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
MST1P2	11209	broad.mit.edu	37	1	16974549	16974549	+	RNA	SNP	C	G	G			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr1:16974549C>G	uc009vow.2	+	5		c.1359C>G			MST1P2_uc010ocg.1_RNA|MST1P2_uc010och.1_RNA|MST1P2_uc010oci.1_RNA|MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA					Homo sapiens cDNA FLJ53774 complete cds, moderately similar to Hepatocyte growth factor-like protein precursor.												0						GGGCTGAGTGCAGCGCCTGCT	0.692000													7	166	---	---	---	---	0	0	0.038147	0	0
MST1P9	11223	broad.mit.edu	37	1	17085452	17085452	+	Silent	SNP	A	G	G	rs3981980	by1000genomes	TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr1:17085452A>G	uc010ock.1	-	10	1239	c.1239T>C	c.(1237-1239)TTT>TTC	p.F413F	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						GAGCGGGAGCAAAATCGTGGC	0.617000													5	136	---	---	---	---	0	0	0.029380	0	0
ASH1L	55870	broad.mit.edu	37	1	155491013	155491013	+	Missense_Mutation	SNP	G	A	A			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr1:155491013G>A	uc009wqq.2	-	2	778	c.298C>T	c.(298-300)CCA>TCA	p.P100S	ASH1L_uc001fkt.2_Missense_Mutation_p.P100S|ASH1L_uc009wqr.1_Missense_Mutation_p.P100S	NM_018489	NP_060959	Q9NR48	ASH1L_HUMAN	absent, small, or homeotic 1-like	100					cell-cell signaling|DNA packaging|regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromosome|Golgi apparatus|nucleus|tight junction	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			skin(5)|ovary(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	11	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			AAGTTCTTTGGAGGTTTTTTA	0.373000													6	220	---	---	---	---	0	0	0.021553	0	0
PLEKHA7	144100	broad.mit.edu	37	11	16863232	16863232	+	Missense_Mutation	SNP	C	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr11:16863232C>T	uc001mmo.2	-	9	749	c.734G>A	c.(733-735)AGC>AAC	p.S245N	PLEKHA7_uc010rcu.1_Missense_Mutation_p.S245N	NM_175058	NP_778228	Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A	245	PH.				epithelial cell-cell adhesion|zonula adherens maintenance	centrosome|zonula adherens	delta-catenin binding			skin(2)|central_nervous_system(1)	3						CGCTGTGGAGCTGTTATAGAT	0.557000													3	70	---	---	---	---	0	0	0.009096	0	0
GRIA4	2893	broad.mit.edu	37	11	105845050	105845050	+	Missense_Mutation	SNP	C	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr11:105845050C>T	uc001pix.2	+	16	2869	c.2423C>T	c.(2422-2424)GCC>GTC	p.A808V	GRIA4_uc001piw.2_Missense_Mutation_p.A808V|GRIA4_uc010rvm.1_RNA|GRIA4_uc009yxl.1_RNA	NM_000829	NP_000820	P48058	GRIA4_HUMAN	glutamate receptor, ionotrophic, AMPA 4 isoform	808	Extracellular (Potential).				glutamate signaling pathway|synaptic transmission	cell junction|endocytic vesicle membrane|integral to membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity			ovary(3)|skin(3)|lung(1)|central_nervous_system(1)	8		Melanoma(852;0.000902)|Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Breast(348;0.0323)		BRCA - Breast invasive adenocarcinoma(274;0.000147)|Epithelial(105;0.0291)|all cancers(92;0.0899)	L-Glutamic Acid(DB00142)	AAGACGAGTGCCTTGAGCCTG	0.463000													4	195	---	---	---	---	0	0	0.009096	0	0
