Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
CROCCL1	84809	broad.mit.edu	37	1	16945452	16945452	+	RNA	SNP	C	T	T	rs11260834		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:16945452C>T	uc010ocf.1	-	4		c.705G>A			CROCCL1_uc009vov.1_RNA|CROCCL1_uc001aze.2_RNA|CROCCL1_uc001azf.2_RNA					Homo sapiens mRNA for FLJ00313 protein.												0						CTCCCTACGACGGCAGGCCTA	0.647000													20	124	---	---	---	---	0	0	0.076483	0	0
NRAS	4893	broad.mit.edu	37	1	115256530	115256530	+	Missense_Mutation	SNP	G	T	T	rs121913254		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:115256530G>T	uc009wgu.2	-	3	435	c.181C>A	c.(181-183)CAA>AAA	p.Q61K		NM_002524	NP_002515	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	61	GTP.		Q -> K (in neuroblastoma cell).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	Golgi membrane|plasma membrane	GTP binding|GTPase activity	p.Q61R(757)|p.Q61K(537)|p.Q61L(147)|p.Q61H(95)|p.Q61P(21)|p.Q61E(9)|p.Q61?(4)|p.Q61Q(3)|p.Q61_E62>HK(1)		haematopoietic_and_lymphoid_tissue(1008)|skin(956)|thyroid(334)|large_intestine(62)|NS(60)|soft_tissue(32)|lung(31)|upper_aerodigestive_tract(25)|urinary_tract(12)|liver(10)|adrenal_gland(9)|autonomic_ganglia(8)|testis(8)|central_nervous_system(8)|prostate(8)|breast(7)|biliary_tract(6)|ovary(6)|stomach(5)|pancreas(5)|endometrium(2)|kidney(2)|cervix(2)|eye(1)	2607	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACTCTTCTTGTCCAGCTGTA	0.458000	Q61K(HT1080_SOFT_TISSUE)|Q61K(OCILY19_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(SKNAS_AUTONOMIC_GANGLIA)|Q61K(HCC15_LUNG)|Q61K(TYKNU_OVARY)|Q61K(SKNSH_AUTONOMIC_GANGLIA)|Q61K(HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(NCIH2087_LUNG)|Q61K(CHP212_AUTONOMIC_GANGLIA)|Q61K(HS944T_SKIN)|Q61K(M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|Q61K(HS936T_SKIN)|Q61K(NCIH1299_LUNG)	50	Mis		melanoma|MM|AML|thyroid				Noonan_syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)			90	204	---	---	---	---	2.48367e-54	3.23956e-54	0.139131	1	0
KIF14	9928	broad.mit.edu	37	1	200539119	200539119	+	Missense_Mutation	SNP	A	T	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:200539119A>T	uc010ppk.1	-	23	4020	c.3581T>A	c.(3580-3582)ATG>AAG	p.M1194K	KIF14_uc010ppj.1_Missense_Mutation_p.M703K	NM_014875	NP_055690	Q15058	KIF14_HUMAN	kinesin family member 14	1194	Required for CIT-binding.				microtubule-based movement	cytoplasm|microtubule|nucleus|spindle	ATP binding|microtubule motor activity|protein binding			breast(3)|ovary(2)|skin(2)	7						TCTGTTCTTCATCAAACTCCT	0.289000													41	84	---	---	---	---	0	0	0.139131	0	0
OR2M2	391194	broad.mit.edu	37	1	248344320	248344320	+	Missense_Mutation	SNP	T	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:248344320T>C	uc010pzf.1	+	1	1033	c.1033T>C	c.(1033-1035)TAC>CAC	p.Y345H		NM_001004688	NP_001004688	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M,	345	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(3)|skin(1)	4	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			ATTGATTATGTACATTGCCTA	0.264000													4	146	---	---	---	---	0	0	0.150653	0	0
KIAA1217	56243	broad.mit.edu	37	10	24669920	24669920	+	Silent	SNP	T	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr10:24669920T>C	uc001iru.3	+	3	880	c.477T>C	c.(475-477)CCT>CCC	p.P159P	KIAA1217_uc001irs.2_Silent_p.P79P|KIAA1217_uc001irt.3_Silent_p.P159P|KIAA1217_uc010qcy.1_Silent_p.P159P|KIAA1217_uc010qcz.1_Silent_p.P159P|KIAA1217_uc001irv.1_Silent_p.P9P|KIAA1217_uc010qda.1_RNA	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1	159					embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						CTCCAACCCCTTTTTCCAGAG	0.542000													4	106	---	---	---	---	0	0	0.014758	0	0
TDRD1	56165	broad.mit.edu	37	10	115978234	115978234	+	Silent	SNP	A	G	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr10:115978234A>G	uc001lbg.1	+	18	2538	c.2385A>G	c.(2383-2385)GTA>GTG	p.V795V	TDRD1_uc001lbf.2_Intron|TDRD1_uc001lbh.1_Silent_p.V786V|TDRD1_uc001lbi.1_Silent_p.V786V|TDRD1_uc010qsc.1_Silent_p.V399V|TDRD1_uc001lbj.2_Silent_p.V504V	NM_198795	NP_942090	Q9BXT4	TDRD1_HUMAN	tudor domain containing 1	795	Tudor 3.				DNA methylation involved in gamete generation|gene silencing by RNA|germ cell development|meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	pi-body	nucleic acid binding|protein binding|zinc ion binding				0		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0343)|all cancers(201;0.0754)		ATGTTAAAGTACATTTTGTGG	0.383000													6	199	---	---	---	---	0	0	0.038147	0	0
MUC2	4583	broad.mit.edu	37	11	1094843	1094843	+	Silent	SNP	C	T	T	rs41417150	by1000genomes	TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:1094843C>T	uc001lsx.1	+	34	13044	c.13017C>T	c.(13015-13017)AAC>AAT	p.N4339N		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	4339						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|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;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	GTGTCCTGAACGACACCTACT	0.617000													6	352	---	---	---	---	0	0	0.029380	0	0
CYB5R2	51700	broad.mit.edu	37	11	7687683	7687683	+	Missense_Mutation	SNP	A	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:7687683A>C	uc001mfm.2	-	8	895	c.657T>G	c.(655-657)ATT>ATG	p.I219M	CYB5R2_uc001mfn.2_RNA|CYB5R2_uc009yfk.2_Missense_Mutation_p.I219M	NM_016229	NP_057313	Q6BCY4	NB5R2_HUMAN	cytochrome b5 reductase b5R.2	219					sterol biosynthetic process	membrane|soluble fraction	cytochrome-b5 reductase activity				0				Epithelial(150;5.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATGTCGTACCAATGGGAGGCC	0.493000											OREG0020724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	14	77	---	---	---	---	0	0	0.163468	0	0
TRIM48	79097	broad.mit.edu	37	11	55035844	55035844	+	Missense_Mutation	SNP	T	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:55035844T>C	uc010rid.1	+	4	660	c.574T>C	c.(574-576)TAC>CAC	p.Y192H		NM_024114	NP_077019	Q8IWZ4	TRI48_HUMAN	tripartite motif-containing 48	176						intracellular	zinc ion binding				0						AGACATATTATACAGGTGAGT	0.338000													3	61	---	---	---	---	0	0	0.014758	0	0
