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
CACHD1	57685	broad.mit.edu	37	1	65113681	65113681	+	Missense_Mutation	SNP	G	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr1:65113681G>A	uc001dbo.1	+	9	1306	c.1201G>A	c.(1201-1203)GTC>ATC	p.V401I	CACHD1_uc001dbp.1_Missense_Mutation_p.V156I|CACHD1_uc001dbq.1_Missense_Mutation_p.V156I	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	cache domain containing 1	452	Extracellular (Potential).				calcium ion transport	integral to membrane				ovary(2)	2						TGATGAAGCCGTCTTCAGCCT	0.488													3	26	---	---	---	---	0	0	0.004672	0	0
ADCY10	55811	broad.mit.edu	37	1	167829094	167829094	+	Missense_Mutation	SNP	A	G	G			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr1:167829094A>G	uc001ger.2	-	16	2145	c.1847T>C	c.(1846-1848)TTG>TCG	p.L616S	ADCY10_uc009wvk.2_Missense_Mutation_p.L524S|ADCY10_uc010plj.1_Missense_Mutation_p.L463S|ADCY10_uc009wvl.2_Missense_Mutation_p.L615S	NM_018417	NP_060887	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10	616					intracellular signal transduction|spermatogenesis	cytoskeleton|cytosol|perinuclear region of cytoplasm|plasma membrane|soluble fraction	adenylate cyclase activity|ATP binding|magnesium ion binding			central_nervous_system(2)|ovary(1)	3						TTGCTTTTTCAAGGTGCTCAT	0.363													4	174	---	---	---	---	0	0	0.014758	0	0
GPRIN2	9721	broad.mit.edu	37	10	46999058	46999058	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr10:46999058C>T	uc001jec.2	+	3	313	c.178C>T	c.(178-180)CAG>TAG	p.Q60*	GPRIN2_uc010qfq.1_5'Flank	NM_014696	NP_055511	O60269	GRIN2_HUMAN	G protein-regulated inducer of neurite outgrowth	60											0						CACCAGACCCCAGGCCCCGGA	0.701													12	54	---	---	---	---	0	0	0.080935	0	0
NCOA4	8031	broad.mit.edu	37	10	51585100	51585100	+	Missense_Mutation	SNP	T	G	G			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr10:51585100T>G	uc001jis.3	+	8	1402	c.1199T>G	c.(1198-1200)GTA>GGA	p.V400G	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Missense_Mutation_p.V416G|NCOA4_uc010qhd.1_Missense_Mutation_p.V416G|NCOA4_uc010qhe.1_Missense_Mutation_p.V300G|NCOA4_uc010qhf.1_Missense_Mutation_p.V234G|NCOA4_uc001jit.2_Missense_Mutation_p.V400G|NCOA4_uc009xoo.2_Missense_Mutation_p.V400G	NM_001145263	NP_001138735	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	400					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2						CCATGTAAGGTAGAGGAGGTG	0.507			T	RET	papillary thyroid 								6	44	---	---	---	---	0	0	0.093190	0	0
HRAS	3265	broad.mit.edu	37	11	533874	533874	+	Missense_Mutation	SNP	T	C	C	rs121913233		TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr11:533874T>C	uc001lpv.2	-	3	370	c.182A>G	c.(181-183)CAG>CGG	p.Q61R	HRAS_uc010qvw.1_Missense_Mutation_p.Q61R|HRAS_uc010qvx.1_Missense_Mutation_p.Q61R|HRAS_uc010qvy.1_RNA	NM_005343	NP_005334	P01112	RASH_HUMAN	v-Ha-ras Harvey rat sarcoma viral oncogene	61	GTP.		Q -> L (in melanoma; strongly reduced GTP hydrolysis in the presence of RAF1; increases transformation of cultured cell lines).	Q->V: Strongly increased transformation of cultured cell lines.|Q->I: Moderately increased transformation of cultured cell lines.	activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding	p.Q61R(112)|p.Q61L(93)|p.Q61K(39)|p.Q61H(20)|p.Q61P(3)|p.Q61Q(1)|p.Q61E(1)		urinary_tract(174)|thyroid(155)|skin(126)|upper_aerodigestive_tract(112)|soft_tissue(37)|prostate(29)|salivary_gland(24)|cervix(23)|stomach(14)|pituitary(10)|lung(9)|haematopoietic_and_lymphoid_tissue(9)|breast(6)|testis(5)|endometrium(4)|bone(3)|large_intestine(2)|oesophagus(2)|penis(2)|kidney(1)|adrenal_gland(1)|thymus(1)	749		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)	GTACTCCTCCTGGCCGGCGGT	0.597	Q61L(KNS62_LUNG)|Q61L(NCIH1915_LUNG)|Q61L(KYSE30_OESOPHAGUS)	6	Mis		infrequent sarcomas|rare other types	rhadomyosarcoma|ganglioneuroblastoma|bladder			Costello_syndrome	HNSCC(11;0.0054)			33	53	---	---	---	---	0	0	0.064281	0	0
