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
NIPAL3	57185	broad.mit.edu	37	1	24766690	24766690	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:24766690T>A	uc001bjh.2	+	3	529	c.122T>A	c.(121-123)ATC>AAC	p.I41N	NIPAL3_uc010oek.1_Missense_Mutation_p.I41N|NIPAL3_uc001bjg.2_Missense_Mutation_p.I41N|NIPAL3_uc009vrc.2_5'UTR	NM_020448	NP_065181	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	41	Helical; (Potential).					integral to membrane					0						CTCTTGGCGATCTTCGGGCAC	0.542													46	95	---	---	---	---	PASS
IPP	3652	broad.mit.edu	37	1	46184982	46184982	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46184982G>C	uc001cou.2	-	6	1346	c.1079C>G	c.(1078-1080)ACT>AGT	p.T360S	IPP_uc001cos.3_Missense_Mutation_p.T360S	NM_005897	NP_005888	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	360	Kelch 2.					actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					ATAGCATTCAGTACAATCAAA	0.373													23	52	---	---	---	---	PASS
IPP	3652	broad.mit.edu	37	1	46184983	46184983	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:46184983T>A	uc001cou.2	-	6	1345	c.1078A>T	c.(1078-1080)ACT>TCT	p.T360S	IPP_uc001cos.3_Missense_Mutation_p.T360S	NM_005897	NP_005888	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	360	Kelch 2.					actin cytoskeleton|cytoplasm	actin binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)					TAGCATTCAGTACAATCAAAA	0.373													23	53	---	---	---	---	PASS
LOC642587	642587	broad.mit.edu	37	1	209605623	209605623	+	Missense_Mutation	SNP	G	A	A	rs12407854		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209605623G>A	uc009xcn.2	+	4	621	c.238G>A	c.(238-240)GCC>ACC	p.A80T		NM_001104548	NP_001098018			hypothetical protein LOC642587												0				OV - Ovarian serous cystadenocarcinoma(81;0.0422)		caccaccgccgccgccaccac	0.284													2	0	---	---	---	---	PASS
CENPF	1063	broad.mit.edu	37	1	214781973	214781973	+	Intron	SNP	T	C	C	rs140032572	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:214781973T>C	uc001hkm.2	+						uc001hkn.1_Missense_Mutation_p.T71A	NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F						cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)|skin(1)	13				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GCGCGCTCCGTCAGGTGCAGC	0.721													4	45	---	---	---	---	PASS
C2orf44	80304	broad.mit.edu	37	2	24261024	24261024	+	Silent	SNP	G	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24261024G>C	uc002rep.2	-	2	1472	c.1341C>G	c.(1339-1341)ACC>ACG	p.T447T	C2orf44_uc010eya.2_Silent_p.T447T	NM_025203	NP_079479	Q9H6R7	CB044_HUMAN	hypothetical protein LOC80304 isoform 1	447							protein binding			ovary(1)|breast(1)	2	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AAGTAGAGTAGGTAGTCTGGC	0.363													102	202	---	---	---	---	PASS
WASH2P	375260	broad.mit.edu	37	2	114355998	114355998	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114355998C>G	uc002tkh.2	+	5	674	c.616C>G	c.(616-618)CAC>GAC	p.H206D	WASH2P_uc002tka.2_RNA|WASH2P_uc002tkb.2_RNA|WASH2P_uc002tkd.2_RNA	NM_182905	NP_878908			WAS protein family homolog 1												0						CCAAGGTGGGCACTTGATGTC	0.612													4	17	---	---	---	---	PASS
SCN1A	6323	broad.mit.edu	37	2	166870294	166870294	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:166870294G>T	uc010zcz.1	-	18	3650	c.3632C>A	c.(3631-3633)ACC>AAC	p.T1211N	SCN1A_uc002udo.3_Missense_Mutation_p.T1091N|SCN1A_uc010fpk.2_Missense_Mutation_p.T1063N	NM_006920	NP_008851	P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha	1222	III.|Helical; Name=S1 of repeat III; (By similarity).					voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(6)|skin(6)|large_intestine(1)	13					Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)	AACAATGAAGGTCTCAAACCA	0.388													64	105	---	---	---	---	PASS
PLEKHM3	389072	broad.mit.edu	37	2	208866412	208866412	+	5'UTR	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:208866412G>A	uc002vcl.2	-	2					PLEKHM3_uc002vcm.2_5'UTR	NM_001080475	NP_001073944	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M,						intracellular signal transduction		metal ion binding			ovary(1)	1						TCCAGAAATGGCTTCATGAAC	0.512													50	94	---	---	---	---	PASS
DOCK10	55619	broad.mit.edu	37	2	225710302	225710302	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:225710302A>C	uc010fwz.1	-	20	2532	c.2293T>G	c.(2293-2295)TAT>GAT	p.Y765D	DOCK10_uc002vob.2_Missense_Mutation_p.Y759D	NM_014689	NP_055504	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	765	DHR-1.						GTP binding			ovary(2)	2		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GTGACGTGATAAAAAGAAAAC	0.403													27	247	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10183747	10183747	+	Silent	SNP	C	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183747C>A	uc003bvc.2	+	1	429	c.216C>A	c.(214-216)TCC>TCA	p.S72S	VHL_uc003bvd.2_Silent_p.S72S	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	72			Missing (in VHLD; type I).		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.S72fs*87(7)|p.E70fs*85(1)|p.S72_V87>L(1)|p.P71fs*84(1)|p.R60fs*35(1)|p.N67_V74del(1)|p.E70_S72>A(1)|p.V74fs*51(1)		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)		GCGAGCCCTCCCAGGTCATCT	0.721		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				12	7	---	---	---	---	PASS
VHL	7428	broad.mit.edu	37	3	10183748	10183748	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183748C>T	uc003bvc.2	+	1	430	c.217C>T	c.(217-219)CAG>TAG	p.Q73*	VHL_uc003bvd.2_Nonsense_Mutation_p.Q73*	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	73			Missing (in VHLD; type I).		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.Q73fs*86(5)|p.Q73*(3)|p.E70fs*85(1)|p.S72_V87>L(1)|p.Q73Q(1)|p.P71fs*84(1)|p.R60fs*35(1)|p.N67_V74del(1)|p.V74fs*58(1)|p.V74fs*51(1)		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)		CGAGCCCTCCCAGGTCATCTT	0.721		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				13	7	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52637711	52637711	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52637711G>A	uc003des.2	-	17	2617	c.2605C>T	c.(2605-2607)CAG>TAG	p.Q869*	PBRM1_uc003dex.2_Intron|PBRM1_uc003deq.2_Nonsense_Mutation_p.Q869*|PBRM1_uc003der.2_Nonsense_Mutation_p.Q837*|PBRM1_uc003det.2_Nonsense_Mutation_p.Q884*|PBRM1_uc003deu.2_Nonsense_Mutation_p.Q884*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.Q869*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.Q869*|PBRM1_uc003dey.2_Nonsense_Mutation_p.Q869*|PBRM1_uc003dez.1_Nonsense_Mutation_p.Q869*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.Q782*|PBRM1_uc003dfa.1_Nonsense_Mutation_p.Q215*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	869					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		AAAAACTGCTGAAGTTCTACT	0.338			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								28	30	---	---	---	---	PASS
ROBO2	6092	broad.mit.edu	37	3	77666705	77666705	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:77666705C>G	uc003dpy.3	+	22	3978	c.3335C>G	c.(3334-3336)ACT>AGT	p.T1112S	ROBO2_uc003dpz.2_Missense_Mutation_p.T1116S|ROBO2_uc011bgj.1_RNA|ROBO2_uc011bgk.1_Missense_Mutation_p.T1116S|ROBO2_uc003dqa.2_Missense_Mutation_p.T239S	NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	1112	Cytoplasmic (Potential).				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|skin(3)|ovary(1)|large_intestine(1)|liver(1)	11				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		CCAGTACAAACTTACTTACAC	0.428													88	59	---	---	---	---	PASS
KIF2A	3796	broad.mit.edu	37	5	61677018	61677018	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61677018C>T	uc003jsy.3	+	19	2284	c.1973C>T	c.(1972-1974)TCA>TTA	p.S658L	KIF2A_uc003jsz.3_Missense_Mutation_p.S696L|KIF2A_uc010iwp.2_Missense_Mutation_p.S639L|KIF2A_uc003jsx.3_Missense_Mutation_p.S638L|KIF2A_uc010iwq.2_Missense_Mutation_p.S461L	NM_004520	NP_004511	O00139	KIF2A_HUMAN	kinesin heavy chain member 2 isoform 1	658					blood coagulation|cell differentiation|cell division|microtubule-based movement|mitotic prometaphase|mitotic spindle organization|nervous system development	centrosome|cytosol|microtubule|spindle pole	ATP binding|microtubule motor activity|protein binding				0		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		GATGTCGATTCATATGCTACA	0.343													149	221	---	---	---	---	PASS
