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	isArtifactMode	oxoGCut
MST1P2	11209	broad.mit.edu	37	1	16974745	16974745	+	RNA	SNP	G	A	A	rs28526603	by1000genomes	TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr1:16974745G>A	uc010och.1	+	7		c.1205G>A			MST1P2_uc001azk.2_RNA|MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						CCTGGAACCGGAGGGCCGGGG	0.711000													4	14					0	0	0	0
ESPNP	284729	broad.mit.edu	37	1	17023110	17023110	+	Missense_Mutation	SNP	G	A	A	rs11260887	by1000genomes	TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr1:17023110G>A	uc001azn.1	-	10	1754	c.1640C>T	c.(1639-1641)CCG>CTG	p.P547L		NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0						GTTGAGCAGCGGCTGAAACCC	0.687000													5	20					0	0	0	0
LRIG2	9860	broad.mit.edu	37	1	113616160	113616160	+	Silent	SNP	C	G	G			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr1:113616160C>G	uc001edf.1	+	1	330	c.132C>G	c.(130-132)CCC>CCG	p.P44P	LRIG2_uc009wgn.1_5'UTR|uc001ede.1_5'Flank	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	44	LRRNT.|Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		GTCTCTGCCCCGCGCCCTGCT	0.657000											OREG0013684	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	206					0	0	0	0
IL6R	3570	broad.mit.edu	37	1	154407116	154407116	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr1:154407116G>A	uc001fez.1	+	4	1017	c.580G>A	c.(580-582)GTC>ATC	p.V194I	IL6R_uc001ffa.1_Missense_Mutation_p.V194I	NM_000565	NP_000556	P08887	IL6RA_HUMAN	interleukin 6 receptor isoform 1 precursor	194	Extracellular (Potential).				acute-phase response|ciliary neurotrophic factor-mediated signaling pathway|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|endocrine pancreas development|hepatic immune response|negative regulation of collagen biosynthetic process|negative regulation of interleukin-8 production|positive regulation of activation of Janus kinase activity|positive regulation of anti-apoptosis|positive regulation of chemokine production|positive regulation of chemokine production|positive regulation of interleukin-6 production|positive regulation of leukocyte chemotaxis|positive regulation of MAPKKK cascade|positive regulation of osteoblast differentiation|positive regulation of smooth muscle cell proliferation|positive regulation of tyrosine phosphorylation of Stat3 protein|regulation of apoptosis	apical plasma membrane|basolateral plasma membrane|extracellular space|interleukin-6 receptor complex	ciliary neurotrophic factor binding|enzyme binding|protein homodimerization activity	p.V194I(1)		ovary(3)|breast(1)	4	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GTCCATGTGCGTCGCCAGTAG	0.532000													6	159					0	0	0	0
DCAF6	55827	broad.mit.edu	37	1	167906205	167906205	+	Missense_Mutation	SNP	T	C	C			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr1:167906205T>C	uc001gew.2	+	1	298	c.56T>C	c.(55-57)CTC>CCC	p.L19P	BRP44_uc001ges.2_5'Flank|BRP44_uc001get.2_5'UTR|BRP44_uc001geu.2_Intron|BRP44_uc009wvn.2_5'Flank|DCAF6_uc001gev.2_Missense_Mutation_p.L19P|DCAF6_uc001gex.2_Missense_Mutation_p.L19P|DCAF6_uc010plk.1_Missense_Mutation_p.L19P	NM_001017977	NP_001017977	Q58WW2	DCAF6_HUMAN	IQ motif and WD repeats 1 isoform b	19					positive regulation of transcription from RNA polymerase II promoter	CUL4 RING ubiquitin ligase complex|nucleus	ligand-dependent nuclear receptor transcription coactivator activity			ovary(1)|central_nervous_system(1)|skin(1)	3						AAAAGGTCCCTCGGGCTGGAG	0.721000													3	23					0	0	0	0