SLC2A14	144195	broad.mit.edu	37	12	7984255	7984255	+	Missense_Mutation	SNP	C	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr12:7984255C>T	uc001qtk.2	-	9	1079	c.286G>A	c.(286-288)GTC>ATC	p.V96I	SLC2A14_uc001qtl.2_Missense_Mutation_p.V73I|SLC2A14_uc001qtm.2_Missense_Mutation_p.V73I|SLC2A14_uc010sgg.1_Intron|SLC2A14_uc001qtn.2_Missense_Mutation_p.V96I|SLC2A14_uc001qto.2_Intron|SLC2A14_uc010sgh.1_Missense_Mutation_p.V111I	NM_153449	NP_703150	Q8TDB8	GTR14_HUMAN	glucose transporter 14	96	Helical; Name=2; (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity			ovary(1)	1				Kidney(36;0.0883)		ATACCCCCGACGGAAAATATG	0.493000											OREG0021654	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	134	---	---	---	---	0	0	0.038147	0	0
DHX37	57647	broad.mit.edu	37	12	125459964	125459964	+	Splice_Site	SNP	C	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr12:125459964C>T	uc001ugy.2	-	6	1079	c.980_splice	c.e6+1	p.R327_splice		NM_032656	NP_116045	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37								ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding			skin(1)	1	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		AGAGCCCTCACCGCTGGGACA	0.652000													7	118	---	---	---	---	0	0	0.029380	0	0
MDGA2	161357	broad.mit.edu	37	14	47426730	47426730	+	Missense_Mutation	SNP	G	C	C			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr14:47426730G>C	uc001wwj.3	-	9	1925	c.1729C>G	c.(1729-1731)CGC>GGC	p.R577G	MDGA2_uc001wwi.3_Missense_Mutation_p.R348G|MDGA2_uc010ani.2_Missense_Mutation_p.R137G	NM_001113498	NP_001106970	Q7Z553	MDGA2_HUMAN	MAM domain containing 1 isoform 1	577	Ig-like 6.				spinal cord motor neuron differentiation	anchored to membrane|plasma membrane				ovary(4)|large_intestine(1)|pancreas(1)	6						TTGCCCAAGCGCCACTCATAG	0.453000													5	125	---	---	---	---	0	0	0.021553	0	0
C16orf80	29105	broad.mit.edu	37	16	58149268	58149268	+	Missense_Mutation	SNP	G	A	A			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr16:58149268G>A	uc002enb.1	-	4	647	c.370C>T	c.(370-372)CGG>TGG	p.R124W		NM_013242	NP_037374	Q9Y6A4	CP080_HUMAN	transcription factor IIB	124					multicellular organismal development						0						TCATCCAGCCGCATGGGCATG	0.532000													4	138	---	---	---	---	0	0	0.014758	0	0
KIAA0513	9764	broad.mit.edu	37	16	85100875	85100875	+	Missense_Mutation	SNP	G	C	C			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr16:85100875G>C	uc002fiu.2	+	2	418	c.198G>C	c.(196-198)TGG>TGC	p.W66C	KIAA0513_uc002fis.3_Missense_Mutation_p.W66C|KIAA0513_uc010voj.1_Missense_Mutation_p.W66C|KIAA0513_uc002fit.2_Missense_Mutation_p.W66C	NM_014732	NP_055547	O60268	K0513_HUMAN	hypothetical protein LOC9764	66						cytoplasm				breast(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.234)		ACCCGTCCTGGGACCAAGACC	0.617000													5	69	---	---	---	---	0	0	0.021553	0	0
Unknown	0	broad.mit.edu	37	17	45128671	45128671	+	5'Flank	SNP	T	G	G	rs1056072	by1000genomes	TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr17:45128671T>G	uc010wkl.1	-						uc010wkm.1_RNA					Homo sapiens cDNA FLJ38031 fis, clone CTONG2013348.																		GCTCACAAAATAAGTTCCAGG	0.308000													3	171	---	---	---	---	0	0	0.009096	0	0
Unknown	0	broad.mit.edu	37	17	45128792	45128792	+	5'Flank	SNP	G	T	T	rs143713325	by1000genomes	TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr17:45128792G>T	uc010wkl.1	-						uc010wkm.1_RNA					Homo sapiens cDNA FLJ38031 fis, clone CTONG2013348.																		AATTCAGGTTGTCAGAATGCA	0.373000													3	77	---	---	---	---	0.004672	0.00520594	0.004672	1	0
