Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
MAST2	23139	broad.mit.edu	37	1	46498015	46498015	+	Missense_Mutation	SNP	T	C	C			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr1:46498015T>C	uc001cov.2	+	25	3636	c.3353T>C	c.(3352-3354)CTG>CCG	p.L1118P	MAST2_uc001cow.2_Missense_Mutation_p.L1118P|MAST2_uc001cpa.2_RNA	NM_015112	NP_055927	Q6P0Q8	MAST2_HUMAN	microtubule associated serine/threonine kinase	1118	PDZ.				regulation of interleukin-12 biosynthetic process|spermatid differentiation	cytoplasm|cytoskeleton|plasma membrane	ATP binding|magnesium ion binding|phosphatase binding|protein serine/threonine kinase activity			ovary(5)|lung(3)|stomach(2)|breast(1)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					GGCTTCACCCTGCGGGCCATT	0.577													4	87					0	0	0.021553	0	0
BARHL2	343472	broad.mit.edu	37	1	91182584	91182584	+	Missense_Mutation	SNP	T	C	C			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr1:91182584T>C	uc001dns.2	-	1	211	c.169A>G	c.(169-171)ACC>GCC	p.T57A		NM_020063	NP_064447	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	57						nucleus	sequence-specific DNA binding			ovary(1)	1		all_lung(203;0.0263)|Lung SC(238;0.128)		all cancers(265;0.000897)|Epithelial(280;0.00516)|OV - Ovarian serous cystadenocarcinoma(397;0.211)		GTCCCTACGGTATCAATCTCC	0.607													3	106					0	0	0.009096	0	0
HLX	3142	broad.mit.edu	37	1	221057861	221057861	+	Missense_Mutation	SNP	G	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr1:221057861G>A	uc001hmv.3	+	4	1739	c.1282G>A	c.(1282-1284)GGC>AGC	p.G428S		NM_021958	NP_068777	Q14774	HLX_HUMAN	H2.0-like homeobox	428	Ser-rich.				cell differentiation	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(2)	2				GBM - Glioblastoma multiforme(131;0.00914)		tgggagcagcggcggcggcgg	0.224													3	19					0	0	0.004672	0	0
PARG	8505	broad.mit.edu	37	10	51093329	51093329	+	Missense_Mutation	SNP	C	T	T			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr10:51093329C>T	uc001jif.2	-	8	2011	c.1750G>A	c.(1750-1752)GCA>ACA	p.A584T	PARG_uc001jih.2_Missense_Mutation_p.A584T|PARG_uc001jig.2_Missense_Mutation_p.A170T|PARG_uc010qgv.1_Intron|PARG_uc009xoi.2_Intron|PARG_uc010qgw.1_Missense_Mutation_p.A475T|PARG_uc009xoj.2_Missense_Mutation_p.A135T|PARG_uc010qgx.1_Missense_Mutation_p.A502T	NM_003631	NP_003622	Q86W56	PARG_HUMAN	poly (ADP-ribose) glycohydrolase	584					carbohydrate metabolic process	nucleus	poly(ADP-ribose) glycohydrolase activity			ovary(2)	2				Epithelial(53;0.213)		TGAGCTTCTGCTTCTTCAAGT	0.318													3	64					0	0	0.004672	0	0
CD44	960	broad.mit.edu	37	11	35201882	35201882	+	Missense_Mutation	SNP	G	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr11:35201882G>A	uc001mvu.2	+	3	729	c.295G>A	c.(295-297)GCA>ACA	p.A99T	CD44_uc001mvv.2_Missense_Mutation_p.A99T|CD44_uc001mvw.2_Missense_Mutation_p.A99T|CD44_uc001mvx.2_Missense_Mutation_p.A99T|CD44_uc001mvy.2_Intron|CD44_uc001mwc.3_Missense_Mutation_p.A99T|CD44_uc010rer.1_Missense_Mutation_p.A99T|CD44_uc009ykh.2_Intron	NM_000610	NP_000601	P16070	CD44_HUMAN	CD44 antigen isoform 1 precursor	99	Extracellular (Potential).|Link.				cell-cell adhesion|cell-matrix adhesion|interferon-gamma-mediated signaling pathway|negative regulation of apoptosis|negative regulation of DNA damage response, signal transduction by p53 class mediator|positive regulation of ERK1 and ERK2 cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-tyrosine phosphorylation	cell surface|Golgi apparatus|integral to plasma membrane	collagen binding|hyaluronic acid binding|receptor activity			pancreas(1)	1	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronidase(DB00070)	CATCTGTGCAGCAAACAACAC	0.493													3	73					0	0	0.009096	0	0
