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	pox_cutoff	isArtifactMode	oxoGCut
PLA2G2D	26279	broad.mit.edu	37	1	20440719	20440719	+	Missense_Mutation	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:20440719C>T	uc001bcz.2	-	4	343	c.326G>A	c.(325-327)TGT>TAT	p.C109Y	PLA2G2D_uc009vpo.2_RNA	NM_012400	NP_036532	Q9UNK4	PA2GD_HUMAN	phospholipase A2, group IID precursor	109					inflammatory response|lipid catabolic process|phospholipid metabolic process	extracellular region	calcium ion binding|phospholipase A2 activity				0		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTCACAGGCACACAGCTGCTG	0.597000										Multiple Myeloma(11;0.12)			14	38					0	0	0.457914	0	0
AGL	178	broad.mit.edu	37	1	100327977	100327977	+	Nonsense_Mutation	SNP	C	G	G			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:100327977C>G	uc001dsi.1	+	4	858	c.458C>G	c.(457-459)TCA>TGA	p.S153*	AGL_uc001dsj.1_Nonsense_Mutation_p.S153*|AGL_uc001dsk.1_Nonsense_Mutation_p.S153*|AGL_uc001dsl.1_Nonsense_Mutation_p.S153*|AGL_uc001dsm.1_Nonsense_Mutation_p.S137*|AGL_uc001dsn.1_Nonsense_Mutation_p.S136*	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,	153	4-alpha-glucanotransferase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		GCAAAAGAATCAGGTAATGTC	0.308000													21	69					0	0	0.592651	0	0
NTRK1	4914	broad.mit.edu	37	1	156843561	156843561	+	Silent	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:156843561C>T	uc001fqh.1	+	8	1043	c.987C>T	c.(985-987)TTC>TTT	p.F329F	NTRK1_uc001fqf.1_Silent_p.F299F|NTRK1_uc009wsi.1_Silent_p.F34F|NTRK1_uc001fqi.1_Silent_p.F329F|NTRK1_uc009wsk.1_Silent_p.F329F	NM_002529	NP_002520	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	329	Ig-like C2-type 2.|Extracellular (Potential).				activation of adenylate cyclase activity|activation of MAPKK activity|activation of phospholipase C activity|cell differentiation|nerve growth factor receptor signaling pathway|nervous system development|phosphatidylinositol-mediated signaling|Ras protein signal transduction	endosome|integral to plasma membrane	ATP binding|neurotrophin receptor activity|transmembrane receptor protein serine/threonine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(9)|ovary(6)|stomach(1)|central_nervous_system(1)	17	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Imatinib(DB00619)	GCTTCATCTTCACTGAGTTCC	0.617000			T	TPM3|TPR|TFG	papillary thyroid					TSP Lung(10;0.080)			7	14					0	0	0.248553	0	0
GORAB	92344	broad.mit.edu	37	1	170501324	170501324	+	Missense_Mutation	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:170501324C>T	uc001gha.2	+	1	62	c.35C>T	c.(34-36)GCG>GTG	p.A12V	GORAB_uc009wvw.2_Missense_Mutation_p.A12V|GORAB_uc001ggz.3_Missense_Mutation_p.A12V|GORAB_uc009wvx.2_5'UTR|GORAB_uc001ghb.2_5'UTR	NM_152281	NP_689494	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting isoform a	12						Golgi apparatus|nucleus					0						GTCGCGGCTGCGAGATTTGGG	0.622000													14	68					0	0	0.479597	0	0
RGS21	431704	broad.mit.edu	37	1	192321246	192321246	+	Missense_Mutation	SNP	C	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:192321246C>A	uc001gsh.2	+	4	332	c.158C>A	c.(157-159)GCC>GAC	p.A53D		NM_001039152	NP_001034241	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	53	RGS.				negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity			ovary(1)|skin(1)	2						TTCTGGCTTGCCTGTGAAGAC	0.328000													10	34					4.1943e-16	5.09896e-16	0.361761	1	0
CDC73	79577	broad.mit.edu	37	1	193099338	193099338	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:193099338G>A	uc001gtb.2	+	3	515	c.272G>A	c.(271-273)CGA>CAA	p.R91Q		NM_024529	NP_078805	Q6P1J9	CDC73_HUMAN	parafibromin	91			R -> P (found in a patient with isolated hyperparathyroidism and parathyroid adenomas).		cell cycle|histone H2B ubiquitination|histone monoubiquitination|transcription, DNA-dependent	Cdc73/Paf1 complex	protein binding			parathyroid(46)|ovary(1)|breast(1)|pancreas(1)	49						AGACCTGATCGAAAAGATCTA	0.249000									Hyperparathyroidism_Familial_Isolated|Hyperparathyroidism-Jaw_Tumor_Syndrome				6	37					0	0	0.248553	0	0
