Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
MST1P2	11209	broad.mit.edu	37	1	16974549	16974549	+	RNA	SNP	C	G	G			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr1:16974549C>G	uc009vow.2	+	5		c.1359C>G			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GGGCTGAGTGCAGCGCCTGCT	0.692													3	62	---	---	---	---	PASS
KIAA0754	643314	broad.mit.edu	37	1	39879328	39879328	+	Missense_Mutation	SNP	G	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr1:39879328G>A	uc009vvt.1	+	1	4153	c.3391G>A	c.(3391-3393)GCC>ACC	p.A1131T	MACF1_uc010ois.1_Intron|MACF1_uc001cda.1_Intron|MACF1_uc001cdc.1_Intron|MACF1_uc010oiu.1_Intron	NM_015038	NP_055853	O94854	K0754_HUMAN	hypothetical protein LOC643314	995	Ala-rich.|10.										0	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AGAGGAGCCCGCCTCCCCAGC	0.711													3	15	---	---	---	---	PASS
EIF2B3	8891	broad.mit.edu	37	1	45363078	45363078	+	Missense_Mutation	SNP	G	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr1:45363078G>C	uc001cmt.1	-	6	732	c.605C>G	c.(604-606)GCC>GGC	p.A202G	EIF2B3_uc001cmu.1_Missense_Mutation_p.A202G|EIF2B3_uc001cmv.1_Missense_Mutation_p.A202G|EIF2B3_uc001cmw.2_Missense_Mutation_p.A202G	NM_020365	NP_065098	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B,	202					negative regulation of translational initiation in response to stress|oligodendrocyte development|response to glucose stimulus|response to heat|response to peptide hormone stimulus	cytosol|eukaryotic translation initiation factor 2B complex	nucleotidyltransferase activity|protein binding|translation initiation factor activity			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					GTAGAGGTGGGCATCCACAAG	0.388													7	32	---	---	---	---	PASS
MFSD4	148808	broad.mit.edu	37	1	205549915	205549915	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr1:205549915C>A	uc001hcv.3	+	3	642	c.556C>A	c.(556-558)CAT>AAT	p.H186N	MFSD4_uc010prk.1_Intron|MFSD4_uc010prl.1_RNA|MFSD4_uc010prm.1_Missense_Mutation_p.H131N	NM_181644	NP_857595	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing	186					transmembrane transport	integral to membrane				skin(2)|central_nervous_system(1)	3	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CCACCTGTTCCATGTCTCCAG	0.617													4	92	---	---	---	---	PASS
RYR2	6262	broad.mit.edu	37	1	237801684	237801684	+	Silent	SNP	C	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr1:237801684C>T	uc001hyl.1	+	45	6940	c.6820C>T	c.(6820-6822)CTG>TTG	p.L2274L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2274	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGGTTGTGGACTGCAAAGTTG	0.413													8	248	---	---	---	---	PASS
SH3BP5L	80851	broad.mit.edu	37	1	249107303	249107303	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr1:249107303C>A	uc001iew.1	-	6	1148	c.596G>T	c.(595-597)CGG>CTG	p.R199L	SH3BP5L_uc010pzp.1_Missense_Mutation_p.R92L|SH3BP5L_uc010pzq.1_Missense_Mutation_p.R167L|SH3BP5L_uc001iev.1_Missense_Mutation_p.R80L	NM_030645	NP_085148	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	199	Potential.										0	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TTGGCACAGCCGAGTCACTCG	0.637													2	5	---	---	---	---	PASS