DYRK4	8798	broad.mit.edu	37	12	4705796	4705796	+	Missense_Mutation	SNP	C	G	G			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr12:4705796C>G	uc001qmx.2	+	6	621	c.461C>G	c.(460-462)GCT>GGT	p.A154G	DYRK4_uc009zeh.1_Missense_Mutation_p.A269G|DYRK4_uc001qmy.1_Missense_Mutation_p.A154G	NM_003845	NP_003836	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation	154	Protein kinase.					Golgi apparatus	ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			lung(2)|skin(1)	3			Colorectal(7;0.103)			ATCCTGGAAGCTCTCAGAAAG	0.498													5	13					0	0	0.014758	0	0
TCL1B	9623	broad.mit.edu	37	14	96157184	96157184	+	Missense_Mutation	SNP	C	G	G			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr14:96157184C>G	uc001yez.2	+	2	316	c.274C>G	c.(274-276)CCC>GCC	p.P92A	TCL1B_uc001yew.2_RNA|TCL1B_uc001yex.2_RNA|TCL1B_uc010avj.2_RNA|TCL1B_uc001yfa.2_Missense_Mutation_p.P92A	NM_004918	NP_004909	O95988	TCL1B_HUMAN	T-cell leukemia/lymphoma 1B	92								p.P92P(1)		ovary(1)	1		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		GCAGCTCTACCCCGGGAGGAA	0.607													3	100					0	0	0.004672	0	0
LOC646214	646214	broad.mit.edu	37	15	21936464	21936464	+	RNA	SNP	C	T	T	rs8025772	by1000genomes	TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr15:21936464C>T	uc010tzj.1	-	1		c.4276G>A				NR_027053				Homo sapiens mRNA for p21-activated kinase 2 variant protein.												0						GTTATGCAGACCATTTCTTTA	0.328													5	10					0	0	0.014758	0	0
MSLNL	401827	broad.mit.edu	37	16	830475	830475	+	Missense_Mutation	SNP	G	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr16:830475G>A	uc002cjz.1	-	3	526	c.526C>T	c.(526-528)CCT>TCT	p.P176S		NM_001025190	NP_001020361	Q96KJ4	MSLNL_HUMAN	mesothelin-like	Error:Variant_position_missing_in_Q96KJ4_after_alignment					cell adhesion	integral to membrane				breast(3)|ovary(1)	4						CAGGCATGAGGCTGTGGATGC	0.562													7	165					0	0	0.020292	0	0
CHST5	23563	broad.mit.edu	37	16	75563706	75563706	+	Missense_Mutation	SNP	C	T	T			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr16:75563706C>T	uc002fei.2	-	3	1972	c.577G>A	c.(577-579)GTG>ATG	p.V193M	CHST5_uc002fej.1_Missense_Mutation_p.V199M	NM_024533	NP_078809	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O)	193	Lumenal (Potential).				N-acetylglucosamine metabolic process|protein sulfation	integral to membrane|intrinsic to Golgi membrane	N-acetylglucosamine 6-O-sulfotransferase activity				0						TTGAGCACCACGTGGCTGTAG	0.657													63	117					0	0	0.048971	0	0
ZNF208	7757	broad.mit.edu	37	19	22155896	22155896	+	Missense_Mutation	SNP	A	C	C			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr19:22155896A>C	uc002nqp.2	-	5	1789	c.1640T>G	c.(1639-1641)ATT>AGT	p.I547S	ZNF208_uc002nqo.1_Intron	NM_007153	NP_009084			zinc finger protein 208											ovary(5)|skin(2)	7		all_lung(12;0.0961)|Lung NSC(12;0.103)				TGAGACCTTAATAAAGGTTTT	0.398													4	104					0	0	0.009096	0	0
SNAR-C3	100170226	broad.mit.edu	37	19	48453574	48453574	+	RNA	SNP	C	G	G			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr19:48453574C>G	uc010xzb.1	+	1		c.22C>G				NR_024221				Homo sapiens small ILF3/NF90-associated RNA C3 (SNAR-C3), non-coding RNA.												0						GTGGCTCCGGCCGGTTGCGCG	0.592													2	2					0	0	0.004672	0	0