SNRPE	6635	broad.mit.edu	37	1	203832834	203832835	+	Missense_Mutation	DNP	GG	AA	AA			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:203832834_203832835GG>AA	uc001hai.2	+	3	173_174	c.125_126GG>AA	c.(124-126)CGG>CAA	p.R42Q	SNRPE_uc010pqn.1_RNA	NM_003094	NP_003085	P62304	RUXE_HUMAN	small nuclear ribonucleoprotein polypeptide E	42					histone mRNA metabolic process|ncRNA metabolic process|spliceosomal snRNP assembly|spliceosome assembly|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nucleoplasm|U12-type spliceosomal complex|U7 snRNP	protein binding|RNA binding				0	all_cancers(21;0.103)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GTGAATATGCGGATAGAAGGCT	0.366000													68	133					0	0	0.115264	0	0
LBR	3930	broad.mit.edu	37	1	225599084	225599084	+	Missense_Mutation	SNP	A	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr1:225599084A>T	uc001hoy.2	-	9	1286	c.1143T>A	c.(1141-1143)TTT>TTA	p.F381L	LBR_uc001hoz.2_Missense_Mutation_p.F381L|LBR_uc001hpa.1_Missense_Mutation_p.F381L	NM_002296	NP_002287	Q14739	LBR_HUMAN	lamin B receptor	381					cholesterol biosynthetic process	integral to nuclear inner membrane	chromo shadow domain binding|delta14-sterol reductase activity|DNA binding|lamin binding|receptor activity			ovary(1)|skin(1)	2	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		ATTTGAGATCAAAAGTACCAA	0.373000													22	91					0	0	0.667858	0	0
OR10Q1	219960	broad.mit.edu	37	11	57996225	57996225	+	Missense_Mutation	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr11:57996225C>T	uc010rkd.1	-	1	123	c.123G>A	c.(121-123)ATG>ATA	p.M41I		NM_001004471	NP_001004471	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q,	41	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(21;0.0589)				CACAGAGGATCATCAAGTAGA	0.527000													28	70					0	0	0.681144	0	0
ZNF385A	25946	broad.mit.edu	37	12	54764720	54764720	+	Silent	SNP	T	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr12:54764720T>C	uc001sfw.1	-	5	948	c.765A>G	c.(763-765)CAA>CAG	p.Q255Q	ZNF385A_uc001sfv.1_Silent_p.Q236Q|ZNF385A_uc009zno.1_RNA|ZNF385A_uc010sov.1_Silent_p.Q174Q|ZNF385A_uc001sfx.1_Silent_p.Q255Q|ZNF385A_uc001sfy.3_Silent_p.Q275Q|ZNF385A_uc001sfz.3_Silent_p.Q194Q	NM_015481	NP_056296	Q96PM9	Z385A_HUMAN	zinc finger protein 385A isoform c	255	Matrin-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding|zinc ion binding			ovary(1)	1						CCTGTTTCAGTTGGACCTCCG	0.597000											OREG0021894	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	28	71					0	0	0.750413	0	0
C12orf74	338809	broad.mit.edu	37	12	93100691	93100691	+	Missense_Mutation	SNP	C	G	G			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr12:93100691C>G	uc001tch.1	+	2	514	c.284C>G	c.(283-285)TCT>TGT	p.S95C	C12orf74_uc001tci.2_Missense_Mutation_p.S95C	NM_001037671	NP_001032760	Q32Q52	CL074_HUMAN	hypothetical protein LOC338809	95											0						CCAAAGGATTCTTCACACTTG	0.582000													23	58					0	0	0.608945	0	0
KCNJ12	3768	broad.mit.edu	37	17	21319100	21319100	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:21319100G>A	uc002gyv.1	+	3	1151	c.446G>A	c.(445-447)CGC>CAC	p.R149H		NM_021012	NP_066292	Q14500	IRK12_HUMAN	potassium inwardly-rectifying channel, subfamily	149	Extracellular (By similarity).				blood circulation|muscle contraction|regulation of heart contraction|synaptic transmission	integral to membrane	inward rectifier potassium channel activity|ion channel inhibitor activity|potassium channel regulator activity			ovary(3)|skin(1)	4				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)	TACGGGCTGCGCTGTGTGACG	0.642000										Prostate(3;0.18)			5	47					0	0	0.184627	0	0