C2orf42	54980	broad.mit.edu	37	2	70402827	70402827	+	Silent	SNP	A	C	C			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr2:70402827A>C	uc002sgh.2	-	5	1345	c.1017T>G	c.(1015-1017)GTT>GTG	p.V339V		NM_017880	NP_060350	Q9NWW7	CB042_HUMAN	hypothetical protein LOC54980	339											0						ACGAGGAAGCAACCACAGGCT	0.438000													7	363	---	---	---	---	0	0	0.058154	0	0
WASH2P	375260	broad.mit.edu	37	2	114355146	114355146	+	Missense_Mutation	SNP	G	A	A			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr2:114355146G>A	uc002tkh.2	+	4	581	c.523G>A	c.(523-525)GGC>AGC	p.G175S	WASH2P_uc002tka.2_RNA|WASH2P_uc002tkb.2_RNA|WASH2P_uc002tkd.2_RNA|WASH2P_uc002tkf.2_RNA	NM_182905	NP_878908			WAS protein family homolog 1												0						TGGGGGCATCGGCAAGGCCAA	0.532000													3	26	---	---	---	---	0	0	0.021553	0	0
THSD7B	80731	broad.mit.edu	37	2	138414527	138414527	+	Missense_Mutation	SNP	C	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr2:138414527C>T	uc002tva.1	+	22	4180	c.4180C>T	c.(4180-4182)CGC>TGC	p.R1394C	THSD7B_uc010zbj.1_Intron	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7				BRCA - Breast invasive adenocarcinoma(221;0.19)		TCTAGAAACACGCCCTTGTAC	0.408000													23	215	---	---	---	---	0	0	0.021523	0	0
FRG1B	284802	broad.mit.edu	37	20	29628245	29628245	+	Missense_Mutation	SNP	G	A	A			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr20:29628245G>A	uc010ztl.1	+	3	189	c.157G>A	c.(157-159)GCC>ACC	p.A53T	FRG1B_uc002wvm.1_RNA|FRG1B_uc010ztj.1_RNA|FRG1B_uc010gdr.1_RNA|FRG1B_uc010ztk.1_Missense_Mutation_p.A5T					Homo sapiens cDNA FLJ32537 fis, clone SMINT2000400, highly similar to Homo sapiens FRG1 mRNA.												0						GGCTTTGTTGGCCTCAAATAG	0.353000													5	279	---	---	---	---	0	0	0.069234	0	0
Unknown	0	broad.mit.edu	37	22	18844888	18844888	+	RNA	SNP	A	G	G			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr22:18844888A>G	uc002zoe.2	+	4		c.2142A>G			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		GCTCACGGAAATACAGCTTCA	0.587000													3	86	---	---	---	---	0	0	0.004672	0	0
GALNT10	55568	broad.mit.edu	37	5	153789197	153789197	+	Missense_Mutation	SNP	G	A	A			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr5:153789197G>A	uc003lvh.2	+	9	1393	c.1261G>A	c.(1261-1263)GCA>ACA	p.A421T	GALNT10_uc010jic.2_RNA|GALNT10_uc010jid.2_Missense_Mutation_p.A262T|uc003lvi.2_Intron|GALNT10_uc003lvj.2_Missense_Mutation_p.A92T	NM_198321	NP_938080	Q86SR1	GLT10_HUMAN	GalNAc transferase 10 isoform a	421	Lumenal (Potential).					Golgi membrane|integral to membrane	metal ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(2)	2	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			tggggatgtcgcagtccagaa	0.299000													5	192	---	---	---	---	0	0	0.014758	0	0
C6orf221	154288	broad.mit.edu	37	6	74073506	74073506	+	Nonsense_Mutation	SNP	C	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr6:74073506C>T	uc003pgt.3	+	3	630	c.577C>T	c.(577-579)CGA>TGA	p.R193*		NM_001017361	NP_001017361	Q587J8	ECAT1_HUMAN	hypothetical protein LOC154288	193										skin(2)	2						GGGGACCCAGCGATCCCCCGA	0.642000													4	74	---	---	---	---	0	0	0.014758	0	0
DPY19L2P2	349152	broad.mit.edu	37	7	102825947	102825947	+	Missense_Mutation	SNP	A	G	G			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr7:102825947A>G	uc003vbh.3	-	20	3239	c.1048T>C	c.(1048-1050)TGT>CGT	p.C350R	DPY19L2P2_uc003vbg.3_RNA|DPY19L2P2_uc010lit.2_RNA	NR_003561				RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						ACAGCTTGACACTTGCCATTG	0.373000													4	91	---	---	---	---	0	0	0.014758	0	0