FAM182B	728882	broad.mit.edu	37	20	25848617	25848617	+	RNA	SNP	A	G	G			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr20:25848617A>G	uc002wvd.1	-	1		c.170T>C								Homo sapiens cDNA FLJ30282 fis, clone BRACE2002803.												0						ggcaggcctgaggctgggatg	0													4	12					0	0	0.009096	0	0
SDC4	6385	broad.mit.edu	37	20	43959044	43959044	+	Missense_Mutation	SNP	T	C	C			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr20:43959044T>C	uc002xnu.2	-	4	447	c.407A>G	c.(406-408)CAG>CGG	p.Q136R	SDC4_uc010zws.1_Missense_Mutation_p.Q64R	NM_002999	NP_002990	P31431	SDC4_HUMAN	syndecan 4 precursor	136	Extracellular (Potential).					extracellular region|integral to plasma membrane	cytoskeletal protein binding|thrombospondin receptor activity				0		Myeloproliferative disorder(115;0.0122)				GTTGCTGCCCTGCACAGTGCT	0.527													41	66					0	0	0.048971	0	0
Unknown	0	broad.mit.edu	37	3	5021633	5021633	+	RNA	SNP	C	G	G			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr3:5021633C>G	uc003bqe.1	-	1		c.14G>C			uc010hce.1_5'UTR|BHLHE40_uc003bqf.2_Intron|BHLHE40_uc011asw.1_Intron					Homo sapiens cDNA FLJ32330 fis, clone PROST2004742.																		CCTTCCTGGTCTCTCTTCCTG	0.602											OREG0015367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	5	46					0	0	0.021553	0	0
FILIP1L	11259	broad.mit.edu	37	3	99567862	99567862	+	Silent	SNP	A	G	G			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr3:99567862A>G	uc003dtm.2	-	5	3121	c.2658T>C	c.(2656-2658)TTT>TTC	p.F886F	C3orf26_uc003dtk.1_Intron|C3orf26_uc003dtl.2_Intron|FILIP1L_uc003dto.2_Silent_p.F886F|FILIP1L_uc010hpf.2_Silent_p.F462F|FILIP1L_uc010hpg.2_Silent_p.F646F|FILIP1L_uc003dtn.2_Silent_p.F646F|FILIP1L_uc003dtp.1_Silent_p.F646F	NM_182909	NP_878913	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like isoform 1	886						cytoplasm|membrane|myosin complex|nucleus				ovary(1)	1						CAGGTTGCACAAAGTTGGCAT	0.448													9	211					0	0	0.105934	0	0
ENPEP	2028	broad.mit.edu	37	4	111434635	111434635	+	Missense_Mutation	SNP	A	T	T			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr4:111434635A>T	uc003iab.3	+	7	1715	c.1373A>T	c.(1372-1374)CAT>CTT	p.H458L		NM_001977	NP_001968	Q07075	AMPE_HUMAN	glutamyl aminopeptidase	458	Extracellular (Potential).				cell migration|cell proliferation|cell-cell signaling|proteolysis	integral to plasma membrane	aminopeptidase activity|metalloexopeptidase activity|zinc ion binding			skin(3)|ovary(1)|breast(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)	L-Glutamic Acid(DB00142)	ATGTCTTCGCATCCAATTATT	0.353													63	75					0	0	0.048971	0	0
PCDHGC4	56098	broad.mit.edu	37	5	140866043	140866043	+	Missense_Mutation	SNP	C	T	T			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr5:140866043C>T	uc003lky.1	+	1	1303	c.1303C>T	c.(1303-1305)CTC>TTC	p.L435F	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc003lkh.1_Intron|PCDHGB6_uc003lkj.1_Intron|PCDHGA10_uc003lkl.1_Intron|PCDHGB7_uc003lkn.1_Intron|PCDHGA11_uc003lkp.1_Intron|PCDHGA11_uc003lkq.1_Intron|PCDHGA12_uc003lkt.1_Intron|PCDHGC3_uc003lkv.1_Intron|PCDHGC3_uc003lkw.1_Intron|PCDHGC4_uc011dbb.1_Missense_Mutation_p.L435F|PCDHGC5_uc011dbc.1_5'Flank|PCDHGC5_uc003lla.1_5'Flank	NM_018928	NP_061751	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4 isoform 1	435	Cadherin 4.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAACCCTCCTCTCAGTACCCA	0.468													26	46					0	0	0.054565	0	0
