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
SPEN	23013	broad.mit.edu	37	1	16257104	16257104	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16257104T>G	uc001axk.1	+	11	4573	c.4369T>G	c.(4369-4371)TCT>GCT	p.S1457A	SPEN_uc010obp.1_Missense_Mutation_p.S1416A	NM_015001	NP_055816	Q96T58	MINT_HUMAN	spen homolog, transcriptional regulator	1457					interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|Notch signaling pathway	nucleus	nucleotide binding|protein binding|RNA binding			ovary(6)|breast(3)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	15		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCTCTCTTCATCTCGTGAAGA	0.363													7	196	---	---	---	---	PASS
SDHB	6390	broad.mit.edu	37	1	17350478	17350478	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17350478A>G	uc001bae.2	-	6	783	c.632T>C	c.(631-633)GTT>GCT	p.V211A		NM_003000	NP_002991	P21912	DHSB_HUMAN	succinate dehydrogenase complex, subunit B, iron	211					respiratory electron transport chain|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	2 iron, 2 sulfur cluster binding|3 iron, 4 sulfur cluster binding|4 iron, 4 sulfur cluster binding|electron carrier activity|metal ion binding|protein binding|succinate dehydrogenase (ubiquinone) activity|ubiquinone binding			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0049)|COAD - Colon adenocarcinoma(227;1.18e-05)|BRCA - Breast invasive adenocarcinoma(304;2.41e-05)|Kidney(64;0.000188)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)	Succinic acid(DB00139)	CTGCATAAGAACTGCAGGCCC	0.502			Mis|N|F			paraganglioma|pheochromocytoma			Familial_Paragangliomas|Carney-Stratakis_syndrome|Cowden_syndrome				11	71	---	---	---	---	PASS
EPHA10	284656	broad.mit.edu	37	1	38227126	38227126	+	Silent	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38227126G>T	uc009vvi.2	-	3	887	c.801C>A	c.(799-801)GGC>GGA	p.G267G	EPHA10_uc001cbw.3_Silent_p.G267G	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	267	Extracellular (Potential).					extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(4)|stomach(3)|lung(1)	8	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGCTGCAGCGGCCCACAGGCA	0.692													5	24	---	---	---	---	PASS
STIL	6491	broad.mit.edu	37	1	47767917	47767917	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:47767917G>C	uc001crc.1	-	4	409	c.254C>G	c.(253-255)ACA>AGA	p.T85R	TAL1_uc001crb.1_Intron|STIL_uc010omn.1_Missense_Mutation_p.T85R|STIL_uc010omo.1_Missense_Mutation_p.T85R|STIL_uc001crd.1_Missense_Mutation_p.T85R|STIL_uc001cre.1_Missense_Mutation_p.T85R|STIL_uc001crg.1_Missense_Mutation_p.T85R	NM_003035	NP_003026	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus isoform 2	85					cell proliferation|multicellular organismal development	centrosome|cytosol				lung(2)|skin(1)	3		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				TTCGTCTGCTGTCAGAGAACC	0.269													5	135	---	---	---	---	PASS
NEGR1	257194	broad.mit.edu	37	1	72400804	72400804	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:72400804G>T	uc001dfw.2	-	2	467	c.367C>A	c.(367-369)CAA>AAA	p.Q123K	NEGR1_uc001dfv.2_5'UTR|NEGR1_uc010oqs.1_Missense_Mutation_p.Q123K	NM_173808	NP_776169	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1 precursor	123	Ig-like C2-type 1.				cell adhesion	anchored to membrane|plasma membrane				ovary(1)	1		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		GGTGTATGTTGAGTCTGAACA	0.378													11	98	---	---	---	---	PASS
HIAT1	64645	broad.mit.edu	37	1	100546150	100546150	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100546150A>C	uc001dst.2	+	11	1201	c.1201A>C	c.(1201-1203)AAA>CAA	p.K401Q		NM_033055	NP_149044	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	401	Cytoplasmic (Potential).				transmembrane transport	integral to membrane|plasma membrane	transporter activity				0		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		TGTGGAACTTAAAGAACTGCC	0.413													33	232	---	---	---	---	PASS
GSTM4	2948	broad.mit.edu	37	1	110198849	110198849	+	5'UTR	SNP	A	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110198849A>C	uc001dyf.2	+	1					GSTM4_uc009wfi.2_5'UTR|GSTM4_uc001dyg.2_5'UTR|GSTM4_uc009wfj.2_5'UTR|GSTM4_uc001dyh.2_5'UTR|GSTM2_uc001dyi.2_5'UTR	NM_000850	NP_000841	Q03013	GSTM4_HUMAN	glutathione S-transferase mu 4 isoform 1						xenobiotic metabolic process	endoplasmic reticulum membrane	glutathione transferase activity				0		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		all cancers(265;0.0123)|Colorectal(144;0.0129)|Epithelial(280;0.0147)|Lung(183;0.0422)|COAD - Colon adenocarcinoma(174;0.0471)|LUSC - Lung squamous cell carcinoma(189;0.227)	Glutathione(DB00143)	ACGACCTTGAAGATCGGCCGG	0.667													2	10	---	---	---	---	PASS
C1orf162	128346	broad.mit.edu	37	1	112019442	112019442	+	Silent	SNP	A	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:112019442A>C	uc001ebe.2	+	3	120	c.60A>C	c.(58-60)ACA>ACC	p.T20T		NM_174896	NP_777556	Q8NEQ5	CA162_HUMAN	hypothetical protein LOC128346	20						integral to membrane				ovary(1)	1		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)		CTCTCTCCACAGCAGCCCCAA	0.453													38	182	---	---	---	---	PASS
C1orf189	388701	broad.mit.edu	37	1	154178091	154178091	+	Silent	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:154178091A>G	uc001fee.1	-	2	83	c.57T>C	c.(55-57)CTT>CTC	p.L19L		NM_001010979	NP_001010979	Q5VU69	CA189_HUMAN	hypothetical protein LOC388701	19											0	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					CCGTCTTCTTAAGTCCCATGG	0.463													7	149	---	---	---	---	PASS
PRG4	10216	broad.mit.edu	37	1	186276075	186276075	+	Silent	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186276075T>C	uc001gru.3	+	7	1275	c.1224T>C	c.(1222-1224)ACT>ACC	p.T408T	PRG4_uc001grt.3_Silent_p.T367T|PRG4_uc009wyl.2_Silent_p.T315T|PRG4_uc009wym.2_Silent_p.T274T|PRG4_uc010poo.1_RNA	NM_005807	NP_005798	Q92954	PRG4_HUMAN	proteoglycan 4 isoform A	408	59 X 8 AA repeats of K-X-P-X-P-T-T-X.|8.				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			skin(1)	1						CACCCACCACTCCCAAGGAGC	0.662													4	37	---	---	---	---	PASS
C1orf65	164127	broad.mit.edu	37	1	223568605	223568605	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:223568605G>T	uc001hoa.2	+	1	1891	c.1788G>T	c.(1786-1788)GAG>GAT	p.E596D		NM_152610	NP_689823	Q8N715	CA065_HUMAN	hypothetical protein LOC164127	596										central_nervous_system(1)|skin(1)	2				GBM - Glioblastoma multiforme(131;0.0704)		CCAGGAGAGAGGAGAGAGCGC	0.562													3	44	---	---	---	---	PASS
OBSCN	84033	broad.mit.edu	37	1	228504428	228504428	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:228504428T>G	uc009xez.1	+	51	13348	c.13304T>G	c.(13303-13305)CTG>CGG	p.L4435R	OBSCN_uc001hsn.2_Missense_Mutation_p.L4435R	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	4435	Ig-like 46.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			stomach(8)|large_intestine(7)|breast(5)|ovary(4)|skin(2)|central_nervous_system(1)|pancreas(1)	28		Prostate(94;0.0405)				CTGGAGATCCTGGAGCCTCTG	0.672													4	16	---	---	---	---	PASS
MXD1	4084	broad.mit.edu	37	2	70164321	70164321	+	Intron	SNP	T	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:70164321T>A	uc002sfy.2	+						MXD1_uc010yqp.1_Intron|MXD1_uc010yqq.1_Intron|MXD1_uc010yqr.1_RNA|MXD1_uc010yqs.1_Intron	NM_002357	NP_002348	Q05195	MAD1_HUMAN	MAX dimerization protein 1						cell proliferation|multicellular organismal development	mitochondrion|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity				0						ATTGCCCATTTAGAGATCTCC	0.532													29	132	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	2	96568655	96568655	+	Intron	SNP	A	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96568655A>T	uc002sva.1	-						uc002suz.1_5'UTR|uc002svb.1_Intron					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		TTTTCTCCATACTTTTTTCCT	0.279													5	21	---	---	---	---	PASS
MGAT4A	11320	broad.mit.edu	37	2	99242002	99242002	+	3'UTR	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:99242002G>T	uc002sze.2	-	16					C2orf64_uc002sza.2_Intron|MGAT4A_uc010yvm.1_Intron|MGAT4A_uc010fil.2_3'UTR	NM_012214	NP_036346	Q9UM21	MGT4A_HUMAN	alpha-1,3-mannosyl-glycoprotein						N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	extracellular region|Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding			skin(1)	1						AAATTCACAGGAAAAAATGTG	0.294													14	75	---	---	---	---	PASS
EPC2	26122	broad.mit.edu	37	2	149501326	149501326	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:149501326G>A	uc010zbt.1	+	3	476	c.449G>A	c.(448-450)AGT>AAT	p.S150N		NM_015630	NP_056445	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2	150					chromatin modification|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus				ovary(1)|breast(1)|pancreas(1)	3				BRCA - Breast invasive adenocarcinoma(221;0.0516)		GAAAAAGCCAGTTCTAATCAG	0.328													4	61	---	---	---	---	PASS
RAPGEF4	11069	broad.mit.edu	37	2	173879257	173879257	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:173879257G>A	uc002uhv.3	+	18	1911	c.1724G>A	c.(1723-1725)AGG>AAG	p.R575K	RAPGEF4_uc002uhw.3_Missense_Mutation_p.R431K	NM_007023	NP_008954	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	575	N-terminal Ras-GEF.				blood coagulation|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|regulation of insulin secretion|regulation of protein phosphorylation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cAMP-dependent protein kinase complex|membrane fraction|plasma membrane	cAMP binding|cAMP-dependent protein kinase regulator activity|Ras GTPase binding|Ras guanyl-nucleotide exchange factor activity			large_intestine(2)|skin(2)|kidney(1)|central_nervous_system(1)	6			OV - Ovarian serous cystadenocarcinoma(117;0.194)			AACAATAAGAGGCGAGTCATC	0.522													11	46	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10183872	10183872	+	Splice_Site	SNP	G	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183872G>C	uc003bvc.2	+	1	553	c.340_splice	c.e1+1	p.G114_splice	VHL_uc003bvd.2_Splice_Site_p.V114_splice	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1						anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(9)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		AGCTACCGAGGTACGGGCCCG	0.622		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				3	6	---	---	---	---	PASS
LEPREL1	55214	broad.mit.edu	37	3	189689771	189689771	+	Silent	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:189689771G>T	uc011bsk.1	-	12	2113	c.1725C>A	c.(1723-1725)CTC>CTA	p.L575L	LEPREL1_uc003fsg.2_Silent_p.L394L	NM_018192	NP_060662	Q8IVL5	P3H2_HUMAN	leprecan-like 1 isoform a	575	Fe2OG dioxygenase.				collagen metabolic process|negative regulation of cell proliferation|peptidyl-proline hydroxylation	basement membrane|endoplasmic reticulum|Golgi apparatus	iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|procollagen-proline 3-dioxygenase activity			breast(3)|ovary(1)	4	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TGGGATGACTGAGGTCATTTC	0.463													11	51	---	---	---	---	PASS
ANKRD17	26057	broad.mit.edu	37	4	73941874	73941874	+	3'UTR	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:73941874A>G	uc003hgp.2	-	34					ANKRD17_uc003hgo.2_3'UTR|ANKRD17_uc003hgq.2_3'UTR|ANKRD17_uc003hgr.2_3'UTR	NM_032217	NP_115593	O75179	ANR17_HUMAN	ankyrin repeat domain protein 17 isoform a						interspecies interaction between organisms	cytoplasm|nucleus	RNA binding			ovary(5)|skin(3)|upper_aerodigestive_tract(1)|lung(1)	10	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			ATTTGGGAGCATAATTTTTTT	0.408													5	18	---	---	---	---	PASS