PTPRZ1	5803	broad.mit.edu	37	7	121652207	121652207	+	Missense_Mutation	SNP	A	G	G			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr7:121652207A>G	uc003vjy.2	+	12	3502	c.3107A>G	c.(3106-3108)GAT>GGT	p.D1036G	PTPRZ1_uc003vjz.2_Intron|PTPRZ1_uc011knt.1_Intron	NM_002851	NP_002842	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type,	1036	Extracellular (Potential).				central nervous system development	integral to plasma membrane	protein binding|protein tyrosine/threonine phosphatase activity|transmembrane receptor protein tyrosine phosphatase activity			ovary(3)|large_intestine(2)|lung(2)|central_nervous_system(1)|kidney(1)	9						GTGTTTGGTGATGATAATAAG	0.363000													4	120	---	---	---	---	0	0	0.009096	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	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	0.368000	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				18	113	---	---	---	---	0	0	0.055883	0	0
VDAC3	7419	broad.mit.edu	37	8	42259489	42259489	+	Silent	SNP	C	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr8:42259489C>T	uc011lct.1	+	7	650	c.507C>T	c.(505-507)TTC>TTT	p.F169F	VDAC3_uc010lxk.2_3'UTR|VDAC3_uc003xpc.2_Silent_p.F170F	NM_005662	NP_005653	Q9Y277	VDAC3_HUMAN	voltage-dependent anion channel 3 isoform b	169	Beta stranded; (By similarity).				adenine transport	mitochondrial outer membrane|pore complex	nucleotide binding|porin activity|protein binding|voltage-gated anion channel activity			upper_aerodigestive_tract(1)	1	all_cancers(6;3.86e-23)|all_lung(13;6.47e-12)|Lung NSC(13;1.08e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00266)|Lung(22;0.00849)|LUSC - Lung squamous cell carcinoma(45;0.024)		Dihydroxyaluminium(DB01375)	AGAATAATTTCGCCCTGGGTT	0.463000													4	77	---	---	---	---	0	0	0.029380	0	0
SHROOM2	357	broad.mit.edu	37	X	9841718	9841718	+	Silent	SNP	G	A	A	rs139542964		TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chrX:9841718G>A	uc004csu.1	+	2	282	c.192G>A	c.(190-192)GCG>GCA	p.A64A		NM_001649	NP_001640	Q13796	SHRM2_HUMAN	apical protein of Xenopus-like	64	PDZ.				apical protein localization|brain development|cell migration|cell morphogenesis|cellular pigment accumulation|ear development|establishment of melanosome localization|eye pigment granule organization|lens morphogenesis in camera-type eye|melanosome organization	apical plasma membrane|cell-cell adherens junction|microtubule|tight junction	actin filament binding|beta-catenin binding|ligand-gated sodium channel activity			ovary(3)|skin(3)|upper_aerodigestive_tract(1)|breast(1)	8		Hepatocellular(5;0.000888)				AAGCCGCGGCGGTCGACAAGT	0.537000											OREG0019659	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	134	---	---	---	---	0	0	0.029380	0	0
MAMLD1	10046	broad.mit.edu	37	X	149631107	149631107	+	Missense_Mutation	SNP	C	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chrX:149631107C>T	uc004fee.1	+	2	242	c.166C>T	c.(166-168)CAT>TAT	p.H56Y	MAMLD1_uc011mxt.1_Missense_Mutation_p.H18Y|MAMLD1_uc011mxu.1_Intron|MAMLD1_uc011mxv.1_Intron	NM_005491	NP_005482	Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	56					male gonad development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0	Acute lymphoblastic leukemia(192;6.56e-05)					AGGAAGAAAGCATCAGGTAAG	0.333000													9	61	---	---	---	---	0	0	0.058154	0	0