NLRC4	58484	broad.mit.edu	37	2	32475161	32475161	+	Missense_Mutation	SNP	A	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr2:32475161A>T	uc002roi.2	-	4	2018	c.1772T>A	c.(1771-1773)ATC>AAC	p.I591N	NLRC4_uc002roj.1_Missense_Mutation_p.I591N|NLRC4_uc010ezt.1_Intron	NM_021209	NP_067032	Q9NPP4	NLRC4_HUMAN	caspase recruitment domain protein 12	591	LRR 3.				activation of caspase activity|defense response to bacterium|detection of bacterium|interleukin-1 beta secretion|positive regulation of apoptosis	cytoplasm	ATP binding|magnesium ion binding|protein homodimerization activity			ovary(3)|large_intestine(1)|lung(1)|skin(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GTAATCGGGGATGTTCCCTGA	0.408													6	245	---	---	---	---	PASS
LTBP1	4052	broad.mit.edu	37	2	33172887	33172887	+	Splice_Site	SNP	T	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr2:33172887T>C	uc002ros.2	+	1	494	c.494_splice	c.e1+2	p.G165_splice		NM_206943	NP_996826	Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding						negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta	proteinaceous extracellular matrix	calcium ion binding|growth factor binding|transforming growth factor beta receptor activity			ovary(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|central_nervous_system(1)	8	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GCTGCAGGGGTAAgcccacac	0.517													2	9	---	---	---	---	PASS
THNSL2	55258	broad.mit.edu	37	2	88478453	88478453	+	Silent	SNP	G	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr2:88478453G>A	uc002ssz.3	+	5	876	c.723G>A	c.(721-723)CAG>CAA	p.Q241Q	THNSL2_uc002ssv.2_RNA|THNSL2_uc002ssw.3_Silent_p.Q241Q|THNSL2_uc002ssx.3_Silent_p.Q209Q|THNSL2_uc002sta.3_Silent_p.Q83Q|THNSL2_uc002ssy.3_Silent_p.Q241Q|THNSL2_uc010fhe.2_Silent_p.Q83Q	NM_018271	NP_060741	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2	241					threonine biosynthetic process		threonine synthase activity			ovary(1)	1						CTTACTTCCAGTGTACGCCAT	0.552													10	447	---	---	---	---	PASS
ANAPC1	64682	broad.mit.edu	37	2	112551673	112551673	+	Silent	SNP	G	A	A	rs141030655	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr2:112551673G>A	uc002thi.2	-	37	4747	c.4500C>T	c.(4498-4500)TCC>TCT	p.S1500S		NM_022662	NP_073153	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	1500	PC 3.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|cytosol|nucleoplasm				skin(2)	2						CATTAGGTGCGGACAAATAAG	0.279													4	23	---	---	---	---	PASS
ULK4	54986	broad.mit.edu	37	3	41939929	41939929	+	Missense_Mutation	SNP	T	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr3:41939929T>A	uc003ckv.3	-	14	1544	c.1343A>T	c.(1342-1344)TAT>TTT	p.Y448F	ULK4_uc003ckw.2_Missense_Mutation_p.Y448F|ULK4_uc003ckx.1_Missense_Mutation_p.Y448F	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	448							ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CCTACCTGAATATGTTGGTAG	0.274													8	212	---	---	---	---	PASS
ULK4	54986	broad.mit.edu	37	3	41939933	41939933	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr3:41939933T>C	uc003ckv.3	-	14	1540	c.1339A>G	c.(1339-1341)ACA>GCA	p.T447A	ULK4_uc003ckw.2_Missense_Mutation_p.T447A|ULK4_uc003ckx.1_Missense_Mutation_p.T447A	NM_017886	NP_060356	Q96C45	ULK4_HUMAN	unc-51-like kinase 4	447							ATP binding|protein serine/threonine kinase activity				0				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CCTGAATATGTTGGTAGATGC	0.279													8	214	---	---	---	---	PASS