COASY	80347	broad.mit.edu	37	17	40717244	40717244	+	Splice_Site	SNP	G	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:40717244G>T	uc002hzz.2	+	7	1460	c.1303_splice	c.e7-1	p.K435_splice	COASY_uc010cyj.2_Splice_Site_p.K464_splice|COASY_uc002iab.2_Splice_Site_p.K140_splice|COASY_uc002iad.2_Splice_Site_p.K435_splice|COASY_uc002iac.2_Splice_Site_p.K435_splice|COASY_uc002iae.2_Splice_Site_p.K230_splice|MLX_uc002iaf.2_5'Flank|MLX_uc002iag.2_5'Flank|MLX_uc002iah.2_5'Flank	NM_001042529	NP_001035994	Q13057	COASY_HUMAN	coenzyme A synthase isoform a						coenzyme A biosynthetic process|pantothenate metabolic process	mitochondrial outer membrane	ATP binding|dephospho-CoA kinase activity|pantetheine-phosphate adenylyltransferase activity				0		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CCCCTCCCCAGAAGCAGCTGA	0.562000													31	140					6.19805e-25	7.68558e-25	0.812448	1	0
AOC2	314	broad.mit.edu	37	17	40997487	40997487	+	Missense_Mutation	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:40997487G>C	uc002ibu.2	+	1	879	c.844G>C	c.(844-846)GTG>CTG	p.V282L	AOC2_uc002ibt.2_Missense_Mutation_p.V282L	NM_009590	NP_033720	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 isoform b	282					catecholamine metabolic process|visual perception	cytoplasm|plasma membrane	aliphatic-amine oxidase activity|aminoacetone:oxygen oxidoreductase(deaminating) activity|copper ion binding|electron carrier activity|phenethylamine:oxygen oxidoreductase (deaminating) activity|primary amine oxidase activity|quinone binding|tryptamine:oxygen oxidoreductase (deaminating) activity			ovary(2)	2		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CCGGTTGGAAGTGGTTAGAGT	0.572000													19	66					0	0	0.575678	0	0
MAPT	4137	broad.mit.edu	37	17	44101444	44101444	+	Silent	SNP	C	G	G			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr17:44101444C>G	uc002ijr.3	+	14	2504	c.2184C>G	c.(2182-2184)GTC>GTG	p.V728V	MAPT_uc010dau.2_Silent_p.V746V|MAPT_uc002ijs.3_Silent_p.V411V|MAPT_uc002ijx.3_Silent_p.V382V|MAPT_uc002ijt.3_Silent_p.V353V|MAPT_uc002iju.3_Silent_p.V322V|MAPT_uc002ijv.3_Silent_p.V329V	NM_016835	NP_058519	P10636	TAU_HUMAN	microtubule-associated protein tau isoform 1	728					cellular component disassembly involved in apoptosis|microtubule cytoskeleton organization|negative regulation of microtubule depolymerization|positive regulation of axon extension|positive regulation of microtubule polymerization|regulation of autophagy	axon|cytosol|growth cone|microtubule|microtubule associated complex|nuclear periphery|plasma membrane|tubulin complex	apolipoprotein E binding|enzyme binding|identical protein binding|lipoprotein particle binding|microtubule binding|protein binding|SH3 domain binding|structural constituent of cytoskeleton			pancreas(1)	1		Melanoma(429;0.216)				TCAGCAATGTCTCCTCCACCG	0.622000													9	117					0	0	0.335167	0	0
TYMS	7298	broad.mit.edu	37	18	662242	662242	+	Missense_Mutation	SNP	A	G	G			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr18:662242A>G	uc010dka.1	+	3	515	c.376A>G	c.(376-378)AGA>GGA	p.R126G	TYMS_uc010dkb.1_Missense_Mutation_p.R126G|TYMS_uc010dkc.1_Intron	NM_001071	NP_001062	P04818	TYSY_HUMAN	thymidylate synthase	126					DNA repair|DNA replication|phosphatidylinositol-mediated signaling|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process|regulation of transcription involved in G1/S phase of mitotic cell cycle|response to organophosphorus	cytosol	thymidylate synthase activity				0					Capecitabine(DB01101)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Gemcitabine(DB00441)|Leucovorin(DB00650)|Pemetrexed(DB00642)|Raltitrexed(DB00293)|Trifluridine(DB00432)	ATTCTCCACCAGAGAAGAAGG	0.498000													56	302					0	0	0.870114	0	0
NDC80	10403	broad.mit.edu	37	18	2616466	2616466	+	Missense_Mutation	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr18:2616466G>C	uc002kli.2	+	17	2004	c.1822G>C	c.(1822-1824)GAT>CAT	p.D608H		NM_006101	NP_006092	O14777	NDC80_HUMAN	kinetochore associated 2	608	Potential.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.|Interaction with NEK2 and ZWINT.				attachment of spindle microtubules to kinetochore|cell division|establishment of mitotic spindle orientation|mitotic prometaphase|mitotic sister chromatid segregation|mitotic spindle organization|phosphatidylinositol-mediated signaling	condensed nuclear chromosome outer kinetochore|cytosol|Ndc80 complex	protein binding			ovary(1)	1						TGCTAAAGTTGATAGAGAATA	0.254000													6	33					0	0	0.500413	0	0