TMCO1	54499	broad.mit.edu	37	1	165712550	165712551	+	Splice_Site	INS	-	A	A			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr1:165712550_165712551insA	uc001gdj.3	-	6	473	c.324_splice	c.e6-1	p.I108_splice	TMCO1_uc001gdl.3_Splice_Site_p.I24_splice|TMCO1_uc001gdm.3_Splice_Site_p.I24_splice|TMCO1_uc001gdk.3_Splice_Site_p.I96_splice|TMCO1_uc001gdn.3_Splice_Site	NM_019026	NP_061899	Q9UM00	TMCO1_HUMAN	transmembrane and coiled-coil domains 1							endoplasmic reticulum membrane|Golgi membrane|integral to membrane				central_nervous_system(1)	1	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					CCATCAAATCTAAAAGAAAAAA	0.381													7	101	---	---	---	---					
TNR	7143	broad.mit.edu	37	1	175372615	175372615	+	Frame_Shift_Del	DEL	C	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr1:175372615delC	uc001gkp.1	-	2	718	c.637delG	c.(637-639)GTGfs	p.V213fs	TNR_uc009wwu.1_Frame_Shift_Del_p.V213fs|TNR_uc010pmz.1_Frame_Shift_Del_p.V213fs	NM_003285	NP_003276	Q92752	TENR_HUMAN	tenascin R precursor	213	Cys-rich.				axon guidance|cell adhesion|signal transduction	proteinaceous extracellular matrix				pancreas(5)|ovary(4)|central_nervous_system(1)|skin(1)	11	Renal(580;0.146)					TCCACACACACCCCCCGGCTG	0.607													7	338	---	---	---	---					
KIAA1462	57608	broad.mit.edu	37	10	30316501	30316503	+	In_Frame_Del	DEL	CTG	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr10:30316501_30316503delCTG	uc001iux.2	-	2	2633_2635	c.2574_2576delCAG	c.(2572-2577)AGCAGT>AGT	p.858_859SS>S	KIAA1462_uc001iuy.2_Intron|KIAA1462_uc001iuz.2_In_Frame_Del_p.720_721SS>S|KIAA1462_uc009xle.1_In_Frame_Del_p.858_859SS>S	NM_020848	NP_065899	Q9P266	K1462_HUMAN	hypothetical protein LOC57608	858_859	Ser-rich.									ovary(4)	4						ACTCTCCTCActgctgctgctgc	0.463													9	141	---	---	---	---					
PCDH15	65217	broad.mit.edu	37	10	55587198	55587200	+	In_Frame_Del	DEL	GGC	-	-	rs12246234		TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr10:55587198_55587200delGGC	uc001jju.1	-	32	4715_4717	c.4320_4322delGCC	c.(4318-4323)CCGCCT>CCT	p.1440_1441PP>P	PCDH15_uc010qhq.1_In_Frame_Del_p.1445_1446PP>P|PCDH15_uc010qhr.1_In_Frame_Del_p.1440_1441PP>P|PCDH15_uc010qhs.1_In_Frame_Del_p.1452_1453PP>P|PCDH15_uc010qht.1_In_Frame_Del_p.1447_1448PP>P|PCDH15_uc010qhu.1_In_Frame_Del_p.1440_1441PP>P|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_In_Frame_Del_p.1437_1438PP>P|PCDH15_uc010qhw.1_In_Frame_Del_p.1400_1401PP>P|PCDH15_uc010qhx.1_In_Frame_Del_p.1369_1370PP>P|PCDH15_uc010qhy.1_In_Frame_Del_p.1445_1446PP>P|PCDH15_uc010qhz.1_In_Frame_Del_p.1440_1441PP>P|PCDH15_uc010qia.1_In_Frame_Del_p.1418_1419PP>P|PCDH15_uc010qib.1_In_Frame_Del_p.1415_1416PP>P	NM_033056	NP_149045	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-4 precursor	1440_1441	Poly-Pro.|Cytoplasmic (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)|upper_aerodigestive_tract(2)|skin(2)	13		Melanoma(3;0.117)|Lung SC(717;0.238)				ACCTggcggaggcggcggcggcg	0.438										HNSCC(58;0.16)			7	143	---	---	---	---					
ADAM21P1	145241	broad.mit.edu	37	14	70714561	70714561	+	5'Flank	DEL	A	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr14:70714561delA	uc010ttg.1	-							NR_003951				SubName: Full=ADAM21-like protein;												0						ATAAGTAAGGAAATCAGGAGA	0.289													5	6	---	---	---	---					