ANKRD56	345079	broad.mit.edu	37	4	77818014	77818014	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:77818014A>G	uc003hki.2	-	1	989	c.989T>C	c.(988-990)GTG>GCG	p.V330A		NM_001029870	NP_001025041	A6NEL2	ANR56_HUMAN	ankyrin repeat domain 56	330											0						GTCTGGCAGCACCGACCAGGC	0.657													3	62	---	---	---	---	PASS
RPS3A	6189	broad.mit.edu	37	4	152025029	152025029	+	Intron	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:152025029C>T	uc003ilz.2	+						RPS3A_uc011cie.1_3'UTR|SNORD73A_uc003ima.1_RNA	NM_001006	NP_000997	P61247	RS3A_HUMAN	ribosomal protein S3a						cell differentiation|endocrine pancreas development|induction of apoptosis|translational elongation|translational initiation|translational termination|viral transcription	cytosolic small ribosomal subunit|nucleolus	protein binding|RNA binding|structural constituent of ribosome			ovary(1)	1	all_hematologic(180;0.093)					GTGATAACAACATTTTTCTGA	0.234													10	68	---	---	---	---	PASS
ADAM29	11086	broad.mit.edu	37	4	175898213	175898213	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:175898213G>A	uc003iuc.2	+	5	2207	c.1537G>A	c.(1537-1539)GCA>ACA	p.A513T	ADAM29_uc003iud.2_Missense_Mutation_p.A513T|ADAM29_uc010irr.2_Missense_Mutation_p.A513T|ADAM29_uc011cki.1_Missense_Mutation_p.A513T	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	513	Cys-rich.|Extracellular (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding	p.A513T(1)		skin(5)|central_nervous_system(3)|ovary(3)|large_intestine(2)|lung(2)|pancreas(1)	16		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		TGGTGCAGGCGCAAATACTGC	0.418													5	158	---	---	---	---	PASS
PIK3R1	5295	broad.mit.edu	37	5	67590479	67590479	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:67590479G>T	uc003jva.2	+	12	2101	c.1541G>T	c.(1540-1542)CGT>CTT	p.R514L	PIK3R1_uc003jvb.2_Missense_Mutation_p.R514L|PIK3R1_uc003jvc.2_Missense_Mutation_p.R214L|PIK3R1_uc003jvd.2_Missense_Mutation_p.R244L|PIK3R1_uc003jve.2_Missense_Mutation_p.R193L|PIK3R1_uc011crb.1_Missense_Mutation_p.R184L	NM_181523	NP_852664	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1	514					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.?(1)		endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)	AAGTTTAAACGTGAAGGCAAT	0.358			Mis|F|O		gliobastoma|ovarian|colorectal					TCGA GBM(4;<1E-08)			13	64	---	---	---	---	PASS
YTHDC2	64848	broad.mit.edu	37	5	112870044	112870044	+	Silent	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112870044A>G	uc003kqn.2	+	6	1068	c.885A>G	c.(883-885)GTA>GTG	p.V295V	YTHDC2_uc010jce.1_Silent_p.V295V|YTHDC2_uc010jcf.1_5'UTR	NM_022828	NP_073739	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	295	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|nucleic acid binding			skin(2)|central_nervous_system(1)	3		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		CTAATGGGGTATTGCTTCGTA	0.348													25	391	---	---	---	---	PASS
BAT2	7916	broad.mit.edu	37	6	31595623	31595623	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31595623T>C	uc003nvb.3	+	12	1621	c.1372T>C	c.(1372-1374)TCT>CCT	p.S458P	BAT2_uc011dnv.1_RNA|BAT2_uc003nvc.3_Missense_Mutation_p.S458P	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	458	4 X 57 AA type A repeats.|2 X type B repeats.					cytoplasm|nucleus	protein binding				0						GCAGTCGTCATCTGAGATTTC	0.627													12	82	---	---	---	---	PASS
DOPEY1	23033	broad.mit.edu	37	6	83823121	83823121	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:83823121T>C	uc003pjs.1	+	7	1021	c.761T>C	c.(760-762)TTT>TCT	p.F254S	DOPEY1_uc011dyy.1_Missense_Mutation_p.F254S|DOPEY1_uc010kbl.1_Missense_Mutation_p.F254S	NM_015018	NP_055833	Q5JWR5	DOP1_HUMAN	dopey family member 1	254					protein transport					ovary(2)|breast(1)|central_nervous_system(1)	4		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CTCTTCTGTTTTCCATTCCAC	0.363													23	124	---	---	---	---	PASS
EPHA7	2045	broad.mit.edu	37	6	93969181	93969181	+	Silent	SNP	G	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:93969181G>C	uc003poe.2	-	10	2056	c.1815C>G	c.(1813-1815)ACC>ACG	p.T605T	EPHA7_uc003pof.2_Silent_p.T600T|EPHA7_uc011eac.1_Silent_p.T601T	NM_004440	NP_004431	Q15375	EPHA7_HUMAN	ephrin receptor EphA7 precursor	605	Cytoplasmic (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			lung(8)|ovary(7)|upper_aerodigestive_tract(3)|central_nervous_system(3)|skin(3)|large_intestine(2)|stomach(1)|pancreas(1)	28		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TGTAGGTTTTGGTGCCTGGAA	0.428													31	223	---	---	---	---	PASS
QRSL1	55278	broad.mit.edu	37	6	107088233	107088233	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:107088233G>A	uc003prm.2	+	2	150	c.34G>A	c.(34-36)GCA>ACA	p.A12T	QRSL1_uc003prl.2_Missense_Mutation_p.A12T	NM_018292	NP_060762	Q9H0R6	QRSL1_HUMAN	glutaminyl-tRNA synthase	12					translation		ATP binding|carbon-nitrogen ligase activity, with glutamine as amido-N-donor				0	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		GGTTTCTGCGGCACTGAAACA	0.408													16	98	---	---	---	---	PASS
TNRC18	84629	broad.mit.edu	37	7	5347894	5347894	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:5347894A>G	uc003soi.3	-	30	9099	c.8750T>C	c.(8749-8751)GTG>GCG	p.V2917A		NM_001080495	NP_001073964	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2917	BAH.						DNA binding				0		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CTTGTGCGACACCGTCTGCAC	0.627													4	24	---	---	---	---	PASS
ANKIB1	54467	broad.mit.edu	37	7	92027912	92027912	+	Silent	SNP	C	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:92027912C>A	uc003ulw.2	+	20	3295	c.2919C>A	c.(2917-2919)ATC>ATA	p.I973I	ANKIB1_uc010lew.1_Silent_p.I242I	NM_019004	NP_061877	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	973							protein binding|zinc ion binding			lung(1)	1	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TCGGCAACATCATGGCTTGGT	0.488													42	196	---	---	---	---	PASS
LMTK2	22853	broad.mit.edu	37	7	97822827	97822827	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:97822827C>G	uc003upd.1	+	11	3343	c.3050C>G	c.(3049-3051)ACT>AGT	p.T1017S		NM_014916	NP_055731	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2 precursor	1017					early endosome to late endosome transport|endocytic recycling|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|protein autophosphorylation|receptor recycling|transferrin transport	early endosome|Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|recycling endosome	ATP binding|myosin VI binding|protein phosphatase inhibitor activity|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(9)|stomach(3)|pancreas(2)|large_intestine(1)|breast(1)	16	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					GGATCTCACACTCCCCAGAAA	0.597													17	110	---	---	---	---	PASS
MUC17	140453	broad.mit.edu	37	7	100677022	100677022	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100677022C>A	uc003uxp.1	+	3	2378	c.2325C>A	c.(2323-2325)AGC>AGA	p.S775R	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	775	Extracellular (Potential).|Ser-rich.|59 X approximate tandem repeats.|11.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					TTGACACAAGCACACATATCA	0.458													10	451	---	---	---	---	PASS
MLL5	55904	broad.mit.edu	37	7	104749515	104749515	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104749515T>C	uc003vcm.2	+	23	4129	c.3595T>C	c.(3595-3597)TGT>CGT	p.C1199R	MLL5_uc010ljc.2_Missense_Mutation_p.C1199R|MLL5_uc010lje.1_RNA|MLL5_uc010ljf.1_RNA|MLL5_uc010ljg.2_Silent_p.A4A|uc003vcp.1_5'Flank|MLL5_uc010ljh.1_Silent_p.A4A	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1199					cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						TGGTGATGGCTGTGCCAGCAG	0.468													17	79	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151873357	151873357	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151873357G>T	uc003wla.2	-	38	9400	c.9181C>A	c.(9181-9183)CAA>AAA	p.Q3061K	MLL3_uc003wkz.2_Missense_Mutation_p.Q2122K|MLL3_uc003wky.2_Missense_Mutation_p.Q570K	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	3061	Potential.|Gln-rich.				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)		TGCCTTTCTTGATCCAAAAGA	0.448			N		medulloblastoma								44	204	---	---	---	---	PASS
LSM1	27257	broad.mit.edu	37	8	38029515	38029515	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:38029515A>G	uc003xkw.2	-	2	271	c.83T>C	c.(82-84)CTT>CCT	p.L28P	LSM1_uc003xkx.2_RNA	NM_014462	NP_055277	O15116	LSM1_HUMAN	Lsm1 protein	28					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|mRNA processing|RNA splicing, via transesterification reactions	cytosol|nucleus|ribonucleoprotein complex	protein binding|RNA binding				0	Colorectal(12;0.000442)					AAAGCCTATAAGTGTCCTTCC	0.343											OREG0018720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	16	161	---	---	---	---	PASS
E2F5	1875	broad.mit.edu	37	8	86119690	86119690	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:86119690C>A	uc003ycz.3	+	5	618	c.581C>A	c.(580-582)TCT>TAT	p.S194Y	E2F5_uc003yda.3_Missense_Mutation_p.S194Y|E2F5_uc010mab.2_Missense_Mutation_p.S33Y|E2F5_uc003ydb.3_Missense_Mutation_p.S13Y	NM_001951	NP_001942	Q15329	E2F5_HUMAN	E2F transcription factor 5 isoform 1	194	Dimerization (Potential).				G1 phase of mitotic cell cycle	transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			ovary(1)	1						CAGGCACCTTCTGGTACACAA	0.294													3	7	---	---	---	---	PASS
KLF10	7071	broad.mit.edu	37	8	103663602	103663602	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103663602C>T	uc011lhk.1	-	3	1112	c.958G>A	c.(958-960)GTG>ATG	p.V320M	KLF10_uc011lhj.1_Missense_Mutation_p.V309M	NM_005655	NP_005646	Q13118	KLF10_HUMAN	Kruppel-like factor 10 isoform a	320					cell proliferation|cell-cell signaling|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|skeletal system development|transforming growth factor beta receptor signaling pathway	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			TGGGGTACCACAAACATGACA	0.602													12	88	---	---	---	---	PASS
DOCK8	81704	broad.mit.edu	37	9	406989	406989	+	Silent	SNP	T	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:406989T>A	uc003zgf.2	+	28	3562	c.3450T>A	c.(3448-3450)ACT>ACA	p.T1150T	DOCK8_uc010mgu.2_Silent_p.T452T|DOCK8_uc010mgv.2_Silent_p.T1050T|DOCK8_uc003zgk.2_Silent_p.T608T	NM_203447	NP_982272	Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1150					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)|central_nervous_system(3)	6		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TCGATCTGACTTCCGAGTACC	0.527													19	144	---	---	---	---	PASS
ZNF510	22869	broad.mit.edu	37	9	99538291	99538291	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99538291C>A	uc004awn.1	-	2	250	c.61G>T	c.(61-63)GCA>TCA	p.A21S	ZNF510_uc004awo.1_Missense_Mutation_p.A21S	NM_014930	NP_055745	Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	21					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Acute lymphoblastic leukemia(62;0.0527)				CCACCTTCTGCAAGTTGGCCC	0.532													4	13	---	---	---	---	PASS
SLC25A25	114789	broad.mit.edu	37	9	130868093	130868093	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:130868093G>A	uc004bte.2	+	6	760	c.731G>A	c.(730-732)CGG>CAG	p.R244Q	SLC25A25_uc004btb.2_Missense_Mutation_p.R278Q|SLC25A25_uc004btc.2_Missense_Mutation_p.R264Q|SLC25A25_uc004btd.2_Missense_Mutation_p.R276Q|SLC25A25_uc004btf.2_Missense_Mutation_p.R141Q	NM_052901	NP_443133	Q6KCM7	SCMC2_HUMAN	solute carrier family 25, member 25 isoform a	244	Solcar 1.|Mitochondrial matrix (Potential).				transmembrane transport	integral to membrane|mitochondrial inner membrane	calcium ion binding				0						TCACTCTGGCGGGGCAATGGC	0.592													11	85	---	---	---	---	PASS