FLI1	2313	broad.mit.edu	37	11	128642762	128642762	+	Silent	SNP	C	T	T			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr11:128642762C>T	uc010sbu.1	+	4	812	c.471C>T	c.(469-471)TCC>TCT	p.S157S	FLI1_uc010sbt.1_Intron|FLI1_uc010sbv.1_Silent_p.S124S|FLI1_uc009zci.2_Silent_p.S91S	NM_002017	NP_002008	Q01543	FLI1_HUMAN	Friend leukemia virus integration 1	157	PNT.				hemostasis|organ morphogenesis	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity		EWSR1/FLI1(2266)	bone(2210)|soft_tissue(48)|autonomic_ganglia(4)|central_nervous_system(4)|lung(3)|ovary(2)|pancreas(2)	2273	all_hematologic(175;0.0641)	Lung NSC(97;0.00588)|all_lung(97;0.00764)|Breast(109;0.0115)|Medulloblastoma(222;0.0523)|all_neural(223;0.0862)|all_hematologic(192;0.182)		OV - Ovarian serous cystadenocarcinoma(99;0.01)|LUSC - Lung squamous cell carcinoma(976;0.0324)|Lung(977;0.0327)		TCGACACATCCTTTTTCCAGA	0.522			T	EWSR1	Ewing sarcoma								4	172	---	---	---	---	0	0	0.009096	0	0
CAPZA3	93661	broad.mit.edu	37	12	18891209	18891209	+	Missense_Mutation	SNP	C	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr12:18891209C>A	uc001rdy.2	+	1	165	c.7C>A	c.(7-9)CTT>ATT	p.L3I	PLCZ1_uc001rdv.3_5'Flank|PLCZ1_uc001rdw.3_5'Flank|PLCZ1_uc010sid.1_5'Flank	NM_033328	NP_201585	Q96KX2	CAZA3_HUMAN	capping protein alpha 3	3					actin cytoskeleton organization|actin filament capping	F-actin capping protein complex	actin binding			ovary(1)|central_nervous_system(1)	2	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				AAACATGACACTTAGCGTGCT	0.438													5	89	---	---	---	---	3.59834e-05	4.65667e-05	0.021553	1	0
C12orf51	283450	broad.mit.edu	37	12	112600941	112600941	+	Missense_Mutation	SNP	C	T	T			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr12:112600941C>T	uc009zwc.2	-	68	11777	c.11759G>A	c.(11758-11760)CGC>CAC	p.R3920H		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)|lung(1)	2						GAACGGGATGCGCTCCTGGTT	0.612													4	103	---	---	---	---	0	0	0.009096	0	0
ARHGEF7	8874	broad.mit.edu	37	13	111862267	111862267	+	Missense_Mutation	SNP	G	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr13:111862267G>A	uc001vrs.2	+	5	699	c.449G>A	c.(448-450)CGC>CAC	p.R150H	ARHGEF7_uc001vrr.2_Missense_Mutation_p.R129H|ARHGEF7_uc001vrt.2_Missense_Mutation_p.R100H|ARHGEF7_uc010tjn.1_Intron|ARHGEF7_uc001vru.1_5'UTR|ARHGEF7_uc001vrv.3_Intron|ARHGEF7_uc001vrw.3_5'UTR|ARHGEF7_uc001vrx.3_5'UTR|ARHGEF7_uc010tjo.1_Missense_Mutation_p.R47H	NM_001113511	NP_001106983	Q14155	ARHG7_HUMAN	PAK-interacting exchange factor beta isoform c	150					apoptosis|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(2)|skin(2)|pancreas(1)|lung(1)|kidney(1)	7	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			TCGTCTCACCGCATAAAGTCT	0.517													5	135	---	---	---	---	0	0	0.014758	0	0
KIAA1409	57578	broad.mit.edu	37	14	94079271	94079271	+	Missense_Mutation	SNP	G	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr14:94079271G>A	uc001ybv.1	+	25	3501	c.3418G>A	c.(3418-3420)GCT>ACT	p.A1140T	KIAA1409_uc001ybs.1_Missense_Mutation_p.A1118T	NM_020818	NP_065869	Q9P2D8	UNC79_HUMAN	hypothetical protein LOC57578	1295						integral to membrane				ovary(10)|skin(4)|large_intestine(3)	17		all_cancers(154;0.0354)|all_epithelial(191;0.216)		Epithelial(152;0.188)		TGAAAGCAGCGCTGAGTCAGA	0.527													22	38	---	---	---	---	0	0	0.076483	0	0