CTNND1	1500	broad.mit.edu	37	11	57573460	57573460	+	Missense_Mutation	SNP	A	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:57573460A>C	uc001nmc.3	+	10	2400	c.1829A>C	c.(1828-1830)AAT>ACT	p.N610T	CTNND1_uc001nlh.1_Missense_Mutation_p.N610T|CTNND1_uc001nlu.3_Missense_Mutation_p.N509T|CTNND1_uc001nlt.3_Missense_Mutation_p.N509T|CTNND1_uc001nls.3_Missense_Mutation_p.N509T|CTNND1_uc001nlw.3_Missense_Mutation_p.N509T|CTNND1_uc001nmf.3_Missense_Mutation_p.N610T|CTNND1_uc001nmd.3_Missense_Mutation_p.N556T|CTNND1_uc001nlk.3_Missense_Mutation_p.N556T|CTNND1_uc001nme.3_Missense_Mutation_p.N610T|CTNND1_uc001nll.3_Missense_Mutation_p.N556T|CTNND1_uc001nmg.3_Missense_Mutation_p.N556T|CTNND1_uc001nlj.3_Missense_Mutation_p.N556T|CTNND1_uc001nlr.3_Missense_Mutation_p.N556T|CTNND1_uc001nlp.3_Missense_Mutation_p.N556T|CTNND1_uc001nlx.3_Missense_Mutation_p.N287T|CTNND1_uc001nlz.3_Missense_Mutation_p.N287T|CTNND1_uc009ymn.2_Missense_Mutation_p.N287T|CTNND1_uc001nlm.3_Missense_Mutation_p.N610T|CTNND1_uc001nly.3_Missense_Mutation_p.N287T|CTNND1_uc001nmb.3_Missense_Mutation_p.N287T|CTNND1_uc001nma.3_Missense_Mutation_p.N287T|CTNND1_uc001nmi.3_Missense_Mutation_p.N509T|CTNND1_uc001nmh.3_Missense_Mutation_p.N610T|CTNND1_uc001nlq.3_Missense_Mutation_p.N509T|CTNND1_uc001nln.3_Missense_Mutation_p.N610T|CTNND1_uc001nli.3_Missense_Mutation_p.N610T|CTNND1_uc001nlo.3_Missense_Mutation_p.N509T|CTNND1_uc001nlv.3_Missense_Mutation_p.N509T	NM_001085458	NP_001078927	O60716	CTND1_HUMAN	catenin, delta 1 isoform 1ABC	610	ARM 6.				adherens junction organization|cell junction assembly|negative regulation of canonical Wnt receptor signaling pathway|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	cytosol|midbody|nucleus	cadherin binding|protein binding|receptor binding			breast(4)|ovary(1)|kidney(1)	6		all_epithelial(135;0.155)				GTTGCCAACAATACTGGGCCA	0.498000													3	29	---	---	---	---	0	0	0.115264	0	0
LOC284232	284232	broad.mit.edu	37	13	19419995	19419995	+	RNA	SNP	C	G	G	rs78291036	by1000genomes	TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr13:19419995C>G	uc010tcj.1	-	1		c.26115G>C				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						GAACTAAGAACAGTTAGATAA	0.294000													6	72	---	---	---	---	0	0	0.038147	0	0
BCL8	606	broad.mit.edu	37	15	20876452	20876452	+	Missense_Mutation	SNP	G	A	A	rs6422239	by1000genomes	TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr15:20876452G>A	uc010tze.1	-	2	368	c.161C>T	c.(160-162)ACA>ATA	p.T54I	BCL8_uc010tzd.1_RNA	NR_027992				RecName: Full=Putative protein BCL8;												0						CTTTGCAGGTGTATGTATCCA	0.333000													4	66	---	---	---	---	0	0	0.014758	0	0
GOLGA6L5	374650	broad.mit.edu	37	15	85055643	85055643	+	RNA	SNP	T	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr15:85055643T>C	uc002bkm.2	-	6		c.917A>G				NR_003246				Homo sapiens cDNA FLJ33459 fis, clone BRAMY2000585.												0						CCTGTTCACGTAGCCTCTCCT	0.547000													2	11	---	---	---	---	0	0	0.115264	0	0
STUB1	10273	broad.mit.edu	37	16	732365	732365	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:732365G>A	uc002cit.2	+	7	1199	c.788G>A	c.(787-789)CGT>CAT	p.R263H	STUB1_uc002ciu.2_Missense_Mutation_p.R191H|STUB1_uc010bqz.2_RNA|STUB1_uc002civ.2_RNA|JMJD8_uc002ciw.1_3'UTR|JMJD8_uc002cix.1_3'UTR|JMJD8_uc002ciy.1_3'UTR	NM_005861	NP_005852	Q9UNE7	CHIP_HUMAN	STIP1 homology and U-box containing protein 1	263	U-box.				cellular response to misfolded protein|DNA repair|misfolded or incompletely synthesized protein catabolic process|positive regulation of cellular chaperone-mediated protein complex assembly|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|proteasomal ubiquitin-dependent protein catabolic process|protein autoubiquitination|protein K63-linked ubiquitination|protein maturation|regulation of glucocorticoid metabolic process|ubiquitin-dependent SMAD protein catabolic process	cytoplasm|nuclear inclusion body|ubiquitin conjugating enzyme complex|ubiquitin ligase complex	Hsp70 protein binding|Hsp90 protein binding|kinase binding|misfolded protein binding|protein binding, bridging|protein homodimerization activity|SMAD binding|TPR domain binding|ubiquitin-ubiquitin ligase activity				0		Hepatocellular(780;0.00335)				TCACTGCAGCGTGTGGGTCAT	0.617000													5	156	---	---	---	---	0	0	0.047766	0	0
PDPR	55066	broad.mit.edu	37	16	70187304	70187304	+	Missense_Mutation	SNP	A	T	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:70187304A>T	uc002eyf.1	+	18	3020	c.2063A>T	c.(2062-2064)CAT>CTT	p.H688L	CLEC18C_uc002exy.2_Intron|PDPR_uc010vlr.1_Missense_Mutation_p.H588L|PDPR_uc002eyg.1_Intron|PDPR_uc002eyh.2_Missense_Mutation_p.H33L|PDPR_uc010vls.1_Missense_Mutation_p.H33L	NM_017990	NP_060460	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory	688					glycine catabolic process|pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix	aminomethyltransferase activity|oxidoreductase activity			breast(1)	1				BRCA - Breast invasive adenocarcinoma(221;0.124)		TACGCCCTGCATGTATACAAT	0.448000													10	47	---	---	---	---	0	0	0.069234	0	0
CDH13	1012	broad.mit.edu	37	16	83520201	83520201	+	Missense_Mutation	SNP	A	G	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:83520201A>G	uc002fgx.2	+	7	1021	c.901A>G	c.(901-903)ATC>GTC	p.I301V	CDH13_uc010vns.1_Missense_Mutation_p.I348V|CDH13_uc010vnt.1_Missense_Mutation_p.I47V|CDH13_uc010vnu.1_Missense_Mutation_p.I262V	NM_001257	NP_001248	P55290	CAD13_HUMAN	cadherin 13 preproprotein	301	Cadherin 2.				adherens junction organization|calcium-dependent cell-cell adhesion|cell junction assembly|endothelial cell migration|homophilic cell adhesion|keratinocyte proliferation|lamellipodium assembly|localization within membrane|low-density lipoprotein particle mediated signaling|negative regulation of cell adhesion|negative regulation of cell proliferation|positive regulation of calcium-mediated signaling|positive regulation of cell migration|positive regulation of cell-matrix adhesion|positive regulation of endothelial cell proliferation|positive regulation of positive chemotaxis|positive regulation of smooth muscle cell proliferation|positive regulation of survival gene product expression|Rac protein signal transduction|regulation of endocytosis|regulation of epidermal growth factor receptor signaling pathway|Rho protein signal transduction|sprouting angiogenesis	anchored to membrane|caveola|extracellular space|integral to membrane|neuron projection	adiponectin binding|cadherin binding|calcium ion binding|low-density lipoprotein particle binding			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CATGTTCTACATCGATCCTGA	0.493000													4	135	---	---	---	---	0	0	0.014758	0	0
Unknown	0	broad.mit.edu	37	17	20319816	20319816	+	RNA	SNP	T	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr17:20319816T>C	uc010vzg.1	+	2		c.187T>C			uc002gwx.2_RNA					Homo sapiens cDNA FLJ59693 complete cds, moderately similar to Ankyrin repeat domain-containing protein 26.																		CAAAGGAAAATGACAGGCCCT	0.507000													6	42	---	---	---	---	0	0	0.029380	0	0
Unknown	0	broad.mit.edu	37	17	45127107	45127107	+	Missense_Mutation	SNP	C	G	G	rs147409399	by1000genomes	TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr17:45127107C>G	uc010wkj.1	+	2	659	c.305C>G	c.(304-306)ACC>AGC	p.T102S	uc010wkl.1_RNA					SubName: Full=Putative uncharacterized protein LRRC37A3;																		CCTTCGTTCACCCAAGAGCAT	0.592000													3	136	---	---	---	---	0	0	0.115264	0	0