FNBP1	23048	broad.mit.edu	37	9	132691916	132691916	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132691916G>A	uc004byw.1	-	7	791	c.572C>T	c.(571-573)TCA>TTA	p.S191L	FNBP1_uc011mbv.1_Missense_Mutation_p.S191L|FNBP1_uc011mbw.1_Missense_Mutation_p.S191L|FNBP1_uc004bza.2_Missense_Mutation_p.S191L|FNBP1_uc004byz.1_Missense_Mutation_p.S191L|FNBP1_uc004byx.1_Missense_Mutation_p.S112L|FNBP1_uc004byy.1_Missense_Mutation_p.S112L	NM_015033	NP_055848	Q96RU3	FNBP1_HUMAN	formin binding protein 1	191	Interaction with microtubules (By similarity).|Self-association, lipid-binding and induction of membrane tubulation.				endocytosis	cell cortex|cytoplasmic membrane-bounded vesicle|cytoskeleton|lysosome|plasma membrane	identical protein binding|lipid binding				0		Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		GAGAATGGATGAGTAATCTGC	0.423			T	MLL	AML								5	197	---	---	---	---	PASS
CCDC3	83643	broad.mit.edu	37	10	12940511	12940511	+	Missense_Mutation	SNP	G	T	T	rs150259960		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:12940511G>T	uc001ilq.1	-	3	852	c.718C>A	c.(718-720)CTG>ATG	p.L240M	CCDC3_uc009xjb.1_RNA|CCDC3_uc001ilr.2_RNA|CCDC3_uc009xjc.1_RNA	NM_031455	NP_113643	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3 precursor	240	Potential.					endoplasmic reticulum|extracellular region				ovary(1)	1		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			TGGTTCGCCAGCTCCAGGTGG	0.692													26	92	---	---	---	---	PASS
SFXN2	118980	broad.mit.edu	37	10	104489089	104489089	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104489089T>C	uc001kwb.2	+	5	611	c.445T>C	c.(445-447)TCC>CCC	p.S149P	SFXN2_uc001kwc.2_Intron|SFXN2_uc001kwd.2_Intron	NM_178858	NP_849189	Q96NB2	SFXN2_HUMAN	sideroflexin 2	149	Helical; (Potential).			QMALSYFTATTTAVATAVGMNMLTKKAPPLVGRWVPFAAVA AANCVNIPMMRQQELIKGI -> KRRPWWAAGCPLPLWLRL TVSISP (in Ref. 2).	iron ion homeostasis	integral to membrane	cation transmembrane transporter activity				0		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		GATGGCCCTTTCCTACTTCAC	0.637											OREG0020485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	49	---	---	---	---	PASS
SORCS1	114815	broad.mit.edu	37	10	108366996	108366996	+	Silent	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:108366996A>G	uc001kym.2	-	23	3101	c.3093T>C	c.(3091-3093)ACT>ACC	p.T1031T	SORCS1_uc001kyl.2_Silent_p.T1031T|SORCS1_uc009xxs.2_Silent_p.T1031T|SORCS1_uc001kyn.1_Silent_p.T1031T|SORCS1_uc001kyo.2_Silent_p.T1031T	NM_052918	NP_443150	Q8WY21	SORC1_HUMAN	SORCS receptor 1 isoform a	1031	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity|protein binding			breast(1)|central_nervous_system(1)	2		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AGAGTTCAGCAGTGGTGGGTA	0.557													13	79	---	---	---	---	PASS
HBE1	3046	broad.mit.edu	37	11	5291073	5291073	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5291073C>A	uc001mal.1	-	1	301	c.48G>T	c.(46-48)TGG>TGT	p.W16C	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Missense_Mutation_p.W16C	NM_005330	NP_005321	P02100	HBE_HUMAN	epsilon globin	16					blood coagulation	hemoglobin complex	heme binding|oxygen binding|oxygen transporter activity				0		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATCTTGCTCCACAGGCTAG	0.502													5	56	---	---	---	---	PASS
SLC6A5	9152	broad.mit.edu	37	11	20629130	20629130	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:20629130T>C	uc001mqd.2	+	5	1190	c.917T>C	c.(916-918)CTA>CCA	p.L306P	SLC6A5_uc009yic.2_Missense_Mutation_p.L71P	NM_004211	NP_004202	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter	306	Extracellular (Potential).		L -> V (in STHE; compound heterozygote with S-509; impairment of glycine transport when coexpressed with S-509 in vitro).		synaptic transmission	integral to membrane|plasma membrane	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(2)|breast(1)|skin(1)	4					Glycine(DB00145)	GTGTCTGTACTACCCTGGGGC	0.418													56	284	---	---	---	---	PASS
PTPRJ	5795	broad.mit.edu	37	11	48166241	48166241	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:48166241G>A	uc001ngp.3	+	13	2945	c.2590G>A	c.(2590-2592)GCA>ACA	p.A864T		NM_002843	NP_002834	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	864	Extracellular (Potential).|Fibronectin type-III 9.				contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity			breast(3)|kidney(3)|ovary(1)|skin(1)	8						TCACCCTTCTGCAGATGTCCT	0.423													13	106	---	---	---	---	PASS
PLA2G16	11145	broad.mit.edu	37	11	63342504	63342504	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63342504G>C	uc001nxh.2	-	4	825	c.402C>G	c.(400-402)ATC>ATG	p.I134M	PLA2G16_uc001nxi.2_Missense_Mutation_p.I146M|PLA2G16_uc009you.1_Missense_Mutation_p.I134M	NM_007069	NP_009000	P53816	PAG16_HUMAN	HRAS-like suppressor 3	134	Helical; (Potential).				lipid catabolic process	integral to membrane|perinuclear region of cytoplasm	hydrolase activity|protein binding			ovary(1)	1						TTGCAGCGATGATGACATCTC	0.483													7	96	---	---	---	---	PASS
PPP2R5B	5526	broad.mit.edu	37	11	64695788	64695788	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64695788G>A	uc001oby.2	+	6	1198	c.613G>A	c.(613-615)GAG>AAG	p.E205K	PPP2R5B_uc001obz.2_Missense_Mutation_p.E205K	NM_006244	NP_006235	Q15173	2A5B_HUMAN	beta isoform of regulatory subunit B56, protein	205					signal transduction	cytoplasm|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(2)	2						ATTTGATAGTGAGGATCCCCG	0.502													12	54	---	---	---	---	PASS
B3GNT1	11041	broad.mit.edu	37	11	66114359	66114359	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:66114359C>T	uc001ohr.2	-	1	803	c.658G>A	c.(658-660)GCC>ACC	p.A220T	BRMS1_uc001ohp.1_5'Flank|BRMS1_uc001oho.1_5'Flank	NM_006876	NP_006867	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal	220	Lumenal (Potential).				poly-N-acetyllactosamine biosynthetic process	integral to Golgi membrane	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity				0						GCATAGTTGGCCCCCTCACGA	0.602													5	101	---	---	---	---	PASS
FAM76B	143684	broad.mit.edu	37	11	95512032	95512032	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:95512032C>T	uc001pfn.2	-	8	1094	c.782G>A	c.(781-783)CGT>CAT	p.R261H	FAM76B_uc001pfm.2_RNA	NM_144664	NP_653265	Q5HYJ3	FA76B_HUMAN	hypothetical protein LOC143684	261	Potential.										0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CTGTAAGAGACGCTTAAGTGA	0.368													5	144	---	---	---	---	PASS
PHC1	1911	broad.mit.edu	37	12	9070228	9070228	+	5'UTR	SNP	C	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9070228C>A	uc001qvd.2	+	2					PHC1_uc001qvc.1_5'UTR|PHC1_uc010sgn.1_5'UTR|PHC1_uc001qve.2_5'UTR	NM_004426	NP_004417	P78364	PHC1_HUMAN	polyhomeotic 1-like						multicellular organismal development	PcG protein complex	DNA binding|zinc ion binding			ovary(1)|breast(1)	2						CCCTCTAGGTCTTGAGTCAGA	0.433													6	15	---	---	---	---	PASS
SOAT2	8435	broad.mit.edu	37	12	53512684	53512684	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53512684G>T	uc001sbv.2	+	9	962	c.874G>T	c.(874-876)GTC>TTC	p.V292F	SOAT2_uc009zms.2_Intron	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2	292					cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1						GACGCCCTATGTCAGGTGGAA	0.532													13	73	---	---	---	---	PASS
SOAT2	8435	broad.mit.edu	37	12	53512685	53512685	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:53512685T>G	uc001sbv.2	+	9	963	c.875T>G	c.(874-876)GTC>GGC	p.V292G	SOAT2_uc009zms.2_Intron	NM_003578	NP_003569	O75908	SOAT2_HUMAN	acyl-CoA:cholesterol acyltransferase 2	292					cholesterol efflux|cholesterol esterification|cholesterol homeostasis|cholesterol metabolic process|macrophage derived foam cell differentiation|very-low-density lipoprotein particle assembly	brush border|endoplasmic reticulum membrane|integral to membrane|microsome	cholesterol binding|cholesterol O-acyltransferase activity|fatty-acyl-CoA binding			ovary(1)	1						ACGCCCTATGTCAGGTGGAAT	0.537													13	73	---	---	---	---	PASS
LOC374491	374491	broad.mit.edu	37	13	25168463	25168463	+	RNA	SNP	T	C	C	rs61946940		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:25168463T>C	uc001upm.2	+	10		c.1135T>C			LOC374491_uc001upn.2_RNA|LOC374491_uc001upo.2_RNA					Homo sapiens mRNA; cDNA DKFZp434J0717 (from clone DKFZp434J0717).												0						TGACAGTCCATCTCTGTACGA	0.363													3	37	---	---	---	---	PASS
CDC16	8881	broad.mit.edu	37	13	115004884	115004884	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:115004884T>G	uc001vuk.1	+	5	498	c.300T>G	c.(298-300)AAT>AAG	p.N100K	CDC16_uc010tkm.1_Missense_Mutation_p.N100K|CDC16_uc001vul.1_Missense_Mutation_p.N100K|CDC16_uc001vum.1_Missense_Mutation_p.N6K|CDC16_uc001vun.1_Missense_Mutation_p.N99K|CDC16_uc001vuo.1_Missense_Mutation_p.N99K	NM_003903	NP_003894	Q13042	CDC16_HUMAN	anaphase-promoting complex, subunit 6	100					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell division|cell proliferation|mitosis|mitotic cell cycle spindle assembly checkpoint|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	binding				0	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			AGCCCATCAATAAAAGATTAT	0.443													18	124	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22788574	22788574	+	Intron	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22788574C>T	uc001wbw.2	+						uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Intron|uc010ajk.1_Intron|uc001wdg.1_Intron|uc010ajl.1_Intron|uc001wdj.2_Intron|uc010ajo.1_Intron|uc010ajp.1_Intron|uc001wdr.2_5'UTR					SubName: Full=Alpha-chain C region; Flags: Fragment;																		AGATATATTCCGAAATCCTCC	0.398													25	259	---	---	---	---	PASS
C14orf39	317761	broad.mit.edu	37	14	60928115	60928115	+	Silent	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60928115C>T	uc001xez.3	-	13	1184	c.1074G>A	c.(1072-1074)CAG>CAA	p.Q358Q	C14orf39_uc010apo.2_Silent_p.Q69Q	NM_174978	NP_777638	Q08AQ4	Q08AQ4_HUMAN	hypothetical protein LOC317761	358										ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TTGATTGTTTCTGTGGGGTTA	0.279													9	95	---	---	---	---	PASS
C14orf39	317761	broad.mit.edu	37	14	60928116	60928116	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:60928116T>C	uc001xez.3	-	13	1183	c.1073A>G	c.(1072-1074)CAG>CGG	p.Q358R	C14orf39_uc010apo.2_Missense_Mutation_p.Q69R	NM_174978	NP_777638	Q08AQ4	Q08AQ4_HUMAN	hypothetical protein LOC317761	358										ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TGATTGTTTCTGTGGGGTTAA	0.279													9	96	---	---	---	---	PASS
LOC646214	646214	broad.mit.edu	37	15	21936992	21936992	+	RNA	SNP	C	T	T	rs4984136		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:21936992C>T	uc010tzj.1	-	1		c.3748G>A				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						TGAGCTTAACCGATCCTTCCA	0.473													3	52	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	28948349	28948349	+	5'Flank	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:28948349T>C	uc001zcd.2	+											DQ593033																		CCACTGGCTCTCAGAAGGGGT	0.567													2	10	---	---	---	---	PASS
UBR1	197131	broad.mit.edu	37	15	43317589	43317589	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43317589G>C	uc001zqq.2	-	24	2640	c.2574C>G	c.(2572-2574)AAC>AAG	p.N858K	UBR1_uc010udk.1_Missense_Mutation_p.N858K	NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin	858					cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			lung(1)	1		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		CTTCATCTTTGTTTTCTTGTT	0.294													10	47	---	---	---	---	PASS