PCDHA12	56137	broad.mit.edu	37	5	140255906	140255906	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140255906G>A	uc003lic.2	+	1	976	c.849G>A	c.(847-849)ATG>ATA	p.M283I	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc003lhx.2_Intron|PCDHA11_uc003lia.2_Intron|PCDHA12_uc011daf.1_Missense_Mutation_p.M283I	NM_018903	NP_061726	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12 isoform 1 precursor	283	Cadherin 3.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding|protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGATCAAAATGATTTTGCCAG	0.363													123	217	---	---	---	---	PASS
CLIC1	1192	broad.mit.edu	37	6	31704181	31704181	+	5'UTR	SNP	G	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31704181G>C	uc003nwr.2	-	1					CLIC1_uc003rje.2_Intron	NM_001288	NP_001279	O00299	CLIC1_HUMAN	chloride intracellular channel 1						signal transduction	brush border|chloride channel complex|cytoplasm|membrane fraction|nuclear membrane|plasma membrane|soluble fraction	protein binding|voltage-gated chloride channel activity			ovary(1)|central_nervous_system(1)	2						CCTAGACCCAGGGCTGTCCCT	0.647													8	7	---	---	---	---	PASS
MRPL2	51069	broad.mit.edu	37	6	43022062	43022062	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43022062G>T	uc003ots.1	-	7	991	c.868C>A	c.(868-870)CCC>ACC	p.P290T	CUL7_uc011dvb.1_5'Flank|CUL7_uc003otq.2_5'Flank|CUL7_uc010jyh.2_5'Flank|KLC4_uc003otr.1_Intron	NM_015950	NP_057034	Q5T653	RM02_HUMAN	mitochondrial ribosomal protein L2 precursor	290					translation	mitochondrion|ribosome	structural constituent of ribosome				0		Ovarian(999;0.0014)	Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|all cancers(41;0.00708)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)	BRCA - Breast invasive adenocarcinoma(397;0.0026)		TTCATGGGGGGTAGTGGCCGA	0.582													4	89	---	---	---	---	PASS
ITGB8	3696	broad.mit.edu	37	7	20438643	20438643	+	Intron	SNP	T	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:20438643T>G	uc003suu.2	+						ITGB8_uc011jyh.1_Intron|ITGB8_uc003sut.2_Missense_Mutation_p.F436C	NM_002214	NP_002205	P26012	ITB8_HUMAN	integrin, beta 8 precursor						cell-matrix adhesion|integrin-mediated signaling pathway|placenta blood vessel development	integrin complex	protein binding|receptor activity			skin(3)	3						TTTTTCCCTTTTAAAATAAAC	0.378													10	28	---	---	---	---	PASS
RABL5	64792	broad.mit.edu	37	7	100959549	100959549	+	Intron	SNP	A	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100959549A>G	uc003uyl.2	-						RABL5_uc011kkk.1_Intron|RABL5_uc011kkl.1_Intron|RABL5_uc003uym.2_Intron|RABL5_uc010lhw.2_Intron|RABL5_uc011kkm.1_3'UTR	NM_022777	NP_073614	Q9H7X7	RABL5_HUMAN	RAB, member RAS oncogene family-like 5 isoform								GTP binding				0	Lung NSC(181;0.215)					GCTGGTTTCTAGGACATGGGA	0.393													3	89	---	---	---	---	PASS
PRKDC	5591	broad.mit.edu	37	8	48794597	48794597	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:48794597T>C	uc003xqi.2	-	38	4895	c.4838A>G	c.(4837-4839)CAC>CGC	p.H1613R	PRKDC_uc003xqj.2_Missense_Mutation_p.H1613R|PRKDC_uc011ldh.1_Intron	NM_006904	NP_008835	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic	1613					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)				CAGTCCTTGGTGTTTCTGGTT	0.453								NHEJ					94	168	---	---	---	---	PASS
SULF1	23213	broad.mit.edu	37	8	70533276	70533276	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:70533276C>T	uc010lza.1	+	14	2101	c.1384C>T	c.(1384-1386)CAA>TAA	p.Q462*	SULF1_uc003xyd.2_Nonsense_Mutation_p.Q462*|SULF1_uc003xye.2_Nonsense_Mutation_p.Q462*|SULF1_uc003xyf.2_Nonsense_Mutation_p.Q462*|SULF1_uc003xyg.2_Nonsense_Mutation_p.Q462*|SULF1_uc003xyh.1_RNA	NM_015170	NP_055985	Q8IWU6	SULF1_HUMAN	sulfatase 1 precursor	462					apoptosis|bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			central_nervous_system(3)|ovary(2)|pancreas(1)|skin(1)	7	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			GCAGAAGTGGCAATGCATTGA	0.453													40	97	---	---	---	---	PASS
KIAA1217	56243	broad.mit.edu	37	10	24498121	24498121	+	5'UTR	SNP	C	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:24498121C>T	uc001iru.3	+	1					KIAA1217_uc001irs.2_Intron|KIAA1217_uc001irt.3_5'UTR|KIAA1217_uc010qcy.1_5'UTR|KIAA1217_uc010qcz.1_5'UTR	NM_019590	NP_062536	Q5T5P2	SKT_HUMAN	sickle tail isoform 1						embryonic skeletal system development	cytoplasm				ovary(5)|skin(2)	7						CAGGCAGAGACAATGGAAGAA	0.542													11	34	---	---	---	---	PASS
NCOA4	8031	broad.mit.edu	37	10	51582253	51582253	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:51582253G>A	uc001jis.3	+	6	754	c.551G>A	c.(550-552)TGT>TAT	p.C184Y	PARG_uc001jih.2_Intron|uc010qha.1_Intron|uc001jin.2_Intron|uc010qhb.1_Intron|uc010qhc.1_Intron|NCOA4_uc009xon.2_Missense_Mutation_p.C200Y|NCOA4_uc010qhd.1_Missense_Mutation_p.C200Y|NCOA4_uc010qhe.1_Missense_Mutation_p.C84Y|NCOA4_uc010qhf.1_Missense_Mutation_p.C18Y|NCOA4_uc001jit.2_Missense_Mutation_p.C184Y|NCOA4_uc009xoo.2_Missense_Mutation_p.C184Y	NM_001145263	NP_001138735	Q13772	NCOA4_HUMAN	nuclear receptor coactivator 4 isoform 3	184					androgen receptor signaling pathway|male gonad development|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	androgen receptor binding|transcription coactivator activity			central_nervous_system(1)|kidney(1)	2						AAGAGAGGCTGTATCTCCATG	0.353			T	RET	papillary thyroid 								48	79	---	---	---	---	PASS
SFTPA2	729238	broad.mit.edu	37	10	81318704	81318704	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:81318704C>A	uc001kal.3	-	4	327	c.230G>T	c.(229-231)GGA>GTA	p.G77V	SFTPA2_uc001kan.3_Missense_Mutation_p.G77V	NM_006926	NP_008857	Q8IWL1	SFPA2_HUMAN	RecName: Full=Pulmonary surfactant-associated protein A2;          Short=SP-A2;          Short=SP-A;          Short=PSP-A;          Short=PSPA; AltName: Full=Alveolar proteinosis protein; AltName: Full=35 kDa pulmonary surfactant-associated protein; Flags: Precursor;	77	Collagen-like.				cell junction assembly|respiratory gaseous exchange	collagen|extracellular space	sugar binding				0	all_cancers(46;0.197)|Breast(12;0.000326)|Prostate(51;0.00985)|all_epithelial(25;0.0149)		Epithelial(14;0.00957)|all cancers(16;0.0179)|Colorectal(32;0.229)			ACCAGGGGCTCCAGGCAGCCC	0.627									Pulmonary_Fibrosis_Idiopathic				6	206	---	---	---	---	PASS
TRIM8	81603	broad.mit.edu	37	10	104404879	104404879	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104404879T>C	uc001kvz.2	+	1	628	c.505T>C	c.(505-507)TAC>CAC	p.Y169H		NM_030912	NP_112174	Q9BZR9	TRIM8_HUMAN	tripartite motif-containing 8	169	B box-type 2.					cytoplasm|PML body	ligase activity|protein homodimerization activity|zinc ion binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GTACTGCTGCTACTACAGCGG	0.637													6	11	---	---	---	---	PASS
GPR123	84435	broad.mit.edu	37	10	134910562	134910562	+	Missense_Mutation	SNP	C	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134910562C>T	uc001llx.3	+	3	524	c.88C>T	c.(88-90)CTC>TTC	p.L30F	GPR123_uc001llw.2_Missense_Mutation_p.L750F	NM_001083909	NP_001077378	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	30	Helical; Name=1; (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity				0		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		CGTCATGCTGCTCTGCCTCCT	0.612													43	30	---	---	---	---	PASS
PHRF1	57661	broad.mit.edu	37	11	608267	608267	+	Silent	SNP	C	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:608267C>A	uc001lqe.2	+	14	2942	c.2811C>A	c.(2809-2811)CCC>CCA	p.P937P	PHRF1_uc010qwc.1_Silent_p.P936P|PHRF1_uc010qwd.1_Silent_p.P935P|PHRF1_uc010qwe.1_Silent_p.P933P|PHRF1_uc009ybz.1_Silent_p.P727P|PHRF1_uc009yca.1_RNA	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	937							RNA polymerase binding|zinc ion binding				0						GGCCATCCCCCCCAGAGCCCT	0.692													9	18	---	---	---	---	PASS
