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	16974243	16974243	+	RNA	SNP	G	C	C	rs142213352	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr1:16974243G>C	uc009vow.2	+	5		c.1053G>C			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_Intron|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_Intron|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_Intron|MST1P2_uc001azm.3_Intron					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GATCTCAGCTGTCGCTCGGGG	0.652													4	28	---	---	---	---	PASS
OR6K2	81448	broad.mit.edu	37	1	158669837	158669837	+	Silent	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr1:158669837G>T	uc001fsu.1	-	1	606	c.606C>A	c.(604-606)GTC>GTA	p.V202V		NM_001005279	NP_001005279	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K,	202	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			pancreas(1)	1	all_hematologic(112;0.0378)					CTGCATGAATGACATCCACTA	0.483													31	194	---	---	---	---	PASS
PLA2G4A	5321	broad.mit.edu	37	1	186915867	186915867	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr1:186915867G>A	uc001gsc.2	+	11	1337	c.1132G>A	c.(1132-1134)GTT>ATT	p.V378I	PLA2G4A_uc010pos.1_Missense_Mutation_p.V318I	NM_024420	NP_077734	P47712	PA24A_HUMAN	cytosolic phospholipase A2, group IVA	378	PLA2c.				phospholipid catabolic process|platelet activating factor biosynthetic process|platelet activation	cytosol|endoplasmic reticulum membrane	calcium ion binding|calcium-dependent phospholipid binding|lysophospholipase activity			lung(2)|breast(1)	3					Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Medrysone(DB00253)|Quinacrine(DB01103)	GGGAACAGTCGTTAAGAAGTA	0.338													21	117	---	---	---	---	PASS
CELSR3	1951	broad.mit.edu	37	3	48680467	48680467	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr3:48680467G>T	uc003cul.2	-	29	8620	c.8339C>A	c.(8338-8340)GCT>GAT	p.A2780D	CELSR3_uc003cuf.1_Missense_Mutation_p.A2878D|CELSR3_uc010hkf.2_Missense_Mutation_p.A70D|CELSR3_uc010hkg.2_Missense_Mutation_p.A763D	NM_001407	NP_001398	Q9NYQ7	CELR3_HUMAN	cadherin EGF LAG seven-pass G-type receptor 3	2780	Cytoplasmic (Potential).				homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CATCCAGGCAGCCCGAGCATC	0.647													7	54	---	---	---	---	PASS
STAB1	23166	broad.mit.edu	37	3	52544480	52544480	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr3:52544480G>C	uc003dej.2	+	25	2818	c.2744G>C	c.(2743-2745)GGC>GCC	p.G915A		NM_015136	NP_055951	Q9NY15	STAB1_HUMAN	stabilin 1 precursor	915	Extracellular (Potential).|EGF-like 8.				cell adhesion|cell-cell signaling|defense response to bacterium|inflammatory response|negative regulation of angiogenesis|receptor-mediated endocytosis	integral to plasma membrane	bacterial cell surface binding|hyaluronic acid binding|low-density lipoprotein receptor activity|protein disulfide oxidoreductase activity|scavenger receptor activity			large_intestine(3)|upper_aerodigestive_tract(2)|central_nervous_system(1)|breast(1)|skin(1)|pancreas(1)	9				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		ATGAGAGGTGGCTGCCACACC	0.652													6	22	---	---	---	---	PASS
FAM86D	692099	broad.mit.edu	37	3	75476630	75476630	+	Silent	SNP	T	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr3:75476630T>G	uc003dpp.3	-	6	794	c.435A>C	c.(433-435)GTA>GTC	p.V145V	FAM86D_uc003dpo.3_Intron|FAM86D_uc003dps.3_Intron|FAM86D_uc003dpq.3_Silent_p.V53V|FAM86D_uc003dpr.3_Intron	NR_024241				RecName: Full=Protein FAM86B1;												0						GGACCGTCGCTACGTCCCAGT	0.582													6	64	---	---	---	---	PASS
TM4SF18	116441	broad.mit.edu	37	3	149040066	149040066	+	Nonsense_Mutation	SNP	C	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr3:149040066C>A	uc003exa.2	-	5	705	c.568G>T	c.(568-570)GGA>TGA	p.G190*		NM_138786	NP_620141	Q96CE8	T4S18_HUMAN	transmembrane 4 L six family member 18	190	Cytoplasmic (Potential).					integral to membrane				ovary(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GAATAGCTTCCACACAGTATC	0.408													3	83	---	---	---	---	PASS