DENND4A	10260	broad.mit.edu	37	15	65983198	65983198	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:65983198C>G	uc002aph.2	-	22	3980	c.3602G>C	c.(3601-3603)AGG>ACG	p.R1201T	DENND4A_uc002api.2_Missense_Mutation_p.R1244T|DENND4A_uc002apj.3_Missense_Mutation_p.R1201T	NM_005848	NP_005839	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A isoform 2	1201					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	4						TAAATCACGCCTAGCAGATGG	0.418													8	54	---	---	---	---	PASS
GNG13	51764	broad.mit.edu	37	16	848396	848396	+	3'UTR	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:848396T>C	uc002ckh.3	-	3						NM_016541	NP_057625	Q9P2W3	GBG13_HUMAN	guanine nucleotide binding protein (G protein),						cellular response to glucagon stimulus|energy reserve metabolic process		signal transducer activity				0		Hepatocellular(780;0.00335)				ggagtggggctgggagtgggg	0.050													3	7	---	---	---	---	PASS
RRN3	54700	broad.mit.edu	37	16	15170407	15170407	+	Intron	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15170407C>T	uc002dde.2	-						PDXDC1_uc002ddc.2_Intron|RRN3_uc010uzp.1_Intron|RRN3_uc010uzq.1_Intron|RRN3_uc002ddf.1_Missense_Mutation_p.S289N	NM_018427	NP_060897	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor						regulation of transcription, DNA-dependent|transcription initiation from RNA polymerase I promoter	nucleolus|nucleoplasm				ovary(1)	1						CATTAATAAACTGCTAACCAT	0.383													20	99	---	---	---	---	PASS
CYLD	1540	broad.mit.edu	37	16	50783997	50783997	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:50783997C>A	uc002egp.1	+	4	803	c.388C>A	c.(388-390)CCT>ACT	p.P130T	CYLD_uc002egn.1_Missense_Mutation_p.P130T|CYLD_uc002ego.2_Missense_Mutation_p.P130T|CYLD_uc010cbs.1_Missense_Mutation_p.P130T|CYLD_uc002egq.1_Missense_Mutation_p.P130T|CYLD_uc002egr.1_Missense_Mutation_p.P130T|CYLD_uc002egs.1_Missense_Mutation_p.P130T	NM_015247	NP_056062	Q9NQC7	CYLD_HUMAN	ubiquitin carboxyl-terminal hydrolase CYLD	130	Interaction with TRIP.				cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3)	28		all_cancers(37;0.0156)				CGTGGGCTGTCCTGTGAAAGT	0.448			Mis|N|F|S		cylindroma	cylindroma			Familial_Cylindromatosis|Multiple_Trichoepithelioma_Familial				33	157	---	---	---	---	PASS
FAM96B	51647	broad.mit.edu	37	16	66966160	66966160	+	Silent	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66966160C>T	uc002eqp.2	-	5	491	c.438G>A	c.(436-438)CTG>CTA	p.L146L	CES2_uc002eqq.2_5'Flank|CES2_uc002eqr.2_5'Flank|CES2_uc002eqs.2_5'Flank	NM_016062	NP_057146	Q9Y3D0	MIP18_HUMAN	hypothetical protein LOC51647	146					chromosome segregation	cytoplasm|MMXD complex|nucleus	protein binding				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)		GGGTGTTCTCCAGGGCAGCTG	0.582													5	46	---	---	---	---	PASS
NUP85	79902	broad.mit.edu	37	17	73204674	73204674	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73204674C>T	uc002jng.1	+	2	346	c.86C>T	c.(85-87)CCA>CTA	p.P29L	NUP85_uc010dgd.1_Missense_Mutation_p.P29L|NUP85_uc010wrv.1_Intron	NM_024844	NP_079120	Q9BW27	NUP85_HUMAN	nucleoporin 85	29					carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	condensed chromosome kinetochore|cytosol|nuclear membrane|Nup107-160 complex|spindle	protein binding			ovary(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			GACTGGGGTCCAGGGGAGATG	0.358													78	404	---	---	---	---	PASS
KIAA0195	9772	broad.mit.edu	37	17	73488654	73488654	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73488654T>A	uc002jnz.3	+	15	1971	c.1696T>A	c.(1696-1698)TCC>ACC	p.S566T	KIAA0195_uc010wsa.1_Missense_Mutation_p.S576T|KIAA0195_uc010wsb.1_Missense_Mutation_p.S206T|KIAA0195_uc002job.3_5'Flank	NM_014738	NP_055553	Q12767	K0195_HUMAN	hypothetical protein LOC9772	566					ATP biosynthetic process|cation transport	integral to membrane	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism			ovary(1)	1	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCAGAACCCCTCCTGCATCCA	0.592													18	75	---	---	---	---	PASS
PIK3C3	5289	broad.mit.edu	37	18	39607334	39607334	+	Intron	SNP	A	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:39607334A>C	uc002lap.2	+						PIK3C3_uc010xcl.1_Intron|PIK3C3_uc002laq.2_5'UTR	NM_002647	NP_002638	Q8NEB9	PK3C3_HUMAN	catalytic phosphatidylinositol 3-kinase 3						cell cycle|cytokinesis|fibroblast growth factor receptor signaling pathway|innate immune response|insulin receptor signaling pathway	midbody|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|protein binding			lung(8)|ovary(1)|breast(1)	10						GTTTTAGTGAAATGATATGAG	0.259										TSP Lung(28;0.18)			4	12	---	---	---	---	PASS
FCGBP	8857	broad.mit.edu	37	19	40354067	40354067	+	3'UTR	SNP	T	C	C	rs2405	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:40354067T>C	uc002omp.3	-	36						NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor							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)			CTTCAGCCACTGCAACCTCCA	0.488													4	35	---	---	---	---	PASS
SPIB	6689	broad.mit.edu	37	19	50926246	50926246	+	Silent	SNP	C	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:50926246C>A	uc002psd.2	+	4	316	c.291C>A	c.(289-291)GCC>GCA	p.A97A	SPIB_uc002pse.2_Silent_p.A97A|SPIB_uc010ycc.1_Intron	NM_003121	NP_003112	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	97					regulation of transcription from RNA polymerase II promoter	cytoplasm|microtubule cytoskeleton|nucleus	sequence-specific DNA binding			lung(1)|kidney(1)	2		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		GCCTGGAGGCCCCGGGGCCTG	0.587													8	103	---	---	---	---	PASS
RPS5	6193	broad.mit.edu	37	19	58906163	58906163	+	3'UTR	SNP	T	C	C	rs2241787	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:58906163T>C	uc002qsn.2	+	6					RPS5_uc002qso.2_3'UTR	NM_001009	NP_001000	P46782	RS5_HUMAN	ribosomal protein S5						endocrine pancreas development|regulation of translational fidelity|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit	mRNA binding|structural constituent of ribosome				0		all_cancers(17;1.71e-22)|all_epithelial(17;1.69e-16)|Lung NSC(17;2.25e-06)|all_lung(17;9.97e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Breast(46;0.0194)|Ovarian(87;0.0443)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.171)|GBM - Glioblastoma multiforme(193;0.0323)|Lung(386;0.0543)|LUSC - Lung squamous cell carcinoma(496;0.176)		TTTGGGGCAGTCCCAGCCACC	0.587													3	63	---	---	---	---	PASS
TOX2	84969	broad.mit.edu	37	20	42680130	42680130	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:42680130C>T	uc002xlf.3	+	4	640	c.623C>T	c.(622-624)GCG>GTG	p.A208V	TOX2_uc010ggo.2_Missense_Mutation_p.A199V|TOX2_uc002xle.3_Missense_Mutation_p.A157V|TOX2_uc010ggp.2_Missense_Mutation_p.A157V|TOX2_uc002xlg.2_Missense_Mutation_p.A157V|TOX2_uc010zwk.1_Missense_Mutation_p.A77V	NM_001098798	NP_001092268	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	208					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			AGCAAGTCAGCGACCCCCTCT	0.627													5	27	---	---	---	---	PASS
SEMG2	6407	broad.mit.edu	37	20	43850086	43850086	+	Intron	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43850086C>T	uc010ggz.2	+						SEMG2_uc002xnk.2_Missense_Mutation_p.A19V|SEMG2_uc002xnl.2_Missense_Mutation_p.A19V	NM_003008	NP_002999	Q02383	SEMG2_HUMAN	semenogelin II precursor						sexual reproduction	extracellular space|stored secretory granule	structural molecule activity			skin(1)	1		Myeloproliferative disorder(115;0.0122)				GAGAAGCAAGCAGCTGTGATG	0.443													10	67	---	---	---	---	PASS
STMN3	50861	broad.mit.edu	37	20	62275107	62275107	+	Splice_Site	SNP	G	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62275107G>T	uc002yfr.1	-	3	373	c.291_splice	c.e3+1	p.K97_splice	STMN3_uc011abb.1_Splice_Site_p.K97_splice	NM_015894	NP_056978	Q9NZ72	STMN3_HUMAN	SCG10-like-protein						cytoplasmic microtubule organization|intracellular signal transduction|negative regulation of Rac protein signal transduction|neuron projection development|regulation of cytoskeleton organization|regulation of Rac GTPase activity	cytoplasm	protein domain specific binding				0	all_cancers(38;2.31e-11)|all_epithelial(29;7.76e-13)		Epithelial(9;1.9e-09)|all cancers(9;1.22e-08)|BRCA - Breast invasive adenocarcinoma(10;8.86e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.00559)			AGGACTCCTTGCCTTCCTCCG	0.657													10	48	---	---	---	---	PASS
DYRK1A	1859	broad.mit.edu	37	21	38845082	38845082	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38845082A>G	uc002ywk.2	+	2	182	c.107A>G	c.(106-108)CAT>CGT	p.H36R	DYRK1A_uc002ywg.1_RNA|DYRK1A_uc010gno.1_RNA|DYRK1A_uc002ywh.1_Missense_Mutation_p.H7R|DYRK1A_uc002ywi.2_Missense_Mutation_p.H36R|DYRK1A_uc002ywj.2_Missense_Mutation_p.H36R|DYRK1A_uc002ywl.2_Missense_Mutation_p.H36R|DYRK1A_uc002ywm.2_Missense_Mutation_p.H36R	NM_001396	NP_001387	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	36					nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4						CAGATGCCCCATTCACATCAG	0.488													22	177	---	---	---	---	PASS
DYRK1A	1859	broad.mit.edu	37	21	38862648	38862648	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:38862648C>G	uc002ywk.2	+	6	911	c.836C>G	c.(835-837)CCA>CGA	p.P279R	DYRK1A_uc002ywi.2_Missense_Mutation_p.P279R|DYRK1A_uc002ywj.2_Missense_Mutation_p.P270R|DYRK1A_uc002ywl.2_Missense_Mutation_p.P279R|DYRK1A_uc002ywm.2_Missense_Mutation_p.P279R|DYRK1A_uc011aei.1_Missense_Mutation_p.P40R	NM_001396	NP_001387	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	279	Protein kinase.				nervous system development|peptidyl-tyrosine phosphorylation|protein autophosphorylation	nuclear speck	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding|protein self-association|protein serine/threonine kinase activity			ovary(2)|lung(1)|breast(1)	4						CTTGCGACTCCAGAACTTAGT	0.423													25	155	---	---	---	---	PASS
CCT8L2	150160	broad.mit.edu	37	22	17073177	17073177	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:17073177C>G	uc002zlp.1	-	1	524	c.264G>C	c.(262-264)TGG>TGC	p.W88C		NM_014406	NP_055221	Q96SF2	TCPQM_HUMAN	T-complex protein 1	88					cellular protein metabolic process	cytoplasm	anion channel activity|ATP binding|calcium-activated potassium channel activity			ovary(1)	1	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CCCGGAGGAGCCATGCTGCTG	0.617													13	52	---	---	---	---	PASS
CACNG2	10369	broad.mit.edu	37	22	36960380	36960380	+	3'UTR	SNP	T	C	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36960380T>C	uc003aps.1	-	4						NM_006078	NP_006069	Q9Y698	CCG2_HUMAN	voltage-dependent calcium channel gamma-2						membrane depolarization|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity				0						CGCGGTCTTCTGGCGAGGCCC	0.428													4	17	---	---	---	---	PASS
FLJ44635	392490	broad.mit.edu	37	X	71380152	71380152	+	3'UTR	SNP	C	T	T	rs7881332	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:71380152C>T	uc004eal.1	+	2						NM_207422	NP_997305	Q56UQ5	TPT1L_HUMAN	hypothetical protein LOC392490											lung(1)	1	Renal(35;0.156)					TGGTGTGACCCGATATATGAT	0.383													3	65	---	---	---	---	PASS
TEX13A	56157	broad.mit.edu	37	X	104464656	104464656	+	Silent	SNP	C	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:104464656C>T	uc004ema.2	-	2	538	c.426G>A	c.(424-426)GAG>GAA	p.E142E	IL1RAPL2_uc004elz.1_Intron|TEX13A_uc004emb.2_Silent_p.E142E	NM_031274	NP_112564	Q9BXU3	TX13A_HUMAN	testis expressed sequence 13A	142						intracellular	zinc ion binding			ovary(2)	2						CCTTGTCTCTCTCTTTCTGCA	0.498													12	28	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	1	20200621	20200635	+	IGR	DEL	CACCACCACCACCAC	-	-	rs144954291		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20200621_20200635delCACCACCACCACCAC								RNF186 (58850 upstream) : OTUD3 (8253 downstream)																							ccaccaccatcaccaccaccaccaccaccaccacc	0.214													4	2	---	---	---	---	