NDC80	10403	broad.mit.edu	37	18	2616517	2616517	+	Missense_Mutation	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr18:2616517G>C	uc002kli.2	+	17	2055	c.1873G>C	c.(1873-1875)GAG>CAG	p.E625Q		NM_006101	NP_006092	O14777	NDC80_HUMAN	kinetochore associated 2	625	Potential.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore|cell division|establishment of mitotic spindle orientation|mitotic prometaphase|mitotic sister chromatid segregation|mitotic spindle organization|phosphatidylinositol-mediated signaling	condensed nuclear chromosome outer kinetochore|cytosol|Ndc80 complex	protein binding			ovary(1)	1						AAATATTAAAGAGATTAGAGA	0.299000													6	26					0	0	0.335167	0	0
FBXW9	84261	broad.mit.edu	37	19	12800616	12800616	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:12800616G>A	uc010dyx.2	-	7	1165	c.1165C>T	c.(1165-1167)CAC>TAC	p.H389Y	FBXW9_uc010xmp.1_RNA|uc002mul.1_3'UTR|FBXW9_uc002mum.1_Missense_Mutation_p.H369Y|FBXW9_uc002mun.1_Missense_Mutation_p.H206Y	NM_032301	NP_115677	Q5XUX1	FBXW9_HUMAN	F-box and WD-40 domain protein 9	399	WD 5.						protein binding			ovary(1)	1						GCGAAGACGTGCAGCAGGCCC	0.647000													17	56					0	0	0.592651	0	0
KLHL26	55295	broad.mit.edu	37	19	18778682	18778682	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:18778682G>A	uc002njz.1	+	3	502	c.475G>A	c.(475-477)GCC>ACC	p.A159T		NM_018316	NP_060786	Q53HC5	KLH26_HUMAN	kelch-like 26	159										ovary(1)	1						CCTGAAGGCGGCCATGAGCGT	0.647000													3	43					0	0	0.115264	0	0
CCDC85A	114800	broad.mit.edu	37	2	56420491	56420491	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr2:56420491G>A	uc002rzn.2	+	2	1658	c.1156G>A	c.(1156-1158)GGA>AGA	p.G386R		NM_001080433	NP_001073902	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	386										breast(3)|ovary(2)	5			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			AGGCAGCGGCGGAGGCAGCAG	0.627000													3	8					0	0	0.115264	0	0
SIRPG	55423	broad.mit.edu	37	20	1615980	1615980	+	Silent	SNP	C	A	A	rs147655438		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr20:1615980C>A	uc002wfm.1	-	4	1079	c.1014G>T	c.(1012-1014)GCG>GCT	p.A338A	SIRPG_uc002wfn.1_Intron|SIRPG_uc002wfo.1_Intron|uc002wfp.1_Intron	NM_018556	NP_061026	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma isoform 1	338	Extracellular (Potential).|Ig-like C1-type 2.				blood coagulation|cell adhesion|cell junction assembly|cell-cell signaling|intracellular signal transduction|leukocyte migration|negative regulation of cell proliferation|positive regulation of cell proliferation|positive regulation of cell-cell adhesion|positive regulation of T cell activation	integral to membrane|intracellular|plasma membrane	protein binding			ovary(1)	1						GTTTGCTGACCGCCAGCTGCC	0.502000													22	54					0.000175454	0.000197785	0.592651	1	0
PRIC285	85441	broad.mit.edu	37	20	62203482	62203482	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr20:62203482G>A	uc002yfm.2	-	2	1149	c.257C>T	c.(256-258)TCC>TTC	p.S86F	PRIC285_uc002yfn.2_Missense_Mutation_p.S86F	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285	86					cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)			CTCGAACTTGGAGAGTCCCGG	0.627000													4	14					0	0	0.150653	0	0
PRPF6	24148	broad.mit.edu	37	20	62642850	62642850	+	Missense_Mutation	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr20:62642850G>C	uc002yho.2	+	11	1686	c.1518G>C	c.(1516-1518)TGG>TGC	p.W506C	PRPF6_uc002yhp.2_Missense_Mutation_p.W506C	NM_012469	NP_036601	O94906	PRP6_HUMAN	PRP6 pre-mRNA processing factor 6 homolog	506					assembly of spliceosomal tri-snRNP|positive regulation of transcription from RNA polymerase II promoter|spliceosome assembly	catalytic step 2 spliceosome|nucleoplasm|U4/U6 snRNP|U4/U6 x U5 tri-snRNP complex|U5 snRNP	androgen receptor binding|ribonucleoprotein binding|transcription coactivator activity			ovary(2)	2	all_cancers(38;6.47e-12)|all_epithelial(29;1.26e-13)|Lung NSC(23;9.37e-10)|all_lung(23;3.23e-09)					GTGAGCAGTGGATCCAGGTGG	0.602000													3	20					0	0	0.115264	0	0