LYVE1	10894	broad.mit.edu	37	11	10580541	10580541	+	3'UTR	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:10580541G>A	uc001miv.2	-	6					uc001miu.2_Intron|LYVE1_uc010rca.1_3'UTR	NM_006691	NP_006682	Q9Y5Y7	LYVE1_HUMAN	lymphatic vessel endothelial hyaluronan receptor						anatomical structure morphogenesis|cell-matrix adhesion|cellular component movement|response to wounding|transport	integral to plasma membrane|membrane fraction				central_nervous_system(1)|skin(1)	2				all cancers(16;7.22e-08)|Epithelial(150;1.03e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0609)		TTCCAGTTAGGAACCAAGGGT	0.502													35	40	---	---	---	---	PASS
CACNA1C	775	broad.mit.edu	37	12	2711091	2711091	+	Silent	SNP	G	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:2711091G>T	uc009zdu.1	+	23	3298	c.2985G>T	c.(2983-2985)CTG>CTT	p.L995L	CACNA1C_uc009zdv.1_Silent_p.L972L|CACNA1C_uc001qkb.2_Silent_p.L975L|CACNA1C_uc001qkc.2_Silent_p.L975L|CACNA1C_uc001qke.2_Silent_p.L975L|CACNA1C_uc001qkf.2_Silent_p.L975L|CACNA1C_uc001qjz.2_Silent_p.L975L|CACNA1C_uc001qkd.2_Silent_p.L975L|CACNA1C_uc001qkg.2_Silent_p.L975L|CACNA1C_uc009zdw.1_Silent_p.L975L|CACNA1C_uc001qkh.2_Silent_p.L975L|CACNA1C_uc001qkl.2_Silent_p.L995L|CACNA1C_uc001qkn.2_Silent_p.L975L|CACNA1C_uc001qko.2_Silent_p.L995L|CACNA1C_uc001qkp.2_Silent_p.L975L|CACNA1C_uc001qkr.2_Silent_p.L975L|CACNA1C_uc001qku.2_Silent_p.L975L|CACNA1C_uc001qkq.2_Silent_p.L975L|CACNA1C_uc001qks.2_Silent_p.L975L|CACNA1C_uc001qkt.2_Silent_p.L975L|CACNA1C_uc001qka.1_Silent_p.L510L|CACNA1C_uc001qki.1_Silent_p.L711L|CACNA1C_uc001qkj.1_Silent_p.L711L|CACNA1C_uc001qkk.1_Silent_p.L711L|CACNA1C_uc001qkm.1_Silent_p.L711L	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	995	Helical; Name=S3 of repeat III; (Potential).|III.				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)	TGGACCTGCTGGTGGTCAGCG	0.572													49	66	---	---	---	---	PASS
PRH1	5554	broad.mit.edu	37	12	11035696	11035696	+	Splice_Site	SNP	C	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:11035696C>T	uc001qzc.2	-	6	653	c.65_splice	c.e6-1	p.D22_splice	PRR4_uc009zhp.2_Intron|PRH1_uc001qzb.3_Splice_Site|PRB4_uc001qzf.1_Intron	NM_006250	NP_006241	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 1							extracellular space	protein binding				0				BRCA - Breast invasive adenocarcinoma(232;0.245)		TGGCTGACATCTAGAAAAGAA	0.403													58	103	---	---	---	---	PASS
UHRF1BP1L	23074	broad.mit.edu	37	12	100433380	100433380	+	Silent	SNP	C	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:100433380C>T	uc001tgq.2	-	20	4498	c.4269G>A	c.(4267-4269)AGG>AGA	p.R1423R	UHRF1BP1L_uc001tgp.2_Silent_p.R1073R	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	1423	Potential.									ovary(2)	2						TTACCTGTTCCCTAGTGAAGT	0.383													59	129	---	---	---	---	PASS
NALCN	259232	broad.mit.edu	37	13	101720338	101720338	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:101720338G>C	uc001vox.1	-	39	4567	c.4378C>G	c.(4378-4380)CAG>GAG	p.Q1460E		NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	1460	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|skin(2)|pancreas(1)|central_nervous_system(1)	16	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTTAAAAGCTGGTCCTCCTCA	0.358													60	105	---	---	---	---	PASS
IPO4	79711	broad.mit.edu	37	14	24655987	24655987	+	Missense_Mutation	SNP	T	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24655987T>G	uc001wmv.1	-	9	898	c.767A>C	c.(766-768)AAT>ACT	p.N256T	IPO4_uc001wmt.1_5'Flank|IPO4_uc001wmu.2_5'UTR|IPO4_uc001wmx.1_Missense_Mutation_p.N120T|IPO4_uc001wmy.1_Missense_Mutation_p.N120T|IPO4_uc010tnz.1_RNA|IPO4_uc001wmw.1_RNA|IPO4_uc001wmz.1_Missense_Mutation_p.N256T	NM_024658	NP_078934	Q8TEX9	IPO4_HUMAN	importin 4	256					intracellular protein transport	cytoplasm|nucleus	protein binding|protein transporter activity			kidney(1)	1				GBM - Glioblastoma multiforme(265;0.0087)		CAGGGCCACATTTCTAGCTAC	0.512													20	38	---	---	---	---	PASS
AKAP6	9472	broad.mit.edu	37	14	33292834	33292834	+	Missense_Mutation	SNP	A	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33292834A>C	uc001wrq.2	+	13	5985	c.5815A>C	c.(5815-5817)ATG>CTG	p.M1939L		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1939					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		TAAAGCACTTATGGATAGTTT	0.368													3	73	---	---	---	---	PASS
RASGRF1	5923	broad.mit.edu	37	15	79356851	79356851	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79356851G>T	uc002beq.2	-	2	669	c.294C>A	c.(292-294)AAC>AAA	p.N98K	RASGRF1_uc002bep.2_Missense_Mutation_p.N98K|RASGRF1_uc010blm.1_Missense_Mutation_p.N20K|RASGRF1_uc002ber.3_Missense_Mutation_p.N98K	NM_002891	NP_002882	Q13972	RGRF1_HUMAN	Ras protein-specific guanine	98	PH 1.				activation of Rac GTPase activity|apoptosis|induction of apoptosis by extracellular signals|long-term memory|nerve growth factor receptor signaling pathway|neuron projection development|regulation of Rac protein signal transduction|small GTPase mediated signal transduction|synaptic transmission	cytosol|growth cone|plasma membrane|synaptosome	Rho guanyl-nucleotide exchange factor activity			skin(4)|ovary(1)|central_nervous_system(1)	6						CATGGCTGAAGTTCACCGTGA	0.478													116	234	---	---	---	---	PASS
AP3S2	10239	broad.mit.edu	37	15	90431758	90431758	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90431758T>C	uc002boq.3	-	3	704	c.268A>G	c.(268-270)ATC>GTC	p.I90V	AP3S2_uc002bos.3_Missense_Mutation_p.I291V|AP3S2_uc010bns.2_RNA|AP3S2_uc002bor.3_RNA|AP3S2_uc010bnt.2_Intron	NM_005829	NP_005820	P59780	AP3S2_HUMAN	adaptor-related protein complex 3, sigma 2	90					intracellular protein transport|vesicle-mediated transport	cytoplasmic vesicle membrane|Golgi apparatus|membrane coat	protein transporter activity				0	Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)			CATACCTGGATGAGGTCCAAG	0.453													27	53	---	---	---	---	PASS
EMP2	2013	broad.mit.edu	37	16	10626630	10626630	+	3'UTR	SNP	T	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10626630T>C	uc002czx.2	-	5						NM_001424	NP_001415	P54851	EMP2_HUMAN	epithelial membrane protein 2						cell proliferation	integral to membrane					0						ttttttttttttttttttttt	0.249													2	4	---	---	---	---	PASS
C17orf103	256302	broad.mit.edu	37	17	21146678	21146678	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:21146678T>A	uc010vzx.1	-	4	292	c.290A>T	c.(289-291)AAG>ATG	p.K97M		NM_152914	NP_690878	Q8N6N6	GTL3B_HUMAN	transcript expressed during hematopoiesis 2	97											0						CTTGACGTACTTCTGGATGTA	0.667													34	54	---	---	---	---	PASS
HOXB3	3213	broad.mit.edu	37	17	46628008	46628008	+	Silent	SNP	C	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46628008C>T	uc002inn.2	-	2	1384	c.984G>A	c.(982-984)GAG>GAA	p.E328E	HOXB3_uc010wlm.1_Silent_p.E255E|HOXB3_uc010dbf.2_Silent_p.E328E|HOXB3_uc010dbg.2_Silent_p.E328E|HOXB3_uc002ino.2_Silent_p.E328E|HOXB3_uc010wlk.1_Silent_p.E196E|HOXB3_uc010wll.1_Silent_p.E255E	NM_002146	NP_002137	P14651	HXB3_HUMAN	homeobox B3	328					angiogenesis	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0						GCGGCTCATACTCGGGCGCCG	0.701											OREG0024516	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	34	59	---	---	---	---	PASS
PRKAR1A	5573	broad.mit.edu	37	17	66511419	66511419	+	Intron	SNP	T	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:66511419T>C	uc002jhg.2	+						PRKAR1A_uc002jhh.2_Intron|PRKAR1A_uc002jhi.2_Intron|PRKAR1A_uc002jhj.2_Intron|PRKAR1A_uc002jhk.2_Intron|PRKAR1A_uc002jhl.2_5'UTR|PRKAR1A_uc002jhm.2_5'Flank	NM_212471	NP_997636	P10644	KAP0_HUMAN	cAMP-dependent protein kinase, regulatory						activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|intracellular signal transduction|nerve growth factor receptor signaling pathway|regulation of insulin secretion|regulation of transcription from RNA polymerase II promoter|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity|protein binding			adrenal_gland(4)|lung(3)|thyroid(2)|soft_tissue(2)|breast(1)	12	Breast(10;1.64e-13)					AAAAACAAAATCTACTTAGAA	0.318			T|Mis|N|F|S	RET	papillary thyroid	myxoma|endocrine|papillary thyroid			Carney_Complex|Primary_Pigmented_Nodular_Adrenocortical_Disease_Familial|Cardiac_Myxomas_Familial_Clustering_of				4	5	---	---	---	---	PASS