CP	1356	broad.mit.edu	37	3	148905905	148905905	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr3:148905905A>C	uc003ewy.3	-	10	2051	c.1798T>G	c.(1798-1800)TTT>GTT	p.F600V	CP_uc011bnr.1_RNA|CP_uc003ewx.3_Missense_Mutation_p.F381V|CP_uc003ewz.2_Missense_Mutation_p.F600V|CP_uc010hvf.1_Missense_Mutation_p.F326V	NM_000096	NP_000087	P00450	CERU_HUMAN	ceruloplasmin precursor	600	Plastocyanin-like 4.|F5/8 type A 2.				cellular iron ion homeostasis|copper ion transport|transmembrane transport	extracellular space	chaperone binding|ferroxidase activity			ovary(1)	1		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GCAGTTGTAAACATTCTAATA	0.343													6	261	---	---	---	---	PASS
ETV5	2119	broad.mit.edu	37	3	185797681	185797681	+	Missense_Mutation	SNP	G	A	A	rs141531791		TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr3:185797681G>A	uc003fpz.2	-	7	822	c.575C>T	c.(574-576)GCG>GTG	p.A192V	ETV5_uc003fpy.2_Missense_Mutation_p.A234V	NM_004454	NP_004445	P41161	ETV5_HUMAN	ets variant gene 5 (ets-related molecule)	192					cellular response to oxidative stress	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding			ovary(2)|skin(2)|breast(1)	5	all_cancers(143;4.06e-12)|Ovarian(172;0.0386)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.62e-24)			TCGGGGGACCGCAAATGTTTG	0.607			T	TMPRSS2|SCL45A3	Prostate 								4	123	---	---	---	---	PASS
DAXX	1616	broad.mit.edu	37	6	33287900	33287900	+	Silent	SNP	C	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr6:33287900C>T	uc003oec.2	-	5	1557	c.1353G>A	c.(1351-1353)GAG>GAA	p.E451E	ZBTB22_uc003oeb.2_5'Flank|ZBTB22_uc010juu.2_5'Flank|DAXX_uc011drd.1_Silent_p.E376E|DAXX_uc011dre.1_Silent_p.E463E|DAXX_uc003oed.2_Silent_p.E451E	NM_001350	NP_001341	Q9UER7	DAXX_HUMAN	death-domain associated protein isoform a	451	Asp/Glu-rich (acidic).|Potential.|Necessary for interaction with USP7.				activation of JUN kinase activity|androgen receptor signaling pathway|apoptosis|induction of apoptosis via death domain receptors|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|regulation of protein ubiquitination|transcription, DNA-dependent	chromosome, centromeric region|cytosol|nucleolus|PML body	androgen receptor binding|heat shock protein binding|p53 binding|protein homodimerization activity|protein N-terminus binding|receptor signaling protein activity|transcription factor binding|ubiquitin protein ligase binding			pancreas(18)|ovary(2)|skin(2)|prostate(1)	23						cttcttcttcctcctcctcct	0.254			Mis|F|N		Pancreatic neuroendocrine tumors								3	91	---	---	---	---	PASS
GABRR2	2570	broad.mit.edu	37	6	89974189	89974189	+	Missense_Mutation	SNP	G	A	A	rs149245573	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr6:89974189G>A	uc003pnb.2	-	8	1111	c.1103C>T	c.(1102-1104)GCG>GTG	p.A368V	GABRR2_uc011dzx.1_Missense_Mutation_p.A244V	NM_002043	NP_002034	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 2	368	Helical; (Potential).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)		GTTGACAGCCGCATACTCCAG	0.597													3	53	---	---	---	---	PASS
ADCY1	107	broad.mit.edu	37	7	45744119	45744119	+	Silent	SNP	C	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr7:45744119C>A	uc003tne.3	+	17	2739	c.2721C>A	c.(2719-2721)CTC>CTA	p.L907L		NM_021116	NP_066939	Q08828	ADCY1_HUMAN	adenylate cyclase 1	907	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	ATP binding|calcium- and calmodulin-responsive adenylate cyclase activity|calmodulin binding|metal ion binding			ovary(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	6					Adenosine(DB00640)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	AAACAAAGCTCATGGAAAAAG	0.498													6	134	---	---	---	---	PASS
