Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	filter
RPS6KA1	6195	broad.mit.edu	37	1	26887302	26887302	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:26887302G>A	uc001bmr.1	+	15	1464	c.1301G>A	c.(1300-1302)CGC>CAC	p.R434H	RPS6KA1_uc010ofe.1_Missense_Mutation_p.R342H|RPS6KA1_uc010off.1_Missense_Mutation_p.R418H|RPS6KA1_uc001bms.1_Missense_Mutation_p.R443H|RPS6KA1_uc009vsl.1_Missense_Mutation_p.R277H	NM_002953	NP_002944	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide	434	Protein kinase 2.				axon guidance|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|stress-activated MAPK cascade|synaptic transmission|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|nucleoplasm	ATP binding|caspase inhibitor activity|magnesium ion binding|protein binding|protein serine/threonine kinase activity			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		GAGTGCAAGCGCTGTGTCCAC	0.572													11	121	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70504369	70504369	+	Silent	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70504369G>A	uc001dep.2	+	19	2778	c.2748G>A	c.(2746-2748)CCG>CCA	p.P916P	LRRC7_uc009wbg.2_Silent_p.P200P|LRRC7_uc001deq.2_Silent_p.P157P	NM_020794	NP_065845	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	916						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						ACTGCCGCCCGGAATCTTCTA	0.398													16	129	---	---	---	---	PASS
FPGT	8790	broad.mit.edu	37	1	74670257	74670257	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74670257G>T	uc001dgb.1	+	4	563	c.526G>T	c.(526-528)GGA>TGA	p.G176*	TNNI3K_uc001dgc.1_Intron|TNNI3K_uc001dgd.2_Intron|TNNI3K_uc001dge.1_Intron|FPGT_uc010oqt.1_Intron|FPGT_uc010oqu.1_Intron|FPGT_uc010oqv.1_Intron	NM_003838	NP_003829	O14772	FPGT_HUMAN	fucose-1-phosphate guanyltransferase	176					fucose metabolic process	cytoplasm	fucose-1-phosphate guanylyltransferase activity|GTP binding			skin(1)	1						TTATAGTATTGGAGAATTTGA	0.358													5	210	---	---	---	---	PASS
GJA8	2703	broad.mit.edu	37	1	147380712	147380712	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:147380712G>T	uc001epu.1	+	2	693	c.630G>T	c.(628-630)TTG>TTT	p.L210F		NM_005267	NP_005258	P48165	CXA8_HUMAN	connexin 50	210	Helical; (Potential).				cell communication|visual perception	connexon complex|integral to plasma membrane	channel activity			ovary(2)|large_intestine(2)|breast(1)|skin(1)	6	all_hematologic(923;0.0276)					TGTTCATGTTGTCTGTGGCCT	0.607													14	130	---	---	---	---	PASS
ATP1A4	480	broad.mit.edu	37	1	160144415	160144415	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:160144415C>T	uc001fve.3	+	15	2668	c.2189C>T	c.(2188-2190)GCG>GTG	p.A730V	ATP1A4_uc001fvf.3_RNA|ATP1A4_uc001fvg.2_Missense_Mutation_p.A233V|ATP1A4_uc001fvh.2_5'Flank	NM_144699	NP_653300	Q13733	AT1A4_HUMAN	Na+/K+ -ATPase alpha 4 subunit isoform 1	730	Cytoplasmic (Potential).				ATP biosynthetic process|ATP hydrolysis coupled proton transport|regulation of cellular pH|sperm motility	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|skin(2)	4	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GACTCCCCTGCGCTGAAGAAG	0.547													27	83	---	---	---	---	PASS
PAPPA2	60676	broad.mit.edu	37	1	176525777	176525777	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176525777G>T	uc001gkz.2	+	2	1483	c.319G>T	c.(319-321)GTT>TTT	p.V107F	PAPPA2_uc001gky.1_Missense_Mutation_p.V107F|PAPPA2_uc009www.2_RNA	NM_020318	NP_064714	Q9BXP8	PAPP2_HUMAN	pappalysin 2 isoform 1	107					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			ovary(7)|central_nervous_system(5)|skin(2)|lung(1)|breast(1)	16						TGTGAGCCTTGTTCCCCCAGA	0.562													15	329	---	---	---	---	PASS