ADAMTSL5	339366	broad.mit.edu	37	19	1508092	1508092	+	Missense_Mutation	SNP	C	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1508092C>G	uc002ltd.2	-	7	950	c.506G>C	c.(505-507)GGG>GCG	p.G169A	ADAMTSL5_uc010dsl.2_5'UTR|ADAMTSL5_uc010xgq.1_Missense_Mutation_p.G179A	NM_213604	NP_998769	Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5 precursor	169						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)		GCCCAACAACCCATCACAGCC	0.672													3	12	---	---	---	---	PASS
ZNF77	58492	broad.mit.edu	37	19	2933730	2933730	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2933730T>A	uc002lws.3	-	4	1526	c.1395A>T	c.(1393-1395)GAA>GAT	p.E465D		NM_021217	NP_067040	Q15935	ZNF77_HUMAN	zinc finger protein 77	465	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|zinc ion binding			ovary(1)	1				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)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		ATTGATTACATTCGTACGGTT	0.498													18	88	---	---	---	---	PASS
TLE6	79816	broad.mit.edu	37	19	2987728	2987728	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:2987728G>A	uc002lwu.2	+	8	596	c.196G>A	c.(196-198)GAA>AAA	p.E66K	TLE6_uc002lwt.2_Missense_Mutation_p.E189K|TLE6_uc010dtg.2_Missense_Mutation_p.E189K|TLE6_uc002lwv.2_5'UTR	NM_024760	NP_079036	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6 isoform 2	66					regulation of transcription, DNA-dependent	nucleus				ovary(1)	1				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)		CCAGGGGCAGGAAAGCAAGGC	0.597													44	131	---	---	---	---	PASS
RNASEH2A	10535	broad.mit.edu	37	19	12917802	12917802	+	Intron	SNP	C	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12917802C>G	uc002mvg.1	+						RNASEH2A_uc002mvf.1_5'UTR	NM_006397	NP_006388	O75792	RNH2A_HUMAN	ribonuclease H2, large subunit						DNA replication|RNA catabolic process	nucleus|ribonuclease H2 complex	metal ion binding|ribonuclease H activity|RNA binding			breast(2)|central_nervous_system(1)	3						TGCCAGAAAACTGACACCCCT	0.572													29	53	---	---	---	---	PASS
MYO9B	4650	broad.mit.edu	37	19	17306197	17306197	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17306197G>A	uc010eak.2	+	22	4113	c.3961G>A	c.(3961-3963)GCC>ACC	p.A1321T	MYO9B_uc002nfi.2_Missense_Mutation_p.A1321T|MYO9B_uc002nfj.1_Missense_Mutation_p.A1321T|MYO9B_uc002nfl.1_5'Flank	NM_004145	NP_004136	Q13459	MYO9B_HUMAN	myosin IXB isoform 1	1321	Tail.				actin filament-based movement	cell cortex|cytosol|filamentous actin|myosin complex|perinuclear region of cytoplasm	actin binding|ADP binding|ATP binding|ATPase activity|calmodulin binding|metal ion binding|microfilament motor activity|Rho GTPase activator activity			breast(1)	1						GCTGGTGGCCGCCGCCAGCCC	0.716													4	3	---	---	---	---	PASS
ANO8	57719	broad.mit.edu	37	19	17439020	17439020	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:17439020G>C	uc002ngf.2	-	13	2336	c.2177C>G	c.(2176-2178)TCG>TGG	p.S726W	ANO8_uc010eap.2_RNA	NM_020959	NP_066010	Q9HCE9	ANO8_HUMAN	anoctamin 8	726	Cytoplasmic (Potential).					chloride channel complex	chloride channel activity			ovary(3)	3						GAGCTGGGGCGAGTGTTCCTC	0.697													14	40	---	---	---	---	PASS
PNMAL2	57469	broad.mit.edu	37	19	46997176	46997176	+	Missense_Mutation	SNP	T	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46997176T>C	uc002pes.2	-	1	1994	c.1547A>G	c.(1546-1548)GAG>GGG	p.E516G	uc002peu.1_5'Flank	NM_020709	NP_065760	Q9ULN7	PNML2_HUMAN	PNMA-like 2	516										central_nervous_system(1)	1		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		CTCGGTGTCCTCCGACTCCTC	0.711													3	73	---	---	---	---	PASS
SYT3	84258	broad.mit.edu	37	19	51135742	51135742	+	Missense_Mutation	SNP	G	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:51135742G>T	uc002pst.2	-	2	1109	c.475C>A	c.(475-477)CCC>ACC	p.P159T	SYT3_uc002psv.2_Missense_Mutation_p.P159T|SYT3_uc010ycd.1_Missense_Mutation_p.P159T	NM_032298	NP_115674	Q9BQG1	SYT3_HUMAN	synaptotagmin III	159	Cytoplasmic (Potential).					cell junction|endosome|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|breast(1)	3		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		AAGTAGGAGGGCTCAGGGGTG	0.652													15	34	---	---	---	---	PASS
EIF2S2	8894	broad.mit.edu	37	20	32699916	32699916	+	Missense_Mutation	SNP	T	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32699916T>A	uc002xaf.2	-	1	170	c.1A>T	c.(1-3)ATG>TTG	p.M1L	EIF2S2_uc002xag.2_Missense_Mutation_p.M1L|EIF2S2_uc010ges.2_5'UTR	NM_003908	NP_003899	P20042	IF2B_HUMAN	eukaryotic translation initiation factor 2 beta	1						cytosol|eukaryotic translation initiation factor 2 complex	metal ion binding|protein binding|translation initiation factor activity			large_intestine(1)	1						TCCCCAGACATGGCTGCGGCT	0.682													4	5	---	---	---	---	PASS
EIF2S2	8894	broad.mit.edu	37	20	32699917	32699917	+	5'UTR	SNP	G	T	T			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32699917G>T	uc002xaf.2	-	1					EIF2S2_uc002xag.2_5'UTR|EIF2S2_uc010ges.2_5'UTR	NM_003908	NP_003899	P20042	IF2B_HUMAN	eukaryotic translation initiation factor 2 beta							cytosol|eukaryotic translation initiation factor 2 complex	metal ion binding|protein binding|translation initiation factor activity			large_intestine(1)	1						CCCCAGACATGGCTGCGGCTC	0.687													4	6	---	---	---	---	PASS
EEF1A2	1917	broad.mit.edu	37	20	62129166	62129166	+	5'UTR	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62129166G>A	uc002yfd.1	-	1					EEF1A2_uc002yfe.1_5'UTR|EEF1A2_uc010gkg.1_5'UTR	NM_001958	NP_001949	Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha							nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			TCTGGCTCAGGGCGAGGGGGG	0.657													42	83	---	---	---	---	PASS
LIPI	149998	broad.mit.edu	37	21	15561671	15561671	+	Missense_Mutation	SNP	G	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:15561671G>A	uc002yjm.2	-	2	189	c.179C>T	c.(178-180)CCG>CTG	p.P60L	LIPI_uc010gkw.1_5'UTR	NM_198996	NP_945347	Q6XZB0	LIPI_HUMAN	lipase, member I	39					lipid catabolic process	extracellular region|extracellular space|membrane|plasma membrane	heparin binding|phospholipase activity			ovary(2)	2				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		CTCTATTCTCGGAATAAATAA	0.343													124	187	---	---	---	---	PASS
CLIC6	54102	broad.mit.edu	37	21	36081739	36081739	+	Missense_Mutation	SNP	G	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:36081739G>C	uc010gmt.1	+	6	1856	c.1856G>C	c.(1855-1857)AGC>ACC	p.S619T	CLIC6_uc002yuf.1_Missense_Mutation_p.S601T	NM_053277	NP_444507	Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	619	GST C-terminal.					chloride channel complex|cytoplasm|plasma membrane	voltage-gated chloride channel activity			ovary(1)|central_nervous_system(1)	2						GATGCCTACAGCACCGAGGAT	0.468													73	119	---	---	---	---	PASS
OSBP2	23762	broad.mit.edu	37	22	31266569	31266569	+	Missense_Mutation	SNP	A	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:31266569A>G	uc003aiy.1	+	3	1111	c.1007A>G	c.(1006-1008)GAG>GGG	p.E336G	OSBP2_uc011ala.1_Missense_Mutation_p.E171G|OSBP2_uc010gwc.1_Missense_Mutation_p.E163G|OSBP2_uc003aix.1_Missense_Mutation_p.E336G|OSBP2_uc011alb.1_Missense_Mutation_p.E336G|OSBP2_uc003aiz.1_Missense_Mutation_p.E336G|OSBP2_uc003aja.1_5'UTR|OSBP2_uc011alc.1_Missense_Mutation_p.E78G	NM_030758	NP_110385	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2 isoform a	336					lipid transport	membrane	lipid binding			breast(1)|skin(1)	2						TCCCTGACAGAGCTGGACGGC	0.562													29	51	---	---	---	---	PASS
SRPX2	27286	broad.mit.edu	37	X	99901384	99901384	+	Missense_Mutation	SNP	C	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99901384C>A	uc004egb.2	+	2	545	c.65C>A	c.(64-66)ACA>AAA	p.T22K		NM_014467	NP_055282	O60687	SRPX2_HUMAN	sushi-repeat-containing protein, X-linked 2	22					angiogenesis|cell motility|cell-cell adhesion|positive regulation of cell migration involved in sprouting angiogenesis|regulation of phosphorylation	cytoplasm|extracellular region	receptor binding			ovary(2)	2						CCGGCAGTGACACCAACATGG	0.458													4	139	---	---	---	---	PASS