TECPR2	9895	broad.mit.edu	37	14	102901026	102901026	+	Silent	SNP	G	A	A	rs145129878		TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr14:102901026G>A	uc001ylw.1	+	9	2020	c.1872G>A	c.(1870-1872)GCG>GCA	p.A624A	TECPR2_uc010awl.2_Silent_p.A624A|TECPR2_uc010txx.1_Intron	NM_014844	NP_055659	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	624							protein binding			lung(1)|central_nervous_system(1)|skin(1)	3						CTCCTGGGGCGCATGATGGGG	0.567													4	35	---	---	---	---	0	0	0.009096	0	0
AHNAK2	113146	broad.mit.edu	37	14	105409862	105409862	+	Missense_Mutation	SNP	G	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr14:105409862G>A	uc010axc.1	-	7	12046	c.11926C>T	c.(11926-11928)CCG>TCG	p.P3976S	AHNAK2_uc001ypx.2_Missense_Mutation_p.P3876S	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3976						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCGAACGACGGCATCTTGAAC	0.617													5	340	---	---	---	---	0	0	0.029380	0	0
WASH3P	374666	broad.mit.edu	37	15	102515344	102515344	+	Missense_Mutation	SNP	A	C	C	rs141089280	by1000genomes	TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr15:102515344A>C	uc002cdi.2	+	9	1988	c.568A>C	c.(568-570)AAG>CAG	p.K190Q	WASH3P_uc002cdl.2_Missense_Mutation_p.K190Q|WASH3P_uc002cdk.2_RNA|WASH3P_uc002cdp.2_Missense_Mutation_p.K190Q|WASH3P_uc010bpo.2_RNA|WASH3P_uc002cdq.2_RNA|WASH3P_uc002cdr.2_RNA	NR_003659				RecName: Full=WAS protein family homolog 2; AltName: Full=Protein FAM39B; AltName: Full=CXYorf1-like protein on chromosome 2;												0						GCTGGAGAAGAAGCAGCAGAA	0.662													2	14	---	---	---	---	0	0	0.004672	0	0
SF3B3	23450	broad.mit.edu	37	16	70569224	70569224	+	Silent	SNP	A	T	T			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr16:70569224A>T	uc002ezf.2	+	6	937	c.726A>T	c.(724-726)TCA>TCT	p.S242S	SNORD111_uc002ezg.1_5'Flank	NM_012426	NP_036558	Q15393	SF3B3_HUMAN	splicing factor 3b, subunit 3	242					protein complex assembly	catalytic step 2 spliceosome|nucleoplasm|small nuclear ribonucleoprotein complex|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(1)	1		Ovarian(137;0.0694)				CAGGAGGGTCAGATGGTCCAA	0.448													92	140	---	---	---	---	0	0	0.048971	0	0
FLJ36000	284124	broad.mit.edu	37	17	21904125	21904125	+	RNA	SNP	G	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr17:21904125G>A	uc002gza.2	+	1		c.64G>A				NR_027084				Homo sapiens cDNA FLJ36000 fis, clone TESTI2015180.												0						ggagtcgcaaggggccgagca	0													3	41	---	---	---	---	0	0	0.009096	0	0
GIP	2695	broad.mit.edu	37	17	47039134	47039134	+	Missense_Mutation	SNP	G	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr17:47039134G>A	uc002iol.1	-	4	403	c.305C>T	c.(304-306)GCC>GTC	p.A102V		NM_004123	NP_004114	P09681	GIP_HUMAN	gastric inhibitory polypeptide preproprotein	102					energy reserve metabolic process|signal transduction	extracellular region|soluble fraction	hormone activity			skin(1)	1						AGCTTGACTGGCCAGCTCCAG	0.617													3	27	---	---	---	---	0	0	0.014758	0	0