TBC1D3P2	440452	broad.mit.edu	37	17	60342311	60342311	+	RNA	SNP	G	T	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr17:60342311G>T	uc010woz.1	-	14		c.1818C>A				NR_027486				Homo sapiens cDNA FLJ60189 complete cds, highly similar to TBC1 domain family member 3.												0						AAAACGAGGAGGCGAAGCTTG	0.458000													5	115	---	---	---	---	6.40141e-05	8.00176e-05	0.080935	1	0
MUC16	94025	broad.mit.edu	37	19	9090831	9090831	+	Silent	SNP	A	G	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr19:9090831A>G	uc002mkp.2	-	1	1188	c.984T>C	c.(982-984)CCT>CCC	p.P328P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	328	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						TCATGGAAAAAGGGATAGCTG	0.522000													3	98	---	---	---	---	0	0	0.115264	0	0
RTN2	6253	broad.mit.edu	37	19	45996575	45996575	+	Missense_Mutation	SNP	A	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr19:45996575A>C	uc002pcb.2	-	5	1104	c.876T>G	c.(874-876)ATT>ATG	p.I292M	RTN2_uc002pcc.2_Intron|RTN2_uc002pcd.2_Intron	NM_005619	NP_005610	O75298	RTN2_HUMAN	reticulon 2 isoform A	292						integral to endoplasmic reticulum membrane	signal transducer activity			ovary(3)	3		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00829)|Epithelial(262;0.184)|GBM - Glioblastoma multiforme(486;0.246)		ACAATTCCAAAATTGGAACCG	0.502000													3	155	---	---	---	---	0	0	0.115264	0	0
COL6A3	1293	broad.mit.edu	37	2	238277411	238277411	+	Silent	SNP	G	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr2:238277411G>A	uc002vwl.2	-	10	4980	c.4695C>T	c.(4693-4695)TCC>TCT	p.S1565S	COL6A3_uc002vwo.2_Silent_p.S1359S|COL6A3_uc010znj.1_Silent_p.S958S	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	1565	VWFA 8.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAATGCCCGAGGAACGGATCA	0.582000													4	221	---	---	---	---	0	0	0.014758	0	0
COL20A1	57642	broad.mit.edu	37	20	61956821	61956821	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr20:61956821G>A	uc011aau.1	+	28	3423	c.3323G>A	c.(3322-3324)GGA>GAA	p.G1108E	COL20A1_uc011aav.1_Missense_Mutation_p.G929E	NM_020882	NP_065933	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1108	Collagen-like 1.				cell adhesion	collagen|extracellular space	structural molecule activity			central_nervous_system(1)	1	all_cancers(38;1.39e-10)					GGAGAGAAGGGAGACCATGGG	0.667000													5	122	---	---	---	---	0	0	0.021553	0	0
DGCR8	54487	broad.mit.edu	37	22	20079439	20079439	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr22:20079439G>A	uc002zri.2	+	7	1902	c.1552G>A	c.(1552-1554)GAG>AAG	p.E518K	DGCR8_uc010grz.2_Missense_Mutation_p.E518K|DGCR8_uc002zrj.2_Missense_Mutation_p.E161K	NM_022720	NP_073557	Q8WYQ5	DGCR8_HUMAN	DiGeorge syndrome critical region gene 8	518	Necessary for interaction with DROSHA.|Necessary for heme-binding and pri-miRNA processing.|DRBM 1.				primary miRNA processing	cytoplasm|cytoplasm|microtubule cytoskeleton|nucleolus|nucleoplasm	double-stranded RNA binding|metal ion binding|protein binding				0	Colorectal(54;0.0993)					CATCCTGCACGAGTACATGCA	0.463000													32	31	---	---	---	---	0	0	0.111260	0	0
LOC96610	96610	broad.mit.edu	37	22	22661478	22661478	+	RNA	SNP	T	G	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr22:22661478T>G	uc011aim.1	+	28		c.1702T>G			LOC96610_uc011aiq.1_RNA|LOC96610_uc011aip.1_RNA|LOC96610_uc010gto.2_RNA					Parts of antibodies, mostly variable regions.												0						CAGATGCGTCTGAAGAAACAT	0.488000													4	93	---	---	---	---	0	0	0.038147	0	0
TMEM89	440955	broad.mit.edu	37	3	48658391	48658391	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr3:48658391G>A	uc011bbo.1	-	2	364	c.364C>T	c.(364-366)CTC>TTC	p.L122F		NM_001008269	NP_001008270	A2RUT3	TMM89_HUMAN	transmembrane protein 89 precursor	122	Cytoplasmic (Potential).					integral to membrane					0				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		ACCCCACGGAGCAGGGTGTGG	0.612000													3	118	---	---	---	---	0	0	0.150653	0	0
LOC348926	348926	broad.mit.edu	37	4	3944111	3944111	+	RNA	SNP	A	T	T	rs147372971	by1000genomes	TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr4:3944111A>T	uc011bvu.1	-	6		c.2971T>A			LOC348926_uc003ghn.2_RNA	NR_024253				Homo sapiens hypothetical protein LOC348926, mRNA (cDNA clone IMAGE:4546485), partial cds.												0						CTTTAGTATTATGCAGATGCT	0.557000													5	40	---	---	---	---	0	0	0.093190	0	0
CPE	1363	broad.mit.edu	37	4	166416761	166416761	+	Missense_Mutation	SNP	A	G	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr4:166416761A>G	uc003irg.3	+	8	1541	c.1264A>G	c.(1264-1266)ACA>GCA	p.T422A		NM_001873	NP_001864	P16870	CBPE_HUMAN	carboxypeptidase E preproprotein	422					cardiac left ventricle morphogenesis|neuropeptide signaling pathway|protein modification process	extracellular region|nucleus|plasma membrane	metallocarboxypeptidase activity|protein binding|zinc ion binding			large_intestine(1)|ovary(1)|skin(1)	3	all_hematologic(180;0.221)	Prostate(90;0.0962)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.137)	Glucagon recombinant(DB00040)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CTATAAACTTACAGCCTCAGC	0.408000													10	181	---	---	---	---	0	0	0.080935	0	0
IK	3550	broad.mit.edu	37	5	140032663	140032663	+	Missense_Mutation	SNP	A	T	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr5:140032663A>T	uc003lgq.2	+	5	448	c.338A>T	c.(337-339)GAT>GTT	p.D113V	IK_uc011czk.1_Missense_Mutation_p.D113V	NM_006083	NP_006074	Q13123	RED_HUMAN	RED protein	113					cell-cell signaling|immune response	extracellular space|nucleus|soluble fraction				large_intestine(1)	1		all_hematologic(541;4.8e-07)|all_lung(500;0.000434)|Lung NSC(810;0.00161)|Breast(839;0.128)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGAACAAAGATTATGAAGAA	0.502000													34	80	---	---	---	---	0	0	0.069456	0	0
ADAMTS2	9509	broad.mit.edu	37	5	178541107	178541107	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr5:178541107G>A	uc003mjw.2	-	22	3397	c.3397C>T	c.(3397-3399)CGG>TGG	p.R1133W	uc003mjv.3_5'Flank	NM_014244	NP_055059	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1	1133					collagen catabolic process	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GGTGATGGCCGCACCTCCATG	0.587000													4	183	---	---	---	---	0	0	0.150653	0	0