MYOM3	127294	broad.mit.edu	37	1	24434680	24434680	+	Intron	DEL	C	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24434680delC	uc001bin.3	-						MYOM3_uc001bio.2_Intron|MYOM3_uc001bip.1_5'UTR	NM_152372	NP_689585	Q5VTT5	MYOM3_HUMAN	myomesin family, member 3											skin(2)|ovary(1)	3		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GGCTGTGCCTCCCTCCTCATA	0.612													6	4	---	---	---	---	
YTHDF2	51441	broad.mit.edu	37	1	29070609	29070610	+	Intron	INS	-	G	G	rs72508792	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:29070609_29070610insG	uc001brc.2	+						YTHDF2_uc001brd.2_Intron|YTHDF2_uc010ofx.1_Intron|YTHDF2_uc001bre.2_Intron	NM_016258	NP_057342	Q9Y5A9	YTHD2_HUMAN	high glucose-regulated protein 8						humoral immune response					ovary(1)|skin(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000601)|all_lung(284;0.000771)|Breast(348;0.00502)|Renal(390;0.00758)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;5.46e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0221)|KIRC - Kidney renal clear cell carcinoma(1967;0.0296)|READ - Rectum adenocarcinoma(331;0.0649)		ATACAGTATCACCTAACAGTTC	0.332													5	5	---	---	---	---	
TMEM48	55706	broad.mit.edu	37	1	54262254	54262254	+	Intron	DEL	A	-	-	rs35930311		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:54262254delA	uc001cvs.2	-						TMEM48_uc010onu.1_Intron|TMEM48_uc001cvt.2_Intron|TMEM48_uc009vzk.2_Intron|TMEM48_uc010onv.1_Intron	NM_018087	NP_060557	Q9BTX1	NDC1_HUMAN	transmembrane protein 48						mRNA transport|nuclear pore complex assembly|nuclear pore distribution|protein transport|transmembrane transport	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore			ovary(1)|pancreas(1)	2						CACGAAGCATAAAAAAAAAAA	0.159													14	7	---	---	---	---	
C1orf177	163747	broad.mit.edu	37	1	55285690	55285691	+	Intron	INS	-	TTCC	TTCC	rs148904661	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55285690_55285691insTTCC	uc001cyb.3	+						C1orf177_uc001cya.3_Intron	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN	hypothetical protein LOC163747 isoform 2												0						cttttccttctttccttccttc	0.000													5	4	---	---	---	---	
LRRC7	57554	broad.mit.edu	37	1	70503603	70503603	+	Intron	DEL	A	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70503603delA	uc001dep.2	+						LRRC7_uc009wbg.2_Intron|LRRC7_uc001deq.2_Intron	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						tattactaggaaaaaaaagtt	0.085													5	3	---	---	---	---	
WDR47	22911	broad.mit.edu	37	1	109560373	109560373	+	Intron	DEL	T	-	-	rs33990918		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109560373delT	uc001dwj.2	-						WDR47_uc001dwl.2_Intron|WDR47_uc001dwi.2_Intron|WDR47_uc001dwk.2_Intron|WDR47_uc010ovf.1_5'Flank	NM_001142551	NP_001136023	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 3											ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		TTTTTCATAAttttttttttt	0.129													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	121137816	121137816	+	IGR	DEL	C	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:121137816delC								FCGR1B (201872 upstream) : LOC647121 (123094 downstream)																							CGGCTTTTTGCCCCCCCGCCG	0.667													9	4	---	---	---	---	
EXO1	9156	broad.mit.edu	37	1	242013582	242013582	+	Intron	DEL	A	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242013582delA	uc001hzh.2	+						EXO1_uc001hzi.2_Intron|EXO1_uc001hzj.2_Intron|EXO1_uc009xgq.2_Intron	NM_130398	NP_569082	Q9UQ84	EXO1_HUMAN	exonuclease 1 isoform b						meiosis|mismatch repair	nucleus	double-stranded DNA specific 5'-3' exodeoxyribonuclease activity|flap endonuclease activity|metal ion binding|protein binding|protein binding|ribonuclease H activity|single-stranded DNA specific 5'-3' exodeoxyribonuclease activity			ovary(2)|lung(2)|skin(1)	5	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			actccgtctcaaaaaaaaaaa	0.104								Direct_reversal_of_damage|Editing_and_processing_nucleases					9	4	---	---	---	---	
KIF26B	55083	broad.mit.edu	37	1	245446118	245446118	+	Intron	DEL	A	-	-	rs34770861		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245446118delA	uc001ibf.1	+						KIF26B_uc010pyq.1_Intron	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B						microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			ccgctcctttaaaAAAAAAGA	0.179													5	6	---	---	---	---	
GREB1	9687	broad.mit.edu	37	2	11725179	11725180	+	Intron	INS	-	A	A	rs78338846		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:11725179_11725180insA	uc002rbk.1	+						GREB1_uc002rbl.2_Intron|GREB1_uc002rbn.1_Intron	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1							integral to membrane				ovary(1)	1	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TCTGTGATTAGAAAAAAAAAAA	0.302													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16134213	16134220	+	IGR	DEL	TTCTTTCT	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16134213_16134220delTTCTTTCT								MYCN (47085 upstream) : FAM49A (599681 downstream)																							tctttctttcttctttctttctttcttt	0.130													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	16179761	16179772	+	IGR	DEL	TTCCTTCCTTCC	-	-	rs148537396	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:16179761_16179772delTTCCTTCCTTCC								MYCN (92633 upstream) : FAM49A (554129 downstream)																							ccttccttctttccttccttccttccttcctt	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	90008306	90008307	+	Intron	INS	-	G	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90008306_90008307insG	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		TTTTGGTAGAAGGGGTCAGGGA	0.485													3	3	---	---	---	---	
TBC1D8	11138	broad.mit.edu	37	2	101645856	101645857	+	Intron	INS	-	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:101645856_101645857insA	uc010fiv.2	-						TBC1D8_uc002tau.3_Intron	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8						blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3						tctgtctcaataaaaaaaaaaa	0.287													15	7	---	---	---	---	
IFIH1	64135	broad.mit.edu	37	2	163167632	163167634	+	Intron	DEL	ACA	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:163167632_163167634delACA	uc002uce.2	-						IFIH1_uc002ucf.2_Intron	NM_022168	NP_071451	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1						detection of virus|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|regulation of apoptosis	cytosol|nucleus	ATP binding|DNA binding|double-stranded RNA binding|helicase activity|protein binding|ribonucleoprotein binding|zinc ion binding			ovary(1)	1						AATCTCCGGGacaacaacaacaa	0.291													4	5	---	---	---	---	
LRP2	4036	broad.mit.edu	37	2	170034062	170034062	+	Intron	DEL	A	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:170034062delA	uc002ues.2	-							NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2						hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	AAAACAAAGGAAAAAAAAAAA	0.308													4	2	---	---	---	---	
KLHL30	377007	broad.mit.edu	37	2	239053066	239053093	+	Intron	DEL	AGGAAGGAAGGCAGGCAGGCAGGCAGGC	-	-	rs72337425	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239053066_239053093delAGGAAGGAAGGCAGGCAGGCAGGCAGGC	uc002vxr.1	+							NM_198582	NP_940984	Q0D2K2	KLH30_HUMAN	kelch-like 30												0		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		gaaggaaggaaggaaggaaggcaggcaggcaggcaggcaggcaggcag	0.211													4	2	---	---	---	---	
RAF1	5894	broad.mit.edu	37	3	12633424	12633425	+	Intron	INS	-	T	T	rs150506410		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:12633424_12633425insT	uc003bxf.3	-						RAF1_uc011aut.1_Intron|RAF1_uc011auu.1_Intron	NM_002880	NP_002871	P04049	RAF1_HUMAN	v-raf-1 murine leukemia viral oncogene homolog						activation of MAPKK activity|apoptosis|axon guidance|cell proliferation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|negative regulation of apoptosis|negative regulation of cell proliferation|negative regulation of protein complex assembly|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of peptidyl-serine phosphorylation|Ras protein signal transduction|synaptic transmission	cytosol|mitochondrial outer membrane|plasma membrane	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|receptor signaling protein activity		ESRP1/RAF1(4)|SRGAP3/RAF1(4)	central_nervous_system(4)|prostate(4)|lung(2)|upper_aerodigestive_tract(1)|stomach(1)|liver(1)|ovary(1)	14					Sorafenib(DB00398)	CAAATTTCCAAttttttttttt	0.168			T	SRGAP3	pilocytic astrocytoma				Noonan_syndrome				3	6	---	---	---	---	
TTC21A	199223	broad.mit.edu	37	3	39168075	39168076	+	Intron	DEL	AC	-	-	rs34422565		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:39168075_39168076delAC	uc003cjc.2	+						TTC21A_uc003cje.2_Intron|TTC21A_uc003cjd.2_Intron|TTC21A_uc011ayx.1_Intron	NM_145755	NP_665698	Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A isoform 2								binding			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CTGGGGTACTACACACACACAC	0.307													4	2	---	---	---	---	
SYNPR	132204	broad.mit.edu	37	3	63466852	63466852	+	Intron	DEL	A	-	-	rs11349566		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:63466852delA	uc003dlq.2	+						SYNPR_uc003dlp.2_Intron|SYNPR_uc011bfk.1_Intron|SYNPR_uc011bfl.1_Intron|SYNPR_uc010hnt.2_Intron|SYNPR_uc011bfm.1_Intron	NM_144642	NP_653243	Q8TBG9	SYNPR_HUMAN	synaptoporin isoform 2							cell junction|integral to membrane|synaptic vesicle membrane|synaptosome	transporter activity				0				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		GACTCTCCTCAAAAAAAAAGA	0.413													3	7	---	---	---	---	
FAM19A1	407738	broad.mit.edu	37	3	68466755	68466755	+	Intron	DEL	T	-	-	rs34877887		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:68466755delT	uc003dnd.2	+						FAM19A1_uc003dne.2_Intron|FAM19A1_uc003dng.2_Intron	NM_213609	NP_998774	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine							endoplasmic reticulum|extracellular region				ovary(1)	1		Lung NSC(201;0.0117)		BRCA - Breast invasive adenocarcinoma(55;7.7e-05)|Epithelial(33;0.000937)|KIRC - Kidney renal clear cell carcinoma(39;0.0579)|Kidney(39;0.0743)		tatttgaatgttttttcccca	0.174													5	6	---	---	---	---	
NCK1	4690	broad.mit.edu	37	3	136586045	136586048	+	Intron	DEL	CCTT	-	-	rs112564204		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:136586045_136586048delCCTT	uc003erh.2	+							NM_006153	NP_006144	P16333	NCK1_HUMAN	NCK adaptor protein 1						axon guidance|positive regulation of actin filament polymerization|positive regulation of T cell proliferation|regulation of translation|signal complex assembly|T cell activation|T cell receptor signaling pathway	cytosol|endoplasmic reticulum|nucleus	cytoskeletal adaptor activity|receptor binding|receptor signaling complex scaffold activity			pancreas(1)	1						ctttcttttcccttccttccttcc	0.029													6	4	---	---	---	---	
SLC9A9	285195	broad.mit.edu	37	3	143486218	143486219	+	Intron	INS	-	TG	TG	rs142594079	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:143486218_143486219insTG	uc003evn.2	-						SLC9A9_uc011bnk.1_Intron	NM_173653	NP_775924	Q8IVB4	SL9A9_HUMAN	solute carrier family 9 (sodium/hydrogen						regulation of pH	integral to membrane|late endosome membrane|recycling endosome	sodium:hydrogen antiporter activity			ovary(2)|skin(1)	3						gtgtctgtgtatgtgtgtgtgt	0.267													2	4	---	---	---	---	