ZNF238	10472	broad.mit.edu	37	1	244217659	244217659	+	Nonsense_Mutation	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr1:244217659C>T	uc001iae.2	+	1	1078	c.556C>T	c.(556-558)CGA>TGA	p.R186*	ZNF238_uc001iad.3_Nonsense_Mutation_p.R195*|ZNF238_uc001iaf.1_Nonsense_Mutation_p.R186*	NM_006352	NP_006343	Q99592	ZN238_HUMAN	zinc finger protein 238 isoform 2	186				KLNILPSKRDLAAEPGNMWMRLPSDSAGIPQAGGEAEPHAT AAGKTVASPCSSTESLSQRSVTSVRDSADVDCVLDLSVKSS LSGVENLNSSYFSSQ -> IEHPAQQKGLGGRAWEHVDAIA LRLSRHPPGWRRGRATRHSSWKNSSQPLQLNRVFVPE (in Ref. 1; AAA81368).	negative regulation of transcription from RNA polymerase II promoter|skeletal muscle tissue development	nuclear chromosome	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)|pancreas(2)	5	all_cancers(71;6.42e-05)|all_epithelial(71;7e-05)|Breast(184;0.0333)|Ovarian(71;0.0619)|all_lung(81;0.089)|all_neural(11;0.101)|Lung NSC(105;0.123)		all cancers(7;1.35e-08)|GBM - Glioblastoma multiforme(7;1e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00223)			CATGTGGATGCGATTGCCCTC	0.572000													7	74					0	0	0	0
ASCL3	56676	broad.mit.edu	37	11	8959494	8959494	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr11:8959494C>T	uc001mhd.1	-	2	275	c.215G>A	c.(214-216)TGC>TAC	p.C72Y		NM_020646	NP_065697	Q9NQ33	ASCL3_HUMAN	ASCL3	71					regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleolus	DNA binding				0				Epithelial(150;1.48e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0228)		AGAGAAGGGGCAGGGTTCACT	0.577000													6	77					0	0	0	0
FJX1	24147	broad.mit.edu	37	11	35640755	35640755	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr11:35640755G>A	uc001mwh.2	+	1	1021	c.571G>A	c.(571-573)GAG>AAG	p.E191K		NM_014344	NP_055159	Q86VR8	FJX1_HUMAN	four jointed box 1 precursor	191						extracellular space					0	all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739)	all_hematologic(20;0.107)				GATTCAGGGCGAGGCCCTGTC	0.731000													7	25					0	0	0	0
AMBRA1	55626	broad.mit.edu	37	11	46564921	46564921	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr11:46564921C>T	uc010rgu.1	-	7	1006	c.646G>A	c.(646-648)GAT>AAT	p.D216N	AMBRA1_uc010rgt.1_5'Flank|AMBRA1_uc009ylc.1_Missense_Mutation_p.D216N|AMBRA1_uc001ncu.1_Missense_Mutation_p.D216N|AMBRA1_uc001ncv.2_Missense_Mutation_p.D216N|AMBRA1_uc001ncw.2_Missense_Mutation_p.D216N|AMBRA1_uc001ncx.2_Missense_Mutation_p.D216N	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	216					autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		TCTGTTCCATCTATGGGGATC	0.542000													16	98					0	0	0	0
OR4A16	81327	broad.mit.edu	37	11	55111250	55111250	+	Missense_Mutation	SNP	T	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr11:55111250T>A	uc010rie.1	+	1	574	c.574T>A	c.(574-576)TTT>ATT	p.F192I		NM_001005274	NP_001005274	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A,	192	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			large_intestine(2)|pancreas(1)	3						TGACACCTACTTTATAGGACT	0.423000													7	145					0	0	0	0
TIGD3	220359	broad.mit.edu	37	11	65124576	65124576	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr11:65124576G>A	uc001odo.3	+	2	1460	c.1297G>A	c.(1297-1299)GAT>AAT	p.D433N		NM_145719	NP_663771	Q6B0B8	TIGD3_HUMAN	tigger transposable element derived 3	433					regulation of transcription, DNA-dependent	chromosome, centromeric region|nucleus	DNA binding				0						CACCAAAGCTGATGCCCTCCG	0.562000													12	109					0	0	0	0
PELI3	246330	broad.mit.edu	37	11	66238754	66238754	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr11:66238754G>A	uc001oic.3	+	4	430	c.266G>A	c.(265-267)CGA>CAA	p.R89Q	PELI3_uc001oib.2_Missense_Mutation_p.R89Q|PELI3_uc001oid.3_Missense_Mutation_p.R65Q|PELI3_uc001oie.3_5'UTR|PELI3_uc010rpd.1_5'Flank	NM_145065	NP_659502	Q8N2H9	PELI3_HUMAN	pellino 3 alpha isoform 1	89						cytosol	protein binding			ovary(1)	1						GGCCGCCGGCGAAGCCGCCTG	0.597000													6	184					0	0	0	0