OGDH	4967	broad.mit.edu	37	7	44663986	44663986	+	Missense_Mutation	SNP	C	T	T	rs150057913		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr7:44663986C>T	uc003tln.2	+	2	153	c.44C>T	c.(43-45)ACG>ATG	p.T15M	OGDH_uc003tlm.2_Missense_Mutation_p.T15M|OGDH_uc011kbx.1_Missense_Mutation_p.T15M|OGDH_uc011kby.1_Missense_Mutation_p.T15M|OGDH_uc003tlp.2_Missense_Mutation_p.T15M|OGDH_uc011kbz.1_Translation_Start_Site	NM_002541	NP_002532	Q02218	ODO1_HUMAN	oxoglutarate dehydrogenase isoform 1 precursor	15					glycolysis|lysine catabolic process|tricarboxylic acid cycle	mitochondrial matrix|mitochondrial membrane	oxoglutarate dehydrogenase (succinyl-transferring) activity|thiamine pyrophosphate binding			upper_aerodigestive_tract(1)|ovary(1)	2					NADH(DB00157)	AGGCCATTGACGGCTTCCCAG	0.398000													4	224	---	---	---	---	0	0	0.014758	0	0
COL22A1	169044	broad.mit.edu	37	8	139890069	139890069	+	Silent	SNP	G	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr8:139890069G>A	uc003yvd.2	-	3	1029	c.582C>T	c.(580-582)TCC>TCT	p.S194S		NM_152888	NP_690848	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	194	VWFA.				cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(11)|pancreas(1)|skin(1)	13	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			AGACGTGGGCGGACTTGGGCT	0.672000										HNSCC(7;0.00092)			3	85	---	---	---	---	0	0	0.115264	0	0
TUBBP5	643224	broad.mit.edu	37	9	141071097	141071097	+	Missense_Mutation	SNP	G	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr9:141071097G>A	uc004com.2	+	4	761	c.500G>A	c.(499-501)TGC>TAC	p.C167Y	TUBBP5_uc010ncq.2_3'UTR					RecName: Full=Putative tubulin beta-4q chain;												0						GTCACCACGTGCCTGCGCTTC	0.577000													4	67	---	---	---	---	0	0	0.014758	0	0
STS	412	broad.mit.edu	37	X	7177465	7177465	+	Missense_Mutation	SNP	A	G	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:7177465A>G	uc004cry.3	+	5	718	c.473A>G	c.(472-474)TAT>TGT	p.Y158C		NM_000351	NP_000342	P08842	STS_HUMAN	steryl-sulfatase precursor	158	Lumenal.				female pregnancy|steroid catabolic process	endoplasmic reticulum membrane|endosome|Golgi apparatus|integral to membrane|lysosome|microsome|plasma membrane	metal ion binding|steryl-sulfatase activity			central_nervous_system(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)			Estrone(DB00655)	GGCTTCAATTATTTCTATGGG	0.522000									Ichthyosis				3	138	---	---	---	---	0	0	0.150653	0	0
AMOT	154796	broad.mit.edu	37	X	112058796	112058796	+	Silent	SNP	C	T	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:112058796C>T	uc004epr.2	-	2	1182	c.1182G>A	c.(1180-1182)CAG>CAA	p.Q394Q	AMOT_uc004eps.2_5'UTR|AMOT_uc004ept.1_Silent_p.Q394Q	NM_001113490	NP_001106962	Q4VCS5	AMOT_HUMAN	angiomotin isoform 1	394					actin cytoskeleton organization|cell-cell junction assembly|negative regulation of angiogenesis|negative regulation of vascular permeability|positive regulation of blood vessel endothelial cell migration|positive regulation of cell size|positive regulation of stress fiber assembly|regulation of cell migration	actin filament|cell surface|cytoplasm|endocytic vesicle|external side of plasma membrane|integral to membrane|lamellipodium|ruffle|stress fiber|tight junction|tight junction	angiostatin binding|protein binding|receptor activity			ovary(1)	1						gctgctgctgctgttgttggt	0.338000													3	33	---	---	---	---	0	0	0.115264	0	0
ZIC3	7547	broad.mit.edu	37	X	136649433	136649433	+	Missense_Mutation	SNP	C	T	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:136649433C>T	uc004fak.2	+	1	1088	c.583C>T	c.(583-585)CGT>TGT	p.R195C		NM_003413	NP_003404	O60481	ZIC3_HUMAN	zinc finger protein of the cerebellum 3	195					cell differentiation|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|breast(1)	3	Acute lymphoblastic leukemia(192;0.000127)					GCTGTTCGGCCGTGCTGACCC	0.672000													4	112	---	---	---	---	0	0	0.021553	0	0
Unknown	0	broad.mit.edu	37	1	59096940	59096941	+	IGR	INS	-	G	G			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:59096940_59096941insG								TACSTD2 (53774 upstream) : MYSM1 (28649 downstream)																							TTTTTGCACAAGGGGGTCTCCA	0.475													7	162	---	---	---	---					
LRRIQ3	127255	broad.mit.edu	37	1	74575212	74575213	+	Frame_Shift_Ins	INS	-	T	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:74575212_74575213insT	uc001dfy.3	-	5	924_925	c.732_733insA	c.(730-735)AAACAGfs	p.K244fs	LRRIQ3_uc001dfz.3_RNA	NM_001105659	NP_001099129	A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	244_245				QQEKII -> TAGKNY (in Ref. 1; BAD18621).						ovary(2)	2						TTTTCCTGCTGTTTTTTTTTGT	0.327													11	152	---	---	---	---					
RPTN	126638	broad.mit.edu	37	1	152127881	152127884	+	Frame_Shift_Del	DEL	TGTC	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:152127881_152127884delTGTC	uc001ezs.1	-	3	1756_1759	c.1691_1694delGACA	c.(1690-1695)AGACAAfs	p.R564fs		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	564_565	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0						GCTCTGGCCTTGTCTGTCTGTCTG	0.485													7	1465	---	---	---	---					
BAT2L2	23215	broad.mit.edu	37	1	171511148	171511149	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:171511148_171511149insA	uc010pmg.1	+	16	4803_4804	c.4537_4538insA	c.(4537-4539)GAAfs	p.E1513fs	BAT2L2_uc010pmh.1_Frame_Shift_Ins_p.E490fs	NM_015172	NP_055987	Q9Y520	PRC2C_HUMAN	HBxAg transactivated protein 2	1513							protein C-terminus binding				0						AGAGAGGGATGAAAAAAAAAAT	0.391													7	110	---	---	---	---					
Unknown	0	broad.mit.edu	37	1	218156531	218156533	+	IGR	DEL	GGA	-	-	rs77544157		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr1:218156531_218156533delGGA								SPATA17 (116029 upstream) : RRP15 (302096 downstream)																							gagggaggagggaggaggaggag	0.389													2	4	---	---	---	---					
LZTS2	84445	broad.mit.edu	37	10	102763415	102763417	+	In_Frame_Del	DEL	CCT	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr10:102763415_102763417delCCT	uc001ksj.2	+	3	629_631	c.560_562delCCT	c.(559-564)GCCTCC>GCC	p.S197del	LZTS2_uc010qpw.1_In_Frame_Del_p.S197del|LZTS2_uc001ksk.2_In_Frame_Del_p.S197del|LZTS2_uc001ksl.2_In_Frame_Del_p.S197del|LZTS2_uc001ksm.2_RNA	NM_032429	NP_115805	Q9BRK4	LZTS2_HUMAN	leucine zipper, putative tumor suppressor 2	197	Ser-rich.|Required for centrosomal localization (By similarity).				cell division|mitosis|Wnt receptor signaling pathway	membrane|microtubule|microtubule organizing center				ovary(2)|large_intestine(1)|breast(1)	4				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		GGGGGCCCTGcctcctcctcctc	0.557													12	372	---	---	---	---					