SEPN1	57190	broad.mit.edu	37	1	26139050	26139055	+	Intron	DEL	ACACAA	-	-	rs72877465		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26139050_26139055delACACAA	uc010oer.1	+						SEPN1_uc010oes.1_Intron	NM_020451	NP_065184	Q9NZV5	SELN_HUMAN	selenoprotein N, 1 isoform 1 precursor							endoplasmic reticulum membrane|extracellular region	protein binding			ovary(2)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0421)|OV - Ovarian serous cystadenocarcinoma(117;1.26e-25)|Colorectal(126;3.01e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0143)|READ - Rectum adenocarcinoma(331;0.0649)		atatgcctacacacaaacacacacac	0.165													4	2	---	---	---	---	
DAB1	1600	broad.mit.edu	37	1	57537753	57537755	+	Intron	DEL	AAC	-	-	rs150894966	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57537753_57537755delAAC	uc001cys.1	-						DAB1_uc001cyt.1_Intron|DAB1_uc001cyq.1_Intron|DAB1_uc001cyr.1_Intron|DAB1_uc009vzw.1_Intron|DAB1_uc009vzx.1_Intron	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1						cell differentiation|nervous system development					skin(2)|ovary(1)	3						aaaaaaaaaaaacagaaaaaaCT	0.340													4	2	---	---	---	---	
HFM1	164045	broad.mit.edu	37	1	91740542	91740543	+	Intron	INS	-	T	T	rs11369914		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:91740542_91740543insT	uc001doa.3	-						HFM1_uc009wdb.2_Intron|HFM1_uc010osu.1_Intron|HFM1_uc001dob.3_Intron|HFM1_uc010osv.1_Intron	NM_001017975	NP_001017975	A2PYH4	HFM1_HUMAN	HFM1 protein								ATP binding|ATP-dependent helicase activity|nucleic acid binding				0		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AAATGTTGGCAttttttttttt	0.198													6	3	---	---	---	---	
RAG1AP1	55974	broad.mit.edu	37	1	155202387	155202388	+	Intron	INS	-	G	G			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:155202387_155202388insG	uc010pey.1	+						uc001fjg.2_5'Flank	NM_018845		Q9BRV3	SWET1_HUMAN	recombination activating gene 1 activating						positive regulation of gene expression, epigenetic	Golgi membrane|integral to membrane|plasma membrane	glucoside transmembrane transporter activity				0	all_epithelial(22;4.71e-30)|all_lung(78;3.15e-27)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;2.28e-10)|all cancers(21;6.16e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000395)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGCTACTGGCTGGGCCCAGGCA	0.614													5	3	---	---	---	---	
FCRL4	83417	broad.mit.edu	37	1	157566292	157566305	+	Intron	DEL	CAGACGCTCAGGCT	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157566292_157566305delCAGACGCTCAGGCT	uc001fqw.2	-						FCRL4_uc010phy.1_Intron	NM_031282	NP_112572	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4 precursor							integral to membrane|plasma membrane	receptor activity			ovary(2)|kidney(1)|skin(1)	4	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				acacagtggccagacgctcaggctgtggactcag	0.168													4	2	---	---	---	---	
FCRL1	115350	broad.mit.edu	37	1	157774046	157774047	+	Intron	INS	-	A	A	rs12133090		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:157774046_157774047insA	uc001frg.2	-						FCRL1_uc001frf.2_5'Flank|FCRL1_uc001frh.2_Intron|FCRL1_uc001fri.2_Intron|FCRL1_uc001frj.2_Intron	NM_052938	NP_443170	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1 isoform 1 precursor							integral to membrane|plasma membrane	receptor activity			skin(4)|ovary(3)	7	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			ACCCCCCCCCCAGTGGCCCATG	0.520													7	6	---	---	---	---	
DEDD	9191	broad.mit.edu	37	1	161093426	161093426	+	Intron	DEL	A	-	-	rs148026706		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161093426delA	uc001fxz.2	-						NIT1_uc001fxw.2_Intron|DEDD_uc009wty.2_Intron|DEDD_uc001fya.2_Intron|DEDD_uc001fyb.2_Intron|DEDD_uc010pkb.1_Intron|DEDD_uc001fyc.2_Intron	NM_001039712	NP_001034801	O75618	DEDD_HUMAN	death effector domain-containing protein						apoptosis|induction of apoptosis via death domain receptors|negative regulation of transcription, DNA-dependent|spermatogenesis|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding				0	all_cancers(52;3.39e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			actctgtctcaaaaaaaaaaa	0.169													3	3	---	---	---	---	
CNTN2	6900	broad.mit.edu	37	1	205036040	205036041	+	Intron	INS	-	G	G	rs151113569	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:205036040_205036041insG	uc001hbr.2	+						CNTN2_uc001hbq.1_Intron|CNTN2_uc001hbs.2_Intron	NM_005076	NP_005067	Q02246	CNTN2_HUMAN	contactin 2 precursor						axon guidance|clustering of voltage-gated potassium channels	anchored to membrane|juxtaparanode region of axon|myelin sheath|node of Ranvier|synapse part	identical protein binding			ovary(1)	1	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			CACACAGCATTGCAGAGGCACC	0.317													4	3	---	---	---	---	
MTR	4548	broad.mit.edu	37	1	237015556	237015557	+	Intron	INS	-	GT	GT	rs145458330	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:237015556_237015557insGT	uc001hyi.3	+						MTR_uc010pxw.1_Intron|MTR_uc010pxx.1_Intron|MTR_uc010pxy.1_Intron	NM_000254	NP_000245	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine						nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	TGTCTTTCtgcgtgtgtgtgtg	0.322													3	3	---	---	---	---	
PLD5	200150	broad.mit.edu	37	1	242383609	242383613	+	Intron	DEL	AAAAG	-	-	rs113967982		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:242383609_242383613delAAAAG	uc001hzn.1	-						PLD5_uc001hzl.3_Intron|PLD5_uc001hzm.3_Intron|PLD5_uc001hzo.1_Intron			Q8N7P1	PLD5_HUMAN	RecName: Full=Inactive phospholipase D5;          Short=Inactive PLD 5; AltName: Full=Inactive choline phosphatase 5; AltName: Full=Inactive phosphatidylcholine-hydrolyzing phospholipase D5; AltName: Full=PLDc;							integral to membrane	catalytic activity			ovary(6)	6	Melanoma(84;0.242)		OV - Ovarian serous cystadenocarcinoma(106;0.0329)			aaagaaaactaaaagaaaagaaaag	0.268													3	3	---	---	---	---	
WDR43	23160	broad.mit.edu	37	2	29129301	29129301	+	Intron	DEL	T	-	-	rs113220687		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:29129301delT	uc002rmo.2	+							NM_015131	NP_055946	Q15061	WDR43_HUMAN	WD repeat domain 43							nucleolus				ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)					cagccttaaattttttttttt	0.194													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	64603095	64603096	+	IGR	INS	-	CACCAC	CACCAC			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64603095_64603096insCACCAC								PELI1 (231490 upstream) : HSPC159 (78231 downstream)																							accaccaccatcaccaccatca	0.000													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	89926005	89926005	+	Intron	DEL	G	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:89926005delG	uc010fhm.2	+											Parts of antibodies, mostly variable regions.																		TAATGGGTCAGGTACTGAGTT	0.448													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	96525717	96525718	+	RNA	INS	-	T	T	rs150334322	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:96525717_96525718insT	uc002sva.1	-	41		c.2149_2150insA			uc002suz.1_Frame_Shift_Ins_p.L290fs|uc002svb.1_Frame_Shift_Ins_p.L290fs					Homo sapiens cDNA FLJ41632 fis, clone FCBBF1000297, highly  similar to Human protein immuno-reactive with anti-PTH polyclonal antibodies mRNA.																		CTTATTTTTCAGTTTTCGAATT	0.282													2	5	---	---	---	---	
TNFAIP6	7130	broad.mit.edu	37	2	152214427	152214427	+	Intron	DEL	T	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:152214427delT	uc002txk.2	+							NM_007115	NP_009046	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6						cell adhesion|cell-cell signaling|inflammatory response|signal transduction		hyaluronic acid binding				0				BRCA - Breast invasive adenocarcinoma(221;0.131)		ATACATACGCTTTTTTTTTTT	0.279													4	2	---	---	---	---	