ATP6V0E1	8992	broad.mit.edu	37	5	172410879	172410879	+	Missense_Mutation	SNP	C	G	G			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr5:172410879C>G	uc003mcd.1	+	1	117	c.16C>G	c.(16-18)CTC>GTC	p.L6V		NM_003945	NP_003936	O15342	VA0E1_HUMAN	ATPase, H+ transporting, lysosomal 9kDa, V0	6					ATP hydrolysis coupled proton transport|cell growth|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport|vacuolar acidification	endosome membrane|integral to membrane|membrane fraction|proton-transporting V-type ATPase, V0 domain|vacuole	proton-transporting ATPase activity, rotational mechanism				0	Renal(175;0.000159)|Lung NSC(126;0.00223)|all_lung(126;0.00391)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			GTATCACGGCCTCACTGTGCC	0.612													7	256					0	0	0.069234	0	0
Unknown	0	broad.mit.edu	37	5	177482813	177482813	+	IGR	SNP	G	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr5:177482813G>A								FAM153C (6725 upstream) : N4BP3 (57743 downstream)																							ACCTTGGCCCGCCGGAAGGGC	0.587													4	104					0	0	0.021553	0	0
CDC5L	988	broad.mit.edu	37	6	44387276	44387276	+	Missense_Mutation	SNP	G	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr6:44387276G>A	uc003oxl.2	+	9	1442	c.1183G>A	c.(1183-1185)GTA>ATA	p.V395I		NM_001253	NP_001244	Q99459	CDC5L_HUMAN	CDC5-like	395	Interaction with PPP1R8.				cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	catalytic step 2 spliceosome|cytoplasm|nuclear speck|nucleolus	DNA binding|RNA binding			lung(3)|ovary(1)|kidney(1)|skin(1)	6	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CTTCTCAGGTGTAACTCCACA	0.423													4	98					0	0	0.014758	0	0
BMP5	653	broad.mit.edu	37	6	55739439	55739439	+	Silent	SNP	G	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr6:55739439G>A	uc003pcq.2	-	1	937	c.225C>T	c.(223-225)TCC>TCT	p.S75S	BMP5_uc011dxf.1_Silent_p.S75S	NM_021073	NP_066551	P22003	BMP5_HUMAN	bone morphogenetic protein 5 preproprotein	75					cartilage development|cell differentiation|growth|ossification	extracellular space	BMP receptor binding|cytokine activity|growth factor activity			ovary(2)	2	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			GAGGTGCAGAGGACGCTTGTT	0.468													4	123					0	0	0.021553	0	0
PIK3CG	5294	broad.mit.edu	37	7	106513029	106513029	+	Silent	SNP	G	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr7:106513029G>A	uc003vdv.3	+	3	2128	c.2043G>A	c.(2041-2043)CTG>CTA	p.L681L	PIK3CG_uc003vdu.2_Silent_p.L681L|PIK3CG_uc003vdw.2_Silent_p.L681L	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	681					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			lung(16)|central_nervous_system(8)|breast(5)|pancreas(3)|stomach(2)|ovary(2)|upper_aerodigestive_tract(1)|skin(1)	38						CCAGATTTCTGCTGAAGCGTG	0.378													10	151					0	0	0.020292	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr7:140453136A>T	uc003vwc.3	-	15	1860	c.1799T>A	c.(1798-1800)GTG>GAG	p.V600E		NM_004333	NP_004324	P15056	BRAF_HUMAN	B-Raf	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(16892)|p.V600?