POLL	27343	broad.mit.edu	37	10	103345131	103345133	+	In_Frame_Del	DEL	GGA	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr10:103345131_103345133delGGA	uc001ktg.1	-	3	1279_1281	c.513_515delTCC	c.(511-516)CCTCCC>CCC	p.171_172PP>P	DPCD_uc010qpz.1_Intron|POLL_uc001ktd.1_5'Flank|POLL_uc001kte.1_5'Flank|POLL_uc001kth.1_Intron|POLL_uc001kti.1_In_Frame_Del_p.171_172PP>P|POLL_uc001ktj.1_In_Frame_Del_p.171_172PP>P|POLL_uc001ktf.2_In_Frame_Del_p.171_172PP>P|POLL_uc001ktk.1_Intron|POLL_uc010qqa.1_Intron|POLL_uc010qqb.1_Intron|POLL_uc001ktm.2_In_Frame_Del_p.171_172PP>P|POLL_uc001ktl.2_In_Frame_Del_p.83_84PP>P|POLL_uc010qqc.1_Intron|POLL_uc010qqd.1_Intron|DPCD_uc001ktn.2_5'Flank	NM_013274	NP_037406	Q9UGP5	DPOLL_HUMAN	DNA-directed DNA polymerase lambda	171_172					DNA replication|nucleotide-excision repair|somatic hypermutation of immunoglobulin genes	nucleus	DNA binding|DNA-directed DNA polymerase activity|lyase activity|metal ion binding				0		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		AGGCCTGGTGGGAGGAGGAGGAG	0.591								DNA_polymerases_(catalytic_subunits)					8	160	---	---	---	---					
TCF7L2	6934	broad.mit.edu	37	10	114925316	114925317	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr10:114925316_114925317insA	uc001lae.3	+	14	1901_1902	c.1394_1395insA	c.(1393-1395)AGAfs	p.R465fs	TCF7L2_uc001lac.3_Frame_Shift_Ins_p.R459fs|TCF7L2_uc010qrk.1_Frame_Shift_Ins_p.E435fs|TCF7L2_uc010qrl.1_Frame_Shift_Ins_p.R442fs|TCF7L2_uc010qrm.1_Frame_Shift_Ins_p.E441fs|TCF7L2_uc010qrn.1_Frame_Shift_Ins_p.E384fs|TCF7L2_uc001lad.3_Frame_Shift_Ins_p.E431fs|TCF7L2_uc001lag.3_Frame_Shift_Ins_p.E465fs|TCF7L2_uc001laf.3_Frame_Shift_Ins_p.R442fs|TCF7L2_uc010qro.1_Frame_Shift_Ins_p.E418fs|TCF7L2_uc001lah.2_3'UTR|TCF7L2_uc010qrp.1_3'UTR|TCF7L2_uc010qrq.1_3'UTR|TCF7L2_uc010qrr.1_Frame_Shift_Ins_p.R397fs|TCF7L2_uc010qrs.1_Frame_Shift_Ins_p.R353fs|TCF7L2_uc010qrt.1_Frame_Shift_Ins_p.R353fs|TCF7L2_uc010qru.1_Frame_Shift_Ins_p.E357fs|TCF7L2_uc010qrv.1_3'UTR|TCF7L2_uc010qrw.1_3'UTR|TCF7L2_uc010qrx.1_3'UTR	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1	482	Promoter-specific activation domain.				anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding	p.R465C(1)		large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		GTTTCTAGGAGAAAAAAAAAGT	0.520													12	304	---	---	---	---					
Unknown	0	broad.mit.edu	37	11	49356208	49356208	+	IGR	DEL	T	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:49356208delT								FOLH1 (125986 upstream) : LOC440040 (223872 downstream)																							GATTCTAGTATTTTTTTTAGT	0.299													8	286	---	---	---	---					
FAU	2197	broad.mit.edu	37	11	64888248	64888250	+	In_Frame_Del	DEL	TCT	-	-	rs1065065		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:64888248_64888250delTCT	uc001ocx.2	-	5	412_414	c.305_307delAGA	c.(304-309)AAGACA>ACA	p.K102del	FAU_uc001ocy.1_3'UTR|MRPL49_uc001ocz.1_5'Flank|MRPL49_uc001oda.1_5'Flank	NM_001997	NP_001988	P35544	UBIM_HUMAN	ubiquitin-like protein fubi and ribosomal	Error:Variant_position_missing_in_P35544_after_alignment											0						GCCCGACCTGTCTTCTTCTTCTT	0.542													9	238	---	---	---	---					
Unknown	0	broad.mit.edu	37	11	128800726	128800727	+	IGR	INS	-	A	A	rs66879759		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr11:128800726_128800727insA								KCNJ5 (12777 upstream) : TP53AIP1 (4545 downstream)																							ttagggaggccggggttaggga	0.000													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	5148154	5148154	+	IGR	DEL	C	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr12:5148154delC								KCNA1 (120734 upstream) : KCNA5 (4931 downstream)																							CTCCTTCCTGCCCCCCCTCCC	0.527													2	4	---	---	---	---					
MIR1244	100302285	broad.mit.edu	37	12	9392182	9392183	+	5'Flank	INS	-	T	T			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr12:9392182_9392183insT	hsa-mir-1244-3|MI0015975	-						uc001qvm.1_5'Flank																	0						TTTTTTACAAGTTTTTTTTTTC	0.371													8	35	---	---	---	---					
PRB2	653247	broad.mit.edu	37	12	11546506	11546508	+	In_Frame_Del	DEL	TTG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr12:11546506_11546508delTTG	uc010shk.1	-	3	539_541	c.504_506delCAA	c.(502-507)AACAAG>AAG	p.N168del		NM_006248	NP_006239			proline-rich protein BstNI subfamily 2												0		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACTTCGGGACTTGTTGTCTCCTT	0.596													11	753	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	24737258	24737263	+	5'Flank	DEL	CCCCCA	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr12:24737258_24737263delCCCCCA	uc001rgb.1	-											Homo sapiens cDNA FLJ32894 fis, clone TESTI2004994.																		CTTCGATTAGcccccacccccacccc	0.432													13	7	---	---	---	---					
R3HDM2	22864	broad.mit.edu	37	12	57674205	57674207	+	In_Frame_Del	DEL	TGC	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr12:57674205_57674207delTGC	uc009zpm.1	-	12	1271_1273	c.1236_1238delGCA	c.(1234-1239)CAGCAA>CAA	p.412_413QQ>Q	R3HDM2_uc010srn.1_RNA|R3HDM2_uc001snu.2_In_Frame_Del_p.73_74QQ>Q|R3HDM2_uc001snr.2_In_Frame_Del_p.139_140QQ>Q|R3HDM2_uc001sns.2_In_Frame_Del_p.412_413QQ>Q|R3HDM2_uc001snt.2_In_Frame_Del_p.426_427QQ>Q|R3HDM2_uc009zpn.1_In_Frame_Del_p.35_36QQ>Q	NM_014925	NP_055740	Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	412_413	Gln-rich.					nucleus	nucleic acid binding			ovary(2)	2						AGCAGGAAGTtgctgctgctgct	0.488													7	144	---	---	---	---					
CUX2	23316	broad.mit.edu	37	12	111758235	111758237	+	In_Frame_Del	DEL	TCC	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr12:111758235_111758237delTCC	uc001tsa.1	+	17	2575_2577	c.2422_2424delTCC	c.(2422-2424)TCCdel	p.S813del		NM_015267	NP_056082	O14529	CUX2_HUMAN	cut-like 2	813	Poly-Ser.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(3)|skin(2)|breast(1)	6						GCCCTCGCTGTCCTCCTCCTCCT	0.749													10	114	---	---	---	---					
SBNO1	55206	broad.mit.edu	37	12	123794283	123794283	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr12:123794283delT	uc010tap.1	-	25	3416	c.3416delA	c.(3415-3417)AATfs	p.N1139fs	SBNO1_uc009zxv.2_RNA|SBNO1_uc010tao.1_Frame_Shift_Del_p.N1138fs|SBNO1_uc010taq.1_Frame_Shift_Del_p.N90fs|SBNO1_uc001ues.1_Frame_Shift_Del_p.N90fs	NM_018183	NP_060653	A3KN83	SBNO1_HUMAN	sno, strawberry notch homolog 1	1139							ATP binding|DNA binding|hydrolase activity			breast(5)|skin(2)|ovary(1)|kidney(1)	9	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		ATATCTTCCATTTTTTTTGGC	0.388													12	200	---	---	---	---					
RXFP2	122042	broad.mit.edu	37	13	32376428	32376429	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr13:32376428_32376429insA	uc001utt.2	+	18	2222_2223	c.2151_2152insA	c.(2149-2154)ATTAAAfs	p.I717fs	RXFP2_uc010aba.2_Frame_Shift_Ins_p.I676fs	NM_130806	NP_570718	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	717_718	Cytoplasmic (Potential).					integral to membrane|plasma membrane					0		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		TTTTCAAAATTAAAAAAAAAAG	0.351													7	199	---	---	---	---					