WDR19	57728	broad.mit.edu	37	4	39245701	39245702	+	Intron	INS	-	A	A	rs142411527	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39245701_39245702insA	uc003gtv.2	+						WDR19_uc011byi.1_Intron|WDR19_uc003gtw.1_Intron	NM_025132	NP_079408	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19						cell projection organization	microtubule basal body|motile cilium|photoreceptor connecting cilium	binding			large_intestine(1)	1						TGGGTTTTTTTAAAAAAAAAAG	0.287													6	6	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	117536739	117536742	+	IGR	DEL	GGAA	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:117536739_117536742delGGAA								MIR1973 (315815 upstream) : TRAM1L1 (467974 downstream)																							aaggaaggagggaaggaaggaagg	0.000													7	6	---	---	---	---	
KIAA1109	84162	broad.mit.edu	37	4	123167688	123167689	+	Intron	DEL	TT	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:123167688_123167689delTT	uc003ieh.2	+						KIAA1109_uc003iek.2_Intron	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein						regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						ATTATGATTATTTTATGAGAAT	0.262													8	8	---	---	---	---	
TBC1D9	23158	broad.mit.edu	37	4	141545654	141545657	+	Intron	DEL	CAAA	-	-	rs5862492		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:141545654_141545657delCAAA	uc010ioj.2	-							NM_015130	NP_055945	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)							intracellular	calcium ion binding|Rab GTPase activator activity			ovary(1)	1	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				cctgatttagcaaacaaacaaaca	0.123													7	4	---	---	---	---	
RNF175	285533	broad.mit.edu	37	4	154652861	154652864	+	Intron	DEL	AAAC	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:154652861_154652864delAAAC	uc003int.2	-						RNF175_uc003inu.1_Intron	NM_173662	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175							integral to membrane	zinc ion binding			ovary(1)|pancreas(1)	2	all_hematologic(180;0.093)	Renal(120;0.118)				ggaaggaaggaaacaaggaaaaaa	0.221													5	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	182675437	182675438	+	IGR	INS	-	CACA	CACA	rs72206458		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:182675437_182675438insCACA								None (None upstream) : MGC45800 (384721 downstream)																							TATATCCCAGTcacacacacac	0.238													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	88504034	88504037	+	IGR	DEL	CACA	-	-	rs56790444	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:88504034_88504037delCACA								MEF2C (304165 upstream) : None (None downstream)																							CGCGCGCGCGcacacacacacaca	0.382													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	103837943	103837944	+	IGR	INS	-	TTCC	TTCC			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:103837943_103837944insTTCC								NUDT12 (939453 upstream) : RAB9BP1 (597231 downstream)																							tcttcctttctttccttccttc	0.000													4	2	---	---	---	---	
SGCD	6444	broad.mit.edu	37	5	155935513	155935513	+	Intron	DEL	A	-	-	rs111768881		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:155935513delA	uc003lwd.3	+						SGCD_uc003lwa.1_Intron|SGCD_uc003lwb.2_Intron|SGCD_uc003lwc.3_Intron	NM_001128209	NP_001121681	Q92629	SGCD_HUMAN	delta-sarcoglycan isoform 3						cytoskeleton organization|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma					0	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTCAAAAATTAAAAAAAAAAA	0.303													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	157575626	157575629	+	IGR	DEL	TTCT	-	-	rs112300868		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:157575626_157575629delTTCT								CLINT1 (289458 upstream) : EBF1 (547295 downstream)																							ccttccttccttcttccctccctc	0.054													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170261195	170261197	+	IGR	DEL	ATT	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170261195_170261197delATT								GABRP (20147 upstream) : RANBP17 (27825 downstream)																							catcatcaccattaccatcacca	0.079													3	3	---	---	---	---	
SYCP2L	221711	broad.mit.edu	37	6	10964195	10964195	+	Intron	DEL	T	-	-	rs149829365		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:10964195delT	uc003mzo.2	+						SYCP2L_uc010jow.2_Intron	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like							nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			AACTTCTCCAttttttttttt	0.224													8	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	18309205	18309206	+	IGR	INS	-	CCCTCCCCTC	CCCTCCCCTC	rs140722672	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:18309205_18309206insCCCTCCCCTC								DEK (44406 upstream) : RNF144B (78388 downstream)																							ccttccttcttccctcccctcc	0.054													4	3	---	---	---	---	
BAI3	577	broad.mit.edu	37	6	69984338	69984341	+	Intron	DEL	TTCC	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:69984338_69984341delTTCC	uc003pev.3	+						BAI3_uc010kak.2_Intron|BAI3_uc011dxx.1_Intron|BAI3_uc003pex.1_Intron	NM_001704	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3						negative regulation of angiogenesis|neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			lung(27)|ovary(8)|skin(6)|pancreas(4)|central_nervous_system(3)|urinary_tract(1)|breast(1)	50		all_lung(197;0.212)				GTGGTTGCATttccttccttcctt	0.201													4	3	---	---	---	---	
DDX43	55510	broad.mit.edu	37	6	74115935	74115936	+	Intron	INS	-	GG	GG	rs143908408	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:74115935_74115936insGG	uc003pgw.2	+						DDX43_uc011dyn.1_Intron	NM_018665	NP_061135	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43							intracellular	ATP binding|ATP-dependent RNA helicase activity|RNA binding			ovary(2)|upper_aerodigestive_tract(1)|skin(1)	4						ttagtagagacggtttctctat	0.000													8	5	---	---	---	---	
PKIB	5570	broad.mit.edu	37	6	122999036	122999039	+	Intron	DEL	CTTT	-	-	rs7752574	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:122999036_122999039delCTTT	uc003pyz.2	+						PKIB_uc003pza.2_Intron|PKIB_uc003pzb.2_Intron|PKIB_uc003pzc.2_Intron	NM_181794	NP_861459	Q9C010	IPKB_HUMAN	cAMP-dependent protein kinase inhibitor beta								cAMP-dependent protein kinase inhibitor activity				0				GBM - Glioblastoma multiforme(226;0.164)		tccttccttccttTCtttctttct	0.093													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	33711997	33712004	+	IGR	DEL	TCCTTCCT	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:33711997_33712004delTCCTTCCT								BBS9 (66317 upstream) : BMPER (233108 downstream)																							cctccctccctccttccttccttccttc	0.005													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	45856865	45856865	+	IGR	DEL	C	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:45856865delC								SEPT7P2 (48248 upstream) : IGFBP1 (71094 downstream)																							GACTGAGGGGCCTGGTAGCTC	0.607													4	2	---	---	---	---	
ARMC10	83787	broad.mit.edu	37	7	102732778	102732778	+	Intron	DEL	A	-	-	rs72173671		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102732778delA	uc003vaw.1	+						ARMC10_uc003vay.1_Intron|ARMC10_uc003vax.1_Intron|ARMC10_uc003vbb.1_Intron|ARMC10_uc011kli.1_Intron|ARMC10_uc010lis.1_Intron|ARMC10_uc003vba.1_Intron|ARMC10_uc003vaz.1_Intron	NM_031905	NP_114111	Q8N2F6	ARM10_HUMAN	SVH protein isoform a						regulation of growth	endoplasmic reticulum membrane|integral to membrane	binding			ovary(1)	1						actccgtctcaaaaaaaaaaa	0.189													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	155953380	155953381	+	IGR	INS	-	GAAG	GAAG	rs138712345	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:155953380_155953381insGAAG								SHH (348413 upstream) : C7orf4 (379804 downstream)																							catctcagaaagaaggaaggaa	0.000													2	4	---	---	---	---	
EFHA2	286097	broad.mit.edu	37	8	16971459	16971461	+	Intron	DEL	AAC	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:16971459_16971461delAAC	uc003wxd.2	+							NM_181723	NP_859074	Q86XE3	EFHA2_HUMAN	EF-hand domain family, member A2							integral to membrane	calcium ion binding			skin(1)	1				Colorectal(111;0.0686)|COAD - Colon adenocarcinoma(73;0.239)		CCAGTTGGAGAACAACGTCAAAA	0.330													4	6	---	---	---	---	
PRKDC	5591	broad.mit.edu	37	8	48774594	48774594	+	Intron	DEL	T	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48774594delT	uc003xqi.2	-						PRKDC_uc003xqj.2_Intron|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic						cellular response to insulin stimulus|double-strand break repair via nonhomologous end joining|peptidyl-serine phosphorylation|positive regulation of transcription from RNA polymerase II promoter	DNA-dependent protein kinase-DNA ligase 4 complex|transcription factor complex	ATP binding|DNA binding|DNA-dependent protein kinase activity|transcription factor binding			lung(12)|central_nervous_system(9)|ovary(6)|skin(4)|large_intestine(3)	34		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)				ACTTGATAAGTTTTTTTTAAC	0.348								NHEJ					4	2	---	---	---	---	
STAU2	27067	broad.mit.edu	37	8	74464094	74464095	+	Intron	DEL	TT	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:74464094_74464095delTT	uc003xzm.2	-						STAU2_uc011lfg.1_Intron|STAU2_uc003xzn.2_Intron|STAU2_uc011lfh.1_Intron|STAU2_uc003xzo.2_3'UTR|STAU2_uc003xzp.2_3'UTR|STAU2_uc011lfi.1_3'UTR|STAU2_uc003xzq.2_3'UTR|STAU2_uc010lzk.2_3'UTR	NM_014393	NP_055208	Q9NUL3	STAU2_HUMAN	staufen homolog 2 isoform e						transport	endoplasmic reticulum|microtubule|nucleolus	double-stranded RNA binding				0	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			TGCATATGGCTTTTTTGTCTGT	0.361													5	4	---	---	---	---	
PKHD1L1	93035	broad.mit.edu	37	8	110509659	110509659	+	Intron	DEL	C	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:110509659delC	uc003yne.2	+							NM_177531	NP_803875	Q86WI1	PKHL1_HUMAN	fibrocystin L precursor						immune response	cytosol|extracellular space|integral to membrane	receptor activity			ovary(9)|central_nervous_system(2)|large_intestine(1)|breast(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AAAAACCGttctttttttttt	0.224										HNSCC(38;0.096)			4	2	---	---	---	---	
TRAPPC9	83696	broad.mit.edu	37	8	141445069	141445069	+	Intron	DEL	A	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141445069delA	uc003yvj.2	-						TRAPPC9_uc003yvh.2_Intron|TRAPPC9_uc003yvi.1_Intron	NM_001160372	NP_001153844	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9 isoform						cell differentiation	endoplasmic reticulum|Golgi apparatus				skin(2)	2						actctgtctcaaaaaaaaaaa	0.109													5	4	---	---	---	---	
PSIP1	11168	broad.mit.edu	37	9	15465782	15465783	+	Intron	INS	-	CCAAA	CCAAA	rs140524451	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:15465782_15465783insCCAAA	uc003zlv.3	-						PSIP1_uc003zlw.3_Intron|SNAPC3_uc003zlu.2_RNA	NM_033222	NP_150091	O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1 isoform 2						initiation of viral infection|interspecies interaction between organisms|nuclear mRNA 5'-splice site recognition|provirus integration|regulation of transcription, DNA-dependent|response to heat|response to oxidative stress|transcription, DNA-dependent	cytosol|nuclear heterochromatin|nuclear periphery|nucleoplasm|nucleoplasm|transcriptionally active chromatin	activating transcription factor binding|chromatin binding|DNA secondary structure binding|RNA polymerase II transcription coactivator activity			breast(1)	1				GBM - Glioblastoma multiforme(50;2.38e-06)		GTATCTTCTTCCCAAAGTAATA	0.312													4	2	---	---	---	---	
