr.1	-	14		c.1814G>C			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		CTGAATCTGTCTGGGACCCCA	0.502													20	171					0	0	0	0
WASH2P	375260	broad.mit.edu	37	2	114355998	114355998	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr2:114355998C>G	uc002tkh.2	+	5	674	c.616C>G	c.(616-618)CAC>GAC	p.H206D	WASH2P_uc002tka.2_RNA|WASH2P_uc002tkb.2_RNA|WASH2P_uc002tkd.2_RNA	NM_182905	NP_878908			WAS protein family homolog 1												0						CCAAGGTGGGCACTTGATGTC	0.612													2	9					0	0	0	0
TTN	7273	broad.mit.edu	37	2	179439605	179439605	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr2:179439605C>T	uc010zfg.1	-	275	63774	c.63550G>A	c.(63550-63552)GAG>AAG	p.E21184K	uc002umo.2_Intron|uc002ump.1_Intron|TTN_uc010zfh.1_Missense_Mutation_p.E14879K|TTN_uc010zfi.1_Missense_Mutation_p.E14812K|TTN_uc010zfj.1_Missense_Mutation_p.E14687K	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	22111							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCATCGTTCTCAGGTGGGTCC	0.453													5	21					0	0	0	0
ERBB4	2066	broad.mit.edu	37	2	212587119	212587119	+	Silent	SNP	T	C	C	rs77309171	byFrequency	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr2:212587119T>C	uc002veg.1	-	7	980	c.882A>G	c.(880-882)CCA>CCG	p.P294P	ERBB4_uc002veh.1_Silent_p.P294P|ERBB4_uc010zji.1_Silent_p.P294P|ERBB4_uc010zjj.1_Silent_p.P294P|ERBB4_uc010fut.1_Silent_p.P294P	NM_005235	NP_005226	Q15303	ERBB4_HUMAN	v-erb-a erythroblastic leukemia viral oncogene	294	Cys-rich.|Extracellular (Potential).				cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent|transmembrane receptor protein tyrosine kinase signaling pathway	basolateral plasma membrane|cytoplasm|integral to membrane|nucleus	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(21)|skin(5)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|large_intestine(1)|pancreas(1)	33		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)		GTTACTTACGTGGACATTTCT	0.313										TSP Lung(8;0.080)			3	46					0	0	0	0
ZNF335	63925	broad.mit.edu	37	20	44592204	44592204	+	Missense_Mutation	SNP	G	A	A	rs141481390		TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr20:44592204G>A	uc002xqw.2	-	9	1564	c.1441C>T	c.(1441-1443)CGC>TGC	p.R481C	ZNF335_uc010zxk.1_Missense_Mutation_p.R326C	NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	481	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(3)|ovary(1)	4		Myeloproliferative disorder(115;0.0122)				ACGTGGAAGCGCAGGTCCTCG	0.587													8	154					0	0	0	0
ZNF334	55713	broad.mit.edu	37	20	45131128	45131128	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr20:45131128G>A	uc002xsc.2	-	5	1034	c.850C>T	c.(850-852)CGA>TGA	p.R284*	ZNF334_uc002xsa.2_Nonsense_Mutation_p.R307*|ZNF334_uc002xsb.2_Nonsense_Mutation_p.R246*|ZNF334_uc002xsd.2_Nonsense_Mutation_p.R246*|ZNF334_uc010ghl.2_Nonsense_Mutation_p.R283*	NM_018102	NP_060572	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334 isoform a	284	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)				TGAATTCTTCGGTGTCGAGTG	0.418													5	126					0	0	0	0
CYP2D7P1	1564	broad.mit.edu	37	22	42538870	42538870	+	Missense_Mutation	SNP	A	C	C	rs2982057	by1000genomes	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr22:42538870A>C	uc003bci.2	-	3	475	c.94T>G	c.(94-96)TCG>GCG	p.S32A	CYP2D7P1_uc003bcg.2_5'Flank|CYP2D7P1_uc003bch.2_5'Flank|CYP2D7P1_uc010gyv.2_Intron|CYP2D7P1_uc010gyw.2_RNA|CYP2D7P1_uc010gyx.1_Missense_Mutation_p.S32A	NR_002570				SubName: Full=Cytochrome P450 2D6;          EC=1.14.14.1;												0						CCATAGCGCGACAGGAACACC	0.687													3	15					0	0	0	0