PRODH2	58510	broad.mit.edu	37	19	36303117	36303117	+	Silent	SNP	C	T	T			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr19:36303117C>T	uc002obx.1	-	4	675	c.657G>A	c.(655-657)CGG>CGA	p.R219R		NM_021232	NP_067055	Q9UF12	PROD2_HUMAN	kidney and liver proline oxidase 1	219					glutamate biosynthetic process|proline catabolic process		proline dehydrogenase activity			ovary(2)	2	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCAGGAGGCCCCGTGACAGGT	0.647													22	45	---	---	---	---	0	0	0.062417	0	0
Unknown	0	broad.mit.edu	37	2	89247307	89247307	+	RNA	SNP	C	G	G			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr2:89247307C>G	uc010ytr.1	-	100		c.7877G>C			uc002stl.2_Intron					Parts of antibodies, mostly variable regions.																		TGTGTCCTGACTGGGTCTGAC	0.562													4	105	---	---	---	---	0	0	0.029380	0	0
LCT	3938	broad.mit.edu	37	2	136567521	136567521	+	Missense_Mutation	SNP	C	T	T			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr2:136567521C>T	uc002tuu.1	-	8	2407	c.2396G>A	c.(2395-2397)CGT>CAT	p.R799H		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	799	Extracellular (Potential).|4 X approximate repeats.|2.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|skin(2)|pancreas(1)|lung(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.169)		AATGAGGGAACGAGCAATGTA	0.418													23	47	---	---	---	---	0	0	0.062417	0	0
DDX27	55661	broad.mit.edu	37	20	47845343	47845343	+	Silent	SNP	C	T	T			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr20:47845343C>T	uc002xuh.2	+	8	952	c.891C>T	c.(889-891)CCC>CCT	p.P297P		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	297	Helicase ATP-binding.					nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TGCTAGTGCCCACCCGAGAGC	0.602													46	42	---	---	---	---	0	0	0.045515	0	0
OGFR	11054	broad.mit.edu	37	20	61444704	61444704	+	Silent	SNP	G	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr20:61444704G>A	uc002ydj.2	+	7	1772	c.1737G>A	c.(1735-1737)TCG>TCA	p.S579S	OGFR_uc002ydk.2_Silent_p.S562S|OGFR_uc002ydl.2_Silent_p.S527S|uc011aam.1_Intron	NM_007346	NP_031372	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	579	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].|4.				regulation of cell growth	cytoplasm|membrane|nucleus	opioid receptor activity				0	Breast(26;3.65e-08)					AGAGCCCATCGGAGACCCCAG	0.741													3	9	---	---	---	---	0	0	0.029380	0	0
C21orf99	149992	broad.mit.edu	37	21	14414844	14414844	+	RNA	SNP	T	C	C	rs148060711	by1000genomes	TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr21:14414844T>C	uc002yiy.3	+	2		c.281T>C			C21orf99_uc002yja.3_RNA					Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						ACTGGGCCTGTGCCAATGGCC	0.433													6	49	---	---	---	---	0	0	0.029380	0	0
C21orf99	149992	broad.mit.edu	37	21	14414902	14414902	+	RNA	SNP	G	A	A	rs2821609	by1000genomes	TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr21:14414902G>A	uc002yiy.3	+	2		c.339G>A			C21orf99_uc002yja.3_RNA					Homo sapiens C21orf99 protein (C21orf99) mRNA, complete cds.												0						CCAGCTTGACGTCCTTGATGG	0.443													6	34	---	---	---	---	0	0	0.038147	0	0
LOC96610	96610	broad.mit.edu	37	22	22664639	22664639	+	RNA	SNP	G	A	A	rs9306349	by1000genomes	TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr22:22664639G>A	uc011aim.1	+	31		c.2154G>A			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						CCAGCCTTCTGTAACCCAGTA	0.428													4	17	---	---	---	---	0	0	0.014758	0	0
ANKRD54	129138	broad.mit.edu	37	22	38236241	38236241	+	Missense_Mutation	SNP	G	C	C			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr22:38236241G>C	uc003auc.2	-	2	387	c.329C>G	c.(328-330)GCT>GGT	p.A110G	ANKRD54_uc003aud.2_5'UTR	NM_138797	NP_620152	Q6NXT1	ANR54_HUMAN	ankyrin repeat domain 54	110	ANK 1.										0	Melanoma(58;0.045)					TCTCTTCAGAGCTGTAAAGAG	0.363													3	100	---	---	---	---	0	0	0.004672	0	0
