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	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	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
LOC200030	200030	broad.mit.edu	37	1	148346958	148346958	+	5'Flank	SNP	A	G	G	rs613569	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148346958A>G	uc001eqe.2	-						LOC200030_uc001eqf.2_5'Flank|LOC200030_uc001eqg.2_5'Flank|NBPF14_uc009wkf.1_5'Flank|uc001erd.3_5'Flank|uc001erc.3_5'Flank|uc010paj.1_5'Flank|uc010pav.1_5'UTR|uc010paw.1_5'UTR			Q86T75	NBPFB_HUMAN	SubName: Full=cDNA FLJ78770;							cytoplasm					0						AACAAGGTTCAAGGTGCCTCA	0.473													2	9	---	---	---	---	PASS
GPATCH4	54865	broad.mit.edu	37	1	156568875	156568875	+	Intron	SNP	G	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:156568875G>T	uc001fpm.2	-						GPATCH4_uc001fpl.2_Translation_Start_Site	NM_015590	NP_056405	Q5T3I0	GPTC4_HUMAN	G patch domain containing 4 isoform 1							intracellular	nucleic acid binding			ovary(1)	1	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ACTCTCACCAGAGAAGAAGAG	0.438													3	71	---	---	---	---	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	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	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
PTPN7	5778	broad.mit.edu	37	1	202119407	202119407	+	Intron	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:202119407G>A	uc001gxm.1	-						PTPN7_uc001gxl.1_Intron|PTPN7_uc001gxn.1_Intron|PTPN7_uc010ppv.1_Intron|PTPN7_uc010ppw.1_Intron|PTPN7_uc010ppx.1_Intron|PTPN7_uc010ppy.1_Intron|PTPN7_uc001gxo.1_Missense_Mutation_p.R293C	NM_002832	NP_002823	P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type							cytosol|internal side of plasma membrane	protein binding|protein tyrosine phosphatase activity			skin(1)	1						ATCCGTTAACGTTGTTGGCCT	0.532													3	22	---	---	---	---	PASS
WDR92	116143	broad.mit.edu	37	2	68384604	68384604	+	5'UTR	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:68384604G>A	uc002see.1	-	1					WDR92_uc002sed.1_RNA|WDR92_uc002sef.1_5'UTR|WDR92_uc002seg.1_5'UTR|PNO1_uc002seh.2_5'Flank	NM_138458	NP_612467	Q96MX6	WDR92_HUMAN	monad						apoptosis|histone lysine methylation		methylated histone residue binding				0						TACGGCAACCGCCACACCCAG	0.552													3	39	---	---	---	---	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	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	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	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	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	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	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
DCTD	1635	broad.mit.edu	37	4	183812459	183812459	+	3'UTR	SNP	G	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183812459G>A	uc003ivf.2	-	6					DCTD_uc003ivg.2_3'UTR|DCTD_uc010irw.2_3'UTR|DCTD_uc003ivh.2_3'UTR	NM_001921	NP_001912	P32321	DCTD_HUMAN	dCMP deaminase isoform b						nucleotide biosynthetic process|pyrimidine base metabolic process|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide metabolic process	cytosol	dCMP deaminase activity|zinc ion binding				0		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)		ATACTGGCTAGTAAGAAGTTA	0.368													10	87	---	---	---	---	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	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
CDH12	1010	broad.mit.edu	37	5	22142968	22142968	+	Intron	SNP	A	C	C			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:22142968A>C	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron|PMCHL1_uc011cnp.1_Intron|PMCHL1_uc010iud.2_Intron|PMCHL1_uc011cnq.1_Intron|PMCHL1_uc011cnr.1_Intron|PMCHL1_uc003jgl.2_Intron|PMCHL1_uc011cns.1_Intron|PMCHL1_uc003jgn.2_Intron|PMCHL1_uc003jgm.2_RNA|PMCHL1_uc010iue.2_Intron|PMCHL1_uc011cnt.1_Intron	NM_004061	NP_004052	P55289	CAD12_HUMAN	cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2						TTCAGCACTCAGCTGTATGCT	0.328										HNSCC(59;0.17)			11	56	---	---	---	---	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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