LYAR	55646	broad.mit.edu	37	4	4276240	4276240	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr4:4276240G>T	uc011bvy.1	-	7	829	c.686C>A	c.(685-687)GCT>GAT	p.A229D	LYAR_uc011bvx.1_Missense_Mutation_p.A112D|LYAR_uc003ght.2_Missense_Mutation_p.A229D	NM_001145725	NP_001139197	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive homolog	229	Lys-rich.					nucleolus	metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CTCAAGGTCAGCCTCCTGTCC	0.453													18	489	---	---	---	---	PASS
GRID2	2895	broad.mit.edu	37	4	94006409	94006409	+	Missense_Mutation	SNP	A	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr4:94006409A>G	uc011cdt.1	+	3	766	c.508A>G	c.(508-510)ATA>GTA	p.I170V	GRID2_uc010ikx.2_Missense_Mutation_p.I170V|GRID2_uc011cdu.1_Intron|GRID2_uc011cdv.1_RNA	NM_001510	NP_001501	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	170	Extracellular (Potential).				glutamate signaling pathway	cell junction|integral to plasma membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(3)|skin(2)|large_intestine(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)	L-Glutamic Acid(DB00142)	GAAATTCATTATATTCTATGA	0.353													4	347	---	---	---	---	PASS
TUBB4Q	56604	broad.mit.edu	37	4	190904645	190904645	+	Missense_Mutation	SNP	G	A	A	rs9995127	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr4:190904645G>A	uc011clg.1	-	4	338	c.335C>T	c.(334-336)ACG>ATG	p.T112M		NM_020040	NP_064424	Q99867	TBB4Q_HUMAN	tubulin, beta polypeptide 4, member Q	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity				0		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;4.1e-31)|Epithelial(3;1.44e-30)|OV - Ovarian serous cystadenocarcinoma(60;2.03e-15)|BRCA - Breast invasive adenocarcinoma(30;8.54e-06)|Lung(3;3.23e-05)|STAD - Stomach adenocarcinoma(60;8.24e-05)|LUSC - Lung squamous cell carcinoma(40;0.000184)|GBM - Glioblastoma multiforme(59;0.00839)|READ - Rectum adenocarcinoma(43;0.155)		CACTGACTCCGTCAGCTCCGC	0.622													4	23	---	---	---	---	PASS
PCDHB14	56122	broad.mit.edu	37	5	140605206	140605206	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr5:140605206C>T	uc003ljb.2	+	1	2129	c.2129C>T	c.(2128-2130)GCG>GTG	p.A710V	PCDHB14_uc011dal.1_Missense_Mutation_p.A557V	NM_018934	NP_061757	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14 precursor	710	Helical; (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGTTCGTGGCGGTGCGGCTG	0.706													23	163	---	---	---	---	PASS
PCDHGA6	56109	broad.mit.edu	37	5	140755446	140755446	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr5:140755446G>T	uc003ljy.1	+	1	1796	c.1796G>T	c.(1795-1797)GGC>GTC	p.G599V	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc011dau.1_Missense_Mutation_p.G599V	NM_018919	NP_061742	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6 isoform 1	599	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGACTCGGGCCAGAACGCC	0.706													8	70	---	---	---	---	PASS
SLC36A2	153201	broad.mit.edu	37	5	150701741	150701741	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr5:150701741C>T	uc003lty.2	-	9	1176	c.1046G>A	c.(1045-1047)GGC>GAC	p.G349D	GM2A_uc011dcs.1_Intron|SLC36A2_uc003ltz.2_RNA|SLC36A2_uc003lua.2_Missense_Mutation_p.G151D|SLC36A2_uc010jhv.2_Missense_Mutation_p.G349D	NM_181776	NP_861441	Q495M3	S36A2_HUMAN	solute carrier family 36, member 2	349	Extracellular (Potential).				cellular nitrogen compound metabolic process	cytoplasm|integral to membrane|plasma membrane	glycine transmembrane transporter activity			ovary(1)|central_nervous_system(1)	2		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCACAGGATGCCGGCAATGTA	0.562													3	80	---	---	---	---	PASS