FTCD	10841	broad.mit.edu	37	21	47571511	47571511	+	Silent	SNP	G	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr21:47571511G>T	uc002zif.2	-	5	641	c.597C>A	c.(595-597)ATC>ATA	p.I199I	FTCD_uc002zig.2_Silent_p.I199I|FTCD_uc002zih.2_Silent_p.I199I|FTCD_uc010gqf.2_Silent_p.I199I|FTCD_uc010gqg.1_Silent_p.I68I	NM_006657	NP_006648	O95954	FTCD_HUMAN	formiminotransferase cyclodeaminase	199	Formiminotransferase C-subdomain (By similarity).				folic acid-containing compound metabolic process|histidine catabolic process	centriole|cytosol|Golgi apparatus	folic acid binding|formimidoyltetrahydrofolate cyclodeaminase activity|glutamate formimidoyltransferase activity			pancreas(1)|skin(1)	2	Breast(49;0.214)			Colorectal(79;0.235)	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Tetrahydrofolic acid(DB00116)	GGTTGAGCGCGATGCGGTGGG	0.647000													21	60					1.55795e-14	1.85755e-14	0.608945	1	0
DGCR2	9993	broad.mit.edu	37	22	19028613	19028613	+	Missense_Mutation	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr22:19028613C>T	uc002zoq.1	-	9	1602	c.1354G>A	c.(1354-1356)GAG>AAG	p.E452K	DGCR2_uc002zor.1_Missense_Mutation_p.E228K|DGCR2_uc011agr.1_Missense_Mutation_p.E408K	NM_005137	NP_005128	P98153	IDD_HUMAN	integral membrane protein DGCR2 precursor	452	Cytoplasmic (Potential).				cell adhesion|organ morphogenesis	integral to membrane	receptor activity|sugar binding			large_intestine(1)	1	Colorectal(54;0.0993)					ATGGAGGCCTCGTAGGGCGGC	0.632000													7	29					0	0	0.248553	0	0
HYAL1	3373	broad.mit.edu	37	3	50340364	50340364	+	Missense_Mutation	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr3:50340364G>C	uc003czp.2	-	2	156	c.24C>G	c.(22-24)ATC>ATG	p.I8M	HYAL1_uc003czm.2_Intron|HYAL1_uc003czo.2_Intron|HYAL1_uc003czq.2_Missense_Mutation_p.I8M|HYAL1_uc003czr.2_Missense_Mutation_p.I8M|HYAL1_uc003czn.2_Intron|HYAL1_uc003czs.2_Missense_Mutation_p.I8M|HYAL1_uc003czt.2_Missense_Mutation_p.I8M	NM_033159	NP_149349	Q12794	HYAL1_HUMAN	hyaluronoglucosaminidase 1 isoform 1	8						extracellular space|lysosome	hyalurononglucosaminidase activity			lung(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)	Hyaluronidase(DB00070)	AGAGGGCGCAGATGGGAAGCA	0.607000													6	34					0	0	0.217242	0	0
SERPINI2	5276	broad.mit.edu	37	3	167170764	167170764	+	Silent	SNP	G	A	A	rs140665807		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr3:167170764G>A	uc003fer.1	-	5	982	c.924C>T	c.(922-924)ACC>ACT	p.T308T	SERPINI2_uc003fes.1_Silent_p.T318T|SERPINI2_uc003fet.1_Silent_p.T308T	NM_006217	NP_006208	O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin),	308					cellular component movement|regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			skin(2)|urinary_tract(1)	3						TAAATATCTCGGTTATGTTCA	0.279000													14	20					0	0	0.500413	0	0
DCK	1633	broad.mit.edu	37	4	71892401	71892401	+	Missense_Mutation	SNP	C	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr4:71892401C>A	uc003hfx.2	+	6	973	c.685C>A	c.(685-687)CAA>AAA	p.Q229K	DCK_uc011cbb.1_Missense_Mutation_p.Q157K	NM_000788	NP_000779	P27707	DCK_HUMAN	deoxycytidine kinase	229					purine base metabolic process|purine-containing compound salvage|pyrimidine base metabolic process|pyrimidine nucleoside salvage|pyrimidine nucleotide metabolic process	cytosol|nucleus	ATP binding|deoxycytidine kinase activity|drug binding|phosphotransferase activity, alcohol group as acceptor|protein homodimerization activity			ovary(1)	1			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Decitabine(DB01262)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	CGATTATCTTCAAGAGGTGCC	0.284000													12	21					0.00010058	0.000115481	0.411799	1	0