SCAMP5	192683	broad.mit.edu	37	15	75311333	75311333	+	3'UTR	SNP	C	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:75311333C>A	uc002azk.1	+	7					SCAMP5_uc002azl.1_3'UTR|SCAMP5_uc002azm.1_3'UTR|SCAMP5_uc002azn.1_3'UTR|SCAMP5_uc010uly.1_3'UTR	NM_138967	NP_620417	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5						exocytosis|negative regulation of endocytosis|positive regulation of calcium ion-dependent exocytosis|positive regulation of cytokine secretion|protein transport|response to endoplasmic reticulum stress	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane|trans-Golgi network membrane	protein binding			ovary(1)	1						GAACCAGCCACGCCTACCAGG	0.582													3	19	---	---	---	---	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	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	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	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	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
LRRC37A4	55073	broad.mit.edu	37	17	43587569	43587569	+	Intron	SNP	G	C	C	rs149697015	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43587569G>C	uc002ije.2	-						uc010wjp.1_RNA					Homo sapiens cDNA FLJ34414 fis, clone HEART2003168, highly similar to Homo sapiens c114 SLIT-like testicular protein (LOC474170), mRNA.												0						aactccgtctgaaaagaaaag	0.144													4	115	---	---	---	---	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	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	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	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	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	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	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	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
HDAC1	3065	broad.mit.edu	37	1	32768050	32768051	+	Intron	INS	-	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32768050_32768051insT	uc001bvb.1	+						HDAC1_uc010ohd.1_Intron|HDAC1_uc010ohe.1_Intron|HDAC1_uc010ohf.1_Intron	NM_004964	NP_004955	Q13547	HDAC1_HUMAN	histone deacetylase 1						anti-apoptosis|blood coagulation|embryonic digit morphogenesis|epidermal cell differentiation|eyelid development in camera-type eye|fungiform papilla formation|hair follicle placode formation|histone H3 deacetylation|histone H4 deacetylation|negative regulation by host of viral transcription|negative regulation of androgen receptor signaling pathway|negative regulation of cell cycle|nerve growth factor receptor signaling pathway|odontogenesis of dentine-containing tooth|positive regulation of cell proliferation|positive regulation of receptor biosynthetic process|positive regulation of transcription from RNA polymerase II promoter	cytosol|NuRD complex|Sin3 complex	activating transcription factor binding|histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|identical protein binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|RNA polymerase II transcription corepressor activity|sequence-specific DNA binding transcription factor activity			ovary(1)|lung(1)|breast(1)	3		Breast(348;0.000523)|Lung NSC(340;0.000992)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Lung SC(1967;0.113)		KIRC - Kidney renal clear cell carcinoma(1967;0.138)	Vorinostat(DB02546)	AGGGTCCCTGCTTTTTTTTTTT	0.426													4	2	---	---	---	---	
GDAP2	54834	broad.mit.edu	37	1	118429438	118429439	+	Intron	INS	-	ACA	ACA	rs143592216	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:118429438_118429439insACA	uc001ehf.2	-						GDAP2_uc001ehg.2_Intron	NM_017686	NP_060156	Q9NXN4	GDAP2_HUMAN	ganglioside induced differentiation associated											ovary(2)	2		all_cancers(81;0.0156)|all_lung(203;5.81e-05)|Lung NSC(69;0.000446)|all_epithelial(167;0.00295)		Lung(183;0.0583)|LUSC - Lung squamous cell carcinoma(189;0.194)		CTACTCTGCAGACAACACCTAT	0.307													5	5	---	---	---	---	