ATN1	1822	broad.mit.edu	37	12	7044927	7044927	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr12:7044927C>G	uc001qrw.1	+	5	734	c.497C>G	c.(496-498)CCT>CGT	p.P166R	ATN1_uc001qrx.1_Missense_Mutation_p.P166R|ATN1_uc001qry.1_Missense_Mutation_p.P165R	NM_001007026	NP_001007027	P54259	ATN1_HUMAN	atrophin-1	166					cell death|central nervous system development	cytoplasm|nucleus	protein domain specific binding			ovary(2)|breast(2)|pancreas(1)|skin(1)	6						CCACTCTTTCCTCCTTCCCCT	0.592000													4	149					0	0	0	0
PRICKLE1	144165	broad.mit.edu	37	12	42854281	42854281	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr12:42854281G>A	uc010skv.1	-	8	2113	c.1826C>T	c.(1825-1827)CCT>CTT	p.P609L	PRICKLE1_uc001rnl.2_Missense_Mutation_p.P609L|PRICKLE1_uc010skw.1_Missense_Mutation_p.P609L|PRICKLE1_uc001rnm.2_Missense_Mutation_p.P609L|PRICKLE1_uc001rnk.1_5'Flank	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	609					negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		CTTCTCTTCAGGCAGGATTTT	0.463000													5	111					0	0	0	0
ACCN2	41	broad.mit.edu	37	12	50472360	50472360	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr12:50472360G>A	uc001rvw.2	+	6	1223	c.994G>A	c.(994-996)GGG>AGG	p.G332R	ACCN2_uc001rvv.2_Missense_Mutation_p.G332R|ACCN2_uc009zln.2_Missense_Mutation_p.G123R|ACCN2_uc009zlo.2_Missense_Mutation_p.G332R	NM_001095	NP_001086	P78348	ACCN2_HUMAN	amiloride-sensitive cation channel 2, neuronal	332	Extracellular (By similarity).				calcium ion transport|response to pH|signal transduction	integral to plasma membrane	ligand-gated sodium channel activity|protein binding			ovary(1)	1					Amiloride(DB00594)	GCACATGCCAGGTCAGGCCTG	0.592000													4	131					0	0	0	0
TRPM1	4308	broad.mit.edu	37	15	31362283	31362283	+	Missense_Mutation	SNP	G	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr15:31362283G>T	uc001zfm.2	-	3	292	c.164C>A	c.(163-165)TCC>TAC	p.S55Y	TRPM1_uc010azy.2_5'Flank|TRPM1_uc001zfl.2_5'Flank|TRPM1_uc001zfn.3_Missense_Mutation_p.S55Y|uc010ubn.1_RNA	NM_002420	NP_002411	Q7Z4N2	TRPM1_HUMAN	transient receptor potential cation channel,	55	Extracellular (Potential).				cellular response to light stimulus|visual perception	integral to plasma membrane	calcium channel activity|receptor activity			ovary(2)|pancreas(1)|skin(1)	4		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AACTCCATAGGAATCTGTTGG	0.483000													12	557					2.27111e-07	8.06969e-07	1	0
ZNF780B	163131	broad.mit.edu	37	19	40540672	40540672	+	Silent	SNP	T	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr19:40540672T>A	uc002omu.2	-	5	2159	c.2094A>T	c.(2092-2094)GTA>GTT	p.V698V	ZNF780B_uc002omv.2_Silent_p.V550V	NM_001005851	NP_001005851	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	698	C2H2-type 20.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					ACTCCTTACATACAAAGGGTT	0.388000													10	137					0	0	0	0
DOK1	1796	broad.mit.edu	37	2	74783609	74783609	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr2:74783609G>C	uc002sms.2	+	5	836	c.814G>C	c.(814-816)GGG>CGG	p.G272R	LOXL3_uc002smp.1_5'Flank|LOXL3_uc002smq.1_5'Flank|LOXL3_uc010ffn.1_5'Flank|DOK1_uc002smr.2_Missense_Mutation_p.G133R|DOK1_uc010ffo.2_Missense_Mutation_p.G133R|DOK1_uc002smt.2_Missense_Mutation_p.G58R|DOK1_uc002smu.2_Missense_Mutation_p.G58R|DOK1_uc010yrz.1_Missense_Mutation_p.G261R|DOK1_uc002smv.2_Missense_Mutation_p.G133R|DOK1_uc002smw.1_Missense_Mutation_p.G58R	NM_001381	NP_001372	Q99704	DOK1_HUMAN	docking protein 1	272					fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	cytosol|perinuclear region of cytoplasm	insulin receptor binding				0						CTCCCATGAAGGGGAGGTGGC	0.612000													4	91					0	0	0	0