CASP10	843	broad.mit.edu	37	2	202050621	202050621	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:202050621delT	uc002uxl.1	+	2	539	c.121delT	c.(121-123)TTTfs	p.F41fs	CASP10_uc002uxi.1_Frame_Shift_Del_p.F41fs|CASP10_uc010zhn.1_RNA|CASP10_uc002uxj.1_Frame_Shift_Del_p.F41fs|CASP10_uc002uxk.1_Frame_Shift_Del_p.F41fs|CASP10_uc010fta.1_Frame_Shift_Del_p.F41fs|CASP10_uc002uxm.1_Frame_Shift_Del_p.F41fs|CASP10_uc010ftb.1_RNA	NM_032974	NP_116756	Q92851	CASPA_HUMAN	caspase 10 isoform b preproprotein	41	DED 1.				apoptosis|induction of apoptosis by extracellular signals|proteolysis	cytosol|plasma membrane	cysteine-type endopeptidase activity|identical protein binding|protein binding			skin(3)|ovary(1)|pancreas(1)|breast(1)	6						GAACCTCAAGTTTCTCTGCAT	0.448													89	47	---	---	---	---	
MUC4	4585	broad.mit.edu	37	3	195494489	195494489	+	Intron	DEL	C	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195494489delC	uc011bto.1	-						MUC4_uc003fuz.2_Intron|MUC4_uc003fva.2_Intron|MUC4_uc003fvb.2_Intron|MUC4_uc003fvc.2_Intron|MUC4_uc003fvd.2_Intron|MUC4_uc003fve.2_Intron|MUC4_uc010hzr.2_Intron|MUC4_uc011btf.1_Intron|MUC4_uc011btg.1_Intron|MUC4_uc011bth.1_Intron|MUC4_uc011bti.1_Intron|MUC4_uc011btj.1_Intron|MUC4_uc011btk.1_Intron|MUC4_uc011btl.1_Intron|MUC4_uc011btm.1_Intron|MUC4_uc011btn.1_Intron|MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a						cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		attgccaccaccatcaccacc	0.000													4	2	---	---	---	---	
DOK7	285489	broad.mit.edu	37	4	3494670	3494671	+	Frame_Shift_Ins	INS	-	A	A			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:3494670_3494671insA	uc003ghd.2	+	7	1027_1028	c.957_958insA	c.(955-960)CCCAAGfs	p.P319fs	DOK7_uc003ghe.2_Frame_Shift_Ins_p.P181fs|DOK7_uc003ghf.2_Frame_Shift_Ins_p.P61fs|DOK7_uc003ghg.1_Frame_Shift_Ins_p.P9fs	NM_173660	NP_775931	Q18PE1	DOK7_HUMAN	downstream of tyrosine kinase 7 isoform 1	319_320	Ser-rich.				positive regulation of protein tyrosine kinase activity	cell junction|synapse	insulin receptor binding|protein kinase binding			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGCCACCCCCCAAGCCGCTGCG	0.688													2	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	28669438	28669442	+	IGR	DEL	CCTTC	-	-	rs5006048		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:28669438_28669442delCCTTC								None (None upstream) : None (None downstream)																							ttcattccttccttcctttccttcc	0.102													7	4	---	---	---	---	
PTPN13	5783	broad.mit.edu	37	4	87553205	87553206	+	Intron	INS	-	TCCTTCCTTCCTTCCT	TCCTTCCTTCCTTCCT	rs148756344	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:87553205_87553206insTCCTTCCTTCCTTCCT	uc003hpz.2	+						PTPN13_uc003hpy.2_Intron|PTPN13_uc003hqa.2_Intron|PTPN13_uc003hqb.2_Intron	NM_080683	NP_542414	Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type							cytoplasm|cytoskeleton|plasma membrane	protein binding|protein binding|protein tyrosine phosphatase activity			ovary(4)|breast(1)|kidney(1)	6		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TTGTCCTTCCATCCTTCCTTAT	0.342													3	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	179875316	179875317	+	IGR	INS	-	CACCACCGTTGC	CACCACCGTTGC	rs140361383	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:179875316_179875317insCACCACCGTTGC								LOC285501 (963413 upstream) : None (None downstream)																							cacaccaccatcaccaccacca	0.054													5	3	---	---	---	---	
SDHA	6389	broad.mit.edu	37	5	218381	218382	+	5'UTR	INS	-	C	C	rs3214561		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:218381_218382insC	uc003jao.3	+	1					CCDC127_uc003jam.1_5'Flank|SDHA_uc003jan.2_5'UTR|SDHA_uc011clv.1_5'UTR|SDHA_uc011clw.1_5'UTR|SDHA_uc003jap.3_5'UTR	NM_004168	NP_004159	P31040	DHSA_HUMAN	succinate dehydrogenase complex, subunit A,						nervous system development|respiratory electron transport chain|succinate metabolic process|transport|tricarboxylic acid cycle	mitochondrial respiratory chain complex II	electron carrier activity|flavin adenine dinucleotide binding|protein binding|succinate dehydrogenase (ubiquinone) activity				0			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	AGGCGCGGTATCCCCCCTCCCC	0.748									Familial_Paragangliomas				5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	170261080	170261082	+	IGR	DEL	CAT	-	-	rs111380690		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:170261080_170261082delCAT								GABRP (20032 upstream) : RANBP17 (27940 downstream)																							ccaccatcaccatcaccaccacc	0.118													7	4	---	---	---	---	
MICA	4276	broad.mit.edu	37	6	31378225	31378226	+	Intron	INS	-	CCT	CCT			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31378225_31378226insCCT	uc003ntk.1	+						MICA_uc003rxz.1_Intron					RecName: Full=MHC class I polypeptide-related sequence A;          Short=MIC-A; Flags: Precursor;												0		Ovarian(999;0.0253)				TGCATTTCCTGCCCCAGGAAGG	0.490													7	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	6	63903575	63903581	+	IGR	DEL	AAGGAGC	-	-	rs70996279		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:63903575_63903581delAAGGAGC								KHDRBS2 (907475 upstream) : LGSN (82276 downstream)																							GAGATTCCAGAAGGAGCAAGGAGCAGG	0.391													4	3	---	---	---	---	
RAB32	10981	broad.mit.edu	37	6	146875689	146875689	+	Frame_Shift_Del	DEL	T	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146875689delT	uc003qln.1	+	3	806	c.626delT	c.(625-627)ATTfs	p.I209fs		NM_006834	NP_006825	Q13637	RAB32_HUMAN	RAB32, member RAS oncogene family	209					protein transport|small GTPase mediated signal transduction	mitochondrion	GTP binding				0		Ovarian(120;0.142)		OV - Ovarian serous cystadenocarcinoma(155;2.68e-09)|GBM - Glioblastoma multiforme(68;0.00608)		GTGGACAAAATTAAGCTAGAT	0.428													67	94	---	---	---	---	
SNX8	29886	broad.mit.edu	37	7	2297644	2297644	+	Intron	DEL	T	-	-	rs71984612		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:2297644delT	uc003slw.2	-							NM_013321	NP_037453	Q9Y5X2	SNX8_HUMAN	sorting nexin 8						cell communication|early endosome to Golgi transport|intracellular protein transport	early endosome membrane	phosphatidylinositol binding|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		CCCAGCAGtcttttttttttt	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	7	65563900	65563902	+	IGR	DEL	GAG	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65563900_65563902delGAG								ASL (5579 upstream) : CRCP (15903 downstream)																							ggagaaggaagaggaggaggagg	0.207													4	3	---	---	---	---	
TFR2	7036	broad.mit.edu	37	7	100230357	100230357	+	Intron	DEL	G	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100230357delG	uc003uvv.1	-						TFR2_uc010lhc.1_Intron|TFR2_uc003uvu.1_Intron	NM_003227	NP_003218	Q9UP52	TFR2_HUMAN	transferrin receptor 2						cellular iron ion homeostasis|iron ion transport|proteolysis	cytoplasm|integral to plasma membrane	peptidase activity|transferrin receptor activity			ovary(1)|pancreas(1)	2	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					aaaaaaaaaagaacctttttt	0.000													4	2	---	---	---	---	
RNF20	56254	broad.mit.edu	37	9	104297516	104297516	+	Intron	DEL	T	-	-	rs76960510		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:104297516delT	uc004bbn.2	+							NM_019592	NP_062538	Q5VTR2	BRE1A_HUMAN	ring finger protein 20						histone H2B ubiquitination|histone monoubiquitination|negative regulation of cell migration|positive regulation of transcription, DNA-dependent|protein polyubiquitination|ubiquitin-dependent protein catabolic process	nucleolus|ubiquitin ligase complex	histone binding|p53 binding|transcription coactivator activity|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(1)|breast(1)|kidney(1)|skin(1)	8		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TACaatttaattttttttttt	0.209													2	4	---	---	---	---	