NBPF7	343505	broad.mit.edu	37	1	120379730	120379731	+	Intron	INS	-	A	A	rs142246355	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:120379730_120379731insA	uc010oxk.1	-							NM_001047980	NP_001041445	P0C2Y1	NBPF7_HUMAN	hypothetical protein LOC343505							cytoplasm				ovary(1)|skin(1)	2	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;3.66e-05)|Lung NSC(69;0.000192)|all_epithelial(167;0.0347)		Lung(183;0.0103)|LUSC - Lung squamous cell carcinoma(189;0.0544)		gactccatctcaaaaaagaaaa	0.124													5	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144863860	144863861	+	Intron	INS	-	T	T	rs137857731		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144863860_144863861insT	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron|PDE4DIP_uc001ema.2_3'UTR	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GGGAACCCTTCTTTTTCATGTC	0.436			T	PDGFRB	MPD								4	2	---	---	---	---	
LOC200030	200030	broad.mit.edu	37	1	148011670	148011671	+	Intron	INS	-	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148011670_148011671insT	uc001eqf.2	-						LOC200030_uc001eqe.2_Intron|LOC200030_uc001eqg.2_Intron|FLJ39739_uc001eqo.1_Intron|NBPF14_uc010pab.1_Intron|NBPF14_uc010pac.1_Intron|NBPF14_uc001eqx.2_Intron|NBPF14_uc001eqq.2_Intron|NBPF14_uc010pad.1_Intron|NBPF14_uc001eqs.1_Intron	NM_017940	NP_060410	Q86T75	NBPFB_HUMAN	hypothetical protein LOC55672							cytoplasm					0						TCCACAATTGCGAAAGTCACCT	0.287													4	3	---	---	---	---	
PTPRC	5788	broad.mit.edu	37	1	198691479	198691480	+	Intron	DEL	AT	-	-	rs71717833		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:198691479_198691480delAT	uc001gur.1	+						PTPRC_uc001gus.1_Intron|PTPRC_uc001gut.1_Intron|PTPRC_uc009wzf.1_Intron|PTPRC_uc010ppg.1_Intron	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C						axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(3)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	12						GTGatatataatatatatatat	0.262													7	4	---	---	---	---	
SPAST	6683	broad.mit.edu	37	2	32312763	32312764	+	Intron	INS	-	TT	TT	rs72286744		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32312763_32312764insTT	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761	Q9UBP0	SPAST_HUMAN	spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					cttttcttttcttttttttttt	0.079													4	3	---	---	---	---	
REG3G	130120	broad.mit.edu	37	2	79254029	79254030	+	Intron	INS	-	A	A	rs34088535		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:79254029_79254030insA	uc002snw.2	+						REG3G_uc002snx.2_Intron|REG3G_uc010ffu.2_Intron	NM_198448	NP_940850	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma precursor						acute-phase response	extracellular region	sugar binding				0						GGAGGGTCTCCTTCAGGAGAGT	0.540													46	9	---	---	---	---	
UGGT1	56886	broad.mit.edu	37	2	128941484	128941485	+	Intron	DEL	GT	-	-	rs67237920		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128941484_128941485delGT	uc002tps.2	+						UGGT1_uc002tpr.2_Intron	NM_020120	NP_064505	Q9NYU2	UGGG1_HUMAN	UDP-glucose ceramide glucosyltransferase-like 1						'de novo' posttranslational protein folding|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen|ER-Golgi intermediate compartment	UDP-glucose:glycoprotein glucosyltransferase activity|unfolded protein binding			ovary(1)	1						TTTTTTCATGgtgtgtgtgtgt	0.292													8	4	---	---	---	---	
BMPR2	659	broad.mit.edu	37	2	203406833	203406833	+	Intron	DEL	A	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203406833delA	uc002uzf.3	+						BMPR2_uc010ftr.2_Intron	NM_001204	NP_001195	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor type II						anterior/posterior pattern formation|BMP signaling pathway|cellular response to starvation|lung alveolus development|mesoderm formation|negative regulation of cell growth|negative regulation of systemic arterial blood pressure|negative regulation of vasoconstriction|positive regulation of BMP signaling pathway|positive regulation of bone mineralization|positive regulation of endothelial cell migration|positive regulation of endothelial cell proliferation|positive regulation of epithelial cell migration|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|regulation of lung blood pressure|transcription from RNA polymerase II promoter|vascular endothelial growth factor receptor signaling pathway	integral to plasma membrane	ATP binding|metal ion binding|transforming growth factor beta receptor activity			ovary(4)|breast(2)|large_intestine(1)|stomach(1)|pancreas(1)	9						gactccgtctaaaaaaaaaaa	0.139													4	2	---	---	---	---	