ATG7	10533	broad.mit.edu	37	3	11389503	11389503	+	Silent	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr3:11389503C>T	uc003bwc.2	+	12	1395	c.1278C>T	c.(1276-1278)CCC>CCT	p.P426P	ATG7_uc003bwd.2_Silent_p.P426P|ATG7_uc011aum.1_Silent_p.P387P	NM_006395	NP_006386	O95352	ATG7_HUMAN	APG7 autophagy 7-like isoform a	426					autophagy|cellular membrane fusion|positive regulation of protein modification process|protein lipidation|protein transport	cytoplasm	APG12 activating enzyme activity|protein homodimerization activity|ubiquitin activating enzyme activity			central_nervous_system(1)	1						AAATATTCCCCGGTGTGGTAT	0.478													8	123					0	0	0	0
TGFBR2	7048	broad.mit.edu	37	3	30713559	30713559	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr3:30713559C>G	uc003ceo.2	+	4	1266	c.884C>G	c.(883-885)TCA>TGA	p.S295*	TGFBR2_uc003cen.2_Nonsense_Mutation_p.S320*	NM_003242	NP_003233	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II	295	Protein kinase.|Cytoplasmic (Potential).				activation of protein kinase activity|brain development|embryonic cranial skeleton morphogenesis|embryonic hemopoiesis|heart development|myeloid dendritic cell differentiation|palate development|pathway-restricted SMAD protein phosphorylation|patterning of blood vessels|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of B cell tolerance induction|positive regulation of mesenchymal cell proliferation|positive regulation of NK T cell differentiation|positive regulation of reactive oxygen species metabolic process|positive regulation of T cell tolerance induction|positive regulation of tolerance induction to self antigen|response to cholesterol|response to drug|transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|vasculogenesis	caveola|external side of plasma membrane	ATP binding|glycosaminoglycan binding|metal ion binding|protein binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity, type II|type I transforming growth factor beta receptor binding|type I transforming growth factor beta receptor binding|type III transforming growth factor beta receptor binding			pancreas(9)|large_intestine(6)|stomach(4)|lung(3)|ovary(3)|central_nervous_system(1)	26						GACATCTTCTCAGACATCAAT	0.493													9	77					0	0	0	0
SLC22A14	9389	broad.mit.edu	37	3	38347718	38347718	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr3:38347718G>C	uc010hhc.1	+	2	243	c.201G>C	c.(199-201)CAG>CAC	p.Q67H	SLC22A14_uc003cia.2_Missense_Mutation_p.Q67H|SLC22A14_uc003cib.2_Missense_Mutation_p.Q67H|SLC22A14_uc011ayo.1_RNA	NM_004803	NP_004794	Q9Y267	S22AE_HUMAN	organic cation transporter like 4	67	Cytoplasmic (Potential).					integral to plasma membrane	organic cation transmembrane transporter activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		CATTCCAGCAGAGGCTAGTAG	0.532													10	85					0	0	0	0
ACOX2	8309	broad.mit.edu	37	3	58514635	58514635	+	Silent	SNP	G	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr3:58514635G>C	uc003dkl.2	-	9	1216	c.1041C>G	c.(1039-1041)CTC>CTG	p.L347L		NM_003500	NP_003491	Q99424	ACOX2_HUMAN	acyl-Coenzyme A oxidase 2	347					bile acid biosynthetic process|fatty acid beta-oxidation using acyl-CoA oxidase	peroxisomal matrix	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity|acyl-CoA dehydrogenase activity|pristanoyl-CoA oxidase activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		GCTGAGGAAAGAGTTTCTGCT	0.463													8	77					0	0	0	0