SERPINB9	5272	broad.mit.edu	37	6	2896330	2896330	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr6:2896330G>A	uc003mug.2	-	3	384	c.263C>T	c.(262-264)ACG>ATG	p.T88M	uc003mue.2_Intron	NM_004155	NP_004146	P50453	SPB9_HUMAN	serpin peptidase inhibitor, clade B, member 9	88					anti-apoptosis|cellular response to estrogen stimulus|immune response|mast cell mediated immunity|regulation of proteolysis	cytosol|extracellular space|nucleus	caspase inhibitor activity|protease binding|serine-type endopeptidase inhibitor activity				0	Ovarian(93;0.0412)	all_hematologic(90;0.108)				CCTGTTGGCCGTTCTCAGCAG	0.443													6	206	---	---	---	---	PASS
C6orf165	154313	broad.mit.edu	37	6	88138375	88138375	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr6:88138375C>G	uc003plv.2	+	9	1084	c.992C>G	c.(991-993)ACC>AGC	p.T331S	C6orf165_uc003plw.2_Missense_Mutation_p.T143S|C6orf165_uc010kbv.1_RNA|C6orf165_uc003plu.1_Missense_Mutation_p.T331S	NM_001031743	NP_001026913	Q8IYR0	CF165_HUMAN	hypothetical protein LOC154313 isoform 1	331										central_nervous_system(1)	1		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		ACTCTGTGGACCAGCTTGCAA	0.368													35	346	---	---	---	---	PASS
ATG5	9474	broad.mit.edu	37	6	106764041	106764041	+	Nonsense_Mutation	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr6:106764041G>A	uc003prf.2	-	2	396	c.43C>T	c.(43-45)CGA>TGA	p.R15*	ATG5_uc010kdb.2_Nonsense_Mutation_p.R15*|ATG5_uc003prg.2_Translation_Start_Site|ATG5_uc010kdc.2_Nonsense_Mutation_p.R15*	NM_004849	NP_004840	Q9H1Y0	ATG5_HUMAN	APG5 autophagy 5-like	15					apoptosis|autophagic vacuole assembly|negative regulation of type I interferon production|post-translational protein modification	autophagic vacuole|pre-autophagosomal structure membrane	protein binding			large_intestine(1)	1	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		GTTGGAATTCGTCCAAACCAC	0.378													42	234	---	---	---	---	PASS
CYP3A43	64816	broad.mit.edu	37	7	99441785	99441785	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr7:99441785C>A	uc003urx.1	+	4	341	c.238C>A	c.(238-240)CCC>ACC	p.P80T	CYP3A43_uc003ury.1_Missense_Mutation_p.P80T|CYP3A43_uc003urz.1_Missense_Mutation_p.P80T|CYP3A43_uc003usa.1_RNA|CYP3A43_uc010lgi.1_Intron|CYP3A43_uc003usb.1_Intron	NM_057095	NP_476436	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A,	80			YGTHSHKLFKKLGIPGPTPLPFLGTILFYLRGLWNFDRECN EKYGEMWGLYEGQQPMLVIMDPD -> LGPIHINFLRSWEF LGQPLCLFWELFCSTLGVFGILTENVMKNTEKCGGCMRGNS PCWSSWIPT (in allele CYP3A43*2).		xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding			ovary(1)|skin(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Cetirizine(DB00341)|Doxycycline(DB00254)	GGGGCAACAGCCCATGCTGGT	0.458													4	82	---	---	---	---	PASS
PVRIG	79037	broad.mit.edu	37	7	99817859	99817859	+	Missense_Mutation	SNP	A	G	G	rs2906645	byFrequency	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr7:99817859A>G	uc003uue.2	+	4	613	c.241A>G	c.(241-243)AAC>GAC	p.N81D	GATS_uc003uty.3_Intron|GATS_uc003utz.3_Intron|GATS_uc003uua.3_Intron|GATS_uc010lgt.2_Intron|GATS_uc011kjl.1_Intron|GATS_uc010lgu.2_Intron|PVRIG_uc003uuf.1_Missense_Mutation_p.N81D	NM_024070	NP_076975	Q6DKI7	PVRIG_HUMAN	poliovirus receptor related immunoglobulin	81						integral to membrane				skin(2)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GGGGGGCCCCAACGGTGCTGG	0.662													8	7	---	---	---	---	PASS
AGK	55750	broad.mit.edu	37	7	141315346	141315346	+	Nonsense_Mutation	SNP	G	T	T	rs141323107		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr7:141315346G>T	uc003vwi.2	+	8	670	c.499G>T	c.(499-501)GAA>TAA	p.E167*	AGK_uc011krg.1_RNA	NM_018238	NP_060708	Q53H12	AGK_HUMAN	acylglycerol kinase precursor	167	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)					CCTCTTTGCCGAAAGTGGAAA	0.443													64	323	---	---	---	---	PASS
AGK	55750	broad.mit.edu	37	7	141315347	141315347	+	Missense_Mutation	SNP	A	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr7:141315347A>T	uc003vwi.2	+	8	671	c.500A>T	c.(499-501)GAA>GTA	p.E167V	AGK_uc011krg.1_RNA	NM_018238	NP_060708	Q53H12	AGK_HUMAN	acylglycerol kinase precursor	167	DAGKc.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway	mitochondrial membrane	acylglycerol kinase activity|ATP binding|diacylglycerol kinase activity|NAD+ kinase activity			ovary(1)|breast(1)	2	Melanoma(164;0.0171)					CTCTTTGCCGAAAGTGGAAAC	0.443													68	321	---	---	---	---	PASS