STAC	6769	broad.mit.edu	37	3	36439959	36439970	+	Intron	DEL	GGAAGGAAGGAG	-	-	rs13083504	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:36439959_36439970delGGAAGGAAGGAG	uc003cgh.1	+						STAC_uc010hgd.1_Intron|STAC_uc011aya.1_Intron	NM_003149	NP_003140	Q99469	STAC_HUMAN	SH3 and cysteine rich domain						intracellular signal transduction	cytoplasm|soluble fraction	metal ion binding			skin(2)|ovary(1)|pancreas(1)	4						aaggaaggaaggaaggaaggagggaaggaaga	0.000													3	3	---	---	---	---	
CHCHD6	84303	broad.mit.edu	37	3	126427494	126427494	+	Intron	DEL	A	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:126427494delA	uc003ejf.1	+						CHCHD6_uc010hsj.1_Intron	NM_032343	NP_115719	Q9BRQ6	CHCH6_HUMAN	coiled-coil-helix-coiled-coil-helix domain												0						ccatctcttgaaaaaaaaaaa	0.000													4	2	---	---	---	---	
PIK3CA	5290	broad.mit.edu	37	3	178937631	178937631	+	Intron	DEL	A	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178937631delA	uc003fjk.2	+							NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha						epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			TTTTATGCTTAAAAAAAAAAA	0.234		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			53	8	---	---	---	---	
Unknown	0	broad.mit.edu	37	3	191759423	191759454	+	IGR	DEL	GAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG	-	-	rs71852976	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:191759423_191759454delGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAG								PYDC2 (580180 upstream) : FGF12 (100230 downstream)																							aagaaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaagga	0.069													1	5	---	---	---	---	
SDHAP1	255812	broad.mit.edu	37	3	195717077	195717078	+	5'UTR	INS	-	GCGCCAG	GCGCCAG			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195717077_195717078insGCGCCAG	uc011btq.1	-	1					SDHAP1_uc003fvx.3_RNA|SDHAP1_uc011btp.1_RNA					SubName: Full=cDNA FLJ56858, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						GGCCAGCGCCAGCGCCAGGCGC	0.490													5	3	---	---	---	---	
TMEM156	80008	broad.mit.edu	37	4	39034067	39034067	+	5'Flank	DEL	A	-	-	rs66913739		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39034067delA	uc003gto.2	-						TMEM156_uc010ifj.2_5'Flank	NM_024943	NP_079219	Q8N614	TM156_HUMAN	transmembrane protein 156							integral to membrane				skin(1)	1						AGTAAGACTTAAAAAAAAAAA	0.348													4	2	---	---	---	---	
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	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	---	---	---	---	
OTUD4	54726	broad.mit.edu	37	4	146067653	146067654	+	Intron	INS	-	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:146067653_146067654insA	uc003ika.3	-						OTUD4_uc003ijz.3_Intron	NM_001102653	NP_001096123	Q01804	OTUD4_HUMAN	OTU domain containing 4 protein isoform 3								protein binding			ovary(2)|breast(1)	3	all_hematologic(180;0.151)					ACATTCTTGTCAAAAAAAAAAA	0.238													4	2	---	---	---	---	
MRS2	57380	broad.mit.edu	37	6	24416483	24416484	+	Intron	INS	-	T	T	rs35657958		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:24416483_24416484insT	uc003neb.2	+						MRS2_uc003nea.2_Intron|MRS2_uc011djl.1_Intron|MRS2_uc011djm.1_Intron|MRS2_uc011djn.1_Intron|MRS2_uc003nec.2_Intron	NM_020662	NP_065713	Q9HD23	MRS2_HUMAN	MRS2-like, magnesium homeostasis factor						ion transport	integral to membrane|mitochondrial inner membrane					0						AAATACTCAACttttttttttt	0.139													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	31733214	31733215	+	IGR	INS	-	A	A	rs141140500	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31733214_31733215insA								MSH5 (592 upstream) : C6orf27 (157 downstream)																							aactacatctcaaaaaaaaaac	0.163													4	2	---	---	---	---	
LAMA4	3910	broad.mit.edu	37	6	112475859	112475859	+	Intron	DEL	T	-	-	rs67359077		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112475859delT	uc003pvu.2	-						LAMA4_uc003pvv.2_Intron|LAMA4_uc003pvt.2_Intron	NM_001105206	NP_001098676	Q16363	LAMA4_HUMAN	laminin, alpha 4 isoform 1 precursor						cell adhesion|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	extracellular matrix structural constituent|receptor binding			ovary(4)|breast(2)|large_intestine(1)|central_nervous_system(1)|pancreas(1)	9		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		CTACATAGCATTTTTTTTTTC	0.219													8	9	---	---	---	---	