ATG2B	55102	broad.mit.edu	37	14	96783571	96783572	+	Frame_Shift_Ins	INS	-	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr14:96783571_96783572insT	uc001yfi.2	-	20	3485_3486	c.3120_3121insA	c.(3118-3123)AAATTAfs	p.K1040fs		NM_018036	NP_060506	Q96BY7	ATG2B_HUMAN	ATG2 autophagy related 2 homolog B	1040_1041										ovary(1)|kidney(1)|skin(1)	3		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TGAGAGTCTAATTTTTTTTTCC	0.371													8	144	---	---	---	---					
GOLGA6B	55889	broad.mit.edu	37	15	72957311	72957313	+	In_Frame_Del	DEL	GAG	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr15:72957311_72957313delGAG	uc010uks.1	+	14	1569_1571	c.1528_1530delGAG	c.(1528-1530)GAGdel	p.E513del	uc002aux.1_5'Flank|uc002auy.1_5'Flank	NM_018652	NP_061122	A6NDN3	GOG6B_HUMAN	golgi autoantigen, golgin subfamily a, 6B	513	Potential.										0						TCTGGACAGTGAGGAGGAGGAGG	0.635													3	5	---	---	---	---					
SLC9A5	6553	broad.mit.edu	37	16	67300017	67300019	+	In_Frame_Del	DEL	GAG	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr16:67300017_67300019delGAG	uc002esm.2	+	15	2170_2172	c.2107_2109delGAG	c.(2107-2109)GAGdel	p.E708del	SLC9A5_uc010cee.2_In_Frame_Del_p.E413del|SLC9A5_uc010vji.1_In_Frame_Del_p.E212del	NM_004594	NP_004585	Q14940	SL9A5_HUMAN	solute carrier family 9 (sodium/hydrogen	708					regulation of pH	integral to membrane|plasma membrane	sodium:hydrogen antiporter activity			ovary(1)|pancreas(1)	2		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		CGTGGAGTCTGAGGAGGAGGAGG	0.571													8	93	---	---	---	---					
MYH10	4628	broad.mit.edu	37	17	8415820	8415822	+	In_Frame_Del	DEL	TTC	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr17:8415820_8415822delTTC	uc002gll.2	-	22	2902_2904	c.2806_2808delGAA	c.(2806-2808)GAAdel	p.E936del	MYH10_uc002glm.2_In_Frame_Del_p.E967del|MYH10_uc010cnx.2_In_Frame_Del_p.E945del	NM_005964	NP_005955	P35580	MYH10_HUMAN	myosin, heavy polypeptide 10, non-muscle	936	Potential.				actin filament-based movement|axon guidance|cytokinesis after mitosis|regulation of cell shape	cell cortex|cleavage furrow|midbody|myosin complex|stress fiber	actin filament binding|actin-dependent ATPase activity|ADP binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(2)	2						TTTGGTTTCTTTCTTCTTCTTCT	0.350													8	118	---	---	---	---					
PPM1D	8493	broad.mit.edu	37	17	58740385	58740386	+	Frame_Shift_Ins	INS	-	A	A			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr17:58740385_58740386insA	uc002iyt.1	+	6	1512_1513	c.1290_1291insA	c.(1288-1293)GTGAATfs	p.V430fs	PPM1D_uc010ddm.1_RNA	NM_003620	NP_003611	O15297	PPM1D_HUMAN	protein phosphatase 1D	430_431					negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity			upper_aerodigestive_tract(1)	1	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)			GGCCAAGGGTGAATTCTAAGGA	0.401											OREG0031485	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	10	211	---	---	---	---					
LMAN1	3998	broad.mit.edu	37	18	57026573	57026574	+	5'Flank	INS	-	C	C	rs140141851	by1000genomes	TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr18:57026573_57026574insC	uc002lhz.2	-						LMAN1_uc010xek.1_5'Flank	NM_005570	NP_005561	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1 precursor						blood coagulation|ER to Golgi vesicle-mediated transport|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine|protein transport	endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|ER-Golgi intermediate compartment membrane|Golgi membrane|integral to membrane	mannose binding|metal ion binding|unfolded protein binding			skin(1)	1		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	AGCCCGGGGGACCCCCAAGGGC	0.752													5	5	---	---	---	---					