NSMAF	8439	broad.mit.edu	37	8	59515931	59515931	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr8:59515931C>T	uc003xtt.2	-	13	1097	c.883G>A	c.(883-885)GAG>AAG	p.E295K	NSMAF_uc011lee.1_Missense_Mutation_p.E326K|NSMAF_uc003xtu.2_Missense_Mutation_p.E295K	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation	295	BEACH.				ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)				GCAGTGTGCTCCGCCACATGG	0.552													23	106	---	---	---	---	PASS
MTSS1	9788	broad.mit.edu	37	8	125597387	125597387	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr8:125597387C>T	uc003yrk.2	-	6	935	c.401G>A	c.(400-402)CGC>CAC	p.R134H	MTSS1_uc003yrj.2_Missense_Mutation_p.R134H|MTSS1_uc003yrl.2_Missense_Mutation_p.R134H	NM_014751	NP_055566	O43312	MTSS1_HUMAN	metastasis suppressor 1	134	IMD.|Potential.				actin cytoskeleton organization|cell adhesion|cellular component movement|filopodium assembly|transmembrane receptor protein tyrosine kinase signaling pathway	actin cytoskeleton|endocytic vesicle|ruffle	actin monomer binding|cytoskeletal adaptor activity|receptor binding|SH3 domain binding			ovary(1)	1	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			TATCTCTTGGCGGGCTTTCTT	0.363													57	305	---	---	---	---	PASS
KANK1	23189	broad.mit.edu	37	9	712060	712060	+	Missense_Mutation	SNP	G	C	C	rs4465020	byFrequency	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr9:712060G>C	uc003zgl.1	+	7	1943	c.1294G>C	c.(1294-1296)GAG>CAG	p.E432Q	KANK1_uc003zgm.2_Missense_Mutation_p.E432Q|KANK1_uc003zgn.1_Missense_Mutation_p.E432Q|KANK1_uc003zgo.1_Missense_Mutation_p.E432Q|KANK1_uc003zgp.1_Missense_Mutation_p.E432Q|KANK1_uc003zgq.2_Missense_Mutation_p.E274Q|KANK1_uc003zgr.1_Missense_Mutation_p.E274Q|KANK1_uc003zgs.1_Missense_Mutation_p.E274Q	NM_015158	NP_055973	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1 isoform a	432					negative regulation of actin filament polymerization	cytoplasm				ovary(2)|central_nervous_system(1)|pancreas(1)	4		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GACACTTGTTGAGATGAGAAA	0.522													3	121	---	---	---	---	PASS
ADAMTSL1	92949	broad.mit.edu	37	9	18662047	18662047	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr9:18662047G>A	uc003zne.3	+	9	1188	c.1061G>A	c.(1060-1062)TGC>TAC	p.C354Y	ADAMTSL1_uc003znb.2_Missense_Mutation_p.C354Y|ADAMTSL1_uc003znc.3_Missense_Mutation_p.C354Y	NM_001040272	NP_001035362	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1 isoform 4 precursor	354						proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(3)|upper_aerodigestive_tract(1)|lung(1)	5				GBM - Glioblastoma multiforme(50;1.29e-17)		CTTCAGGAGTGCAACTTGGAT	0.408													38	209	---	---	---	---	PASS
FAM27A	548321	broad.mit.edu	37	9	45728087	45728087	+	RNA	SNP	A	G	G	rs149365398	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr9:45728087A>G	uc004adn.3	+	2		c.507A>G				NR_024060				Homo sapiens cDNA FLJ27519 fis, clone TST09087.												0						CTCCCTGGACAAGCCACCCTT	0.597													3	4	---	---	---	---	PASS
ZNF438	220929	broad.mit.edu	37	10	31133925	31133925	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr10:31133925C>G	uc010qdz.1	-	8	2887	c.2452G>C	c.(2452-2454)GGA>CGA	p.G818R	ZNF438_uc001ivn.2_Missense_Mutation_p.G769R|ZNF438_uc010qdy.1_Missense_Mutation_p.G808R|ZNF438_uc001ivo.3_Missense_Mutation_p.G382R|ZNF438_uc009xlg.2_Missense_Mutation_p.G818R|ZNF438_uc001ivp.3_Missense_Mutation_p.G808R|ZNF438_uc010qea.1_Missense_Mutation_p.G818R|ZNF438_uc010qeb.1_Missense_Mutation_p.G818R	NM_182755	NP_877432	Q7Z4V0	ZN438_HUMAN	zinc finger protein 438 isoform a	818					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|breast(1)	2		Prostate(175;0.0587)				TCGATCACTCCCTGGTTGGAG	0.542													80	364	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73270958	73270958	+	Missense_Mutation	SNP	C	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr10:73270958C>A	uc001jrx.3	+	6	795	c.418C>A	c.(418-420)CGC>AGC	p.R140S	CDH23_uc001jrw.3_Missense_Mutation_p.R140S|CDH23_uc001jrv.2_Missense_Mutation_p.R135S|CDH23_uc009xql.2_Missense_Mutation_p.R185S	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	140	Cadherin 2.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						CTACAGCGTCCGCATCCCTGA	0.572													3	57	---	---	---	---	PASS