(325)|p.V600K(176)|p.V600R(36)|p.V600M(25)|p.V600A(23)|p.V600D(21)|p.V600G(11)|p.V600_K601>E(8)|p.T599_V600insTT(3)|p.T599_R603>I(2)|p.T599_V600>IAL(2)|p.V600L(2)|p.T599_V600insT(2)|p.V600_W604del(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insV(1)|p.T599_V600insDFGLAT(1)	KIAA1549/BRAF(229)|AKAP9_ENST00000356239/BRAF(10)|AGTRAP/BRAF(2)|FCHSD1/BRAF(2)|SLC45A3/BRAF(2)	thyroid(8166)|large_intestine(5052)|skin(3798)|NS(368)|central_nervous_system(284)|ovary(236)|lung(78)|eye(53)|prostate(44)|endometrium(30)|biliary_tract(28)|soft_tissue(27)|haematopoietic_and_lymphoid_tissue(22)|breast(18)|upper_aerodigestive_tract(13)|stomach(13)|pancreas(10)|small_intestine(10)|testis(7)|bone(6)|cervix(5)|genital_tract(4)|oesophagus(3)|urinary_tract(3)|adrenal_gland(3)|gastrointestinal_tract_(site_indeterminate)(2)|liver(2)|meninges(1)|kidney(1)|autonomic_ganglia(1)|pituitary(1)|salivary_gland(1)	18290	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368	V600E(UACC257_SKIN)|V600D(K029AX_SKIN)|V600E(HS695T_SKIN)|V600E(COLO679_SKIN)|V600E(BT474_BREAST)|V600E(IGR39_SKIN)|V600E(A101D_SKIN)|V600E(COLO783_SKIN)|V600E(IGR37_SKIN)|V600E(A375_SKIN)|V600E(WM793_SKIN)|V600E(COLO818_SKIN)|V600E(HS294T_SKIN)|V600E(SKMEL28_SKIN)|V600E(DU4475_BREAST)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(IGR1_SKIN)|V600E(SKHEP1_LIVER)|V600E(WM983B_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(RVH421_SKIN)|V600D(WM2664_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(SKMEL24_SKIN)|V600D(WM115_SKIN)|V600E(MALME3M_SKIN)|V600E(A673_BONE)|V600E(C32_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO800_SKIN)|V600E(COLO741_SKIN)|V600E(HS939T_SKIN)|V600E(COLO205_LARGE_INTESTINE)|V600E(K029AX_SKIN)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(SH4_SKIN)|V600E(WM88_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(COLO849_SKIN)|V600E(MELHO_SKIN)|V600E(BHT101_THYROID)|V600E(G361_SKIN)|V600E(UACC62_SKIN)|V600E(BCPAP_THYROID)|V600E(8505C_THYROID)|V600E(SW1417_LARGE_INTESTINE)|V600E(COLO829_SKIN)|V600E(RKO_LARGE_INTESTINE)|V600E(A2058_SKIN)|V600E(RPMI7951_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(SKMEL5_SKIN)|V600E(ES2_OVARY)|V600E(LOXIMVI_SKIN)	61	Mis|T|O	AKAP9|KIAA1549	melanoma|colorectal|papillary thyroid|borderline ov|Non small-cell lung cancer (NSCLC)|cholangiocarcinoma|pilocytic astrocytoma		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous_syndrome				29	49					0	0	0.050027	0	0
FRMPD1	22844	broad.mit.edu	37	9	37745690	37745690	+	Missense_Mutation	SNP	G	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr9:37745690G>A	uc004aag.1	+	16	3705	c.3661G>A	c.(3661-3663)GTC>ATC	p.V1221I	FRMPD1_uc004aah.1_Missense_Mutation_p.V1221I	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1221						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|skin(2)|breast(1)	9				GBM - Glioblastoma multiforme(29;0.00655)		TTCACCAGCCGTCCCTCCAGA	0.527													4	124					0	0	0.029380	0	0
Unknown	0	broad.mit.edu	37	MT	15299	15299	+	Missense_Mutation	SNP	T	C	C			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chrM:15299T>C	uc004coy.2	+	1	539	c.464T>C	c.(463-465)CTT>CCT	p.L155P	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		TTCACTTCATCTTACCCTTCA	0.483											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	61	6					0	0	0.048971	0	0
ZNF280C	55609	broad.mit.edu	37	X	129354452	129354452	+	Missense_Mutation	SNP	T	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chrX:129354452T>A	uc004evm.2	-	13	1552	c.1398A>T	c.(1396-1398)AAA>AAT	p.K466N	ZNF280C_uc010nrf.1_Missense_Mutation_p.K417N	NM_017666	NP_060136	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	466					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)|ovary(1)	3						GAACTCCTTTTTTCTGTTTAC	0.343													25	39					0	0	0.041601	0	0