AP3B1	8546	broad.mit.edu	37	5	77452179	77452179	+	Missense_Mutation	SNP	G	C	C			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr5:77452179G>C	uc003kfj.2	-	14	1501	c.1376C>G	c.(1375-1377)GCT>GGT	p.A459G		NM_003664	NP_003655	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1	459					endocytosis|melanosome organization	clathrin coated vesicle membrane|Golgi apparatus|membrane coat	protein phosphatase binding|protein transporter activity			central_nervous_system(1)	1		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		CACACTTTCAGCAACAACTAT	0.294									Hermansky-Pudlak_syndrome				27	43	---	---	---	---	0	0	0.030593	0	0
PCDHB6	56130	broad.mit.edu	37	5	140531461	140531461	+	Missense_Mutation	SNP	C	A	A	rs61730259		TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr5:140531461C>A	uc003lir.2	+	1	1623	c.1623C>A	c.(1621-1623)AGC>AGA	p.S541R	PCDHB6_uc011dah.1_Missense_Mutation_p.S405R	NM_018939	NP_061762	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6 precursor	541	Cadherin 5.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding			skin(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGTTGAGCAGCGAGGCGCTGG	0.682													3	102	---	---	---	---	0.004672	0.00587337	0.004672	1	0
MUC17	140453	broad.mit.edu	37	7	100679466	100679466	+	Missense_Mutation	SNP	C	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr7:100679466C>A	uc003uxp.1	+	3	4822	c.4769C>A	c.(4768-4770)GCT>GAT	p.A1590D	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1590	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|24.					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)					AGTTCTGAGGCTAACACCCTT	0.488													83	173	---	---	---	---	6.11987e-43	8.41483e-43	0.048971	1	0
SLA	6503	broad.mit.edu	37	8	134062170	134062170	+	Missense_Mutation	SNP	T	C	C			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr8:134062170T>C	uc003ytz.2	-	5	1057	c.225A>G	c.(223-225)ATA>ATG	p.I75M	TG_uc003ytw.2_Intron|TG_uc010mdw.2_Intron|TG_uc011ljb.1_Intron|TG_uc011ljc.1_Intron|SLA_uc011lje.1_Missense_Mutation_p.I92M|SLA_uc011ljf.1_Translation_Start_Site|SLA_uc011ljg.1_Missense_Mutation_p.I92M|SLA_uc010mdy.1_Missense_Mutation_p.I75M|SLA_uc010mdz.1_Missense_Mutation_p.I75M|SLA_uc010mea.2_RNA|SLA_uc011ljd.1_Missense_Mutation_p.I115M	NM_001045556	NP_001039021	Q13239	SLAP1_HUMAN	Src-like-adaptor isoform a	75	SH3.					endosome	SH3/SH2 adaptor activity			lung(1)|liver(1)	2	all_epithelial(106;3.51e-21)|Lung NSC(106;4.24e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0279)|Breast(495;0.037)	BRCA - Breast invasive adenocarcinoma(115;0.000701)			TGGCCACACATATTCCAGGGA	0.448													22	33	---	---	---	---	0	0	0.091800	0	0
TMEM38B	55151	broad.mit.edu	37	9	108510354	108510354	+	Silent	SNP	C	T	T			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr9:108510354C>T	uc004bcu.1	+	5	660	c.543C>T	c.(541-543)TAC>TAT	p.Y181Y	TMEM38B_uc010mtn.1_Intron	NM_018112	NP_060582	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	181	Lumenal (Potential).					integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2						TTATTTTCAGCCCTGCCAAGG	0.363													4	58	---	---	---	---	0	0	0.009096	0	0
TSIX	9383	broad.mit.edu	37	X	73043675	73043675	+	RNA	SNP	A	G	G			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chrX:73043675A>G	uc004ebn.2	+	1		c.31636A>G			XIST_uc004ebm.1_RNA	NR_003255				Homo sapiens XIST antisense RNA (non-protein coding) (TSIX), non-coding RNA.												0						TCACACCTATATTACTTCATT	0.368													4	105	---	---	---	---	0	0	0.014758	0	0