PEX1	5189	broad.mit.edu	37	7	92147136	92147136	+	Silent	SNP	G	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr7:92147136G>A	uc003uly.2	-	5	789	c.693C>T	c.(691-693)AAC>AAT	p.N231N	PEX1_uc011khr.1_Silent_p.N23N|PEX1_uc010ley.2_Silent_p.N231N|PEX1_uc011khs.1_Intron|PEX1_uc011kht.1_RNA	NM_000466	NP_000457	O43933	PEX1_HUMAN	peroxin1	231					microtubule-based peroxisome localization|protein import into peroxisome matrix	cytosol|nucleus|peroxisomal membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding|protein complex binding			ovary(1)|central_nervous_system(1)	2	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TCTCTGACTCGTTTTCATTAG	0.363													6	147	---	---	---	---	PASS
CHMP7	91782	broad.mit.edu	37	8	23114023	23114023	+	Silent	SNP	C	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr8:23114023C>T	uc003xdc.2	+	5	1356	c.708C>T	c.(706-708)GAC>GAT	p.D236D	CHMP7_uc011kzs.1_RNA|CHMP7_uc003xdd.2_Silent_p.D126D|CHMP7_uc003xde.2_Silent_p.D94D	NM_152272	NP_689485	Q8WUX9	CHMP7_HUMAN	CHMP family, member 7	236					cellular membrane organization|late endosome to vacuole transport	cytosol|ESCRT III complex	protein transporter activity				0		Prostate(55;0.0513)		Colorectal(74;0.0155)|COAD - Colon adenocarcinoma(73;0.0632)		CAGTCAATGACGTAGATGTTG	0.502													5	299	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413572	68413572	+	RNA	SNP	C	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr9:68413572C>T	uc004aex.2	+	1		c.127C>T								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		CCAGTGGCGCCGGATCTAGGA	0.567													2	4	---	---	---	---	PASS
FAM75C1	441452	broad.mit.edu	37	9	90535283	90535283	+	Missense_Mutation	SNP	T	C	C	rs118048695	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr9:90535283T>C	uc010mqi.2	+	4	490	c.461T>C	c.(460-462)ATG>ACG	p.M154T	FAM75C1_uc004apq.3_Missense_Mutation_p.M137T	NM_001145124	NP_001138596			family with sequence similarity 75, member C1												0						CATGAGCCTATGGAAGATGCT	0.582													5	298	---	---	---	---	PASS
FAM75C1	441452	broad.mit.edu	37	9	90535290	90535290	+	Silent	SNP	T	C	C	rs55701842	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr9:90535290T>C	uc010mqi.2	+	4	497	c.468T>C	c.(466-468)GAT>GAC	p.D156D	FAM75C1_uc004apq.3_Silent_p.D139D	NM_001145124	NP_001138596			family with sequence similarity 75, member C1												0						CTATGGAAGATGCTGCTCCCA	0.592													5	302	---	---	---	---	PASS
MRPL50	54534	broad.mit.edu	37	9	104152773	104152773	+	Missense_Mutation	SNP	T	C	C	rs75793839		TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr9:104152773T>C	uc004bbe.2	-	2	497	c.452A>G	c.(451-453)AAT>AGT	p.N151S	MRPL50_uc011lvj.1_Intron	NM_019051	NP_061924	Q8N5N7	RM50_HUMAN	mitochondrial ribosomal protein L50	151						mitochondrion|ribosome					0		Acute lymphoblastic leukemia(62;0.0559)				GATTTTCAAATTGGGGGGCAG	0.398													6	170	---	---	---	---	PASS
MRPL50	54534	broad.mit.edu	37	9	104152775	104152775	+	Silent	SNP	G	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr9:104152775G>A	uc004bbe.2	-	2	495	c.450C>T	c.(448-450)CCC>CCT	p.P150P	MRPL50_uc011lvj.1_Intron	NM_019051	NP_061924	Q8N5N7	RM50_HUMAN	mitochondrial ribosomal protein L50	150						mitochondrion|ribosome					0		Acute lymphoblastic leukemia(62;0.0559)				TTTTCAAATTGGGGGGCAGAT	0.403													6	172	---	---	---	---	PASS