GPR15	2838	broad.mit.edu	37	3	98251012	98251012	+	Silent	SNP	G	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr3:98251012G>T	uc011bgy.1	+	1	135	c.135G>T	c.(133-135)CTG>CTT	p.L45L		NM_005290	NP_005281	P49685	GPR15_HUMAN	G protein-coupled receptor 15	45	Helical; Name=1; (Potential).					integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(1)	1		Lung NSC(201;7.93e-06)|all_neural(597;0.00172)|Hepatocellular(537;0.00825)|Myeloproliferative disorder(1037;0.0255)		Lung(72;0.246)		CTGTGTTCCTGACTGGAGTGC	0.502													7	68					8.12818e-05	8.941e-05	1	0
SLC34A2	10568	broad.mit.edu	37	4	25667818	25667818	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr4:25667818G>A	uc003grr.2	+	5	529	c.448G>A	c.(448-450)GGG>AGG	p.G150R	SLC34A2_uc003grs.2_Missense_Mutation_p.G149R|SLC34A2_uc010iev.2_Missense_Mutation_p.G149R	NM_006424	NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (sodium phosphate),	150	Helical; Name=M2; (Potential).				cellular phosphate ion homeostasis	apical plasma membrane|brush border membrane|integral to plasma membrane	phosphate binding|sodium ion binding|sodium-dependent phosphate transmembrane transporter activity|sodium:phosphate symporter activity			skin(3)|ovary(1)|kidney(1)	5		Breast(46;0.0503)				GCTGGTGATCGGGGTGCTGGT	0.507													6	100					0	0	0	0
FAT4	79633	broad.mit.edu	37	4	126412367	126412367	+	Missense_Mutation	SNP	C	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr4:126412367C>A	uc003ifj.3	+	17	14390	c.14390C>A	c.(14389-14391)ACA>AAA	p.T4797K	FAT4_uc011cgp.1_Missense_Mutation_p.T3038K|FAT4_uc003ifi.1_Missense_Mutation_p.T2274K	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	4797	Cytoplasmic (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						AGGCTCAACACACCTCGCCCT	0.527													6	71					3.59834e-05	4.04813e-05	1	0
TRIO	7204	broad.mit.edu	37	5	14504668	14504668	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr5:14504668G>C	uc003jff.2	+	55	8584	c.8578G>C	c.(8578-8580)GAG>CAG	p.E2860Q	TRIO_uc003jfg.2_RNA	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2860	Protein kinase.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|stomach(2)|breast(2)|upper_aerodigestive_tract(1)|kidney(1)	18	Lung NSC(4;0.000742)					CGACACCTTTGAGACCCCCAC	0.582													8	228					0	0	0	0
SLC4A9	83697	broad.mit.edu	37	5	139747331	139747331	+	Silent	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr5:139747331C>G	uc003lfm.2	+	16	2309	c.2274C>G	c.(2272-2274)CTC>CTG	p.L758L	SLC4A9_uc003lfj.2_Silent_p.L734L|SLC4A9_uc011czg.1_Silent_p.L671L|SLC4A9_uc003lfl.2_Silent_p.L734L|SLC4A9_uc003lfk.2_Silent_p.L720L	NM_031467	NP_113655	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate	758	Helical; (Potential).|Membrane (anion exchange).					integral to membrane|plasma membrane	inorganic anion exchanger activity|sodium:bicarbonate symporter activity			large_intestine(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCTGGACCTCTTCTGTGTGG	0.582													4	38					0	0	0	0
PCDHGA12	26025	broad.mit.edu	37	5	140812277	140812277	+	Missense_Mutation	SNP	C	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr5:140812277C>A	uc003lkt.1	+	1	2120	c.1951C>A	c.(1951-1953)CAG>AAG	p.Q651K	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc011dba.1_Missense_Mutation_p.Q651K	NM_003735	NP_003726	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12 isoform 1	651	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|pancreas(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCACGGCCAGCCCCCTCT	0.697													10	121					6.40141e-05	7.12067e-05	1	0