TIAM1	7074	broad.mit.edu	37	21	32502548	32502548	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr21:32502548C>G	uc002yow.1	-	26	4500	c.4028G>C	c.(4027-4029)CGA>CCA	p.R1343P	TIAM1_uc011adk.1_Missense_Mutation_p.R1343P|TIAM1_uc011adl.1_Missense_Mutation_p.R1283P	NM_003253	NP_003244	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1343	PH 2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cell-cell junction|cytosol	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|breast(3)|ovary(2)|large_intestine(2)	10						CGCCAAAGCTCGAACCTGCAG	0.483000													3	214					0	0	0	0
Unknown	0	broad.mit.edu	37	22	18846140	18846140	+	RNA	SNP	T	C	C			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr22:18846140T>C	uc002zoe.2	+	5		c.2502T>C			uc002zof.2_5'Flank					Homo sapiens cDNA FLJ76361 complete cds.																		TAGGGCACCTTGGACCTCTCT	0.617000													3	20					0	0	0	0
DEPDC5	9681	broad.mit.edu	37	22	32289633	32289633	+	Missense_Mutation	SNP	C	G	G			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr22:32289633C>G	uc003als.2	+	38	4148	c.4006C>G	c.(4006-4008)CTG>GTG	p.L1336V	DEPDC5_uc011als.1_Missense_Mutation_p.L1267V|DEPDC5_uc011alu.1_Missense_Mutation_p.L1367V|DEPDC5_uc011alv.1_RNA|DEPDC5_uc003alt.2_Missense_Mutation_p.L1358V|DEPDC5_uc003alu.2_Missense_Mutation_p.L785V|DEPDC5_uc003alv.2_RNA|DEPDC5_uc003alw.2_Missense_Mutation_p.L634V|DEPDC5_uc011alx.1_Missense_Mutation_p.L184V|DEPDC5_uc010gwk.2_Missense_Mutation_p.L362V|DEPDC5_uc011aly.1_Missense_Mutation_p.L184V	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1	1336					intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						CACAGACCGGCTGGAGTGGTG	0.557000													5	59					0	0	0	0
CCDC80	151887	broad.mit.edu	37	3	112324348	112324348	+	Silent	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr3:112324348G>A	uc003dzf.2	-	8	2987	c.2769C>T	c.(2767-2769)TAC>TAT	p.Y923Y	CCDC80_uc011bhv.1_Silent_p.Y896Y|CCDC80_uc003dzg.2_Silent_p.Y923Y	NM_199512	NP_955806	Q76M96	CCD80_HUMAN	steroid-sensitive protein 1 precursor	923										ovary(2)	2						GGTAACTATGGTAACCATAGC	0.463000													4	83					0	0	0	0
SOX2	6657	broad.mit.edu	37	3	181430843	181430843	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr3:181430843C>T	uc003fkx.2	+	1	1122	c.695C>T	c.(694-696)ACC>ATC	p.T232I	SOX2OT_uc003fkv.2_Intron|SOX2OT_uc003fkw.3_Intron	NM_003106	NP_003097	P48431	SOX2_HUMAN	sex-determining region Y-box 2	232					cell cycle arrest|chromatin organization|eye development|glial cell fate commitment|inner ear development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of epithelial cell proliferation|negative regulation of neuron differentiation|osteoblast differentiation|pituitary gland development|positive regulation of MAPKKK cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of caspase activity|response to growth factor stimulus|response to wounding|somatic stem cell maintenance	cytosol|transcription factor complex	miRNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding				0	all_cancers(143;1.22e-16)|Ovarian(172;0.0283)		all cancers(12;1.82e-48)|Epithelial(37;9.85e-40)|OV - Ovarian serous cystadenocarcinoma(80;7.37e-23)|Lung(8;2.01e-21)|GBM - Glioblastoma multiforme(1;2.13e-08)			CAGCAGGGCACCCCTGGCATG	0.642000			A		NSCLC|oesophageal squamous carcinoma		MICROPHTHALMIA AND ESOPHAGEAL ATRESIA SYNDROME						7	71					0	0	0	0