UBAP2	55833	broad.mit.edu	37	9	33956316	33956316	+	Intron	DEL	T	-	-	rs68127153		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:33956316delT	uc003ztq.1	-						UBAP2_uc011loc.1_Intron|UBAP2_uc011lod.1_Intron|UBAP2_uc011loe.1_Intron|UBAP2_uc011lof.1_Intron|UBAP2_uc011log.1_Intron|UBAP2_uc003ztr.2_Intron	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2											ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		GTGAATGCAAttttttttttt	0.159													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	34923047	34923047	+	IGR	DEL	T	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34923047delT								C9orf144 (84464 upstream) : KIAA1045 (34474 downstream)																							TTTGTTTTTGTTTTTTttttt	0.308													2	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	78808345	78808345	+	IGR	DEL	A	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78808345delA								PCSK5 (7 upstream) : RFK (192088 downstream)																							agccaaaaagaaaaaaaaaaa	0.229													4	3	---	---	---	---	
KIAA0368	23392	broad.mit.edu	37	9	114206518	114206519	+	Intron	INS	-	A	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114206518_114206519insA	uc004bfe.1	-						KIAA0368_uc010muc.1_Intron	NM_001080398	NP_001073867			KIAA0368 protein												0						GTGTGTCATTTAAAAAAAAAAA	0.332													4	3	---	---	---	---	
RPL35	11224	broad.mit.edu	37	9	127620481	127620482	+	Intron	DEL	AT	-	-	rs143690124		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:127620481_127620482delAT	uc004boy.1	-							NM_007209	NP_009140	P42766	RL35_HUMAN	ribosomal protein L35						endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosolic large ribosomal subunit|nucleolus	mRNA binding|protein binding|structural constituent of ribosome			ovary(1)	1				GBM - Glioblastoma multiforme(294;0.182)		CAGGCCACacatgtcactaact	0.327													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	4734408	4734418	+	IGR	DEL	GGTAGGTGAAG	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:4734408_4734418delGGTAGGTGAAG								LOC100216001 (14146 upstream) : AKR1E2 (133984 downstream)																							aaggaaggaaggtaggtgaagggaaggaagg	0.071													5	3	---	---	---	---	
VCL	7414	broad.mit.edu	37	10	75803109	75803110	+	Intron	INS	-	T	T	rs145684984		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:75803109_75803110insT	uc001jwd.2	+						VCL_uc009xrr.2_Intron|VCL_uc010qky.1_Intron|VCL_uc001jwe.2_Intron|VCL_uc010qkz.1_Intron	NM_014000	NP_054706	P18206	VINC_HUMAN	vinculin isoform meta-VCL						adherens junction assembly|apical junction assembly|cell-matrix adhesion|cellular component movement|epithelial cell-cell adhesion|lamellipodium assembly|morphogenesis of an epithelium|muscle contraction|negative regulation of cell migration|platelet activation|platelet degranulation|protein localization at cell surface	costamere|cytosol|extracellular region|focal adhesion	actin binding|alpha-catenin binding|beta-catenin binding|beta-dystroglycan binding|cadherin binding|structural molecule activity		VCL/ALK(4)	kidney(4)|ovary(1)|central_nervous_system(1)	6	Prostate(51;0.0112)					TGACATAATAAttttttttttt	0.099													6	3	---	---	---	---	
SEC31B	25956	broad.mit.edu	37	10	102275671	102275672	+	Intron	INS	-	G	G	rs143845466	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:102275671_102275672insG	uc001krc.1	-						SEC31B_uc010qpo.1_Intron|SEC31B_uc001krd.1_Intron|SEC31B_uc001krf.1_Intron|SEC31B_uc001kre.1_Intron|SEC31B_uc010qpp.1_Intron|SEC31B_uc009xwn.1_Intron|SEC31B_uc009xwo.1_Intron|SEC31B_uc010qpq.1_Intron|SEC31B_uc010qpr.1_Intron	NM_015490	NP_056305	Q9NQW1	SC31B_HUMAN	SEC31 homolog B						protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane				ovary(1)	1		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CTGACTGGAAAGGGGGGGGGTG	0.480													5	7	---	---	---	---	
NAP1L4	4676	broad.mit.edu	37	11	3000198	3000199	+	Intron	INS	-	A	A	rs142571211	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3000198_3000199insA	uc001lxc.2	-						NAP1L4_uc010qxm.1_Intron|NAP1L4_uc010qxn.1_Intron	NM_005969	NP_005960	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4						nucleosome assembly	chromatin assembly complex|cytoplasm	unfolded protein binding			ovary(1)	1		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)		CCAGGGGTGTTAAAGCATGGAG	0.401													3	4	---	---	---	---	
C11orf36	283303	broad.mit.edu	37	11	3238012	3238013	+	5'Flank	INS	-	CCTT	CCTT	rs148237917	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:3238012_3238013insCCTT	uc001lxo.2	+						C11orf36_uc001lxn.2_5'Flank	NR_027138				RecName: Full=Uncharacterized protein C11orf36;												0						AACTTGGATCCccttccttcct	0.178													10	6	---	---	---	---	
EIF3M	10480	broad.mit.edu	37	11	32609935	32609942	+	Intron	DEL	AAAAAAAA	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:32609935_32609942delAAAAAAAA	uc001mtu.2	+						EIF3M_uc010ref.1_Intron	NM_006360	NP_006351	Q7L2H7	EIF3M_HUMAN	eukaryotic translation initiation factor 3,							eukaryotic translation initiation factor 3 complex	protein binding|translation initiation factor activity			ovary(1)|breast(1)|skin(1)	3	Breast(20;0.109)					acttcatctgaaaaaaaaaaaaaaaaaa	0.125													3	3	---	---	---	---	
KBTBD4	55709	broad.mit.edu	37	11	47597411	47597412	+	Intron	INS	-	T	T	rs35653820		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47597411_47597412insT	uc001nfx.2	-						NDUFS3_uc001nft.3_Intron|KBTBD4_uc001nfw.1_Intron|KBTBD4_uc001nfz.2_Intron|KBTBD4_uc001nfy.2_Intron	NM_016506	NP_057590	Q9NVX7	KBTB4_HUMAN	kelch repeat and BTB (POZ) domain containing 4											ovary(1)|central_nervous_system(1)	2						CCTAAAATTGCttttttttttt	0.173													9	4	---	---	---	---	
ANO1	55107	broad.mit.edu	37	11	69995756	69995756	+	Intron	DEL	A	-	-	rs72410022		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:69995756delA	uc001opj.2	+						ANO1_uc001opk.1_Intron|ANO1_uc001opl.1_Intron|ANO1_uc010rqk.1_Intron	NM_018043	NP_060513	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel						multicellular organismal development	chloride channel complex|cytoplasm|plasma membrane	intracellular calcium activated chloride channel activity			ovary(1)|pancreas(1)	2						aactctgtctaaaaaaaaaaa	0.234													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	134310587	134310590	+	Intron	DEL	TCCA	-	-	rs71472116		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134310587_134310590delTCCA	uc001qhs.2	+											Homo sapiens cDNA FLJ37762 fis, clone BRHIP2024347, weakly similar to GALECTIN-3.																		catccatccgtccatccatccatc	0.000													5	3	---	---	---	---	
APOBEC1	339	broad.mit.edu	37	12	7806968	7806969	+	Intron	INS	-	T	T	rs148121076		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7806968_7806969insT	uc001qtb.2	-						APOBEC1_uc001qtc.2_Intron|APOBEC1_uc010sgf.1_Intron	NM_001644	NP_001635	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme						cytidine to uridine editing|DNA demethylation|lipid metabolic process|mRNA modification|mRNA processing|negative regulation of methylation-dependent chromatin silencing	nucleoplasm	cytidine deaminase activity|RNA binding|zinc ion binding				0						TCCACAGTTCCttttttttttt	0.069													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	12	10392084	10392087	+	IGR	DEL	CTTC	-	-	rs147106286		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10392084_10392087delCTTC								GABARAPL1 (16362 upstream) : KLRD1 (64963 downstream)																							ttccttccttcttccttccttcct	0.039													8	4	---	---	---	---	
TROAP	10024	broad.mit.edu	37	12	49719150	49719150	+	Intron	DEL	A	-	-	rs111795391		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:49719150delA	uc001rtx.3	+						TROAP_uc009zlh.2_Intron|TROAP_uc001rty.2_5'Flank	NM_005480	NP_005471	Q12815	TROAP_HUMAN	tastin isoform 1						cell adhesion	cytoplasm				ovary(1)	1						tctatttcttaaaaaaaaaaa	0.199													2	4	---	---	---	---	
GOLGA2B	55592	broad.mit.edu	37	12	100562234	100562234	+	Intron	DEL	T	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100562234delT	uc001tgu.2	-						GOLGA2B_uc001tgy.3_5'Flank|GOLGA2B_uc001tgz.3_RNA	NM_017600	NP_060070			golgi autoantigen, golgin subfamily a, 2-like 1												0						CCGCACCCCCTAGCCTGTTGA	0.547													4	3	---	---	---	---	
IGF1	3479	broad.mit.edu	37	12	102809375	102809378	+	Intron	DEL	TCCC	-	-	rs111541926	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102809375_102809378delTCCC	uc001tjm.2	-						IGF1_uc001tjn.2_Intron|IGF1_uc001tjo.2_Intron	NM_001111283	NP_001104753	P05019	IGF1_HUMAN	insulin-like growth factor 1 isoform 1						anti-apoptosis|bone mineralization involved in bone maturation|cellular component movement|DNA replication|glycolate metabolic process|muscle hypertrophy|myoblast differentiation|myoblast proliferation|myotube cell development|negative regulation of smooth muscle cell apoptosis|phosphatidylinositol-mediated signaling|platelet activation|platelet degranulation|positive regulation of activated T cell proliferation|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|positive regulation of fibroblast proliferation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of mitosis|positive regulation of osteoblast differentiation|positive regulation of phosphatidylinositol 3-kinase cascade|positive regulation of Ras protein signal transduction|positive regulation of smooth muscle cell migration|positive regulation of smooth muscle cell proliferation|positive regulation of transcription from RNA polymerase II promoter|positive regulation of tyrosine phosphorylation of Stat5 protein|Ras protein signal transduction|regulation of multicellular organism growth|satellite cell maintenance involved in skeletal muscle regeneration	platelet alpha granule lumen	growth factor activity|hormone activity|insulin receptor binding|insulin-like growth factor receptor binding|integrin binding			central_nervous_system(1)|pancreas(1)	2						cttccttccttccctccctccctc	0.147													4	2	---	---	---	---	
BAZ1A	11177	broad.mit.edu	37	14	35252661	35252662	+	Intron	INS	-	CTCCTGAG	CTCCTGAG			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:35252661_35252662insCTCCTGAG	uc001wsk.2	-						BAZ1A_uc001wsl.2_Intron	NM_013448	NP_038476	Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A						chromatin remodeling|regulation of transcription, DNA-dependent|transcription, DNA-dependent	ACF complex	zinc ion binding			lung(2)|central_nervous_system(2)|ovary(1)|breast(1)|skin(1)	7	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		cgtgcctcaacctcctgagtag	0.020													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	71328853	71328854	+	IGR	INS	-	AGGA	AGGA	rs141178617	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:71328853_71328854insAGGA								MAP3K9 (52965 upstream) : PCNX (45268 downstream)																							ggaagggaggtaggaaggaagg	0.035													8	4	---	---	---	---	
SCAPER	49855	broad.mit.edu	37	15	76763440	76763441	+	Intron	INS	-	TC	TC	rs34088021		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:76763440_76763441insTC	uc002bby.2	-						SCAPER_uc010bkr.2_Intron|SCAPER_uc002bbx.2_Intron|SCAPER_uc002bbz.1_Intron	NM_020843	NP_065894	Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER							endoplasmic reticulum|nucleus	zinc ion binding			large_intestine(1)|lung(1)|ovary(1)	3						cttcttcttctttttttttttt	0.262													16	7	---	---	---	---	
PSTPIP1	9051	broad.mit.edu	37	15	77321836	77321836	+	Intron	DEL	G	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:77321836delG	uc002bcf.2	+						PSTPIP1_uc010bkt.1_Intron|PSTPIP1_uc010umo.1_Intron|PSTPIP1_uc010bku.1_Intron|PSTPIP1_uc002bcg.2_Intron|PSTPIP1_uc010bkv.1_Intron|PSTPIP1_uc010bkw.1_Intron|PSTPIP1_uc002bch.1_Intron|PSTPIP1_uc002bci.1_5'Flank	NM_003978	NP_003969	O43586	PPIP1_HUMAN	proline-serine-threonine phosphatase interacting						cell adhesion|signal transduction	cleavage furrow|lamellipodium|perinuclear region of cytoplasm	catalytic activity			ovary(1)	1						TCCTGGGGCAGGGGCTTAGCG	0.637													2	4	---	---	---	---	