ZNF442	79973	broad.mit.edu	37	19	12461741	12461741	+	Frame_Shift_Del	DEL	A	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr19:12461741delA	uc002mtr.1	-	6	1269	c.658delT	c.(658-660)TGGfs	p.W220fs	ZNF442_uc010xmk.1_Frame_Shift_Del_p.W151fs	NM_030824	NP_110451	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	220	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|breast(1)|kidney(1)	4						AAACTAGGCCAAAAAAAGGCT	0.403													7	248	---	---	---	---					
RAB11FIP5	26056	broad.mit.edu	37	2	73315337	73315339	+	In_Frame_Del	DEL	TGG	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr2:73315337_73315339delTGG	uc002siu.3	-	3	1648_1650	c.1407_1409delCCA	c.(1405-1410)CACCAA>CAA	p.H469del	RAB11FIP5_uc002sit.3_In_Frame_Del_p.H391del	NM_015470	NP_056285	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	469					protein transport	mitochondrial outer membrane|recycling endosome membrane	gamma-tubulin binding				0						ACTTAGGCCTTGGTGGTGGTGGT	0.635													8	294	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	73851205	73851207	+	IGR	DEL	TCC	-	-	rs112833082		TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr2:73851205_73851207delTCC								ALMS1 (14159 upstream) : NAT8 (16643 downstream)																							CAGCTTCTGGtcctcctcctcct	0.340													4	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	2	159719223	159719223	+	IGR	DEL	T	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr2:159719223delT								DAPL1 (46729 upstream) : TANC1 (105923 downstream)																							CTATGACCGGTTTGTAGCCAT	0.458													2	4	---	---	---	---					
IRS1	3667	broad.mit.edu	37	2	227664854	227664854	+	5'Flank	DEL	G	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr2:227664854delG	uc002voh.3	-							NM_005544	NP_005535	P35568	IRS1_HUMAN	insulin receptor substrate 1						fibroblast growth factor receptor signaling pathway|glucose homeostasis|insulin receptor signaling pathway|negative regulation of insulin receptor signaling pathway|negative regulation of insulin secretion|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive regulation of fatty acid beta-oxidation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of insulin receptor signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity	caveola|cytosol|insulin receptor complex|microsome|nucleus	insulin receptor binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase binding|protein kinase C binding|SH2 domain binding|transmembrane receptor protein tyrosine kinase adaptor activity			lung(5)|central_nervous_system(4)|ovary(2)|pancreas(1)	12		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		GGGGGGCCACGGGGGGGCACT	0.706													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	3	143610906	143610906	+	IGR	DEL	T	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr3:143610906delT								SLC9A9 (43560 upstream) : C3orf58 (79734 downstream)																							ctcactttccttttccctctc	0.149													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	4	3578072	3578074	+	5'Flank	DEL	GAA	-	-	rs111370021		TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr4:3578072_3578074delGAA	uc003ghj.1	+						uc003ghk.1_5'Flank					Homo sapiens cDNA FLJ35424 fis, clone SMINT2001461.																		