PCDH15	65217	broad.mit.edu	37	10	56287578	56287578	+	Silent	SNP	G	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr10:56287578G>T	uc001jju.1	-	3	546	c.151C>A	c.(151-153)CGG>AGG	p.R51R	PCDH15_uc010qhq.1_Silent_p.R56R|PCDH15_uc010qhr.1_Silent_p.R51R|PCDH15_uc010qhs.1_Silent_p.R56R|PCDH15_uc010qht.1_Silent_p.R51R|PCDH15_uc010qhu.1_Silent_p.R51R|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Silent_p.R51R|PCDH15_uc010qhw.1_Silent_p.R51R|PCDH15_uc010qhx.1_Silent_p.R51R|PCDH15_uc010qhy.1_Silent_p.R56R|PCDH15_uc010qhz.1_Silent_p.R51R|PCDH15_uc010qia.1_Intron|PCDH15_uc010qib.1_Intron|PCDH15_uc001jjw.2_Silent_p.R51R	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	51	Cadherin 1.|Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				TTACCATTCCGACTTTCTTCA	0.343										HNSCC(58;0.16)			6	123	---	---	---	---	PASS
TSG101	7251	broad.mit.edu	37	11	18524118	18524118	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr11:18524118G>T	uc001mor.2	-	7	681	c.555C>A	c.(553-555)TAC>TAA	p.Y185*	TSG101_uc001mos.1_Nonsense_Mutation_p.Y133*|TSG101_uc009yhs.1_RNA	NM_006292	NP_006283	Q99816	TS101_HUMAN	tumor susceptibility gene 101	185					cell division|cellular membrane organization|endosome transport|interspecies interaction between organisms|non-lytic virus budding|protein transport|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	early endosome|late endosome membrane|multivesicular body|nucleolus|plasma membrane	calcium-dependent protein binding|DNA binding|transcription corepressor activity|ubiquitin binding|ubiquitin protein ligase binding				0						GACAGCCTGGGTAACCACTAA	0.428													6	14	---	---	---	---	PASS
PDE2A	5138	broad.mit.edu	37	11	72301503	72301503	+	Missense_Mutation	SNP	G	A	A	rs341047	byFrequency	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr11:72301503G>A	uc010rrc.1	-	8	914	c.671C>T	c.(670-672)ACC>ATC	p.T224I	PDE2A_uc001oso.2_Missense_Mutation_p.T203I|PDE2A_uc010rra.1_Missense_Mutation_p.T217I|PDE2A_uc001osn.2_Intron|PDE2A_uc010rrb.1_Missense_Mutation_p.T215I|PDE2A_uc010rrd.1_Missense_Mutation_p.T109I	NM_002599	NP_002590	O00408	PDE2A_HUMAN	phosphodiesterase 2A isoform 1	224					platelet activation|signal transduction	cytosol	3',5'-cyclic-AMP phosphodiesterase activity|3',5'-cyclic-GMP phosphodiesterase activity|cGMP binding|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity|metal ion binding			ovary(2)|breast(1)|skin(1)	4			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Sildenafil(DB00203)|Sulindac(DB00605)	GTCGCGGTCGGTGTACGCCGC	0.736													8	9	---	---	---	---	PASS
NARS2	79731	broad.mit.edu	37	11	78277317	78277317	+	Missense_Mutation	SNP	T	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr11:78277317T>C	uc001ozi.2	-	4	750	c.374A>G	c.(373-375)GAT>GGT	p.D125G	NARS2_uc010rsq.1_5'UTR	NM_024678	NP_078954	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial	125					asparaginyl-tRNA aminoacylation	mitochondrial matrix	asparagine-tRNA ligase activity|ATP binding|nucleic acid binding			ovary(2)	2	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GATGGGGAAATCCTGCCAATA	0.363													13	59	---	---	---	---	PASS
IL10RA	3587	broad.mit.edu	37	11	117864125	117864125	+	Silent	SNP	G	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr11:117864125G>A	uc001prv.2	+	4	614	c.537G>A	c.(535-537)ACG>ACA	p.T179T	IL10RA_uc010rxl.1_Silent_p.T159T|IL10RA_uc010rxm.1_Silent_p.T159T|IL10RA_uc010rxn.1_Silent_p.T30T|IL10RA_uc001prw.2_Silent_p.T30T	NM_001558	NP_001549	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha precursor	179	Extracellular (Potential).					integral to membrane|plasma membrane	interleukin-10 receptor activity			ovary(1)	1	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		GAAACTTCACGGTATGGGGTT	0.562													3	83	---	---	---	---	PASS