SHPRH	257218	broad.mit.edu	37	6	146242677	146242677	+	Intron	DEL	T	-	-	rs146207931		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146242677delT	uc003qlf.2	-						SHPRH_uc003qld.2_Intron|SHPRH_uc003qle.2_Intron|SHPRH_uc003qlg.1_Intron|SHPRH_uc003qlh.2_Intron|SHPRH_uc003qli.1_Intron	NM_001042683	NP_001036148	Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase isoform a						DNA repair|nucleosome assembly	nucleosome|nucleus	ATP binding|DNA binding|helicase activity|ligase activity|zinc ion binding			ovary(1)|kidney(1)|central_nervous_system(1)	3		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		ATTTGGCCAGTTTTTTTTTTT	0.303													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	149915719	149915720	+	IGR	DEL	AA	-	-	rs113339415		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:149915719_149915720delAA								C6orf72 (3652 upstream) : KATNA1 (452 downstream)																							TTTATATACCaaaaaaaaaaaa	0.406													3	3	---	---	---	---	
C7orf28B	221960	broad.mit.edu	37	7	6859772	6859773	+	Intron	INS	-	A	A	rs147091531	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:6859772_6859773insA	uc003sqx.1	-						C7orf28B_uc011jxd.1_Intron	NM_198097	NP_932765	P86791	CCZ1_HUMAN	hypothetical protein LOC221960							lysosomal membrane					0		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)		AAAGTTCAAACTATCTACTTAA	0.257													4	2	---	---	---	---	
NDUFB2	4708	broad.mit.edu	37	7	140404902	140404902	+	Intron	DEL	T	-	-	rs72099907		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:140404902delT	uc003vwa.2	+						NDUFB2_uc010lnl.2_Intron	NM_004546	NP_004537	O95178	NDUB2_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta						mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity			ovary(1)|central_nervous_system(1)	2	Melanoma(164;0.00956)				NADH(DB00157)	CTGTATCTGCttttttttttt	0.164													5	3	---	---	---	---	
MLL3	58508	broad.mit.edu	37	7	152100795	152100802	+	Intron	DEL	ACACATAC	-	-	rs71273890	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:152100795_152100802delACACATAC	uc003wla.2	-							NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3						intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		aaaaactgggacacatacacacacacac	0.000			N		medulloblastoma								4	2	---	---	---	---	
ZMAT4	79698	broad.mit.edu	37	8	40389934	40389935	+	Intron	DEL	AA	-	-	rs35797324		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:40389934_40389935delAA	uc003xnr.2	-						ZMAT4_uc003xns.2_Intron	NM_024645	NP_078921	Q9H898	ZMAT4_HUMAN	zinc finger, matrin type 4 isoform a							nucleus	DNA binding|zinc ion binding			pancreas(1)|central_nervous_system(1)|skin(1)	3	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			CTGTATATATAAAATATCTCCA	0.302													3	5	---	---	---	---	
GGH	8836	broad.mit.edu	37	8	63928200	63928201	+	Intron	INS	-	A	A			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:63928200_63928201insA	uc003xuw.2	-							NM_003878	NP_003869	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase precursor						glutamine metabolic process	extracellular space|lysosome|melanosome	gamma-glutamyl-peptidase activity				0	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|L-Glutamic Acid(DB00142)	acttactttcCAAAAAAAAAAA	0.248													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	68419306	68419307	+	IGR	DEL	CA	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68419306_68419307delCA								FAM27B (625117 upstream) : MIR1299 (582932 downstream)																							tacaccacaccacacacacatt	0.000													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	133834150	133834152	+	IGR	DEL	CAC	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:133834150_133834152delCAC								FIBCD1 (19695 upstream) : LAMC3 (50352 downstream)																							ccatcaccatcaccaccaccacc	0.000													8	4	---	---	---	---	