Unknown	0	broad.mit.edu	37	1	27976271	27976271	+	IGR	DEL	A	-	-			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr1:27976271delA								FGR (14544 upstream) : IFI6 (16301 downstream)																							AAACTTTTGTAAAAAAAAAAA	0.318													3	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	1	60563282	60563282	+	IGR	DEL	A	-	-			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr1:60563282delA								C1orf87 (23856 upstream) : NFIA (979664 downstream)																							GGTTTGATATAAGAAATTCTT	0.423													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	15	60061388	60061389	+	IGR	DEL	AA	-	-	rs9646206		TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr15:60061388_60061389delAA								BNIP2 (79746 upstream) : FOXB1 (235032 downstream)																							TGCTATTTGTaaaaaaaaaaaa	0.312													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	22253184	22253185	+	IGR	INS	-	A	A	rs2202992		TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr17:22253184_22253185insA								FLJ36000 (340114 upstream) : None (None downstream)																							cgcacagaactaaacagaagca	0.000													10	22	---	---	---	---					
ANKLE1	126549	broad.mit.edu	37	19	17394682	17394682	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr19:17394682delT	uc002nga.2	+	5	1385	c.1109delT	c.(1108-1110)CTCfs	p.L370fs	ANKLE1_uc010xpm.1_RNA|ANKLE1_uc010eao.1_Frame_Shift_Del_p.L392fs|ANKLE1_uc010xpn.1_Frame_Shift_Del_p.L424fs|ANKLE1_uc002nfy.2_Frame_Shift_Del_p.L359fs|ANKLE1_uc002nfz.2_Frame_Shift_Del_p.L76fs	NM_152363	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat domain 41	370	LEM.					nuclear envelope					0						CTGAAGGGACTCCGAGCACTT	0.577													21	39	---	---	---	---					
POLR1B	84172	broad.mit.edu	37	2	113332659	113332661	+	In_Frame_Del	DEL	CCA	-	-			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr2:113332659_113332661delCCA	uc002thw.2	+	15	3341_3343	c.2761_2763delCCA	c.(2761-2763)CCAdel	p.P921del	POLR1B_uc010fkn.2_In_Frame_Del_p.P865del|POLR1B_uc002thx.2_In_Frame_Del_p.P782del|POLR1B_uc010fko.2_In_Frame_Del_p.P738del|POLR1B_uc010fkp.2_In_Frame_Del_p.P360del|POLR1B_uc010yxn.1_In_Frame_Del_p.P959del|POLR1B_uc002thy.2_In_Frame_Del_p.P782del|POLR1B_uc010yxo.1_In_Frame_Del_p.P698del	NM_019014	NP_061887	Q9H9Y6	RPA2_HUMAN	RNA polymerase I polypeptide B isoform 1	921					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1						CCATGGTTTTCCATCCCGCATGA	0.507													40	88	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	99685055	99685056	+	IGR	INS	-	A	A			TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr9:99685055_99685056insA								LOC441454 (12319 upstream) : FAM22G (5536 downstream)																							gactccgtctcaaaaaaaaaaa	0.178													2	4	---	---	---	---					
TMEM8C	389827	broad.mit.edu	37	9	136379889	136379890	+	Frame_Shift_Ins	INS	-	G	G	rs17758315	byFrequency	TCGA-BJ-A2P4-01A-11D-A18F-08	TCGA-BJ-A2P4-10A-01D-A18F-08									Somatic	Phase_I	Capture				Illumina GAIIx	64bb0fec-acc3-43ac-b80d-c267d9fca3e9	464d968e-2efa-4aa0-8483-4cfa938005f7	g.chr9:136379889_136379890insG	uc011mdk.1	-	5	534_535	c.534_535insC	c.(532-537)TATGTCfs	p.Y178fs		NM_001080483	NP_001073952	A6NI61	TMM8C_HUMAN	transmembrane protein 8C	178_179	Helical; (Potential).					integral to membrane					0						AAGCTGTGGACATAAGTGTAGT	0.634													11	46	---	---	---	---					