CPSF2	53981	broad.mit.edu	37	14	92608697	92608697	+	Splice_Site	SNP	T	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr14:92608697T>C	uc001yah.1	+	8	1086	c.849_splice	c.e8+2	p.Q283_splice		NM_017437	NP_059133	Q9P2I0	CPSF2_HUMAN	cleavage and polyadenylation specific factor 2						histone mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	hydrolase activity|protein binding|RNA binding			ovary(2)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.222)		AAGTCCCAGGTTTGTTCTCAT	0.383													5	286	---	---	---	---	PASS
LOC646214	646214	broad.mit.edu	37	15	21938316	21938316	+	RNA	SNP	A	C	C	rs111913251	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr15:21938316A>C	uc010tzj.1	-	1		c.2424T>G				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						aaacctgacaaaaacaagaaa	0.010													4	18	---	---	---	---	PASS
CDAN1	146059	broad.mit.edu	37	15	43022880	43022880	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr15:43022880A>C	uc001zql.2	-	14	2207	c.2090T>G	c.(2089-2091)GTG>GGG	p.V697G	CDAN1_uc001zqj.2_RNA|CDAN1_uc001zqk.2_Missense_Mutation_p.W23G	NM_138477	NP_612486	Q8IWY9	CDAN1_HUMAN	codanin 1	697						integral to membrane	protein binding			ovary(2)	2		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GAGAAACTCCACCAGCCAGGG	0.637													6	41	---	---	---	---	PASS
CSPG4	1464	broad.mit.edu	37	15	75980335	75980335	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr15:75980335C>A	uc002baw.2	-	3	3164	c.3071G>T	c.(3070-3072)AGC>ATC	p.S1024I		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4 precursor	1024	Interaction with COL5A1 (By similarity).|Extracellular (Potential).|Gly/Ser-rich (glycosaminoglycan attachment domain).|CSPG 6.|Interaction with COL6A2 (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			ovary(2)|pancreas(1)	3						GAAGATCCGGCTGATGGTCTG	0.657													4	118	---	---	---	---	PASS
GOLGA6L5	374650	broad.mit.edu	37	15	85055872	85055872	+	RNA	SNP	C	T	T	rs62029638	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr15:85055872C>T	uc002bkm.2	-	6		c.688G>A				NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						CTCCTGTTCACGTAGCCTCTC	0.547													6	10	---	---	---	---	PASS
ATP2C2	9914	broad.mit.edu	37	16	84402275	84402275	+	Silent	SNP	G	C	C	rs62048787	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr16:84402275G>C	uc002fhx.2	+	1	143	c.54G>C	c.(52-54)GGG>GGC	p.G18G	ATP2C2_uc010chj.2_Silent_p.G18G	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	18	Cytoplasmic (Potential).				ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						TCTCGGGCGGGGGCCGCCAGT	0.706													3	9	---	---	---	---	PASS
MUC16	94025	broad.mit.edu	37	19	9075833	9075833	+	Silent	SNP	C	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr19:9075833C>T	uc002mkp.2	-	3	11817	c.11613G>A	c.(11611-11613)GAG>GAA	p.E3871E		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	3872	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						ATTTTTCTTTCTCATTCCAGG	0.448													8	100	---	---	---	---	PASS
PBX4	80714	broad.mit.edu	37	19	19675795	19675795	+	Missense_Mutation	SNP	G	A	A	rs139542458		TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr19:19675795G>A	uc002nmy.2	-	6	873	c.872C>T	c.(871-873)ACG>ATG	p.T291M	PBX4_uc010xqz.1_RNA|PBX4_uc010xra.1_Missense_Mutation_p.T126M	NM_025245	NP_079521	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	291							sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			large_intestine(1)|ovary(1)	2						CCCAACTTCCGTGGTATCCAC	0.527													9	377	---	---	---	---	PASS