C10orf18	54906	broad.mit.edu	37	10	5804474	5804474	+	Intron	DEL	G	-	-	rs59569509	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:5804474delG	uc001iij.2	+						C10orf18_uc001iik.2_Intron	NM_017782	NP_060252	Q5VWN6	CJ018_HUMAN	hypothetical protein LOC54906											ovary(1)|central_nervous_system(1)	2						ACCAAAAGTTGTTTTTTTTTT	0.308													62	9	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	52467884	52467886	+	IGR	DEL	TCC	-	-	rs57441530		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:52467884_52467886delTCC								SGMS1 (82961 upstream) : ASAH2B (31810 downstream)																							CATCTTCACGTCCTTCTCTCACA	0.389													5	4	---	---	---	---	
IPO7	10527	broad.mit.edu	37	11	9436166	9436166	+	Intron	DEL	C	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:9436166delC	uc001mho.2	+							NM_006391	NP_006382	O95373	IPO7_HUMAN	importin 7						interspecies interaction between organisms|signal transduction	Golgi apparatus|nuclear pore|soluble fraction	protein transporter activity|Ran GTPase binding|small GTPase regulator activity			lung(1)|breast(1)	2				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		CCTAATGAATCtttttttttt	0.149													4	2	---	---	---	---	
TPCN2	219931	broad.mit.edu	37	11	68844539	68844546	+	Intron	DEL	CTTGCCCT	-	-	rs72570552	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68844539_68844546delCTTGCCCT	uc001oos.2	+						TPCN2_uc009ysk.1_Intron|TPCN2_uc001oor.2_Intron|TPCN2_uc010rqg.1_Intron|TPCN2_uc001oot.2_Intron	NM_139075	NP_620714	Q8NHX9	TPC2_HUMAN	two pore segment channel 2						cellular calcium ion homeostasis|smooth muscle contraction	endosome membrane|integral to membrane|lysosomal membrane	NAADP-sensitive calcium-release channel activity|voltage-gated calcium channel activity				0			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGTCCCTCCActtgccctcctgccctcc	0.053													4	2	---	---	---	---	
FAT3	120114	broad.mit.edu	37	11	92142411	92142412	+	Intron	DEL	GT	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92142411_92142412delGT	uc001pdj.3	+							NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3						homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TGAAGCTTTCgtgtgtgtgtgt	0.238										TCGA Ovarian(4;0.039)			4	2	---	---	---	---	
GRIN2B	2904	broad.mit.edu	37	12	13717796	13717797	+	Intron	INS	-	G	G	rs138212867	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:13717796_13717797insG	uc001rbt.2	-							NM_000834	NP_000825	Q13224	NMDE2_HUMAN	N-methyl-D-aspartate receptor subunit 2B						response to ethanol	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|outer membrane-bounded periplasmic space|postsynaptic membrane	glycine binding|N-methyl-D-aspartate selective glutamate receptor activity|zinc ion binding			central_nervous_system(4)|ovary(3)|skin(3)|lung(2)	12					Felbamate(DB00949)|Haloperidol(DB00502)|L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Memantine(DB01043)	TGGCCATCAGAGGGGGGGGCAT	0.460													3	3	---	---	---	---	
SLC2A13	114134	broad.mit.edu	37	12	40206204	40206207	+	Intron	DEL	CTTC	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:40206204_40206207delCTTC	uc010skm.1	-						C12orf40_uc009zjv.1_Intron	NM_052885	NP_443117	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose							integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			ovary(1)	1		Lung NSC(34;0.105)|all_lung(34;0.123)				ctctctctttcttccttccttcct	0.020										HNSCC(50;0.14)			4	2	---	---	---	---	
ANKS1B	56899	broad.mit.edu	37	12	99639945	99639945	+	Intron	DEL	T	-	-	rs35408837		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:99639945delT	uc001tge.1	-						ANKS1B_uc001tgf.1_Intron|ANKS1B_uc001tgk.2_Intron	NM_152788	NP_690001	Q7Z6G8	ANS1B_HUMAN	cajalin 2 isoform a							Cajal body|cell junction|cytoplasm|dendritic spine|postsynaptic density|postsynaptic membrane					0		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		AGCCGTATGCTTTTTTTTTTC	0.393													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	111837697	111837698	+	IGR	INS	-	AGAA	AGAA			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111837697_111837698insAGAA								FAM109A (30772 upstream) : SH2B3 (6054 downstream)																							aagactctgtcAgaaagaaaga	0.000													4	2	---	---	---	---	