Unknown	0	broad.mit.edu	37	1	2776114	2776114	+	IGR	DEL	G	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr1:2776114delG								MMEL1 (211633 upstream) : ACTRT2 (161932 downstream)																							gagggaggaaggagggaggaa	0.055													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	1	38242625	38242625	+	IGR	DEL	T	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr1:38242625delT								EPHA10 (11801 upstream) : MANEAL (17149 downstream)																							CCAGCCTGCCTTCATGGGCTC	0.532													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	38047615	38047615	+	IGR	DEL	T	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr12:38047615delT								None (None upstream) : ALG10B (662942 downstream)																							gatagagcagttttgaaactc	0.000													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	12	131962224	131962225	+	IGR	INS	-	ATA	ATA	rs67902503		TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr12:131962224_131962225insATA								LOC116437 (264749 upstream) : SFRS8 (233410 downstream)																							tggtaatggtggtgatgatggt	0.005													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	14	59502047	59502049	+	IGR	DEL	CCT	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr14:59502047_59502049delCCT								DACT1 (387011 upstream) : DAAM1 (153350 downstream)																							ttccccttcccctcctcctcctc	0.010													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	16	27311479	27311482	+	IGR	DEL	GTGT	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr16:27311479_27311482delGTGT								NSMCE1 (31366 upstream) : IL4R (13769 downstream)																							GAGAGGAGGGgtgtgtgtgtgtgt	0.324													3	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	17	48026282	48026283	+	IGR	INS	-	GT	GT	rs147308847	by1000genomes	TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr17:48026282_48026283insGT								TAC4 (100903 upstream) : DLX4 (20279 downstream)																							GGAGGTGGGAGGGGGCAGAGGG	0.629													4	8	---	---	---	---					
CA10	56934	broad.mit.edu	37	17	50236292	50236294	+	5'Flank	DEL	GAG	-	-	rs78051960	by1000genomes	TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr17:50236292_50236294delGAG	uc002itw.3	-						CA10_uc002itv.3_5'Flank|CA10_uc002itx.3_Intron|CA10_uc002ity.3_Intron|CA10_uc002itz.2_Intron	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			GCGCGGCCATGAGGAGGAGGAGG	0.778													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	19	16361069	16361070	+	IGR	DEL	GT	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr19:16361069_16361070delGT								AP1M1 (14913 upstream) : KLF2 (74581 downstream)																							CAATTTCACCgtgtgtgtgtga	0.099													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	16409482	16409483	+	IGR	INS	-	C	C	rs149678427	by1000genomes	TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr2:16409482_16409483insC								MYCN (322354 upstream) : FAM49A (324418 downstream)																							TCCTTCCTGGGaccccgccccg	0.411													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	75654263	75654264	+	IGR	DEL	GT	-	-	rs112676502		TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr2:75654263_75654264delGT								TACR1 (227618 upstream) : FAM176A (65180 downstream)																							gggacaaagcgtgtgtgtgtgt	0.000													3	5	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	133025925	133025925	