GAK	2580	broad.mit.edu	37	4	861163	861163	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr4:861163G>C	uc003gbm.3	-	21	2652	c.2453C>G	c.(2452-2454)GCC>GGC	p.A818G	GAK_uc003gbn.3_Missense_Mutation_p.A739G|GAK_uc010ibk.1_Missense_Mutation_p.A712G|GAK_uc010ibi.2_5'UTR|GAK_uc010ibj.2_RNA|GAK_uc003gbl.3_Missense_Mutation_p.A682G	NM_005255	NP_005246	O14976	GAK_HUMAN	cyclin G associated kinase	818					cell cycle	focal adhesion|Golgi apparatus|perinuclear region of cytoplasm	ATP binding|heat shock protein binding|protein serine/threonine kinase activity			lung(2)|central_nervous_system(1)|skin(1)	4				Colorectal(103;0.219)		CTCCATCAGGGCAGACTCGCT	0.597000													5	128					0	0	0	0
CAMK2D	817	broad.mit.edu	37	4	114680566	114680566	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr4:114680566C>T	uc003ibi.2	-	2	929	c.70G>A	c.(70-72)GCA>ACA	p.A24T	CAMK2D_uc003ibj.2_Missense_Mutation_p.A24T|CAMK2D_uc003ibk.2_Missense_Mutation_p.A24T|CAMK2D_uc003ibo.3_Missense_Mutation_p.A24T|CAMK2D_uc003ibm.2_Missense_Mutation_p.A24T|CAMK2D_uc003ibn.2_Missense_Mutation_p.A24T|CAMK2D_uc003ibl.2_Missense_Mutation_p.A24T	NM_001221	NP_001212	Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II	24	ATP (By similarity).|Protein kinase.				interferon-gamma-mediated signaling pathway|regulation of cell growth|synaptic transmission	calcium- and calmodulin-dependent protein kinase complex|cytosol|endocytic vesicle membrane|nucleoplasm|plasma membrane	ATP binding|calmodulin binding|calmodulin-dependent protein kinase activity			ovary(1)	1		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		ACTGAGAATGCCCCCCTGGAA	0.318000													4	87					0	0	0	0
KIAA1109	84162	broad.mit.edu	37	4	123147970	123147970	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr4:123147970C>T	uc003ieh.2	+	22	2947	c.2902C>T	c.(2902-2904)CGT>TGT	p.R968C	KIAA1109_uc003iei.1_Missense_Mutation_p.R721C|KIAA1109_uc010ins.1_Missense_Mutation_p.R311C|KIAA1109_uc003iej.1_3'UTR	NM_015312	NP_056127	Q2LD37	K1109_HUMAN	fragile site-associated protein	968					regulation of cell growth|regulation of epithelial cell differentiation	integral to membrane|nucleus				ovary(8)|skin(2)|pancreas(1)|central_nervous_system(1)	12						TGGAATTGATCGTCGGTTCTG	0.338000													5	74					0	0	0	0
C6	729	broad.mit.edu	37	5	41159281	41159281	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr5:41159281G>A	uc003jmk.2	-	12	1969	c.1759C>T	c.(1759-1761)CGA>TGA	p.R587*	C6_uc003jml.1_Nonsense_Mutation_p.R587*	NM_000065	NP_000056	P13671	CO6_HUMAN	complement component 6 precursor	587	TSP type-1 3.				complement activation, classical pathway|cytolysis|innate immune response	membrane attack complex	protein binding			ovary(3)|central_nervous_system(2)|skin(2)	7		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				TTGCATTCTCGGGTTCTCGAT	0.493000													5	105					0	0	0	0
LOC100133050	100133050	broad.mit.edu	37	5	99715528	99715528	+	RNA	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr5:99715528C>T	uc011cuw.1	-	4		c.382G>A				NR_027503				Homo sapiens glucuronidase, beta pseudogene (LOC100133050), non-coding RNA.												0						AGCGGACAGTCGAAGCCCTTC	0.607000													3	10					0	0	0	0
PCDHA3	56145	broad.mit.edu	37	5	140181071	140181071	+	Missense_Mutation	SNP	G	C	C			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr5:140181071G>C	uc003lhf.2	+	1	289	c.289G>C	c.(289-291)GGG>CGG	p.G97R	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.G97R	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	97	Cadherin 1.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAACTGTGCGGGCGGAGCGC	0.557000													6	268					0	0	0	0