NAA16	79612	broad.mit.edu	37	13	41897181	41897181	+	Intron	DEL	T	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:41897181delT	uc001uyf.2	+						NAA16_uc010tfg.1_Intron|NAA16_uc001uye.3_Intron|NAA16_uc001uyd.3_Intron	NM_024561	NP_078837	Q6N069	NAA16_HUMAN	NMDA receptor regulated 1-like protein isoform						N-terminal protein amino acid acetylation|positive regulation of transcription, DNA-dependent	cytoplasm|transcription factor complex	binding			central_nervous_system(1)	1						AAGTTAAAACTTTTTTTTTAG	0.333													261	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	26355374	26355375	+	IGR	DEL	CA	-	-	rs146744363		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:26355374_26355375delCA								HS3ST4 (206366 upstream) : C16orf82 (722844 downstream)																							TGCTTacatgcacacacacaca	0.376													4	3	---	---	---	---	
CDH8	1006	broad.mit.edu	37	16	61689778	61689778	+	Intron	DEL	T	-	-	rs66728481		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:61689778delT	uc002eog.1	-							NM_001796	NP_001787	P55286	CADH8_HUMAN	cadherin 8, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(6)|skin(2)|breast(1)	9		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		GTCTCCGCACttttttttttt	0.224													5	3	---	---	---	---	
CLEC18A	348174	broad.mit.edu	37	16	69988604	69988605	+	Intron	INS	-	T	T			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:69988604_69988605insT	uc010vlo.1	+						CLEC18C_uc002exy.2_Intron|CLEC18A_uc002exz.2_Intron|CLEC18A_uc002eya.2_Intron|CLEC18A_uc010vlp.1_Intron	NM_001136214	NP_001129686	A5D8T8	CL18A_HUMAN	secretory protein LOC348174 precursor							extracellular region	sugar binding				0						TTTAGttttacttttttttttt	0.223													6	3	---	---	---	---	
GAN	8139	broad.mit.edu	37	16	81387847	81387847	+	Intron	DEL	A	-	-	rs139978939		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81387847delA	uc002fgo.2	+							NM_022041	NP_071324	Q9H2C0	GAN_HUMAN	gigaxonin						cell death	cytoplasm|neurofilament	protein binding			ovary(2)	2		Colorectal(91;0.153)				CAACTCTTGGAAAAAAAAAAA	0.259													4	4	---	---	---	---	
LRRC37A	9884	broad.mit.edu	37	17	44383412	44383412	+	Intron	DEL	A	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44383412delA	uc002ikg.2	+						ARL17A_uc002iki.3_Intron|ARL17A_uc002ikh.3_Intron|ARL17B_uc002ikf.2_Intron	NM_014834	NP_055649	A6NMS7	L37A1_HUMAN	leucine rich repeat containing 37A precursor							integral to membrane					0		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		TTTTGTATCTAATGCACCACG	0.284													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	46791071	46791072	+	IGR	INS	-	A	A	rs71369208		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46791071_46791072insA								MIR196A1 (81150 upstream) : PRAC (8020 downstream)																							gactccttctcaaaaaaaaaaa	0.223													4	2	---	---	---	---	
MED13	9969	broad.mit.edu	37	17	60070140	60070141	+	Intron	INS	-	T	T	rs138009503	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:60070140_60070141insT	uc002izo.2	-							NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13						androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			large_intestine(1)|ovary(1)	2						cttattattacttttttttgag	0.000													6	3	---	---	---	---	
EIF4A3	9775	broad.mit.edu	37	17	78114113	78114113	+	Intron	DEL	T	-	-	rs34004549		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:78114113delT	uc010wuc.1	-						EIF4A3_uc002jxs.2_Intron	NM_014740	NP_055555	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A,						mRNA transport|negative regulation of translation|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|positive regulation of translation|rRNA processing	catalytic step 2 spliceosome|cytoplasm|exon-exon junction complex|nuclear speck	ATP binding|ATP-dependent RNA helicase activity|poly(A) RNA binding|protein binding			ovary(1)	1	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			TTAAttttgcttttttttttt	0.164													4	2	---	---	---	---	
LOC647946	647946	broad.mit.edu	37	18	37248401	37248401	+	Intron	DEL	G	-	-	rs3067224		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:37248401delG	uc010xcj.1	-						LOC647946_uc002lal.1_Intron	NR_024391				Homo sapiens cDNA FLJ33284 fis, clone ASTRO2009458.												0						aaggaaggaaggaaagaagga	0.144													4	2	---	---	---	---	