CYP2B6	1555	broad.mit.edu	37	19	41497274	41497274	+	Missense_Mutation	SNP	C	T	T	rs8192709	byFrequency	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr19:41497274C>T	uc002opr.1	+	1	71	c.64C>T	c.(64-66)CGC>TGC	p.R22C	CYP2A7_uc002opo.2_Intron	NM_000767	NP_000758	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B,	22					cellular ketone metabolic process|exogenous drug catabolic process|steroid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(1)|skin(1)	2			LUSC - Lung squamous cell carcinoma(20;0.00322)		Bupropion(DB01156)|Butalbital(DB00241)|Carbamazepine(DB00564)|Clopidogrel(DB00758)|Cyclophosphamide(DB00531)|Efavirenz(DB00625)|Ifosfamide(DB01181)|Memantine(DB01043)|Meperidine(DB00454)|Mephenytoin(DB00532)|Methadone(DB00333)|Methylphenobarbital(DB00849)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicotine(DB00184)|Orphenadrine(DB01173)|Phenytoin(DB00252)|Propofol(DB00818)|Ritonavir(DB00503)|Selegiline(DB01037)|Sertraline(DB01104)|Ticlopidine(DB00208)|Troleandomycin(DB01361)	CCTGGTTCAGCGCCACCCTAA	0.592													15	491	---	---	---	---	PASS
NSFL1C	55968	broad.mit.edu	37	20	1433675	1433675	+	Splice_Site	SNP	C	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr20:1433675C>T	uc002wfc.2	-	6	1595	c.647_splice	c.e6+1	p.G216_splice	NSFL1C_uc002wfd.2_Splice_Site_p.G105_splice|NSFL1C_uc002wfe.2_Splice_Site_p.G185_splice|NSFL1C_uc002wff.2_Splice_Site|NSFL1C_uc010gag.2_Translation_Start_Site	NM_016143	NP_057227	Q9UNZ2	NSF1C_HUMAN	p47 protein isoform a							chromosome|Golgi stack|nucleus	lipid binding|protein binding				0						TTTTCACTCACCCTCTGCGGA	0.453													7	354	---	---	---	---	PASS
SLC4A11	83959	broad.mit.edu	37	20	3209652	3209652	+	Missense_Mutation	SNP	A	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr20:3209652A>C	uc002wig.2	-	16	2120	c.2072T>G	c.(2071-2073)GTG>GGG	p.V691G	SLC4A11_uc010zqe.1_Missense_Mutation_p.V718G|SLC4A11_uc002wih.2_RNA|SLC4A11_uc010zqf.1_Missense_Mutation_p.V675G	NM_032034	NP_114423	Q8NBS3	S4A11_HUMAN	solute carrier family 4 member 11	691	Membrane (bicarbonate transporter).				cellular cation homeostasis|fluid transport|phosphoenolpyruvate-dependent sugar phosphotransferase system	basolateral plasma membrane|integral to membrane	bicarbonate transmembrane transporter activity|borate transmembrane transporter activity|hydrogen ion channel activity|inorganic anion exchanger activity|sodium channel activity|sugar:hydrogen symporter activity			ovary(1)	1						AGTGCCCTTCACCAGCCTGCA	0.667													8	25	---	---	---	---	PASS
RAE1	8480	broad.mit.edu	37	20	55948583	55948583	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr20:55948583C>T	uc002xyg.2	+	9	1036	c.695C>T	c.(694-696)GCC>GTC	p.A232V	RAE1_uc010gis.1_Missense_Mutation_p.A185V|RAE1_uc010git.1_Missense_Mutation_p.A232V|RAE1_uc002xyh.2_Missense_Mutation_p.A232V|RAE1_uc002xyi.2_Missense_Mutation_p.A232V	NM_003610	NP_003601	P78406	RAE1L_HUMAN	RAE1 (RNA export 1, S.pombe) homolog	232					carbohydrate metabolic process|glucose transport|mRNA export from nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|cytoskeleton|nuclear outer membrane|nuclear pore	microtubule binding|RNA binding				0	Lung NSC(12;0.00263)|all_lung(29;0.00828)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;3.7e-14)|Epithelial(14;1.07e-09)|all cancers(14;1.11e-08)			ACTGGTTTTGCCCTGGGAAGT	0.398													4	137	---	---	---	---	PASS