FAT4	79633	broad.mit.edu	37	4	126371574	126371574	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr4:126371574G>A	uc003ifj.3	+	9	9403	c.9403G>A	c.(9403-9405)GGC>AGC	p.G3135S	FAT4_uc011cgp.1_Missense_Mutation_p.G1433S|FAT4_uc003ifi.1_Missense_Mutation_p.G613S	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN	FAT tumor suppressor homolog 4 precursor	3135	Cadherin 30.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						AAATGAAGAAGGCATTTTTGC	0.388000													13	18					0	0	0.457914	0	0
PCDHA6	56142	broad.mit.edu	37	5	140209735	140209735	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr5:140209735G>A	uc003lho.2	+	1	2086	c.2059G>A	c.(2059-2061)GCG>ACG	p.A687T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc011dab.1_Missense_Mutation_p.A687T	NM_018909	NP_061732	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6 isoform 1 precursor	687	Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			haematopoietic_and_lymphoid_tissue(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGGGCGCCGCGGGCCCAGA	0.672000													5	68					0	0	0.217242	0	0
ARHGAP26	23092	broad.mit.edu	37	5	142601928	142601928	+	Missense_Mutation	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr5:142601928C>T	uc011dbj.1	+	23	2397	c.2362C>T	c.(2362-2364)CCA>TCA	p.P788S	ARHGAP26_uc003lmt.2_Missense_Mutation_p.P733S|ARHGAP26_uc003lmw.2_Missense_Mutation_p.P696S	NM_015071	NP_055886	Q9UNA1	RHG26_HUMAN	GTPase regulator associated with the focal	788	SH3.				actin cytoskeleton organization|filopodium assembly|nervous system development|small GTPase mediated signal transduction	cytoskeleton|cytosol|focal adhesion	cytoskeletal adaptor activity|Rho GTPase activator activity|SH3 domain binding			ovary(1)	1		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TACAGTTCACCCATCTCAGGA	0.463000													3	52					0	0	0.150653	0	0
HIST1H4C	8364	broad.mit.edu	37	6	26104205	26104205	+	Silent	SNP	C	G	G	rs139978722		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:26104205C>G	uc003ngi.2	+	1	30	c.30C>G	c.(28-30)GGC>GGG	p.G10G		NM_003542	NP_003533	P62805	H4_HUMAN	histone cluster 1, H4c	10					CenH3-containing nucleosome assembly at centromere|negative regulation of megakaryocyte differentiation|phosphatidylinositol-mediated signaling|telomere maintenance	nucleoplasm|nucleosome	DNA binding|protein binding				0						GCGGAAAAGGCTTGGGGAAGG	0.532000													16	53					0	0	0.557998	0	0
ZNF192	7745	broad.mit.edu	37	6	28116192	28116192	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:28116192G>A	uc003nkn.1	+	2	191	c.7G>A	c.(7-9)GAA>AAA	p.E3K	ZNF192_uc010jqx.1_Missense_Mutation_p.E3K|ZNF192_uc010jqy.1_5'UTR|ZNF192_uc011dkz.1_5'UTR	NM_006298	NP_006289	Q15776	ZN192_HUMAN	zinc finger protein 192	3					viral reproduction	cytoplasm|nucleolus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						TCTAATGGCTGAAGAATCAAG	0.473000													7	19					0	0	0.335167	0	0
CRISP3	10321	broad.mit.edu	37	6	49696475	49696475	+	Missense_Mutation	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:49696475C>T	uc003ozs.2	-	8	721	c.706G>A	c.(706-708)GCC>ACC	p.A236T		NM_006061	NP_006052	P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3 precursor	236					innate immune response	proteinaceous extracellular matrix|specific granule				skin(2)	2	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			TTGCAGGAGGCCTTGCAACTG	0.403000													33	71					0	0	0.779181	0	0
COL9A1	1297	broad.mit.edu	37	6	70990561	70990561	+	Missense_Mutation	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:70990561G>A	uc003pfg.3	-	10	1088	c.929C>T	c.(928-930)CCG>CTG	p.P310L	COL9A1_uc003pfe.3_5'Flank|COL9A1_uc003pff.3_Missense_Mutation_p.P67L	NM_001851	NP_001842	P20849	CO9A1_HUMAN	alpha 1 type IX collagen isoform 1 precursor	310	Triple-helical region (COL3).				axon guidance|cell adhesion|organ morphogenesis	collagen type IX	metal ion binding			ovary(4)	4						TGGCTTTCCCGGTTCACCTGC	0.627000													8	17					0	0	0.307466	0	0