+	IGR	DEL	G	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr2:133025925delG								NCRNA00164 (10383 upstream) : GPR39 (148222 downstream)																							GGCGGGGGGTGGGGGTTTGGG	0.612													3	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	133118724	133118724	+	IGR	DEL	G	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr2:133118724delG								NCRNA00164 (103182 upstream) : GPR39 (55423 downstream)																							TGCAGGCACAGGGCAGGCATT	0.726													7	6	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	177706539	177706541	+	IGR	DEL	TCC	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr2:177706539_177706541delTCC								MIR1246 (240759 upstream) : HNRNPA3 (370881 downstream)																							tcctcctccttcctcctcctcct	0.000													2	4	---	---	---	---					
COL6A3	1293	broad.mit.edu	37	2	238322874	238322875	+	5'Flank	INS	-	C	C			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr2:238322874_238322875insC	uc002vwl.2	-						COL6A3_uc002vwo.2_5'Flank|COL6A3_uc010znj.1_5'Flank|COL6A3_uc002vwq.2_5'Flank|COL6A3_uc002vwr.2_5'Flank|COL6A3_uc010znk.1_5'Flank	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor						axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		ctcctcctcctcctccctcccg	0.391													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	239887273	239887274	+	IGR	INS	-	T	T	rs72541496	by1000genomes	TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr2:239887273_239887274insT								TWIST2 (55036 upstream) : HDAC4 (82591 downstream)																							AGTTGCTTCCCCCATGGCCTAG	0.639													3	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	21	10735736	10735736	+	IGR	DEL	C	-	-	rs111875771		TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr21:10735736delC								None (None upstream) : TPTE (171007 downstream)																							tctcagattgcttctgtctgg	0.015													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	21	10779645	10779645	+	IGR	DEL	G	-	-	rs112487535		TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr21:10779645delG								None (None upstream) : TPTE (127098 downstream)																							ggaaggggaaggaatggaatt	0.000													4	3	---	---	---	---					
SMC4	10051	broad.mit.edu	37	3	160143939	160143940	+	Frame_Shift_Ins	INS	-	A	A			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr3:160143939_160143940insA	uc003fdh.2	+	17	2669_2670	c.2556_2557insA	c.(2554-2559)GACAAAfs	p.D852fs	IFT80_uc003fda.2_Intron|SMC4_uc003fdi.2_Frame_Shift_Ins_p.D827fs|SMC4_uc003fdj.2_Frame_Shift_Ins_p.D852fs|SMC4_uc010hwd.2_Frame_Shift_Ins_p.D852fs|SMC4_uc003fdl.2_Frame_Shift_Ins_p.D555fs	NM_001002800	NP_001002800	Q9NTJ3	SMC4_HUMAN	SMC4 structural maintenance of chromosomes	852_853	Potential.				cell division|mitotic chromosome condensation	condensin complex|cytoplasm|nucleus	ATP binding|protein heterodimerization activity			ovary(1)|breast(1)	2			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CAGCCCCTGACAAAAAAAAGCA	0.322													8	254	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	9240393	9240394	+	5'Flank	INS	-	AG	AG			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr4:9240393_9240394insAG	uc011bwo.1	+											RecName: Full=Ubiquitin carboxyl-terminal hydrolase 17-like protein 2;          EC=3.1.2.15; AltName: Full=Ubiquitin thioesterase 17-like protein 2; AltName: Full=Ubiquitin-specific-processing protease 17-like protein 2; AltName: Full=Deubiquitinating