TNKS2	80351	broad.mit.edu	37	10	93600428	93600428	+	Silent	SNP	A	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr10:93600428A>G	uc001khp.2	+	14	1935	c.1638A>G	c.(1636-1638)CTA>CTG	p.L546L		NM_025235	NP_079511	Q9H2K2	TNKS2_HUMAN	tankyrase, TRF1-interacting ankyrin-related	546	ANK 10.				positive regulation of canonical Wnt receptor signaling pathway|protein auto-ADP-ribosylation|protein localization to chromosome, telomeric region|protein polyubiquitination|Wnt receptor signaling pathway	Golgi membrane|microsome|nuclear envelope|pericentriolar material|perinuclear region of cytoplasm	NAD+ ADP-ribosyltransferase activity|protein binding			kidney(3)|skin(3)|ovary(1)|lung(1)	8		Colorectal(252;0.162)				AATATCTGCTACAGCATGGAG	0.433													7	330	---	---	---	---	PASS
PKD2L1	9033	broad.mit.edu	37	10	102051147	102051147	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr10:102051147C>T	uc001kqx.1	-	12	2301	c.1918G>A	c.(1918-1920)GCC>ACC	p.A640T	PKD2L1_uc009xwm.1_Missense_Mutation_p.A593T	NM_016112	NP_057196	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	640	Cytoplasmic (Potential).				signal transduction	integral to membrane	calcium activated cation channel activity|calcium ion binding|cytoskeletal protein binding			ovary(4)	4		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		GTGAAGGTGGCCGTGAGCTCA	0.507													4	168	---	---	---	---	PASS
MUC6	4588	broad.mit.edu	37	11	1019457	1019457	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr11:1019457G>A	uc001lsw.2	-	30	3899	c.3848C>T	c.(3847-3849)ACA>ATA	p.T1283I		NM_005961	NP_005952	Q6W4X9	MUC6_HUMAN	mucin 6, gastric	1283	Pro-rich.|Thr-rich.				maintenance of gastrointestinal epithelium	extracellular region	extracellular matrix structural constituent			ovary(1)	1		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CAGCCCTGATGTGGCTTGTGG	0.642													5	188	---	---	---	---	PASS
OR52E6	390078	broad.mit.edu	37	11	5862984	5862984	+	Missense_Mutation	SNP	G	C	C	rs10769272	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr11:5862984G>C	uc010qzq.1	-	1	144	c.144C>G	c.(142-144)TTC>TTG	p.F48L	TRIM5_uc001mbq.1_Intron	NM_001005167	NP_001005167	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E,	48	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGATCACAAAGAAGATAGCAG	0.483													3	184	---	---	---	---	PASS
RPS6KB2	6199	broad.mit.edu	37	11	67196653	67196653	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr11:67196653G>A	uc001old.2	+	3	264	c.182G>A	c.(181-183)CGC>CAC	p.R61H	RPS6KB2_uc001olf.2_5'UTR|RPS6KB2_uc001olg.2_Missense_Mutation_p.R61H|RPS6KB2_uc009yrq.2_5'UTR|RPS6KB2_uc001ole.2_RNA|RPS6KB2_uc001olh.2_RNA|RPS6KB2_uc009yrr.2_5'Flank	NM_003952	NP_003943	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide	61					nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of translational initiation|translation	nucleoplasm	ATP binding|protein serine/threonine kinase activity			ovary(2)|central_nervous_system(2)|stomach(1)|lung(1)|salivary_gland(1)	7			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			GGCCCAGAGCGCATCGGGCCC	0.622													4	192	---	---	---	---	PASS
HEPHL1	341208	broad.mit.edu	37	11	93754497	93754497	+	Translation_Start_Site	SNP	C	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr11:93754497C>A	uc001pep.2	+	1	120	c.-37C>A	c.(-39--35)CCCTG>CCATG			NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1 precursor						copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity			ovary(3)	3		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				GATTTGTCCCCTGTGCAGGCT	0.577													3	92	---	---	---	---	PASS