HIST1H1C	3006	broad.mit.edu	37	6	26056369	26056369	+	Silent	SNP	C	G	G			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr6:26056369C>G	uc003nfw.2	-	1	331	c.288G>C	c.(286-288)ACG>ACC	p.T96T		NM_005319	NP_005310	P16403	H12_HUMAN	histone cluster 1, H1c	96	H15.				nucleosome assembly	nucleosome|nucleus	DNA binding			ovary(3)|skin(2)	5						CGGTGCCTTTCGTTTGCACCA	0.532000													6	178					0	0	0	0
BAT2	7916	broad.mit.edu	37	6	31604566	31604566	+	Silent	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr6:31604566G>A	uc003nvb.3	+	28	6240	c.5991G>A	c.(5989-5991)CCG>CCA	p.P1997P	BAT2_uc003nvc.3_Silent_p.P1997P	NM_080686	NP_542417	P48634	PRC2A_HUMAN	HLA-B associated transcript-2	1997	3-2.|3 X 50 AA type C repeats.					cytoplasm|nucleus	protein binding				0						GCTCCCTGCCGCCAGCACCAC	0.612000													8	282					0	0	0	0
GPR6	2830	broad.mit.edu	37	6	110300574	110300574	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr6:110300574G>A	uc011eaw.1	+	2	439	c.259G>A	c.(259-261)GCT>ACT	p.A87T	GPR6_uc011eav.1_Missense_Mutation_p.A102T|GPR6_uc003ptu.2_Missense_Mutation_p.A87T	NM_005284	NP_005275	P46095	GPR6_HUMAN	G protein-coupled receptor 6	87	Helical; Name=1; (Potential).					integral to plasma membrane					0		all_cancers(87;1.64e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;2.83e-05)|all_lung(197;0.00016)|Lung NSC(302;0.000318)|Colorectal(196;0.0488)		BRCA - Breast invasive adenocarcinoma(108;8.01e-05)|Epithelial(106;8.76e-05)|all cancers(137;0.000197)|OV - Ovarian serous cystadenocarcinoma(136;0.0307)		GACAGTGATCGCTGGAGAAAA	0.672000													7	157					0	0	0	0
LPA	4018	broad.mit.edu	37	6	160952810	160952810	+	Missense_Mutation	SNP	C	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr6:160952810C>A	uc003qtl.2	-	40	6194	c.6074G>T	c.(6073-6075)CGT>CTT	p.R2025L		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	4533	Peptidase S1.				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|skin(2)|pancreas(1)	6		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	CCTTGAAACACGAGCATAGAC	0.458000													6	82					4.096e-09	1.48703e-08	1	0
SUN1	23353	broad.mit.edu	37	7	891656	891656	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr7:891656G>A	uc011jvp.1	+	8	906	c.827G>A	c.(826-828)TGG>TAG	p.W276*	GET4_uc003sjj.1_RNA|SUN1_uc003sjf.2_Nonsense_Mutation_p.W193*|SUN1_uc011jvq.1_Nonsense_Mutation_p.W174*|SUN1_uc003sjg.2_Nonsense_Mutation_p.W181*|SUN1_uc011jvr.1_Nonsense_Mutation_p.W85*|SUN1_uc003sji.2_Nonsense_Mutation_p.W114*|SUN1_uc003sjk.2_5'Flank	NM_001130965	NP_001124437	O94901	SUN1_HUMAN	unc-84 homolog A isoform a	303	Nuclear.				cytoskeletal anchoring at nuclear membrane|nuclear matrix anchoring at nuclear membrane	integral to membrane|nuclear inner membrane|SUN-KASH complex	protein binding				0						TTGATTTCTTGGCTGAATGTG	0.433000													4	111					0	0	0	0
MAFK	7975	broad.mit.edu	37	7	1579888	1579888	+	Silent	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr7:1579888C>T	uc003skr.2	+	3	559	c.348C>T	c.(346-348)ACC>ACT	p.T116T	MAFK_uc003sks.1_RNA	NM_002360	NP_002351	O60675	MAFK_HUMAN	v-maf musculoaponeurotic fibrosarcoma oncogene	116					blood coagulation	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.75e-15)		CGCTGCAGACCTTCGCGCGCA	0.682000													5	29					0	0	0	0