COL5A1	1289	broad.mit.edu	37	9	137709530	137709531	+	Intron	DEL	CA	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137709530_137709531delCA	uc004cfe.2	+							NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein						axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)	11		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCTGCAGGCCACACACACACA	0.688													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	30986206	30986207	+	Intron	INS	-	TT	TT			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:30986206_30986207insTT	uc010qdx.1	+											SubName: Full=cDNA FLJ59642, highly similar to Supervillin;																		AGACAAGACTCTAGAAGTGAAA	0.550													2	4	---	---	---	---	
ACTR1A	10121	broad.mit.edu	37	10	104242537	104242538	+	Intron	INS	-	A	A	rs113812056		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:104242537_104242538insA	uc001kvv.2	-						ACTR1A_uc010qqn.1_Intron|ACTR1A_uc010qqo.1_Intron	NM_005736	NP_005727	P61163	ACTZ_HUMAN	ARP1 actin-related protein 1 homolog A,						G2/M transition of mitotic cell cycle|vesicle-mediated transport	centrosome|cytosol|dynactin complex	ATP binding			central_nervous_system(1)	1		Colorectal(252;0.122)		Epithelial(162;5.34e-09)|all cancers(201;1.43e-07)|BRCA - Breast invasive adenocarcinoma(275;0.222)		gctgctgagctaaaaaaaaaaa	0.010													3	3	---	---	---	---	
KCNK18	338567	broad.mit.edu	37	10	118960801	118960801	+	Intron	DEL	A	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118960801delA	uc010qsr.1	+							NM_181840	NP_862823	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18							integral to membrane|plasma membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;0.19)		all cancers(201;0.0211)		CACCGTGGGTAAGTGCAAAGC	0.537													45	63	---	---	---	---	
HRAS	3265	broad.mit.edu	37	11	534404	534415	+	Intron	DEL	CCCAGGCCCAGC	-	-	rs45443193		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:534404_534415delCCCAGGCCCAGC	uc001lpv.2	-						HRAS_uc010qvw.1_Intron|HRAS_uc010qvx.1_Intron|HRAS_uc010qvy.1_Intron	NM_005343	NP_005334	P01112	RASH_HUMAN	v-Ha-ras Harvey rat sarcoma viral oncogene						activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding			urinary_tract(174)|thyroid(155)|skin(126)|upper_aerodigestive_tract(112)|soft_tissue(37)|prostate(29)|salivary_gland(24)|cervix(23)|stomach(14)|pituitary(10)|lung(9)|haematopoietic_and_lymphoid_tissue(9)|breast(6)|testis(5)|endometrium(4)|bone(3)|large_intestine(2)|oesophagus(2)|penis(2)|kidney(1)|adrenal_gland(1)|thymus(1)	749		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Sulindac(DB00605)	CTCAGCCAGGCCCAGGCCCAGCCCCAGGCCCC	0.698		6	Mis		infrequent sarcomas|rare other types	rhadomyosarcoma|ganglioneuroblastoma|bladder			Costello_syndrome	HNSCC(11;0.0054)			12	6	---	---	---	---	
TRPM5	29850	broad.mit.edu	37	11	2441272	2441286	+	Intron	DEL	CCCAGGCCCCCACGG	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:2441272_2441286delCCCAGGCCCCCACGG	uc001lwm.3	-						TRPM5_uc010qxl.1_Intron|TRPM5_uc009ydn.2_Intron	NM_014555	NP_055370	Q9NZQ8	TRPM5_HUMAN	transient receptor potential cation channel,							integral to membrane|plasma membrane	receptor activity|voltage-gated ion channel activity			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		AGCTCCTCCTCCCAGGCCCCCACGGCCCAGGCCCC	0.665													6	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	68646559	68646562	+	IGR	DEL	TTCC	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:68646559_68646562delTTCC								CPT1A (37160 upstream) : MRPL21 (12185 downstream)																							TTttctttctttccttccttcctt	0.142													10	8	---	---	---	---	
MYO7A	4647	broad.mit.edu	37	11	76892814	76892820	+	Intron	DEL	TTTTTTT	-	-	rs10522799		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:76892814_76892820delTTTTTTT	uc001oyb.2	+						MYO7A_uc010rsl.1_Intron|MYO7A_uc010rsm.1_Intron|MYO7A_uc001oyc.2_Intron|MYO7A_uc001oyd.2_Intron|MYO7A_uc009yus.1_Intron|MYO7A_uc009yut.1_Intron	NM_000260	NP_000251	Q13402	MYO7A_HUMAN	myosin VIIA isoform 1						actin filament-based movement|equilibrioception|lysosome organization|sensory perception of sound|visual perception	cytosol|lysosomal membrane|myosin complex|photoreceptor inner segment|photoreceptor outer segment|synapse	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|breast(1)	4						CCTTCTCAAGtttttttttttgttttt	0.295													6	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	128799552	128799553	+	IGR	DEL	CC	-	-	rs67455375		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:128799552_128799553delCC								KCNJ5 (11603 upstream) : TP53AIP1 (5719 downstream)																							CCGAGGGGAGCCCCCCCCTCCC	0.589													3	3	---	---	---	---	
GLB1L3	112937	broad.mit.edu	37	11	134178195	134178196	+	Intron	INS	-	TGT	TGT	rs146163748	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134178195_134178196insTGT	uc009zdf.2	+						GLB1L3_uc010scu.1_Intron|GLB1L3_uc001qho.3_Intron	NM_001080407	NP_001073876	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1 like 3						carbohydrate metabolic process		cation binding|hydrolase activity, hydrolyzing O-glycosyl compounds			pancreas(1)	1	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		caccaccaccaccaccaccact	0.000													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	14	75340955	75340955	+	IGR	DEL	T	-	-	rs35863744		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:75340955delT								PROX2 (10418 upstream) : DLST (7639 downstream)																							ATCATACAAGttttttttttt	0.199													4	3	---	---	---	---	
LGMN	5641	broad.mit.edu	37	14	93184931	93184931	+	Intron	DEL	A	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:93184931delA	uc001yav.2	-						LGMN_uc001yat.2_Intron|LGMN_uc001yau.2_Intron|LGMN_uc001yaw.2_Intron|LGMN_uc010aul.2_Intron|LGMN_uc001yax.2_Intron|LGMN_uc001yay.2_Intron	NM_001008530	NP_001008530	Q99538	LGMN_HUMAN	legumain preproprotein						hormone biosynthetic process|negative regulation of neuron apoptosis|vitamin D metabolic process	lysosome	cysteine-type endopeptidase activity|protein serine/threonine kinase activity			skin(1)	1		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		aaataataataaaaaaaaaaa	0.184													3	4	---	---	---	---	
FMN1	342184	broad.mit.edu	37	15	33256125	33256126	+	Intron	DEL	CA	-	-	rs35753530		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33256125_33256126delCA	uc001zhf.3	-							NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1						actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TCCTATGAATcacacacacaca	0.302													6	4	---	---	---	---	
TP53BP1	7158	broad.mit.edu	37	15	43747919	43747919	+	Intron	DEL	A	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43747919delA	uc001zrs.2	-						TP53BP1_uc010udp.1_Intron|TP53BP1_uc001zrq.3_Intron|TP53BP1_uc001zrr.3_Intron|TP53BP1_uc010udq.1_Intron	NM_005657	NP_005648	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1 isoform 3						double-strand break repair via homologous recombination|positive regulation of transcription from RNA polymerase II promoter	condensed chromosome kinetochore|cytoplasm|nucleoplasm	p53 binding|RNA polymerase II activating transcription factor binding|RNA polymerase II transcription cofactor activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)|kidney(1)	7		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		actctgtctcaaaaaaaaaaa	0.139								Direct_reversal_of_damage|Other_conserved_DNA_damage_response_genes					4	2	---	---	---	---	
SHF	90525	broad.mit.edu	37	15	45466031	45466036	+	Intron	DEL	GGCAGA	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:45466031_45466036delGGCAGA	uc001zuy.2	-						SHF_uc010uen.1_Intron|SHF_uc010ueo.1_Intron|SHF_uc010uep.1_Intron|SHF_uc010ueq.1_Intron|SHF_uc010uer.1_Intron|SHF_uc010ues.1_Intron|SHF_uc010uet.1_Intron|SHF_uc010ueu.1_Intron	NM_138356	NP_612365	Q7M4L6	SHF_HUMAN	Src homology 2 domain containing F											ovary(1)	1		all_cancers(109;8.13e-11)|all_epithelial(112;6.29e-09)|Lung NSC(122;3.57e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;4.1e-16)|GBM - Glioblastoma multiforme(94;5.98e-06)		aatgaggaggggcagaggcagaggca	0.257													4	2	---	---	---	---	