OR2J2	26707	broad.mit.edu	37	6	29141890	29141890	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr6:29141890C>T	uc011dlm.1	+	1	580	c.478C>T	c.(478-480)CAT>TAT	p.H160Y		NM_030905	NP_112167	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J,	160	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0						CTCAGCACTTCATTCCTCCTT	0.463													19	250					0	0	0	0
TDRD6	221400	broad.mit.edu	37	6	46658969	46658969	+	Missense_Mutation	SNP	A	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr6:46658969A>G	uc003oyj.2	+	1	3104	c.3104A>G	c.(3103-3105)AAC>AGC	p.N1035S	TDRD6_uc010jze.2_Missense_Mutation_p.N1029S	NM_001010870	NP_001010870	O60522	TDRD6_HUMAN	tudor domain containing 6	1035	Tudor 5.				cell differentiation|multicellular organismal development|spermatogenesis	chromatoid body	nucleic acid binding			breast(3)|ovary(2)|skin(1)	6			Lung(136;0.192)			TCTCCCTTGAACCCTGGAACC	0.368													4	83					0	0	0	0
AIM1	202	broad.mit.edu	37	6	106967352	106967352	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr6:106967352G>A	uc003prh.2	+	2	1532	c.1045G>A	c.(1045-1047)GAA>AAA	p.E349K		NM_001624	NP_001615	Q9Y4K1	AIM1_HUMAN	absent in melanoma 1	349							sugar binding			breast(4)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|skin(1)	9	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		TACCGTCTCGGAAGAAGAGAT	0.438													8	67					0	0	0	0
MYO1G	64005	broad.mit.edu	37	7	45010270	45010270	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:45010270G>A	uc003tmh.2	-	9	1282	c.1138C>T	c.(1138-1140)CGG>TGG	p.R380W	MYO1G_uc003tmf.2_5'Flank|MYO1G_uc003tmg.2_Missense_Mutation_p.R142W|MYO1G_uc010kym.2_Missense_Mutation_p.R265W|MYO1G_uc003tmi.1_Missense_Mutation_p.R292W|MYO1G_uc003tmj.2_Missense_Mutation_p.R142W	NM_033054	NP_149043	B0I1T2	MYO1G_HUMAN	myosin IG	380	Myosin head-like.					myosin complex|plasma membrane	actin binding|ATP binding|calmodulin binding|motor activity			breast(2)|ovary(1)|pancreas(1)	4						CGAGGATCCCGGCCCCGGGGT	0.602													12	118					0	0	0	0
SUMF2	25870	broad.mit.edu	37	7	56136270	56136270	+	Missense_Mutation	SNP	C	T	T	rs150976522	byFrequency	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:56136270C>T	uc003trv.2	+	2	251	c.220C>T	c.(220-222)CGG>TGG	p.R74W	PSPH_uc003trj.2_Intron|SUMF2_uc003tro.2_Missense_Mutation_p.R74W|SUMF2_uc011kcv.1_RNA|SUMF2_uc011kcw.1_Missense_Mutation_p.R74W|SUMF2_uc011kcx.1_Missense_Mutation_p.R74W|SUMF2_uc003trt.2_Intron|SUMF2_uc011kcy.1_Missense_Mutation_p.R74W|SUMF2_uc011kcz.1_Missense_Mutation_p.R74W|SUMF2_uc003tru.2_RNA|SUMF2_uc011kda.1_5'UTR|SUMF2_uc003trx.2_RNA	NM_001130069	NP_001123541	Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2 isoform e	55						endoplasmic reticulum lumen	metal ion binding			ovary(1)|skin(1)	2	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CGGGCCTGTGCGGGAGGCGAC	0.507													4	46					0	0	0	0
RABGEF1	27342	broad.mit.edu	37	7	66262383	66262383	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:66262383G>C	uc011kee.1	+	6	824	c.660G>C	c.(658-660)AAG>AAC	p.K220N	RABGEF1_uc003tvf.2_Missense_Mutation_p.K79N|RABGEF1_uc003tvg.2_Missense_Mutation_p.K14N|RABGEF1_uc010lag.2_Missense_Mutation_p.K206N|RABGEF1_uc003tvh.2_Missense_Mutation_p.K206N|RABGEF1_uc003tvi.2_Missense_Mutation_p.K40N	NM_014504	NP_055319	Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	423					endocytosis|protein transport	early endosome|recycling endosome	DNA binding|protein binding|zinc ion binding			ovary(1)	1						GAGTCGAGAAGATAATGGATC	0.279													4	46					0	0	0	0