WDR93	56964	broad.mit.edu	37	15	90260276	90260277	+	Intron	INS	-	T	T	rs148200475		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90260276_90260277insT	uc002boj.2	+						WDR93_uc010bnr.2_Intron	NM_020212	NP_064597	Q6P2C0	WDR93_HUMAN	WD repeat domain 93						electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			ctttttctttcttttttttttt	0.079													10	5	---	---	---	---	
MSLNL	401827	broad.mit.edu	37	16	820382	820383	+	Intron	INS	-	T	T	rs11384995		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:820382_820383insT	uc002cjz.1	-							NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like						cell adhesion	integral to membrane				breast(3)|ovary(1)	4						GATGGGGCAGATGGCGGGAGTG	0.673													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	3395810	3395813	+	IGR	DEL	TCCT	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3395810_3395813delTCCT								ZNF75A (27236 upstream) : OR2C1 (10076 downstream)																							ctcttttctctccttccttccttc	0.000													4	2	---	---	---	---	
ABCC6	368	broad.mit.edu	37	16	16306170	16306170	+	Intron	DEL	T	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16306170delT	uc002den.3	-						ABCC6_uc010bvo.2_Intron|ABCC6_uc010uzz.1_Intron	NM_001171	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C, member 6						response to drug|visual perception	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			skin(2)|ovary(1)	3				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)		GAACTGTGTAttttttttttt	0.264													9	5	---	---	---	---	
NOMO2	283820	broad.mit.edu	37	16	18549711	18549712	+	Intron	INS	-	AA	AA			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:18549711_18549712insAA	uc002dfe.2	-						NOMO2_uc002dff.2_Intron|NOMO2_uc010bvx.2_Intron	NM_001004060	NP_001004060	Q5JPE7	NOMO2_HUMAN	nodal modulator 2 isoform 1							endoplasmic reticulum membrane|integral to membrane	carbohydrate binding|carboxypeptidase activity|protein binding			skin(1)	1						ctctgtctctcaaaaaaaaaaa	0.173													7	5	---	---	---	---	
TMC7	79905	broad.mit.edu	37	16	19056911	19056913	+	Intron	DEL	TTC	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:19056911_19056913delTTC	uc002dfq.2	+						TMC7_uc002dfp.2_Intron|TMC7_uc010vap.1_Intron	NM_024847	NP_079123	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7 isoform a							integral to membrane				skin(2)|ovary(1)	3						ACTGGTAACtttctttttttttt	0.202													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	55375588	55375589	+	IGR	INS	-	TGTG	TGTG	rs145799229	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:55375588_55375589insTGTG								IRX6 (10917 upstream) : MMP2 (137492 downstream)																							ATAAATCTGCAtgtgtgtgtgt	0.173													4	2	---	---	---	---	
HSBP1	3281	broad.mit.edu	37	16	83843068	83843068	+	Intron	DEL	T	-	-	rs149539074		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:83843068delT	uc002fgy.1	+							NM_001537	NP_001528	O75506	HSBP1_HUMAN	heat shock factor binding protein 1						negative regulation of transcription from RNA polymerase II promoter	nucleus	transcription corepressor activity				0		all_cancers(2;0.00573)|all_epithelial(2;0.0309)		BRCA - Breast invasive adenocarcinoma(80;0.0404)		ttttcttttcttttttttttt	0.199													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	15796782	15796783	+	IGR	INS	-	CCTT	CCTT			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15796782_15796783insCCTT								MEIS3P1 (103765 upstream) : ADORA2B (51448 downstream)																							AGATAATCAGCccttccttcct	0.267													4	2	---	---	---	---	
MAP2K3	5606	broad.mit.edu	37	17	21204581	21204584	+	Intron	DEL	TGTG	-	-	rs34743272		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21204581_21204584delTGTG	uc002gys.2	+						MAP2K3_uc002gyt.2_Intron|MAP2K3_uc002gyu.2_Intron	NM_145109	NP_659731	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3						activation of MAPK activity|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of transcription, DNA-dependent|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|MAP kinase kinase activity|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity				0				COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CAGTTCTGTCTGTGTGACCATTCG	0.417													4	2	---	---	---	---	
ATAD5	79915	broad.mit.edu	37	17	29195527	29195528	+	Intron	INS	-	T	T	rs71994777		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29195527_29195528insT	uc002hfs.1	+						ATAD5_uc002hft.1_Intron	NM_024857	NP_079133	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5						response to DNA damage stimulus	nucleus	ATP binding|nucleoside-triphosphatase activity			ovary(3)	3		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				tttttttttaattttttttttt	0.094													6	3	---	---	---	---	
CCDC47	57003	broad.mit.edu	37	17	61841924	61841925	+	Intron	INS	-	T	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61841924_61841925insT	uc002jbs.3	-						CCDC47_uc010ddx.2_Intron|CCDC47_uc002jbt.2_Intron	NM_020198	NP_064583	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47 precursor							integral to membrane	protein binding				0						GTAGGTGTTGATTTTTTTTTTT	0.356													6	3	---	---	---	---	
RGS9	8787	broad.mit.edu	37	17	63197235	63197238	+	Intron	DEL	ACAG	-	-	rs9911951	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:63197235_63197238delACAG	uc002jfe.2	+						RGS9_uc010dem.2_Intron|RGS9_uc002jfd.2_Intron|RGS9_uc002jff.2_Intron|RGS9_uc002jfg.2_Intron	NM_003835	NP_003826	O75916	RGS9_HUMAN	regulator of G-protein signaling 9 isoform 1						intracellular signal transduction|negative regulation of signal transduction|regulation of G-protein coupled receptor protein signaling pathway|visual perception	cytoplasm|heterotrimeric G-protein complex	GTPase activator activity|signal transducer activity			ovary(2)|skin(2)	4						acacacacacacagacacacacac	0.338													4	2	---	---	---	---	
PIGN	23556	broad.mit.edu	37	18	59712910	59712911	+	3'UTR	INS	-	A	A	rs145916087	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:59712910_59712911insA	uc002lii.3	-	32					PIGN_uc002lij.3_3'UTR	NM_176787	NP_789744	O95427	PIGN_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						C-terminal protein lipidation|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphotransferase activity, for other substituted phosphate groups			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5		Colorectal(73;0.187)				GCAAAACCTAGAAAAAAAAAGA	0.366													3	4	---	---	---	---	
ADAMTSL5	339366	broad.mit.edu	37	19	1509665	1509666	+	Intron	INS	-	AAGGGAAGG	AAGGGAAGG	rs149580059	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1509665_1509666insAAGGGAAGG	uc002ltd.2	-						ADAMTSL5_uc010dsl.2_Intron|ADAMTSL5_uc010xgq.1_Intron	NM_213604	NP_998769	Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5 precursor							proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		gggaagggagaaagggaaggaa	0.243													3	4	---	---	---	---	
INSR	3643	broad.mit.edu	37	19	7149948	7149975	+	Intron	DEL	GAAGGAAGGAAGGAAGGAAGGAAGGAAG	-	-	rs8105223	by1000genomes	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7149948_7149975delGAAGGAAGGAAGGAAGGAAGGAAGGAAG	uc002mgd.1	-						INSR_uc002mge.1_Intron	NM_000208	NP_000199	P06213	INSR_HUMAN	insulin receptor isoform Long precursor						activation of MAPK activity|activation of protein kinase B activity|carbohydrate metabolic process|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|glucose homeostasis|heart morphogenesis|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of cell proliferation|positive regulation of developmental growth|positive regulation of DNA replication|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of glycolysis|positive regulation of MAPKKK cascade|positive regulation of mitosis|positive regulation of nitric oxide biosynthetic process|positive regulation of protein kinase B signaling cascade|positive regulation of protein phosphorylation|positive regulation of respiratory burst|protein autophosphorylation|protein heterotetramerization|regulation of embryonic development|regulation of transcription, DNA-dependent|transformation of host cell by virus	caveola|endosome membrane|insulin receptor complex|microsome	ATP binding|GTP binding|insulin binding|insulin receptor activity|insulin receptor substrate binding|insulin-like growth factor I binding|insulin-like growth factor II binding|insulin-like growth factor receptor binding|metal ion binding|phosphatidylinositol 3-kinase binding|PTB domain binding|receptor signaling protein tyrosine kinase activity|SH2 domain binding			ovary(4)|lung(3)|central_nervous_system(2)|large_intestine(1)|stomach(1)|skin(1)	12					Insulin Glargine recombinant(DB00047)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	aaaaaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaagga	0.171													4	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	13709248	13709251	+	IGR	DEL	AAGG	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13709248_13709251delAAGG								CACNA1A (91974 upstream) : CCDC130 (133323 downstream)																							gaaaaaagaaaaggaaggaaggag	0.034											OREG0025297	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	19	32882998	32882998	+	IGR	DEL	A	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:32882998delA								ZNF507 (4427 upstream) : DPY19L3 (13679 downstream)																							agagaaagagaaaaaaaaaaa	0.000													4	2	---	---	---	---	
TMC4	147798	broad.mit.edu	37	19	54665102	54665103	+	Intron	INS	-	T	T	rs75907120		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54665102_54665103insT	uc010erf.2	-						LENG1_uc002qdm.2_5'Flank|TMC4_uc002qdn.2_Intron|TMC4_uc002qdo.2_Intron	NM_001145303	NP_001138775	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4 isoform 1							integral to membrane				pancreas(1)	1	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					gtcgcccaggcttttttttttg	0.144													5	3	---	---	---	---	
PLCB1	23236	broad.mit.edu	37	20	8528925	8528928	+	Intron	DEL	TTTC	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8528925_8528928delTTTC	uc002wnb.2	+						PLCB1_uc010zrb.1_Intron|PLCB1_uc010gbv.1_Intron|PLCB1_uc002wmz.1_Intron|PLCB1_uc002wna.2_Intron	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1						activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12						tctttcattttttctttctttctt	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	57104966	57104966	+	Intron	DEL	C	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57104966delC	uc002xzg.1	+											Homo sapiens cDNA FLJ30075 fis, clone BGGI11000285.																		ttttttttttcttccttcttc	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	31761554	31761555	+	IGR	DEL	GA	-	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31761554_31761555delGA								PATZ1 (19305 upstream) : DRG1 (33984 downstream)																							gagagaaagtgagagagagaga	0.015													4	2	---	---	---	---	
DEPDC5	9681	broad.mit.edu	37	22	32180607	32180607	+	Intron	DEL	A	-	-	rs36118041		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32180607delA	uc003als.2	+						DEPDC5_uc011als.1_Intron|DEPDC5_uc011alu.1_Intron|DEPDC5_uc011alv.1_Intron|DEPDC5_uc003alt.2_Intron|DEPDC5_uc003alr.1_Intron|DEPDC5_uc011alt.1_Intron	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						ctcccatctcaaaaaaaaaaa	0.154													3	3	---	---	---	---	