SGCE	8910	broad.mit.edu	37	7	94230126	94230126	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr7:94230126C>T	uc003unl.2	-	7	980	c.869G>A	c.(868-870)CGT>CAT	p.R290H	SGCE_uc003unk.2_Missense_Mutation_p.R122H|SGCE_uc003unm.2_Missense_Mutation_p.R290H|SGCE_uc003unn.2_Missense_Mutation_p.R290H|SGCE_uc011kic.1_Missense_Mutation_p.R249H|SGCE_uc011kid.1_Missense_Mutation_p.R326H	NM_003919	NP_003910	O43556	SGCE_HUMAN	sarcoglycan, epsilon isoform 2	290	Cys-rich.|Extracellular (Potential).				cell-matrix adhesion|muscle organ development	cytoplasm|cytoskeleton|integral to plasma membrane|sarcoglycan complex|sarcolemma	calcium ion binding			ovary(1)	1	all_cancers(62;8.26e-10)|all_epithelial(64;5.59e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			CCCCTCTCCACGAATCACTTC	0.378000													9	39					0	0	0	0
SDCBP	6386	broad.mit.edu	37	8	59492228	59492228	+	Missense_Mutation	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr8:59492228G>A	uc003xtn.2	+	7	775	c.625G>A	c.(625-627)GTT>ATT	p.V209I	SDCBP_uc003xto.2_Missense_Mutation_p.V208I|SDCBP_uc003xtr.2_Missense_Mutation_p.V208I|SDCBP_uc003xtp.2_Missense_Mutation_p.V203I|SDCBP_uc003xtq.2_Missense_Mutation_p.V209I|SDCBP_uc003xts.2_Missense_Mutation_p.V215I|SDCBP_uc011led.1_Missense_Mutation_p.V150I	NM_005625	NP_005616	O00560	SDCB1_HUMAN	syntenin isoform 1	209	PDZ 2.				actin cytoskeleton organization|axon guidance|positive regulation of phosphorylation|protein targeting to membrane|substrate-dependent cell migration, cell extension|synaptic transmission	cytoskeleton|cytosol|endoplasmic reticulum membrane|focal adhesion|interleukin-5 receptor complex|melanosome|nucleus	cytoskeletal adaptor activity|frizzled binding|interleukin-5 receptor binding|protein heterodimerization activity|protein N-terminus binding|syndecan binding				0		all_lung(136;0.0271)|Lung NSC(129;0.0351)|all_epithelial(80;0.0554)				CACTGGACATGTTGGTTTTAT	0.338000													5	72					0	0	0	0
CA8	767	broad.mit.edu	37	8	61135309	61135309	+	Missense_Mutation	SNP	G	A	A	rs145210688	by1000genomes	TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr8:61135309G>A	uc003xtz.1	-	7	885	c.637C>T	c.(637-639)CGG>TGG	p.R213W	CA8_uc003xua.1_Missense_Mutation_p.R213W	NM_004056	NP_004047	P35219	CAH8_HUMAN	carbonic anhydrase VIII	213					one-carbon metabolic process		carbonate dehydratase activity|zinc ion binding				0		all_cancers(86;0.172)|all_epithelial(80;0.0383)|all_lung(136;0.0413)|Lung NSC(129;0.0474)				CAGTAATCCCGCAGCAGAGGG	0.438000													15	77					0	0	0	0
KIAA1539	80256	broad.mit.edu	37	9	35107547	35107547	+	Missense_Mutation	SNP	C	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr9:35107547C>T	uc003zwl.2	-	3	1050	c.725G>A	c.(724-726)CGA>CAA	p.R242Q	KIAA1539_uc003zwm.2_Missense_Mutation_p.R242Q|KIAA1539_uc003zwn.2_5'UTR|KIAA1539_uc003zwo.2_Missense_Mutation_p.R242Q|KIAA1539_uc003zwp.1_Missense_Mutation_p.R242Q|KIAA1539_uc010mkk.1_RNA	NM_025182	NP_079458	Q7L5A3	K1539_HUMAN	hypothetical protein LOC80256	242						nucleus				ovary(2)	2	all_epithelial(49;0.217)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			AAGCAGCCTTCGCTTGGTGGG	0.697000													5	139					0	0	0	0
AWAT1	158833	broad.mit.edu	37	X	69455618	69455618	+	Silent	SNP	G	A	A			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chrX:69455618G>A	uc004dxy.2	+	2	170	c.129G>A	c.(127-129)CCG>CCA	p.P43P		NM_001013579	NP_001013597	Q58HT5	AWAT1_HUMAN	wax synthase 1	43	Helical; (Potential).				lipid biosynthetic process	endoplasmic reticulum membrane|integral to membrane	long-chain-alcohol O-fatty-acyltransferase activity			ovary(3)	3						CCTTGTGGCCGCTACCAGTGC	0.488000													6	243					0	0	0	0
F9	2158	broad.mit.edu	37	X	138643694	138643694	+	Missense_Mutation	SNP	A	T	T			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chrX:138643694A>T	uc004fas.1	+	8	879	c.850A>T	c.(850-852)ATT>TTT	p.I284F	F9_uc004fat.1_Missense_Mutation_p.I246F	NM_000133	NP_000124	P00740	FA9_HUMAN	coagulation factor IX preproprotein	284	Peptidase S1.				blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen|plasma membrane	calcium ion binding|serine-type endopeptidase activity			lung(2)|ovary(1)	3	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Heparin(DB01109)|Menadione(DB00170)	TGAACATAATATTGAGGAGAC	0.333000													13	90					0	0	0	0