ATCAY	85300	broad.mit.edu	37	19	3924772	3924772	+	3'UTR	DEL	T	-	-	rs11306255		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3924772delT	uc002lyy.3	+	13					ATCAY_uc010xhz.1_3'UTR|ATCAY_uc010dts.2_3'UTR	NM_033064	NP_149053	Q86WG3	ATCAY_HUMAN	caytaxin						transport		protein binding			breast(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00485)|STAD - Stomach adenocarcinoma(1328;0.183)		AAACATTGTATTTTTTTTTTT	0.502													3	6	---	---	---	---	
SLC5A5	6528	broad.mit.edu	37	19	17991503	17991504	+	Intron	INS	-	CAAAA	CAAAA	rs144134876	by1000genomes	TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17991503_17991504insCAAAA	uc002nhr.3	+							NM_000453	NP_000444	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium iodide						cellular nitrogen compound metabolic process|cellular response to cAMP|cellular response to gonadotropin stimulus|hormone biosynthetic process	integral to membrane|nucleus|plasma membrane	iodide transmembrane transporter activity|sodium:iodide symporter activity			skin(2)|ovary(1)|central_nervous_system(1)	4						agatcttttctcaaaacaaaac	0.005													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	49715837	49715838	+	IGR	INS	-	CTTC	CTTC	rs76677262		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49715837_49715838insCTTC								TRPM4 (746 upstream) : SLC6A16 (77056 downstream)																							AATGTAACCTActtccttcctt	0.035													4	2	---	---	---	---	
SYT3	84258	broad.mit.edu	37	19	51132916	51132917	+	Intron	DEL	CC	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51132916_51132917delCC	uc002pst.2	-						SYT3_uc002psv.2_Intron|SYT3_uc010ycd.1_Intron	NM_032298	NP_115674	Q9BQG1	SYT3_HUMAN	synaptotagmin III							cell junction|endosome|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|breast(1)	3		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		ggagtccaggcccccagcccct	0.000													5	4	---	---	---	---	
ZNFX1	57169	broad.mit.edu	37	20	47870567	47870567	+	Intron	DEL	T	-	-	rs11353174		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47870567delT	uc002xui.2	-							NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1								metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ttcttttttcttttttttttt	0.194													12	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	25157654	25157669	+	IGR	DEL	AAGGAAGGAAGGAAGA	-	-	rs71182204		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:25157654_25157669delAAGGAAGGAAGGAAGA								None (None upstream) : None (None downstream)																							gggagggaggaaggaaggaaggaagaaaggaaggaa	0.000													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	16920274	16920275	+	IGR	DEL	AT	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:16920274_16920275delAT								OR11H1 (470470 upstream) : CCT8L2 (151373 downstream)																							TTATAGTGACATGTATGAAAAC	0.267													6	4	---	---	---	---	
NUP50	10762	broad.mit.edu	37	22	45577017	45577019	+	Intron	DEL	CCC	-	-	rs66468525		TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45577017_45577019delCCC	uc003bfr.2	+						NUP50_uc003bfs.2_Intron|NUP50_uc011aqn.1_Intron|NUP50_uc003bft.2_Intron|NUP50_uc011aqo.1_Intron	NM_007172	NP_009103	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa isoform b						carbohydrate metabolic process|glucose transport|intracellular transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear membrane|nuclear pore|nucleoplasm	protein binding				0		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTTCTGGCATCCCCCCCCCCCCC	0.404													6	3	---	---	---	---	
FBLN1	2192	broad.mit.edu	37	22	45970657	45970657	+	Intron	DEL	C	-	-			TCGA-EJ-5512-01A-01D-1576-08	TCGA-EJ-5512-10A-01D-1577-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:45970657delC	uc003bgj.1	+							NM_006486	NP_006477	P23142	FBLN1_HUMAN	fibulin 1 isoform D						interspecies interaction between organisms	extracellular space|soluble fraction	calcium ion binding|extracellular matrix structural constituent|protein binding			ovary(1)|central_nervous_system(1)	2		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GCAGAACtttctttttttttt	0.289													5	3	---	---	---	---	