BNIP2	663	broad.mit.edu	37	15	59960956	59960957	+	Intron	INS	-	AC	AC	rs140314308	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59960956_59960957insAC	uc010uhc.1	-						BNIP2_uc002agi.3_Intron|BNIP2_uc010uhb.1_Intron	NM_004330	NP_004321	Q12982	BNIP2_HUMAN	BCL2/adenovirus E1B 19kD interacting protein 2						anti-apoptosis|apoptosis|positive regulation of muscle cell differentiation	nuclear envelope|perinuclear region of cytoplasm	calcium ion binding|GTPase activator activity|protein binding			ovary(1)	1						TTTTCTTTGTTACACACACACA	0.376													6	3	---	---	---	---	
LRRC28	123355	broad.mit.edu	37	15	99925966	99925966	+	Intron	DEL	C	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:99925966delC	uc002bva.1	+						LRRC28_uc002bvb.1_Intron|LRRC28_uc010urt.1_Intron|LRRC28_uc002bvc.1_Intron|LRRC28_uc010uru.1_Intron|LRRC28_uc002bvd.1_Intron	NM_144598	NP_653199	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28												0	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			TTTTTTTTTTCTTAGTTTCTA	0.279													4	2	---	---	---	---	
EMP2	2013	broad.mit.edu	37	16	10631618	10631619	+	Intron	DEL	CA	-	-	rs34790340		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10631618_10631619delCA	uc002czx.2	-							NM_001424	NP_001415	P54851	EMP2_HUMAN	epithelial membrane protein 2						cell proliferation	integral to membrane					0						TGCATGCGCCcacacacacaca	0.342													9	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	16696737	16696738	+	IGR	INS	-	CTTC	CTTC			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:16696737_16696738insCTTC								LOC339047 (252300 upstream) : XYLT1 (499445 downstream)																							tccctccctttcttccttcctt	0.000													8	5	---	---	---	---	
PIGS	94005	broad.mit.edu	37	17	26880657	26880658	+	3'UTR	INS	-	AC	AC	rs145536032	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:26880657_26880658insAC	uc002hbo.2	-	12					UNC119_uc002hbk.2_5'Flank|UNC119_uc002hbm.2_5'Flank|PIGS_uc002hbn.2_3'UTR|PIGS_uc010wap.1_3'UTR	NM_033198	NP_149975	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis,						attachment of GPI anchor to protein|C-terminal protein lipidation	GPI-anchor transamidase complex	protein binding			breast(2)|urinary_tract(1)|kidney(1)	4	Lung NSC(42;0.00431)					tGGAACCTCTGacacacacaca	0.223													4	5	---	---	---	---	
AATK	9625	broad.mit.edu	37	17	79098839	79098847	+	Intron	DEL	GCAGGGTGA	-	-	rs141491493		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79098839_79098847delGCAGGGTGA	uc010dia.2	-						AATK_uc010dhz.2_5'Flank|hsa-mir-3065|MI0014228_5'Flank	NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase							integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			aggggcaggggcagggtgagcagggtgag	0.330													7	5	---	---	---	---	
DLGAP1	9229	broad.mit.edu	37	18	3741135	3741136	+	Intron	INS	-	C	C			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:3741135_3741136insC	uc002kmf.2	-						DLGAP1_uc010wyz.1_Intron|DLGAP1_uc002kme.1_Intron|DLGAP1_uc010dkn.2_Intron|DLGAP1_uc010wyw.1_Intron|DLGAP1_uc010wyx.1_Intron|DLGAP1_uc010wyy.1_Intron|DLGAP1_uc002kmg.2_Intron|DLGAP1_uc002kmk.2_Intron	NM_004746	NP_004737	O14490	DLGP1_HUMAN	discs large homolog-associated protein 1 isoform						synaptic transmission	cell junction|postsynaptic density|postsynaptic membrane				ovary(2)|pancreas(1)|skin(1)	4		Colorectal(8;0.0257)				caccaccaccacatcaccatca	0.000													4	2	---	---	---	---	
FARSA	2193	broad.mit.edu	37	19	13036039	13036039	+	Intron	DEL	T	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13036039delT	uc002mvs.2	-						FARSA_uc002mvt.2_Intron|FARSA_uc010xmv.1_Intron|FARSA_uc010dyy.1_Intron	NM_004461	NP_004452	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit						phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|phenylalanine-tRNA ligase activity|protein binding|tRNA binding			ovary(1)	1					L-Phenylalanine(DB00120)	TTCCCACCCCttttttttttt	0.299													3	3	---	---	---	---	
GGN	199720	broad.mit.edu	37	19	38879051	38879052	+	5'Flank	INS	-	AGCCCCTCCTATTTCG	AGCCCCTCCTATTTCG	rs145320261	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38879051_38879052insAGCCCCTCCTATTTCG	uc002oij.1	-						GGN_uc002oik.1_5'Flank|GGN_uc010efy.1_5'Flank|SPRED3_uc002oil.1_5'Flank|SPRED3_uc002oim.2_5'Flank	NM_152657	NP_689870	Q86UU5	GGN_HUMAN	gametogenetin						cell differentiation|multicellular organismal development|spermatogenesis						0	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GCCAGGCACCCAAGCCACAGCG	0.599													4	2	---	---	---	---	
HNRNPUL1	11100	broad.mit.edu	37	19	41797899	41797900	+	Intron	INS	-	A	A	rs66916970		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41797899_41797900insA	uc002oqb.3	+						CYP2F1_uc010xvw.1_Intron|HNRNPUL1_uc002opz.3_Intron|HNRNPUL1_uc002oqa.3_Intron|HNRNPUL1_uc010ehm.2_Intron|HNRNPUL1_uc002oqc.3_Intron|HNRNPUL1_uc002oqe.3_Intron|HNRNPUL1_uc002oqd.3_Intron|HNRNPUL1_uc010ehn.2_Intron|HNRNPUL1_uc010eho.2_Intron|HNRNPUL1_uc010xvy.1_Intron|HNRNPUL1_uc010ehp.2_Intron|HNRNPUL1_uc010ehl.1_Intron	NM_007040	NP_008971	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1						nuclear mRNA splicing, via spliceosome|regulation of transcription, DNA-dependent|response to virus|transcription, DNA-dependent	heterogeneous nuclear ribonucleoprotein complex|nucleoplasm	enzyme binding|RNA binding			central_nervous_system(1)|skin(1)	2						aaaaaaaaaacaaaaaaaaaaa	0.208													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	20	37281795	37281797	+	IGR	DEL	ATG	-	-	rs112245163		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:37281795_37281797delATG								ADIG (64691 upstream) : SLC32A1 (71308 downstream)																							ggtgatgataatgatggtggtgg	0.005													4	4	---	---	---	---	
C20orf166	128826	broad.mit.edu	37	20	61150006	61150008	+	Intron	DEL	CCT	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:61150006_61150008delCCT	uc011aaj.1	+						C20orf200_uc002ycy.2_5'Flank|C20orf200_uc002ycz.1_5'Flank|uc011aak.1_5'Flank|MIR1-1_hsa-mir-1-1|MI0000651_5'Flank	NM_178463	NP_848558	Q9H1L0	CT166_HUMAN	hypothetical protein LOC128826												0	Breast(26;1.04e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)			ACCCTGCAGGcctcctcctcctc	0.586													4	2	---	---	---	---	
MX1	4599	broad.mit.edu	37	21	42820858	42820865	+	Intron	DEL	TGTGTGTG	-	-	rs35875316		TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:42820858_42820865delTGTGTGTG	uc002yzh.2	+						MX1_uc002yzi.2_Intron|MX1_uc010goq.2_Intron	NM_001144925	NP_001138397	P20591	MX1_HUMAN	myxovirus resistance protein 1						induction of apoptosis|response to virus|type I interferon-mediated signaling pathway	cytosol	GTP binding|GTPase activity|protein binding			ovary(1)	1		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				GATCTGGTTTtgtgtgtgtgtgtgtgtg	0.317													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	22	25855682	25855683	+	Intron	INS	-	GTGT	GTGT	rs138963277	by1000genomes	TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25855682_25855683insGTGT	uc003abt.2	+						uc003abu.2_Intron|uc003abv.2_Intron					Homo sapiens cDNA clone IMAGE:3542716, partial cds.																		CCTGGCAGCTGgtgtgtgtgtg	0.406													8	5	---	---	---	---	
TAB1	10454	broad.mit.edu	37	22	39815792	39815792	+	Intron	DEL	A	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39815792delA	uc003axt.2	+						TAB1_uc003axr.2_Intron|TAB1_uc011aok.1_Intron|TAB1_uc003axu.1_Intron	NM_006116	NP_006107	Q15750	TAB1_HUMAN	mitogen-activated protein kinase kinase kinase 7						activation of MAPK activity|activation of MAPKKK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|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|endosome membrane	catalytic activity|protein binding			breast(1)	1						accctgtctcaaaaaaaaaaa	0.249													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	X	448557	448560	+	IGR	DEL	GGAA	-	-			TCGA-BP-5180-01A-01D-1429-08	TCGA-BP-5180-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:448557_448560delGGAA								PPP2R3B (100930 upstream) : SHOX (136519 downstream)																							GAGACaggatggaaggaaggaagg	0.025													12	7	---	---	---	---	