COL4A1	1282	broad.mit.edu	37	13	110857850	110857850	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr13:110857850delT	uc001vqw.3	-	16	1016	c.894delA	c.(892-894)AAAfs	p.K298fs	COL4A1_uc010agl.2_Intron	NM_001845	NP_001836	P02462	CO4A1_HUMAN	alpha 1 type IV collagen preproprotein	298	Triple-helical region.				angiogenesis|axon guidance		extracellular matrix structural constituent|platelet-derived growth factor binding			ovary(3)|lung(1)|central_nervous_system(1)|pancreas(1)	6	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CGGGACTCCCTTTTTCCCCTT	0.398													11	427	---	---	---	---					
NR2E3	10002	broad.mit.edu	37	15	72101852	72101852	+	5'Flank	DEL	G	-	-	rs34325422		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr15:72101852delG	uc002ati.2	+						NR2E3_uc002ath.1_5'Flank	NM_014249	NP_055064	Q9Y5X4	NR2E3_HUMAN	photoreceptor-specific nuclear receptor isoform						phototransduction|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription from RNA polymerase II promoter|visual perception	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding				0						GAGCAGCGCAGGGGGCTGGTG	0.647													4	3	---	---	---	---					
IQGAP1	8826	broad.mit.edu	37	15	91019925	91019925	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr15:91019925delA	uc002bpl.1	+	24	2916	c.2815delA	c.(2815-2817)AAAfs	p.K939fs		NM_003870	NP_003861	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	939					energy reserve metabolic process|regulation of insulin secretion|small GTPase mediated signal transduction	actin filament|cytoplasm|midbody|nucleus|plasma membrane	calmodulin binding|GTPase inhibitor activity|protein phosphatase binding|Ras GTPase activator activity			ovary(2)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	8	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AAAACTTACCAAAAAAAATAA	0.363													7	205	---	---	---	---					
Unknown	0	broad.mit.edu	37	16	13966971	13966973	+	IGR	DEL	TGG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:13966971_13966973delTGG								SHISA9 (632699 upstream) : ERCC4 (47041 downstream)																							gtggtggtgatggtggtggtggt	0.177													5	9	---	---	---	---					
Unknown	0	broad.mit.edu	37	16	18762017	18762020	+	IGR	DEL	GGGA	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:18762017_18762020delGGGA								ABCC6P1 (152412 upstream) : RPS15A (32257 downstream)																							ggcaggggaggggagggagggagg	0.034													2	4	---	---	---	---					
SLC5A11	115584	broad.mit.edu	37	16	24921737	24921739	+	In_Frame_Del	DEL	CAG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:24921737_24921739delCAG	uc002dmu.2	+	15	1993_1995	c.1761_1763delCAG	c.(1759-1764)GCCAGC>GCC	p.S592del	SLC5A11_uc002dms.2_In_Frame_Del_p.S528del|SLC5A11_uc010vcd.1_In_Frame_Del_p.S557del|SLC5A11_uc002dmt.2_In_Frame_Del_p.S436del|SLC5A11_uc010vce.1_In_Frame_Del_p.S522del|SLC5A11_uc010bxt.2_In_Frame_Del_p.S528del|SLC5A11_uc002dmv.2_In_Frame_Del_p.S215del	NM_052944	NP_443176	Q8WWX8	SC5AB_HUMAN	solute carrier family 5 (sodium/glucose	592	Cytoplasmic (Potential).				apoptosis|carbohydrate transport|sodium ion transport	integral to membrane|plasma membrane	polyol transmembrane transporter activity|symporter activity			ovary(2)	2				GBM - Glioblastoma multiforme(48;0.0365)		TGCCAGAGGCCAGCAGCAGCAGC	0.542													7	159	---	---	---	---					
SRCAP	10847	broad.mit.edu	37	16	30736370	30736371	+	Frame_Shift_Ins	INS	-	C	C			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:30736370_30736371insC	uc002dze.1	+	25	6010_6011	c.5625_5626insC	c.(5623-5628)CAGCCCfs	p.Q1875fs	SRCAP_uc002dzf.2_RNA|SRCAP_uc002dzg.1_Frame_Shift_Ins_p.Q1670fs|SRCAP_uc010bzz.1_Frame_Shift_Ins_p.Q1445fs	NM_006662	NP_006653	Q6ZRS2	SRCAP_HUMAN	Snf2-related CBP activator protein	1875_1876	Pro-rich.				interspecies interaction between organisms|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	Golgi apparatus|nucleus|protein complex	ATP binding|DNA binding|helicase activity|histone acetyltransferase activity|transcription coactivator activity			ovary(3)|skin(1)	4			Colorectal(24;0.198)			CTCGACGCCAGCCCCCCCCACC	0.569													14	356	---	---	---	---					
ACD	65057	broad.mit.edu	37	16	67693646	67693648	+	In_Frame_Del	DEL	GCA	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr16:67693646_67693648delGCA	uc002etq.3	-	3	888_890	c.551_553delTGC	c.(550-555)CTGCAG>CAG	p.L184del	ACD_uc002etp.3_In_Frame_Del_p.L181del|ACD_uc002etr.3_In_Frame_Del_p.L181del|ACD_uc010vjt.1_In_Frame_Del_p.L174del|PARD6A_uc002ets.2_5'Flank|PARD6A_uc002ett.2_5'Flank|PARD6A_uc002etu.2_5'Flank	NM_001082486	NP_001075955	Q96AP0	ACD_HUMAN	adrenocortical dysplasia homolog isoform 1	184					intracellular protein transport|negative regulation of telomere maintenance via telomerase|positive regulation of single-stranded telomeric DNA binding|positive regulation of telomerase activity|protection from non-homologous end joining at telomere|protein localization to chromosome, telomeric region|telomere assembly	nuclear telomere cap complex|nucleoplasm	DNA binding|DNA polymerase binding			pancreas(1)	1		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0143)|Epithelial(162;0.047)|all cancers(182;0.228)		CCGCAGTCCTGCAGCAGCAGCAG	0.650													8	384	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	19015728	19015729	+	5'Flank	INS	-	A	A			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr17:19015728_19015729insA	uc010vym.1	-											DL492381																		CATCAAGAAGGAAAAaccactc	0.277													7	61	---	---	---	---					
NUDT19	390916	broad.mit.edu	37	19	33200189	33200190	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr19:33200189_33200190delCT	uc010edf.2	+	2	813_814	c.813_814delCT	c.(811-816)GCCTCTfs	p.A271fs		NM_001105570	NP_001099040	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety	271_272						mitochondrion|peroxisome	hydrolase activity|metal ion binding				0	Esophageal squamous(110;0.137)					CAAACTTTGCCTCTCTCTCTGA	0.450													7	328	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	52233917	52233918	+	IGR	INS	-	G	G	rs76664622		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr19:52233917_52233918insG								HAS1 (6696 upstream) : FPR1 (15109 downstream)																							gaggagggggtgggggGGCTGG	0.203													4	3	---	---	---	---					