AKAP9	10142	broad.mit.edu	37	7	91682106	91682106	+	Nonsense_Mutation	SNP	C	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:91682106C>G	uc003ulg.2	+	22	5660	c.5435C>G	c.(5434-5436)TCA>TGA	p.S1812*	AKAP9_uc003ulf.2_Nonsense_Mutation_p.S1812*|AKAP9_uc003uli.2_Nonsense_Mutation_p.S1435*	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2	1824					G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AACATGTGGTCAAAAGTAACT	0.373			T	BRAF	papillary thyroid								9	61					0	0	0	0
PCOLCE	5118	broad.mit.edu	37	7	100205594	100205594	+	Silent	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:100205594G>A	uc003uvo.2	+	9	1416	c.1218G>A	c.(1216-1218)GAG>GAA	p.E406E	PCOLCE_uc010lhb.1_RNA|PCOLCE_uc003uvp.1_RNA	NM_002593	NP_002584	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	406	NTR.				multicellular organismal development	extracellular space	collagen binding|heparin binding|peptidase activator activity				0	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					AGGTAGAAGAGAACAGAGGCC	0.547													12	105					0	0	0	0
MUC17	140453	broad.mit.edu	37	7	100685103	100685103	+	Missense_Mutation	SNP	C	T	T	rs146748610	byFrequency	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:100685103C>T	uc003uxp.1	+	3	10459	c.10406C>T	c.(10405-10407)CCG>CTG	p.P3469L	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	3469	Extracellular (Potential).|Ser-rich.|56.|59 X approximate tandem repeats.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					AGTACCACGCCGGTGGCCAGT	0.498													33	350					0	0	0	0
PIK3CG	5294	broad.mit.edu	37	7	106520087	106520087	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:106520087C>T	uc003vdv.3	+	6	2600	c.2515C>T	c.(2515-2517)CGC>TGC	p.R839C	PIK3CG_uc003vdu.2_Missense_Mutation_p.R839C|PIK3CG_uc003vdw.2_Missense_Mutation_p.R839C	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	839	PI3K/PI4K.				G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding	p.R839C(1)		lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						TGATGATCTGCGCCAAGACAT	0.333													6	67					0	0	0	0
LAMB1	3912	broad.mit.edu	37	7	107572693	107572693	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:107572693C>T	uc003vew.2	-	28	4653	c.4318G>A	c.(4318-4320)GCC>ACC	p.A1440T	LAMB1_uc003vev.2_Missense_Mutation_p.A1464T|LAMB1_uc003veu.2_5'Flank	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	1440	Domain I.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	TTCTGCCAGGCGTTGTGTGCA	0.552													19	179					0	0	0	0
OR6B1	135946	broad.mit.edu	37	7	143701885	143701885	+	Missense_Mutation	SNP	T	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:143701885T>G	uc003wdt.1	+	1	796	c.796T>G	c.(796-798)TTC>GTC	p.F266V		NM_001005281	NP_001005281	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B,	266	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.0783)					TATCCATGCCTTCAACATGAA	0.428													8	90					0	0	0	0
PRKAG2	51422	broad.mit.edu	37	7	151573605	151573605	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:151573605C>T	uc003wkk.2	-	1	712	c.101G>A	c.(100-102)CGC>CAC	p.R34H	PRKAG2_uc010lqe.1_RNA|PRKAG2_uc003wkm.1_Missense_Mutation_p.R34H|uc003wko.1_5'Flank	NM_016203	NP_057287	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit	34					ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			breast(1)|kidney(1)	2	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)		AATGTGCACGCGCAGCGAACG	0.647													7	68					0	0	0	0