ggaggagaaggaagaggaggagg	0.177													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	5	110285304	110285305	+	IGR	INS	-	T	T			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr5:110285304_110285305insT								SLC25A46 (186822 upstream) : TSLP (120473 downstream)																							AATCATTAAACTTTGTTTTCCA	0.436													7	437	---	---	---	---					
Unknown	0	broad.mit.edu	37	7	158791139	158791139	+	IGR	DEL	C	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr7:158791139delC								WDR60 (52257 upstream) : LOC154822 (9906 downstream)																							CCCCTCCACACCCCCCACGTG	0.697													3	3	---	---	---	---					
NECAB1	64168	broad.mit.edu	37	8	91804128	91804128	+	Frame_Shift_Del	DEL	A	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr8:91804128delA	uc011lgg.1	+	1	208	c.14delA	c.(13-15)CAGfs	p.Q5fs	TMEM64_uc003yeo.2_5'Flank	NM_022351	NP_071746	Q8N987	NECA1_HUMAN	N-terminal EF-hand calcium binding protein 1	5					antibiotic biosynthetic process	cytoplasm	calcium ion binding|oxidoreductase activity			central_nervous_system(1)	1			BRCA - Breast invasive adenocarcinoma(11;0.0499)			GAAGATTCCCAGGAGACATCG	0.647													2	4	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	44109175	44109177	+	IGR	DEL	AAC	-	-	rs145089083		TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr9:44109175_44109177delAAC								FAM75A6 (478445 upstream) : FAM27C (881059 downstream)																							AAGGTAGACTAACTCTTCGCTAT	0.340													5	10	---	---	---	---					
Unknown	0	broad.mit.edu	37	9	82974407	82974408	+	IGR	INS	-	GCCGGG	GCCGGG			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chr9:82974407_82974408insGCCGGG								TLE4 (632750 upstream) : None (None downstream)																							AGCAGGGAGCAgccggggctgg	0.540													2	4	---	---	---	---					
ATRX	546	broad.mit.edu	37	X	76778785	76778787	+	In_Frame_Del	DEL	TCT	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chrX:76778785_76778787delTCT	uc004ecp.3	-	31	7024_7026	c.6792_6794delAGA	c.(6790-6795)GAAGAG>GAG	p.2264_2265EE>E	ATRX_uc004ecq.3_In_Frame_Del_p.2226_2227EE>E|ATRX_uc004eco.3_In_Frame_Del_p.2049_2050EE>E	NM_000489	NP_000480	P46100	ATRX_HUMAN	transcriptional regulator ATRX isoform 1	2264_2265	Poly-Glu.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding			haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30					Phosphatidylserine(DB00144)	TTCAGTCAACTCTTCTTCTTCTT	0.369			Mis|F|N		Pancreatic neuroendocrine tumors		ATR-X (alpha thalassemia/mental retardation) syndrome						7	479	---	---	---	---					
MAGEA10	4109	broad.mit.edu	37	X	151303906	151303908	+	In_Frame_Del	DEL	AGG	-	-			TCGA-FY-A3R7-01A-11D-A21Z-08	TCGA-FY-A3R7-10A-01D-A21Z-08									Somatic	Phase_I	Capture				Illumina GAIIx	70bcbd8b-101e-4fd8-aed8-acb251f4e31d	97a1bdbf-7d65-4bc2-b8ce-f13f9c221b73	g.chrX:151303906_151303908delAGG	uc004ffk.2	-	5	593_595	c.185_187delCCT	c.(184-189)TCCTGC>TGC	p.S62del	MAGEA10_uc004ffl.2_In_Frame_Del_p.S62del	NM_001011543	NP_001011543	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	62	Poly-Ser.										0	Acute lymphoblastic leukemia(192;6.56e-05)					AGAGGATAGCaggaggaggagga	0.419													7	204	---	---	---	---					