C21orf70	85395	broad.mit.edu	37	21	46387079	46387079	+	Missense_Mutation	SNP	C	A	A			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr21:46387079C>A	uc002zgl.2	+	4	501	c.483C>A	c.(481-483)AGC>AGA	p.S161R	C21orf70_uc002zgm.2_Missense_Mutation_p.S146R	NM_058190	NP_478070	Q9NSI2	CU070_HUMAN	hypothetical protein LOC85395	161											0				Colorectal(79;0.248)		AGGCTGGCAGCCGGCGCCAAG	0.716													3	22	---	---	---	---	PASS
XRCC6	2547	broad.mit.edu	37	22	42057337	42057337	+	Missense_Mutation	SNP	C	T	T			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr22:42057337C>T	uc003bao.1	+	12	1595	c.1525C>T	c.(1525-1527)CCC>TCC	p.P509S	XRCC6_uc003bap.1_Missense_Mutation_p.P468S|XRCC6_uc011apc.1_Missense_Mutation_p.P459S|XRCC6_uc003baq.1_Missense_Mutation_p.P509S|XRCC6_uc003bar.1_Missense_Mutation_p.P509S|XRCC6_uc003bas.1_Missense_Mutation_p.P459S	NM_001469	NP_001460	P12956	XRCC6_HUMAN	ATP-dependent DNA helicase II, 70 kDa subunit	509					DNA ligation|double-strand break repair via nonhomologous end joining|initiation of viral infection|negative regulation of transcription, DNA-dependent|positive regulation of transcription from RNA polymerase II promoter|provirus integration|telomere maintenance|transcription, DNA-dependent	DNA-dependent protein kinase-DNA ligase 4 complex|Ku70:Ku80 complex|membrane fraction|nuclear telomere cap complex|transcription factor complex	5'-deoxyribose-5-phosphate lyase activity|ATP binding|ATP-dependent DNA helicase activity|double-stranded DNA binding|protein C-terminus binding|transcription regulatory region DNA binding			skin(2)|ovary(1)|lung(1)|kidney(1)	5						TTTTCTAGTGCCCAAGGTTGA	0.473								Direct_reversal_of_damage|NHEJ					7	250	---	---	---	---	PASS
MAGEB6	158809	broad.mit.edu	37	X	26212305	26212305	+	Silent	SNP	T	G	G	rs4997767	by1000genomes	TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chrX:26212305T>G	uc004dbr.2	+	2	491	c.342T>G	c.(340-342)TCT>TCG	p.S114S	MAGEB6_uc010ngc.1_Intron	NM_173523	NP_775794	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	114	Ser-rich.									ovary(3)	3						CCACTGGCTCTCCTGATGCAG	0.537													3	75	---	---	---	---	PASS
XIST	7503	broad.mit.edu	37	X	73066367	73066367	+	RNA	SNP	T	C	C			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chrX:73066367T>C	uc004ebm.1	-	1		c.6222A>G				NR_001564				Homo sapiens cDNA: FLJ21545 fis, clone COL06195.												0						AGTAGGACCTTATTCACATGG	0.448													6	127	---	---	---	---	PASS
PPP1R3A	5506	broad.mit.edu	37	7	113519968	113519968	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr7:113519968delT	uc010ljy.1	-	4	1210	c.1179delA	c.(1177-1179)AAAfs	p.K393fs		NM_002711	NP_002702	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory (inhibitor)	393					glycogen metabolic process	integral to membrane				lung(9)|ovary(9)|pancreas(7)|skin(6)|breast(2)|prostate(1)	34						CTGAGGAATATTTTTCATTGC	0.393													413	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68413562	68413563	+	RNA	INS	-	G	G	rs71256949		TCGA-CH-5789-01A-11D-1576-08	TCGA-CH-5789-10A-01D-1576-08									Somatic	Phase_I	Capture				Illumina GAIIx	b68c5ec2-0875-4d77-b4b7-738d2b2f313c	ce3a5af9-17c9-4195-8da2-1bee4bac3cac	g.chr9:68413562_68413563insG	uc004aex.2	+	1		c.117_118insG								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		TTCAGCTCCCCCAGTGGCGCCG	0.535													5	3	---	---	---	---	