PREX2	80243	broad.mit.edu	37	8	69005941	69005941	+	Silent	SNP	T	C	C			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr8:69005941T>C	uc003xxv.1	+	21	2379	c.2352T>C	c.(2350-2352)TTT>TTC	p.F784F	PREX2_uc003xxu.1_Silent_p.F784F|PREX2_uc011lez.1_Silent_p.F719F	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	784					G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17						GGGATGCTTTTGACTGTAAAG	0.403													9	102					0	0	0	0
C8orf34	116328	broad.mit.edu	37	8	69358591	69358591	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr8:69358591G>A	uc010lyz.2	+	3	294	c.245G>A	c.(244-246)AGA>AAA	p.R82K	C8orf34_uc010lyx.1_Missense_Mutation_p.R82K|C8orf34_uc010lyy.1_Missense_Mutation_p.R82K|C8orf34_uc003xyb.2_Missense_Mutation_p.R57K	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328	82					signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			AGGGATTTCAGAAGCTATGAT	0.348													4	58					0	0	0	0
RSPO2	340419	broad.mit.edu	37	8	109001316	109001316	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr8:109001316C>T	uc003yms.2	-	3	909	c.251G>A	c.(250-252)GGA>GAA	p.G84E	RSPO2_uc003ymq.2_Missense_Mutation_p.G17E|RSPO2_uc003ymr.2_Intron	NM_178565	NP_848660	Q6UXX9	RSPO2_HUMAN	R-spondin family, member 2 precursor	84					Wnt receptor signaling pathway	extracellular region	heparin binding			skin(3)|ovary(2)|pancreas(1)|lung(1)	7			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			GGCTCGGTGTCCATAGTACCC	0.488													4	78					0	0	0	0
CSMD3	114788	broad.mit.edu	37	8	113308235	113308235	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr8:113308235G>A	uc003ynu.2	-	54	8600	c.8441C>T	c.(8440-8442)GCG>GTG	p.A2814V	CSMD3_uc003yns.2_Missense_Mutation_p.A2016V|CSMD3_uc003ynt.2_Missense_Mutation_p.A2774V|CSMD3_uc011lhx.1_Missense_Mutation_p.A2645V	NM_198123	NP_937756	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3 isoform 1	2814	Extracellular (Potential).|Sushi 17.					integral to membrane|plasma membrane				ovary(21)|lung(11)|skin(11)|kidney(8)|large_intestine(6)|upper_aerodigestive_tract(2)|central_nervous_system(2)|urinary_tract(1)|breast(1)	63						ACAATGACCCGCTGAAATACG	0.299										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			4	35					0	0	0	0
GLIS3	169792	broad.mit.edu	37	9	4285986	4285986	+	Missense_Mutation	SNP	G	C	C	rs10758591	by1000genomes	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr9:4285986G>C	uc003zii.1	-	2	1153	c.440C>G	c.(439-441)CCC>CGC	p.P147R	GLIS3_uc003zhx.1_Intron|GLIS3_uc003zic.1_Intron|GLIS3_uc003zie.1_Intron|GLIS3_uc010mhh.1_Intron|GLIS3_uc003zid.1_Intron|GLIS3_uc010mhi.1_Intron|GLIS3_uc003zif.1_Intron|GLIS3_uc003zig.1_Intron|GLIS3_uc003zih.1_Intron			Q8NEA6	GLIS3_HUMAN	SubName: Full=GLIS family zinc finger 3 transcript variant TS2; SubName: Full=GLIS family zinc finger 3 transcript variant TS3; SubName: Full=GLIS family zinc finger 3 transcript variant TS4; SubName: Full=GLIS family zinc finger 3 transcript variant TS5; Flags: Fragment;	Error:Variant_position_missing_in_Q8NEA6_after_alignment					negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter		DNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		AATGGGATGGGGGAGAAAAAA	0.408													4	68					0	0	0	0