IMPG1	3617	broad.mit.edu	37	6	76660465	76660465	+	Missense_Mutation	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660465G>C	uc003pik.1	-	13	1768	c.1638C>G	c.(1636-1638)TTC>TTG	p.F546L		NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1	546					visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TATCCTCCAAGAAATGATCTG	0.483000													13	45					0	0	0.457914	0	0
IMPG1	3617	broad.mit.edu	37	6	76660636	76660636	+	Silent	SNP	G	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:76660636G>A	uc003pik.1	-	13	1597	c.1467C>T	c.(1465-1467)ATC>ATT	p.I489I		NM_001563	NP_001554	Q17R60	IMPG1_HUMAN	interphotoreceptor matrix proteoglycan 1	489					visual perception	proteinaceous extracellular matrix	extracellular matrix structural constituent|receptor activity			ovary(2)|skin(1)	3		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				CCAGTTGGCTGATTGCAGAAT	0.498000													15	50					0	0	0.539581	0	0
LAMA4	3910	broad.mit.edu	37	6	112454683	112454683	+	Silent	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr6:112454683G>C	uc003pvu.2	-	27	3873	c.3564C>G	c.(3562-3564)CTC>CTG	p.L1188L	LAMA4_uc003pvv.2_Silent_p.L1181L|LAMA4_uc003pvt.2_Silent_p.L1181L	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor	1188	Laminin G-like 2.				cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		GGTGTGCTCTGAGGGCCCTGG	0.438000													24	76					0	0	0.681144	0	0
MSRA	4482	broad.mit.edu	37	8	9912062	9912062	+	Silent	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:9912062C>T	uc003wsx.2	+	1	233	c.36C>T	c.(34-36)CTC>CTT	p.L12L	MSRA_uc011kwx.1_Silent_p.L12L	NM_012331	NP_036463	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A isoform a	12				Missing (in Ref. 6; AAG09689).|Missing: Impaired subcellular location.	methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	GCCAGCTCCTCCTCCTCCACA	0.716000													12	23					0	0	0.479597	0	0
MSRA	4482	broad.mit.edu	37	8	9912103	9912103	+	Missense_Mutation	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:9912103C>T	uc003wsx.2	+	1	274	c.77C>T	c.(76-78)TCG>TTG	p.S26L	MSRA_uc011kwx.1_Missense_Mutation_p.S26L	NM_012331	NP_036463	Q9UJ68	MSRA_HUMAN	methionine sulfoxide reductase A isoform a	26					methionine metabolic process|protein modification process|response to oxidative stress	mitochondrion|nucleus	peptide-methionine-(S)-S-oxide reductase activity				0		Myeloproliferative disorder(644;0.178)			L-Methionine(DB00134)	ATGGGCAACTCGGCCTCGAAC	0.697000													13	29					0	0	0.457914	0	0
FAM74A3	728495	broad.mit.edu	37	9	40716117	40716117	+	RNA	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr9:40716117G>C	uc010mmk.2	+	1		c.594G>C				NR_026801				Homo sapiens family with sequence similarity 74, member A3 (FAM74A3), non-coding RNA.											skin(1)	1				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		CTGTCTGCAAGAAGACGTGCA	0.527000													6	38					0	0	0.217242	0	0
ZNF189	7743	broad.mit.edu	37	9	104170234	104170234	+	Missense_Mutation	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr9:104170234G>C	uc004bbh.1	+	3	460	c.184G>C	c.(184-186)GAG>CAG	p.E62Q	ZNF189_uc004bbg.1_Missense_Mutation_p.E20Q|ZNF189_uc004bbi.1_Missense_Mutation_p.E48Q|ZNF189_uc011lvk.1_Missense_Mutation_p.E47Q	NM_003452	NP_003443	O75820	ZN189_HUMAN	zinc finger protein 189 isoform 1	62	KRAB.				negative regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|skin(2)|kidney(1)|central_nervous_system(1)	6		Acute lymphoblastic leukemia(62;0.0559)				AGATAAGGATGAGGAGCCAAC	0.368000													4	9					0	0	0.184627	0	0
MSN	4478	broad.mit.edu	37	X	64936758	64936758	+	Missense_Mutation	SNP	G	C	C			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:64936758G>C	uc004dwf.2	+	2	289	c.91G>C	c.(91-93)GAC>CAC	p.D31H	MSN_uc010nkp.1_RNA	NM_002444	NP_002435	P26038	MOES_HUMAN	moesin	31	FERM.				leukocyte cell-cell adhesion|leukocyte migration|membrane to membrane docking	apical plasma membrane|cytoskeleton|extrinsic to membrane|microvillus membrane|nucleolus	cell adhesion molecule binding|receptor binding|structural constituent of cytoskeleton		MSN/ALK(6)	haematopoietic_and_lymphoid_tissue(6)|ovary(3)|lung(1)	10						GCAGCTATTTGACCAGGTAAG	0.507000			T	ALK	ALCL								12	53					0	0	0.387290	0	0