RPL13AP20	387841	broad.mit.edu	37	12	13028751	13028751	+	Missense_Mutation	SNP	G	C	C			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr12:13028751G>C	uc010sho.1	+	1	341	c.319G>C	c.(319-321)GGC>CGC	p.G107R		NR_003932				SubName: Full=Ribosomal protein L13a variant; Flags: Fragment;												0						GGTGTTTGACGGCATCCCACC	0.612													3	21	---	---	---	---	PASS
ATF7IP	55729	broad.mit.edu	37	12	14628823	14628823	+	Splice_Site	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr12:14628823G>T	uc001rbw.2	+	11	3021	c.2863_splice	c.e11-1	p.C955_splice	ATF7IP_uc001rbu.2_Splice_Site_p.C955_splice|ATF7IP_uc001rbv.1_Splice_Site_p.C954_splice|ATF7IP_uc001rbx.2_Splice_Site_p.C954_splice|ATF7IP_uc001rby.3_Splice_Site_p.C955_splice|ATF7IP_uc001rca.2_Splice_Site_p.C955_splice	NM_018179	NP_060649	Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting						DNA methylation|interspecies interaction between organisms|positive regulation of transcription, DNA-dependent|regulation of RNA polymerase II transcriptional preinitiation complex assembly|transcription, DNA-dependent		protein binding			lung(3)|ovary(1)|skin(1)	5						TTGTTTTTCAGTGTGGAAAAG	0.363													18	101	---	---	---	---	PASS
LST-3TM12	338821	broad.mit.edu	37	12	21196342	21196342	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr12:21196342G>T	uc010sin.1	+	6	661	c.661G>T	c.(661-663)GTA>TTA	p.V221L	SLCO1B3_uc010sil.1_Intron|LST-3TM12_uc010sim.1_Missense_Mutation_p.V268L	NM_001009562	NP_001009562	Q71QF0	Q71QF0_HUMAN	liver-specific organic anion transporter 3TM12	221						membrane	transporter activity				0						GTCTGGAATAGTATCCATTAT	0.373													11	213	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	19857036	19857036	+	RNA	SNP	A	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr14:19857036A>G	uc001vvq.1	-	5		c.494T>C								Homo sapiens cDNA FLJ12852 fis, clone NT2RP2003445.																		CTGGATAATAAAGTTCATCTC	0.373													10	190	---	---	---	---	PASS
MYH7	4625	broad.mit.edu	37	14	23901077	23901077	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr14:23901077C>T	uc001wjx.2	-	7	638	c.532G>A	c.(532-534)GGA>AGA	p.G178R		NM_000257	NP_000248	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	178	ATP.|Myosin head-like.				adult heart development|muscle filament sliding|regulation of heart rate|ventricular cardiac muscle tissue morphogenesis	focal adhesion|muscle myosin complex|myosin filament|nucleus|sarcomere	actin binding|actin-dependent ATPase activity|ATP binding|calmodulin binding|microfilament motor activity|structural constituent of muscle			ovary(3)|skin(1)	4	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		CCGGATTCTCCGCTGTGAAGA	0.547													22	92	---	---	---	---	PASS
FMN1	342184	broad.mit.edu	37	15	33261343	33261343	+	Silent	SNP	T	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr15:33261343T>G	uc001zhf.3	-	4	1890	c.1890A>C	c.(1888-1890)GCA>GCC	p.A630A		NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1	853					actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TTGGCTGGAGTGCTGCATGGA	0.532													8	34	---	---	---	---	PASS
CAPN3	825	broad.mit.edu	37	15	42676689	42676689	+	Silent	SNP	C	T	T	rs117609395	byFrequency	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr15:42676689C>T	uc001zpn.1	+	2	624	c.318C>T	c.(316-318)TGC>TGT	p.C106C	CAPN3_uc001zpk.1_5'UTR|CAPN3_uc001zpl.1_Silent_p.C19C|CAPN3_uc010udf.1_Silent_p.C19C|CAPN3_uc010udg.1_Silent_p.C19C|CAPN3_uc001zpo.1_Silent_p.C106C|CAPN3_uc001zpp.1_Silent_p.C106C	NM_000070	NP_000061	P20807	CAN3_HUMAN	calpain 3 isoform a	106	Calpain catalytic.				muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			central_nervous_system(1)	1		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AGGAAATTTGCGAGAATCCCC	0.323													4	183	---	---	---	---	PASS