GNE	10020	broad.mit.edu	37	9	36236908	36236908	+	Silent	SNP	T	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr9:36236908T>A	uc010mlh.2	-	4	905	c.690A>T	c.(688-690)ATA>ATT	p.I230I	CLTA_uc003zzf.1_Intron|GNE_uc010mlg.2_Silent_p.I230I|GNE_uc011lpl.1_Intron|GNE_uc010mli.2_Silent_p.I261I|GNE_uc010mlj.2_Silent_p.I225I	NM_005476	NP_005467	Q9Y223	GLCNE_HUMAN	UDP-N-acetylglucosamine-2-epimerase/N-	230	UDP-N-acetylglucosamine 2-epimerase.				cell adhesion|lipopolysaccharide biosynthetic process|N-acetylneuraminate metabolic process|UDP-N-acetylglucosamine metabolic process		ATP binding|N-acylmannosamine kinase activity|UDP-N-acetylglucosamine 2-epimerase activity				0			STAD - Stomach adenocarcinoma(86;0.228)			CAAACATTTTTATGGAATGCT	0.348													6	70					0	0	0	0
FAM75A6	389730	broad.mit.edu	37	9	43625382	43625382	+	Missense_Mutation	SNP	G	A	A	rs143826416	by1000genomes	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr9:43625382G>A	uc011lrb.1	-	4	3334	c.3305C>T	c.(3304-3306)CCT>CTT	p.P1102L		NM_001145196	NP_001138668	Q5VVP1	F75A6_HUMAN	hypothetical protein LOC389730	1102						integral to membrane					0						CTTGTGAATAGGGGGAAACAT	0.483													7	125					0	0	0	0
NOTCH1	4851	broad.mit.edu	37	9	139411828	139411828	+	Missense_Mutation	SNP	C	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr9:139411828C>A	uc004chz.2	-	9	1451	c.1451G>T	c.(1450-1452)GGT>GTT	p.G484V		NM_017617	NP_060087	P46531	NOTC1_HUMAN	notch1 preproprotein	484	Extracellular (Potential).|EGF-like 12; calcium-binding (Potential).				aortic valve morphogenesis|immune response|negative regulation of BMP signaling pathway|negative regulation of cell-substrate adhesion|negative regulation of myoblast differentiation|negative regulation of osteoblast differentiation|negative regulation of transcription, DNA-dependent|Notch receptor processing	cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to membrane|nucleoplasm|plasma membrane	calcium ion binding|protein binding|receptor activity	p.G484V(2)		haematopoietic_and_lymphoid_tissue(791)|upper_aerodigestive_tract(29)|lung(13)|central_nervous_system(10)|breast(9)|large_intestine(1)|skin(1)|oesophagus(1)|pancreas(1)	856	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GCAGTGCACACCCTCGTAGCC	0.652			T|Mis|O	TRB@	T-ALL					HNSCC(8;0.001)			3	16					0.004672	0.00502748	1	0
GLRA2	2742	broad.mit.edu	37	X	14550468	14550468	+	Missense_Mutation	SNP	A	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chrX:14550468A>G	uc010nep.2	+	3	508	c.176A>G	c.(175-177)GAT>GGT	p.D59G	GLRA2_uc010neq.2_Missense_Mutation_p.D59G|GLRA2_uc004cwe.3_Missense_Mutation_p.D59G|GLRA2_uc011mio.1_5'UTR|GLRA2_uc011mip.1_Missense_Mutation_p.D37G	NM_001118885	NP_001112357	P23416	GLRA2_HUMAN	glycine receptor, alpha 2 isoform A	59	Extracellular (Probable).				neuropeptide signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|receptor activity|transmitter-gated ion channel activity			ovary(1)|lung(1)	2	Hepatocellular(33;0.128)				Ethanol(DB00898)|Glycine(DB00145)	TCAGGATATGATGCAAGAATC	0.378													10	43					0	0	0	0
RBBP7	5931	broad.mit.edu	37	X	16870184	16870184	+	Missense_Mutation	SNP	T	G	G			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chrX:16870184T>G	uc004cxt.2	-	9	1383	c.1025A>C	c.(1024-1026)AAT>ACT	p.N342T	RBBP7_uc004cxs.1_Missense_Mutation_p.N386T|RBBP7_uc004cxu.2_Missense_Mutation_p.N333T	NM_002893	NP_002884	Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	342	WD 6.				cell proliferation|cellular heat acclimation|CenH3-containing nucleosome assembly at centromere|DNA replication|multicellular organismal development|negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ESC/E(Z) complex|NuRD complex	protein binding			upper_aerodigestive_tract(1)|ovary(1)	2	Hepatocellular(33;0.0997)					ATCCCACACATTCAGGCGGCG	0.368													17	111					0	0	0	0