OGT	8473	broad.mit.edu	37	X	70782731	70782731	+	Missense_Mutation	SNP	C	T	T			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:70782731C>T	uc004eaa.1	+	16	2229	c.2012C>T	c.(2011-2013)GCG>GTG	p.A671V	BCYRN1_uc011mpt.1_Intron|OGT_uc004eab.1_Missense_Mutation_p.A661V|OGT_uc004eac.2_Missense_Mutation_p.A532V|OGT_uc004ead.2_Missense_Mutation_p.A290V	NM_181672	NP_858058	O15294	OGT1_HUMAN	O-linked GlcNAc transferase isoform 1	671					cellular response to retinoic acid|positive regulation of granulocyte differentiation|positive regulation of histone H3-K4 methylation|positive regulation of proteolysis|protein O-linked glycosylation|signal transduction	cytosol|MLL5-L complex	enzyme activator activity|protein binding|protein N-acetylglucosaminyltransferase activity			ovary(3)|kidney(1)|pancreas(1)	5	Renal(35;0.156)					ACGAGTGGTGCGCTTTTCATG	0.353000													27	77					0	0	0.706142	0	0
STAG2	10735	broad.mit.edu	37	X	123197834	123197834	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chrX:123197834C>A	uc004etz.3	+	19	2297	c.1958C>A	c.(1957-1959)TCA>TAA	p.S653*	STAG2_uc004eua.2_Nonsense_Mutation_p.S653*|STAG2_uc004eub.2_Nonsense_Mutation_p.S653*|STAG2_uc004euc.2_Nonsense_Mutation_p.S653*|STAG2_uc004eud.2_Nonsense_Mutation_p.S653*|STAG2_uc004eue.2_Nonsense_Mutation_p.S653*	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform b	653					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5						GTAGATATTTCAAGAAGTCAA	0.333000													13	45					1.49906e-05	1.75362e-05	0.457914	1	0
LYPD3	27076	broad.mit.edu	37	19	43967294	43967300	+	Frame_Shift_Del	DEL	GTTGCCG	-	-			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr19:43967294_43967300delGTTGCCG	uc002owl.1	-	4	630_636	c.522_528delCGGCAAC	c.(520-528)GACGGCAACfs	p.D174fs	LYPD3_uc002owm.2_3'UTR	NM_014400	NP_055215	O95274	LYPD3_HUMAN	GPI-anchored metastasis-associated protein	174_176	UPAR/Ly6 2.					anchored to plasma membrane				pancreas(1)	1		Prostate(69;0.0153)				TCAAGGTGACGTTGCCGTCGAAGCAGC	0.647													20	78	---	---	---	---					
RAB11FIP1	80223	broad.mit.edu	37	8	37730588	37730589	+	Frame_Shift_Ins	INS	-	G	G			TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr8:37730588_37730589insG	uc003xkm.1	-	4	1775_1776	c.1731_1732insC	c.(1729-1734)CCCTCTfs	p.P577fs	RAB11FIP1_uc010lvz.1_Intron|RAB11FIP1_uc003xkn.1_Intron|RAB11FIP1_uc003xkl.1_5'UTR|RAB11FIP1_uc003xko.1_5'UTR|RAB11FIP1_uc003xkp.1_Intron	NM_001002814	NP_001002814	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 isoform 3	577_578	Ser-rich.				protein transport	centrosome|phagocytic vesicle membrane|recycling endosome	protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			CCCAATTCAGAGGGGACAGATG	0.559													26	49	---	---	---	---					
TSC1	7248	broad.mit.edu	37	9	135796822	135796826	+	Splice_Site	DEL	GGCTA	-	-	rs118203425		TCGA-A4-7287-01A-11D-2136-08	TCGA-A4-7287-10A-01D-2136-08									Somatic	Phase_I	Capture				Illumina GAIIx	11ea8c34-5b98-4a26-9312-6d92ea3eb990	93eabf7d-e975-4f03-a638-5bc360235ff1	g.chr9:135796822_135796826delGGCTA	uc004cca.2	-	8	898	c.664_splice	c.e8-1	p.P222_splice	TSC1_uc004ccb.3_Splice_Site_p.P222_splice|TSC1_uc011mcq.1_Splice_Site_p.P171_splice|TSC1_uc011mcr.1_Splice_Site_p.P101_splice|TSC1_uc011mcs.1_Splice_Site_p.P101_splice|TSC1_uc004ccc.1_Splice_Site_p.P222_splice|TSC1_uc004ccd.2_Splice_Site_p.P222_splice|TSC1_uc004cce.1_Splice_Site_p.P222_splice	NM_000368	NP_000359	Q92574	TSC1_HUMAN	tuberous sclerosis 1 protein isoform 1						activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding			lung(4)|central_nervous_system(3)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|skin(1)|ovary(1)|bone(1)	14				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CTCCATCATTGGCTAGAAGAGTTGG	0.283			D|Mis|N|F|S			hamartoma|renal cell			Tuberous_Sclerosis				9	21	---	---	---	---					