SQRDL	58472	broad.mit.edu	37	15	45965849	45965849	+	Silent	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr15:45965849G>T	uc001zvt.2	+	6	693	c.504G>T	c.(502-504)TCG>TCT	p.S168S	SQRDL_uc001zvu.2_Silent_p.S168S|SQRDL_uc001zvv.2_Silent_p.S168S	NM_021199	NP_067022	Q9Y6N5	SQRD_HUMAN	sulfide dehydrogenase like precursor	168							oxidoreductase activity			ovary(1)	1		Lung NSC(122;0.000117)|all_lung(180;0.000737)|Melanoma(134;0.0417)		all cancers(107;5.89e-18)|GBM - Glioblastoma multiforme(94;1.21e-06)|COAD - Colon adenocarcinoma(120;0.17)|Colorectal(133;0.188)		AAATAGGGTCGAATTATTCAG	0.398													60	278	---	---	---	---	PASS
KIF23	9493	broad.mit.edu	37	15	69740133	69740133	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr15:69740133G>A	uc002asb.2	+	23	2987	c.2870G>A	c.(2869-2871)CGC>CAC	p.R957H	KIF23_uc002asc.2_Missense_Mutation_p.R853H|KIF23_uc010bii.2_Missense_Mutation_p.R763H|KIF23_uc010ukc.1_Missense_Mutation_p.R670H	NM_138555	NP_612565	Q02241	KIF23_HUMAN	kinesin family member 23 isoform 1	957					blood coagulation|cytokinesis|microtubule-based movement|mitosis|mitotic spindle elongation	cytosol|kinesin complex|microtubule|midbody|nucleoplasm|spindle	ATP binding|microtubule motor activity|protein binding				0						TGTTTTAGGCGCAAAAAGCCA	0.398													4	217	---	---	---	---	PASS
JPH3	57338	broad.mit.edu	37	16	87678351	87678351	+	Silent	SNP	C	T	T	rs144950183	byFrequency	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr16:87678351C>T	uc002fkd.2	+	2	1124	c.870C>T	c.(868-870)GGC>GGT	p.G290G	JPH3_uc010vou.1_RNA	NM_020655	NP_065706	Q8WXH2	JPH3_HUMAN	junctophilin 3	290	Cytoplasmic (Potential).|MORN 7.				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane|plasma membrane	protein binding			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0287)		CCTACGTGGGCGAGTGGAAGA	0.672													4	90	---	---	---	---	PASS
TRPV2	51393	broad.mit.edu	37	17	16321054	16321054	+	Missense_Mutation	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr17:16321054G>T	uc002gpy.2	+	2	439	c.72G>T	c.(70-72)GAG>GAT	p.E24D	TRPV2_uc002gpz.2_Translation_Start_Site	NM_016113	NP_057197	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel,	24	Cytoplasmic (Potential).|Required for interaction with SLC50A1 (By similarity).				sensory perception	integral to plasma membrane|melanosome	calcium channel activity			ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		ATGGCTCTGAGGCGGACAGAG	0.577													4	109	---	---	---	---	PASS
CRLF3	51379	broad.mit.edu	37	17	29111372	29111372	+	Missense_Mutation	SNP	T	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr17:29111372T>G	uc002hfr.3	-	8	1271	c.1162A>C	c.(1162-1164)ACT>CCT	p.T388P	CRLF3_uc010wbr.1_Missense_Mutation_p.T272P	NM_015986	NP_057070	Q8IUI8	CRLF3_HUMAN	cytokine receptor-like factor 3	388					negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|positive regulation of cell cycle arrest|positive regulation of JAK-STAT cascade|positive regulation of transcription from RNA polymerase II promoter	cytoplasm					0		all_hematologic(16;0.014)|Acute lymphoblastic leukemia(14;0.0236)|Myeloproliferative disorder(56;0.0255)				GTTCCTAGAGTCACGGCTTCA	0.388													3	137	---	---	---	---	PASS
ACACA	31	broad.mit.edu	37	17	35600381	35600381	+	Missense_Mutation	SNP	C	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr17:35600381C>T	uc002hnm.2	-	22	2917	c.2726G>A	c.(2725-2727)CGC>CAC	p.R909H	ACACA_uc002hnk.2_Missense_Mutation_p.R831H|ACACA_uc002hnl.2_Missense_Mutation_p.R851H|ACACA_uc002hnn.2_Missense_Mutation_p.R909H|ACACA_uc002hno.2_Missense_Mutation_p.R946H|ACACA_uc010cuz.2_Missense_Mutation_p.R909H	NM_198836	NP_942133	Q13085	ACACA_HUMAN	acetyl-Coenzyme A carboxylase alpha isoform 2	909					acetyl-CoA metabolic process|energy reserve metabolic process|fatty acid biosynthetic process|long-chain fatty-acyl-CoA biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|triglyceride biosynthetic process	cytosol	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			large_intestine(1)|ovary(1)	2		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	GGGGGGAATGCGGCCAGACAC	0.473													6	475	---	---	---	---	PASS