HAUS7	55559	broad.mit.edu	37	X	152730472	152730472	+	Missense_Mutation	SNP	C	A	A	rs141087618		TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chrX:152730472C>A	uc004fho.1	-	3	854	c.296G>T	c.(295-297)GGG>GTG	p.G99V	HAUS7_uc004fhl.2_RNA|HAUS7_uc004fhm.2_RNA|HAUS7_uc004fhn.1_Missense_Mutation_p.G99V|HAUS7_uc004fhp.1_Intron|HAUS7_uc011myq.1_RNA	NM_017518	NP_059988	Q99871	HAUS7_HUMAN	HAUS augmin-like complex subunit 7	99					cell division|centrosome organization|mitosis|spindle assembly	centrosome|HAUS complex|microtubule|nucleolus|plasma membrane|spindle	thioesterase binding				0						TGTTGGGACCCCTTTCAGTGA	0.577000													17	359					1.56452e-12	5.80612e-12	1	0
CHAT	1103	broad.mit.edu	37	10	50872950	50872952	+	In_Frame_Del	DEL	CTT	-	-			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr10:50872950_50872952delCTT	uc001jhz.2	+	15	2258_2260	c.2105_2107delCTT	c.(2104-2109)ACTTCT>ACT	p.S705del	CHAT_uc001jhv.1_In_Frame_Del_p.S587del|CHAT_uc001jhx.1_In_Frame_Del_p.S587del|CHAT_uc001jhy.1_In_Frame_Del_p.S587del|CHAT_uc001jia.2_In_Frame_Del_p.S587del|CHAT_uc010qgs.1_Intron	NM_020549	NP_065574	P28329	CLAT_HUMAN	choline acetyltransferase isoform 2	705					neurotransmitter biosynthetic process|neurotransmitter secretion	cytosol|nucleus	choline O-acetyltransferase activity			central_nervous_system(3)	3		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)	TGCAAAGAGACTTCTTCTAGCAA	0.502													---	---	---							
Unknown	0	broad.mit.edu	37	15	22118395	22118396	+	IGR	DEL	AC	-	-	rs139043886		TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr15:22118395_22118396delAC								CXADRP2 (101517 upstream) : LOC727924 (159636 downstream)																							ATAAATTATAACATTCTTTTTG	0.342													---	---	---							
KBTBD13	390594	broad.mit.edu	37	15	65369216	65369216	+	Frame_Shift_Del	DEL	C	-	-			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr15:65369216delC	uc010uis.1	+	1	63	c.63delC	c.(61-63)GACfs	p.D21fs	RASL12_uc010uir.1_5'Flank	NM_001101362	NP_001094832	C9JR72	KBTBD_HUMAN	hypothetical protein LOC390594	21	BTB.					cytoplasm					0						TCCAAGCCGACCGCGCCCTGC	0.721													---	---	---							
Unknown	0	broad.mit.edu	37	2	128824754	128824754	+	IGR	DEL	A	-	-	rs113610724		TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr2:128824754delA								SAP130 (39121 upstream) : UGGT1 (24000 downstream)																							gactccatctaaaaaaaaaaa	0.174													---	---	---							
NBEAL1	65065	broad.mit.edu	37	2	203922058	203922058	+	Frame_Shift_Del	DEL	A	-	-			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr2:203922058delA	uc002uzt.3	+	6	730	c.397delA	c.(397-399)AAAfs	p.K133fs	NBEAL1_uc002uzq.3_Frame_Shift_Del_p.K133fs|NBEAL1_uc010zid.1_Frame_Shift_Del_p.K82fs|NBEAL1_uc010zie.1_RNA	NM_001114132	NP_001107604	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1 isoform 3	133							binding			ovary(1)|skin(1)	2						GTTAAAAAGCAAAAAAAAAGA	0.318													---	---	---							
Unknown	0	broad.mit.edu	37	2	219818739	219818739	+	IGR	DEL	G	-	-			TCGA-CR-7392-01A-11D-2012-08	TCGA-CR-7392-10A-01D-2013-08									Somatic	Phase_I	Capture				Illumina GAIIx	0616d3e5-9641-4329-a65a-19f4c6918e1c	6af45747-7234-43ab-a250-f346349301fd	g.chr2:219818739delG								WNT10A (60088 upstream) : CDK5R2 (5659 downstream)																							GCCTCAGCCCGACTGTGGATG	0.408													---	---	---							