enzyme 17-like protein 2; AltName: Full=Deubiquitinating protein 3;          Short=DUB-3;																		caaacacacacacacacgcccc	0.312													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	41951770	41951770	+	IGR	DEL	C	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr5:41951770delC								FBXO4 (10107 upstream) : GHR (472256 downstream)																							TTCTTGGCCACCATCCACCAC	0.488													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	50728058	50728061	+	IGR	DEL	GAGA	-	-	rs67129718	by1000genomes	TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr5:50728058_50728061delGAGA								ISL1 (37501 upstream) : None (None downstream)																							gtgtgtgtgtgagagagagagaga	0.230													2	4	---	---	---	---					
NRG2	9542	broad.mit.edu	37	5	139422565	139422567	+	In_Frame_Del	DEL	GCT	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr5:139422565_139422567delGCT	uc003lex.1	-	1	313_315	c.88_90delAGC	c.(88-90)AGCdel	p.S30del	NRG2_uc003lev.1_In_Frame_Del_p.S30del|NRG2_uc003lew.1_In_Frame_Del_p.S30del|NRG2_uc003ley.1_In_Frame_Del_p.S30del	NM_004883	NP_004874	O14511	NRG2_HUMAN	neuregulin 2 isoform 1	30	Poly-Ser.				embryo development	extracellular region|integral to membrane|plasma membrane	growth factor activity			pancreas(2)|breast(2)|ovary(1)|skin(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tgctcctctcgctgctgctgctg	0.320													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	2292527	2292528	+	IGR	DEL	CT	-	-	rs147898362		TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr7:2292527_2292528delCT								NUDT1 (1747 upstream) : SNX8 (2113 downstream)																							tgcccccttgctctctcacccc	0.000													3	3	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	55847406	55847408	+	IGR	DEL	TCC	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr7:55847406_55847408delTCC								FKBP9L (75146 upstream) : SEPT14 (13829 downstream)																							ttcttcctcttcctcctcctcct	0.030													3	3	---	---	---	---					
SLC39A4	55630	broad.mit.edu	37	8	145639747	145639747	+	Frame_Shift_Del	DEL	A	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chr8:145639747delA	uc003zcq.2	-	6	1148	c.1048delT	c.(1048-1050)TGCfs	p.C350fs	SLC39A4_uc003zcm.1_5'Flank|SLC39A4_uc003zcn.2_5'Flank|SLC39A4_uc003zco.2_Frame_Shift_Del_p.C74fs|SLC39A4_uc003zcp.2_Frame_Shift_Del_p.C325fs	NM_130849	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter),	350	Cytoplasmic (Potential).					cytoplasmic membrane-bounded vesicle|integral to membrane|recycling endosome membrane	zinc ion transmembrane transporter activity				0	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			CAGCCAGTGCAGGTCAGCAGC	0.657													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	M	14659	14660	+	5'Flank	INS	-	T	T			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chrM:14659_14660insT	uc004coy.2	+						uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		CTCAACAGAAACAAAGCATACA	0.421													138	14	---	---	---	---					
Unknown	0	broad.mit.edu	37	X	8434947	8434950	+	IGR	DEL	GGGA	-	-			TCGA-EL-A3GS-01A-11D-A20C-08	TCGA-EL-A3GS-10A-01D-A20C-08									Somatic	Phase_I	Capture				Illumina GAIIx	a0284b66-384e-4381-8417-b75de48de723	e8912aa1-848f-4ab7-b099-c4a4dff101d6	g.chrX:8434947_8434950delGGGA								VCX3B (397 upstream) : KAL1 (61966 downstream)																							gaggtgtgtggggagggagggagg	0.000													2	4	---	---	---	---					