SSX6	280657	broad.mit.edu	37	X	47970673	47970673	+	Missense_Mutation	SNP	C	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chrX:47970673C>A	uc004dix.1	+	4	336	c.214C>A	c.(214-216)CGT>AGT	p.R72S	SSX6_uc011mlv.1_Missense_Mutation_p.R72S	NM_173357	NP_775493			SubName: Full=Putative uncharacterized protein SSX1;												0						ACTTTTCATGCGTAATAAACG	0.383													4	15					0.00909568	0.0096825	1	0
ELF4	2000	broad.mit.edu	37	X	129201444	129201444	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chrX:129201444G>A	uc004evd.3	-	9	1629	c.1244C>T	c.(1243-1245)TCG>TTG	p.S415L	ELF4_uc004eve.3_Missense_Mutation_p.S415L	NM_001421	NP_001412	Q99607	ELF4_HUMAN	E74-like factor 4	415					natural killer cell proliferation|NK T cell proliferation|positive regulation of transcription from RNA polymerase II promoter	PML body	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1						GGTCAGGGCCGAGCCCGACCC	0.587			T	ERG	AML								12	46					0	0	0	0
TP53	7157	broad.mit.edu	37	17	7579698	7579699	+	Splice_Site	INS	-	CC	CC			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr17:7579698_7579699insCC	uc002gim.2	-	3	290	c.96_splice	c.e3+1	p.L32_splice	TP53_uc002gig.1_Splice_Site_p.L32_splice|TP53_uc002gih.2_Splice_Site_p.L32_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_5'Flank|TP53_uc010cng.1_5'Flank|TP53_uc002gii.1_5'Flank|TP53_uc010cnh.1_Splice_Site_p.L32_splice|TP53_uc010cni.1_Splice_Site_p.L32_splice|TP53_uc002gij.2_Splice_Site_p.L32_splice|TP53_uc010cnj.1_5'Flank|TP53_uc002gin.2_Splice_Site_p.L32_splice|TP53_uc002gio.2_Intron|TP53_uc010vug.1_Splice_Site|TP53_uc010cnk.1_Splice_Site_p.L47_splice	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.0?(7)|p.?(2)|p.S33fs*10(1)|p.P13fs*18(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		CCTTGTCCTTACCAGAACGTTG	0.381		111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---							
POLDIP2	26073	broad.mit.edu	37	17	26684390	26684391	+	Splice_Site	INS	-	C	C	rs148075904	by1000genomes	TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr17:26684390_26684391insC	uc002haz.2	-	3	211	c.79_splice	c.e3+0	p.P27_splice	POLDIP2_uc010wag.1_RNA|TMEM199_uc002hba.2_5'Flank|SARM1_uc010wah.1_5'Flank	NM_015584	NP_056399	Q9Y2S7	PDIP2_HUMAN	DNA polymerase delta interacting protein 2							mitochondrial nucleoid|nucleus					0	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		GCACAGAGCGGCTTTGCCACCG	0.762													---	---	---							
H1FX	8971	broad.mit.edu	37	3	129034495	129034495	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr3:129034495delT	uc003elx.2	-	1	626	c.251delA	c.(250-252)AATfs	p.N84fs	C3orf47_uc011bkv.1_5'Flank	NM_006026	NP_006017	Q92522	H1X_HUMAN	H1 histone family, member X	84	H15.				nucleosome assembly	nucleosome|nucleus	DNA binding				0						GGTGCGCCCATTCTGCTGGTC	0.612													---	---	---							
INTS1	26173	broad.mit.edu	37	7	1546840	1546840	+	5'Flank	DEL	T	-	-	rs111819550		TCGA-CR-7376-01A-11D-2129-08	TCGA-CR-7376-10A-01D-2129-08									Somatic	Phase_I	Capture				Illumina GAIIx	a6b11f68-79da-4542-818d-f404116c0bf8	47cf1857-e93d-470f-abe2-bebe102fb2c1	g.chr7:1546840delT	uc003skn.2	-						INTS1_uc003skq.2_5'Flank	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1						snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTCAttattcttttttttttt	0.269													---	---	---							