COIL	8161	broad.mit.edu	37	17	55028287	55028287	+	Missense_Mutation	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr17:55028287G>A	uc002iuu.2	-	2	347	c.316C>T	c.(316-318)CTT>TTT	p.L106F		NM_004645	NP_004636	P38432	COIL_HUMAN	coilin	106						Cajal body|nucleolus	protein C-terminus binding			ovary(1)	1	Breast(9;6.15e-08)					GCTTTTCTAAGAGATAAATTA	0.378													4	230	---	---	---	---	PASS
CD79B	974	broad.mit.edu	37	17	62007651	62007651	+	Silent	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr17:62007651G>A	uc002jdq.1	-	3	296	c.213C>T	c.(211-213)TCC>TCT	p.S71S	CD79B_uc002jdo.1_Silent_p.S45S|CD79B_uc002jdp.1_Silent_p.S72S|CD79B_uc002jdr.1_Intron	NM_000626	NP_000617	P40259	CD79B_HUMAN	CD79B antigen isoform 1 precursor	71	Extracellular (Potential).|Ig-like V-type.				cell surface receptor linked signaling pathway|immune response	Golgi apparatus|integral to plasma membrane|nucleus	transmembrane receptor activity				0						TCACATTGCCGGAGGCGCTGT	0.567			Mis|O		DLBCL								12	88	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40384050	40384050	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr19:40384050C>G	uc002omp.3	-	21	9568	c.9560G>C	c.(9559-9561)GGC>GCC	p.G3187A		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	3187	TIL 7.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCACTGGCAGCCCTCCACACA	0.662													12	21	---	---	---	---	PASS
SIRPB1	10326	broad.mit.edu	37	20	1559075	1559075	+	Silent	SNP	G	A	A	rs142943219		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr20:1559075G>A	uc010gai.2	-	2	441	c.342C>T	c.(340-342)GAC>GAT	p.D114D	SIRPB1_uc002wfk.3_Silent_p.D114D	NM_006065	NP_006056	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1 isoform 1	114	Extracellular (Potential).|Ig-like V-type.				cell junction assembly|cell surface receptor linked signaling pathway	integral to plasma membrane	protein binding			ovary(1)	1						AGGTGCCGGCGTCTGCTGGGG	0.522													9	289	---	---	---	---	PASS
LOC96610	96610	broad.mit.edu	37	22	22664606	22664606	+	RNA	SNP	A	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr22:22664606A>G	uc011aim.1	+	31		c.2121A>G			LOC96610_uc011aiq.1_RNA					Parts of antibodies, mostly variable regions.												0						GTCTTCATGCAAACTTGGTAT	0.398													3	52	---	---	---	---	PASS
PARVB	29780	broad.mit.edu	37	22	44527372	44527372	+	Missense_Mutation	SNP	C	G	G			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr22:44527372C>G	uc003ben.2	+	5	434	c.382C>G	c.(382-384)CTG>GTG	p.L128V	PARVB_uc003bem.2_Missense_Mutation_p.L161V|PARVB_uc010gzn.2_Missense_Mutation_p.L76V|PARVB_uc003beo.2_Missense_Mutation_p.L91V	NM_013327	NP_037459	Q9HBI1	PARVB_HUMAN	parvin, beta isoform b	128	CH 1.				cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)				TGCAGAAAAACTGGCAGGGTG	0.388													7	78	---	---	---	---	PASS
MIR509-3	100126337	broad.mit.edu	37	X	146341191	146341191	+	RNA	SNP	C	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chrX:146341191C>T	hsa-mir-509-3|MI0005717	-			c.54C>T			MIR509-2_hsa-mir-509-2|MI0005530_5'Flank																	0						TACCCACAGACGTACCAATCA	0.463													81	126	---	---	---	---	PASS
BMP2K	55589	broad.mit.edu	37	4	79792164	79792166	+	In_Frame_Del	DEL	CAC	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	49224380-bffd-4048-93a7-fb4b19285c35	05c383c1-ef34-477c-b518-2b48a62f2443	g.chr4:79792164_79792166delCAC	uc003hlk.2	+	11	1625_1627	c.1459_1461delCAC	c.(1459-1461)CACdel	p.H494del	BMP2K_uc010ijl.1_RNA|BMP2K_uc003hlj.2_In_Frame_Del_p.H494del|BMP2K_uc003hll.2_5'Flank	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a	494	Gln/His-rich.					nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1						gcagcagcagcaccaccaccacc	0.172													68	8	---	---	---	---	