CNOT3	4849	broad.mit.edu	37	19	54649671	54649671	+	Frame_Shift_Del	DEL	T	-	-	rs36665	byFrequency	TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr19:54649671delT	uc002qdj.1	+	9	1040	c.729delT	c.(727-729)CCCfs	p.P243fs	CNOT3_uc010yel.1_Frame_Shift_Del_p.P243fs|CNOT3_uc002qdi.2_Frame_Shift_Del_p.P156fs|CNOT3_uc002qdk.1_Frame_Shift_Del_p.P243fs|CNOT3_uc010ere.1_RNA	NM_014516	NP_055331	O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	243					nuclear-transcribed mRNA poly(A) tail shortening|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasmic mRNA processing body|cytosol|nucleus	protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCACCTCCCCTCCCAGCCACA	0.632													8	252	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	127489361	127489363	+	IGR	DEL	GCA	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr2:127489361_127489363delGCA								GYPC (35116 upstream) : BIN1 (316244 downstream)																							CCAAAAAGATgcagcagcagcag	0.502													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	132768083	132768084	+	IGR	INS	-	G	G	rs111469343	by1000genomes	TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr2:132768083_132768084insG								C2orf27B (208849 upstream) : NCRNA00164 (137080 downstream)																							TCTTGATGTTAACTATcagctg	0.218													3	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	133019311	133019315	+	IGR	DEL	GCACA	-	-	rs78165606		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr2:133019311_133019315delGCACA								NCRNA00164 (3769 upstream) : GPR39 (154832 downstream)																							CCCAACTCTTGCACAGCACAAGTAC	0.395													8	219	---	---	---	---					
ALPP	250	broad.mit.edu	37	2	233243529	233243531	+	In_Frame_Del	DEL	TGC	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr2:233243529_233243531delTGC	uc002vsq.2	+	1	182_184	c.17_19delTGC	c.(16-21)ATGCTG>ATG	p.L13del	ALPP_uc002vsr.2_5'Flank	NM_001632	NP_001623	P05187	PPB1_HUMAN	placental alkaline phosphatase preproprotein	13						anchored to membrane|cell surface|integral to membrane|plasma membrane	alkaline phosphatase activity|metal ion binding			ovary(1)	1		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GGGCCCTGCAtgctgctgctgct	0.542													10	108	---	---	---	---					
FRG1B	284802	broad.mit.edu	37	20	29625899	29625900	+	Frame_Shift_Ins	INS	-	AT	AT			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr20:29625899_29625900insAT	uc010ztl.1	+	2	85_86	c.53_54insAT	c.(52-54)AAAfs	p.K18fs	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Intron					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						GGCTATGGAAAATATCTTGGTA	0.342													7	193	---	---	---	---					
DDX27	55661	broad.mit.edu	37	20	47858504	47858504	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr20:47858504delA	uc002xuh.2	+	17	2126	c.2065delA	c.(2065-2067)AAAfs	p.K689fs		NM_017895	NP_060365	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	689						nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			kidney(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GAAGGATGCCAAAAAAAAGGG	0.488													11	169	---	---	---	---					
Unknown	0	broad.mit.edu	37	21	10899065	10899066	+	IGR	INS	-	T	T	rs113335631		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr21:10899065_10899066insT								None (None upstream) : TPTE (7677 downstream)																							ACCATTTGCTATTTTTTTTTTA	0.431													13	233	---	---	---	---					
Unknown	0	broad.mit.edu	37	21	47555751	47555764	+	IGR	DEL	CCCAGCCTCCCCTC	-	-	rs72149464		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr21:47555751_47555764delCCCAGCCTCCCCTC								COL6A2 (2988 upstream) : FTCD (413 downstream)																							agcgttccctcccagcctcccctccccagcctcc	0.271													4	6	---	---	---	---					
MED12L	116931	broad.mit.edu	37	3	151148114	151148116	+	In_Frame_Del	DEL	CAG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr3:151148114_151148116delCAG	uc003eyp.2	+	42	6369_6371	c.6331_6333delCAG	c.(6331-6333)CAGdel	p.Q2115del	MED12L_uc011bnz.1_In_Frame_Del_p.Q1779del	NM_053002	NP_443728	Q86YW9	MD12L_HUMAN	mediator of RNA polymerase II transcription,	2115	Gln-rich.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	mediator complex				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCAGCAGACCCAGCAGCAGCAGC	0.527													8	139	---	---	---	---					
FXR1	8087	broad.mit.edu	37	3	180666228	180666228	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr3:180666228delA	uc003fkq.2	+	5	386	c.364delA	c.(364-366)AAAfs	p.K122fs	FXR1_uc003fkp.2_Frame_Shift_Del_p.K37fs|FXR1_uc003fkr.2_Frame_Shift_Del_p.K122fs|FXR1_uc011bqj.1_Frame_Shift_Del_p.K36fs|FXR1_uc003fks.2_Frame_Shift_Del_p.K36fs|FXR1_uc011bqk.1_Frame_Shift_Del_p.K73fs|FXR1_uc011bql.1_Frame_Shift_Del_p.K109fs	NM_005087	NP_005078	P51114	FXR1_HUMAN	fragile X mental retardation-related protein 1	122					apoptosis|cell differentiation|muscle organ development	nucleolus|polysome				breast(1)	1	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			TAAAACTGTCAAAAAAAATAC	0.333													7	151	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	177400751	177400765	+	IGR	DEL	GAGGAAGAGGAGGAA	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr4:177400751_177400765delGAGGAAGAGGAGGAA								SPCS3 (147357 upstream) : VEGFC (203926 downstream)																							agaggaataggaggaagaggaggaagaggaagagg	0.084													9	5	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	5417142	5417142	+	IGR	DEL	G	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr5:5417142delG								ADAMTS16 (96731 upstream) : KIAA0947 (5665 downstream)																							aggaggaggaggagaaggGGC	0.209													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	104043368	104043370	+	IGR	DEL	GAG	-	-	rs71588364		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr5:104043368_104043370delGAG								None (None upstream) : RAB9BP1 (391805 downstream)																							ggaggaggaagaggaggaggagg	0.089													3	5	---	---	---	---					
MCC	4163	broad.mit.edu	37	5	112824048	112824049	+	In_Frame_Ins	INS	-	GCC	GCC			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr5:112824048_112824049insGCC	uc003kql.3	-	1	479_480	c.63_64insGGC	c.(61-66)insGGC	p.21_22insG		NM_001085377	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers isoform 1	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell migration|negative regulation of epithelial cell proliferation|Wnt receptor signaling pathway	cytoplasm|nucleus|plasma membrane	protein binding|receptor activity			ovary(1)	1		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		ctgctgccgctgccgccgccgc	0.391													8	23	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	7518105	7518106	+	IGR	INS	-	T	T	rs150873580		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr6:7518105_7518106insT								RIOK1 (99837 upstream) : DSP (23764 downstream)																							AAGTGAATCAAttttttttttt	0.173													10	18	---	---	---	---					
GABRR2	2570	broad.mit.edu	37	6	89975427	89975429	+	In_Frame_Del	DEL	AAG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr6:89975427_89975429delAAG	uc003pnb.2	-	7	875_877	c.867_869delCTT	c.(865-870)TTCTTG>TTG	p.F289del	GABRR2_uc011dzx.1_In_Frame_Del_p.F165del	NM_002043	NP_002034	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) receptor, rho 2	289	Helical; (Potential).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity				0		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)		TGTTTGGAGCAAGAAGAAGAAGA	0.517													7	121	---	---	---	---					
Unknown	0	broad.mit.edu	37	6	170402621	170402622	+	IGR	DEL	GG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr6:170402621_170402622delGG								C6orf208 (199652 upstream) : LOC154449 (160800 downstream)																							agcgtggtgtggggggggaccg	0.248													4	8	---	---	---	---					
MPP6	51678	broad.mit.edu	37	7	24705666	24705666	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr7:24705666delA	uc003swx.2	+	9	1209	c.910delA	c.(910-912)AAAfs	p.K304fs	MPP6_uc003swy.2_Frame_Shift_Del_p.K304fs|MPP6_uc010kur.2_5'UTR	NM_016447	NP_057531	Q9NZW5	MPP6_HUMAN	membrane protein, palmitoylated 6	304					protein complex assembly		protein binding				0						TATAAGTAGCAAAAAAAAGAA	0.299													8	274	---	---	---	---					
TMEM60	85025	broad.mit.edu	37	7	77423460	77423460	+	Frame_Shift_Del	DEL	T	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr7:77423460delT	uc003ugn.2	-	2	458	c.231delA	c.(229-231)AAAfs	p.K77fs		NM_032936	NP_116325	Q9H2L4	TMM60_HUMAN	transmembrane protein 60	77						integral to membrane					0						GGTACCAGGCTTTTTTTTTAA	0.408													7	126	---	---	---	---					
PTCD1	26024	broad.mit.edu	37	7	99032605	99032607	+	In_Frame_Del	DEL	CTC	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr7:99032605_99032607delCTC	uc003uqh.2	-	2	390_392	c.259_261delGAG	c.(259-261)GAGdel	p.E87del	PTCD1_uc011kiw.1_In_Frame_Del_p.E136del	NM_015545	NP_056360	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	87										ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			TCCCAAAACTCTCCTCCTCCTCC	0.606													7	241	---	---	---	---					
LUC7L2	51631	broad.mit.edu	37	7	139094365	139094366	+	Frame_Shift_Del	DEL	AG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr7:139094365_139094366delAG	uc003vux.2	+	7	1118_1119	c.744_745delAG	c.(742-747)GAAGAGfs	p.E248fs	LUC7L2_uc011kqs.1_Frame_Shift_Del_p.E245fs|LUC7L2_uc011kqt.1_Frame_Shift_Del_p.E314fs|LUC7L2_uc003vuy.2_Frame_Shift_Del_p.E247fs|LUC7L2_uc003vuz.1_Frame_Shift_Del_p.E195fs|LUC7L2_uc003vva.2_Frame_Shift_Del_p.E195fs	NM_016019	NP_057103	Q9Y383	LC7L2_HUMAN	LUC7-like 2	248_249	Arg/Ser-rich.						enzyme binding|metal ion binding				0	Melanoma(164;0.242)					AACGAAGAGAAGAGAGAGAGAG	0.391													8	59	---	---	---	---					
Unknown	0	broad.mit.edu	37	8	128098663	128098671	+	IGR	DEL	CAGCAGCTG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr8:128098663_128098671delCAGCAGCTG								FAM84B (528197 upstream) : LOC727677 (203391 downstream)																							gcaggggtcacagcagctgcagcagctgc	0.191													10	23	---	---	---	---					
Unknown	0	broad.mit.edu	37	8	142724261	142724269	+	IGR	DEL	TGGTGATGG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr8:142724261_142724269delTGGTGATGG								FLJ43860 (206931 upstream) : MIR1302-7 (143334 downstream)																							atgatggtgatggtgatggtggtgatggt	0.029													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	3661724	3661726	+	IGR	DEL	CTG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr9:3661724_3661726delCTG								RFX3 (135741 upstream) : GLIS3 (162402 downstream)																							gctgttatcactgctgctgctgc	0.384													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	68433481	68433482	+	IGR	INS	-	CTC	CTC	rs144672547		TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr9:68433481_68433482insCTC								FAM27B (639292 upstream) : MIR1299 (568757 downstream)																							CATTTCTTCTTCTGCTGTTTTA	0.342													15	77	---	---	---	---					
C9orf43	257169	broad.mit.edu	37	9	116187646	116187648	+	In_Frame_Del	DEL	GCA	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chr9:116187646_116187648delGCA	uc004bho.3	+	10	1284_1286	c.888_890delGCA	c.(886-891)CGGCAG>CGG	p.Q304del	C9orf43_uc004bhp.2_In_Frame_Del_p.Q304del	NM_152786	NP_689999	Q8TAL5	CI043_HUMAN	hypothetical protein LOC257169	304	Gln-rich.										0						agcagcagcggcagcagcagcag	0.438													7	116	---	---	---	---					
Unknown	0	broad.mit.edu	37	X	8435065	8435067	+	IGR	DEL	GGT	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:8435065_8435067delGGT								VCX3B (515 upstream) : KAL1 (61849 downstream)																							gggaggaagaggtggtgtgtggg	0.000													3	6	---	---	---	---					
CNKSR2	22866	broad.mit.edu	37	X	21627678	21627680	+	In_Frame_Del	DEL	GAG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:21627678_21627680delGAG	uc004czx.1	+	20	2671_2673	c.2635_2637delGAG	c.(2635-2637)GAGdel	p.E886del	CNKSR2_uc004czw.2_In_Frame_Del_p.E886del|CNKSR2_uc011mjn.1_In_Frame_Del_p.E837del|CNKSR2_uc011mjo.1_In_Frame_Del_p.E856del|CNKSR2_uc004czy.2_In_Frame_Del_p.E478del	NM_014927	NP_055742	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras	886	Potential.|Poly-Glu.				regulation of signal transduction	cytoplasm|membrane	protein binding			large_intestine(1)|lung(1)	2						ggtggaggaagaggaggaggagg	0.379													7	86	---	---	---	---					
NUDT11	55190	broad.mit.edu	37	X	51239296	51239309	+	Translation_Start_Site	DEL	TCCTCGAGGCAGCC	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:51239296_51239309delTCCTCGAGGCAGCC	uc010njt.2	-	1						NM_018159	NP_060629	Q96G61	NUD11_HUMAN	nudix-type motif 11							cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|metal ion binding				0	Ovarian(276;0.236)					TTGCACTTCATCCTCGAGGCAGCCTCCTCGAGGC	0.584										HNSCC(48;0.14)			8	29	---	---	---	---					
CD99L2	83692	broad.mit.edu	37	X	149984524	149984526	+	In_Frame_Del	DEL	GTG	-	-			TCGA-EM-A3AP-01A-12D-A20C-08	TCGA-EM-A3AP-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	03ca262c-a3df-4cca-94ed-46e626da1321	fcd4c6c0-a804-409c-a0d3-950106b65912	g.chrX:149984524_149984526delGTG	uc004fel.2	-	3	274_276	c.156_158delCAC	c.(154-159)ACCACA>ACA	p.52_53TT>T	CD99L2_uc004fek.2_5'Flank|CD99L2_uc004fem.2_Intron|CD99L2_uc004fen.2_Intron|CD99L2_uc004feo.2_RNA|CD99L2_uc011myb.1_In_Frame_Del_p.52_53TT>T	NM_031462	NP_113650	Q8TCZ2	C99L2_HUMAN	CD99 antigen-like 2 isoform E3'-E4'-E3-E4	52_53	Extracellular (Potential).|Poly-Thr.				cell adhesion	cell junction|integral to membrane				large_intestine(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;6.56e-05)					CCTATTGGTTGTGGTGGTGGTGG	0.552													12	544	---	---	---	---					