MR1	3140	broad.mit.edu	37	1	181019499	181019499	+	Intron	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:181019499A>T	uc001goq.1	+						MR1_uc001gop.2_3'UTR|MR1_uc001gor.1_Intron|MR1_uc001gos.1_Intron|MR1_uc010pns.1_Intron	NM_001531	NP_001522	Q95460	HMR1_HUMAN	major histocompatibility complex, class						antigen processing and presentation of peptide antigen via MHC class I|immune response	endoplasmic reticulum|extracellular region|integral to membrane|MHC class I protein complex	MHC class I receptor activity			skin(1)	1						AATCTAGGTTATATCCACTGT	0.423													5	22	---	---	---	---	PASS
DHX9	1660	broad.mit.edu	37	1	182841497	182841497	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:182841497G>A	uc001gpr.2	+	15	1746	c.1583G>A	c.(1582-1584)CGT>CAT	p.R528H	DHX9_uc001gps.2_Missense_Mutation_p.R314H	NM_001357	NP_001348	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 9	528	Helicase ATP-binding.				CRD-mediated mRNA stabilization|nuclear mRNA splicing, via spliceosome	centrosome|CRD-mediated mRNA stability complex|nucleolus|nucleoplasm|ribonucleoprotein complex	ATP binding|ATP-dependent DNA helicase activity|ATP-dependent RNA helicase activity|DNA binding|double-stranded RNA binding|protein binding			ovary(2)	2						GTAGTACTGCGTGATGTTGTT	0.323													61	239	---	---	---	---	PASS
FAM5C	339479	broad.mit.edu	37	1	190068181	190068181	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:190068181G>A	uc001gse.1	-	8	1500	c.1268C>T	c.(1267-1269)ACG>ATG	p.T423M	FAM5C_uc010pot.1_Missense_Mutation_p.T321M	NM_199051	NP_950252	Q76B58	FAM5C_HUMAN	family with sequence similarity 5, member C	423						extracellular region				lung(2)|ovary(1)|kidney(1)|skin(1)	5	Prostate(682;0.198)					GCACGAGTGCGTCTCTTCTGA	0.547													11	53	---	---	---	---	PASS
TP53I3	9540	broad.mit.edu	37	2	24307098	24307098	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24307098C>A	uc002rey.1	-	2	159	c.99G>T	c.(97-99)AAG>AAT	p.K33N	LOC375190_uc002rew.2_Intron|TP53I3_uc002rex.1_Missense_Mutation_p.K33N|TP53I3_uc002rez.1_Missense_Mutation_p.K33N|TP53I3_uc010ykk.1_Translation_Start_Site	NM_147184	NP_671713	Q53FA7	QORX_HUMAN	tumor protein p53 inducible protein 3	33					induction of apoptosis by oxidative stress|NADP metabolic process		NADPH binding|NADPH:quinone reductase activity|protein homodimerization activity|quinone binding|zinc ion binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGCCGCCACCTTCAGGAGGA	0.657											OREG0014492	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	8	61	---	---	---	---	PASS
TP53I3	9540	broad.mit.edu	37	2	24307099	24307099	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24307099T>C	uc002rey.1	-	2	158	c.98A>G	c.(97-99)AAG>AGG	p.K33R	LOC375190_uc002rew.2_Intron|TP53I3_uc002rex.1_Missense_Mutation_p.K33R|TP53I3_uc002rez.1_Missense_Mutation_p.K33R|TP53I3_uc010ykk.1_5'UTR	NM_147184	NP_671713	Q53FA7	QORX_HUMAN	tumor protein p53 inducible protein 3	33					induction of apoptosis by oxidative stress|NADP metabolic process		NADPH binding|NADPH:quinone reductase activity|protein homodimerization activity|quinone binding|zinc ion binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCCGCCACCTTCAGGAGGAC	0.652											OREG0014492	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	65	---	---	---	---	PASS
TP53I3	9540	broad.mit.edu	37	2	24307100	24307100	+	Nonsense_Mutation	SNP	T	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24307100T>A	uc002rey.1	-	2	157	c.97A>T	c.(97-99)AAG>TAG	p.K33*	LOC375190_uc002rew.2_Intron|TP53I3_uc002rex.1_Nonsense_Mutation_p.K33*|TP53I3_uc002rez.1_Nonsense_Mutation_p.K33*|TP53I3_uc010ykk.1_5'UTR	NM_147184	NP_671713	Q53FA7	QORX_HUMAN	tumor protein p53 inducible protein 3	33					induction of apoptosis by oxidative stress|NADP metabolic process		NADPH binding|NADPH:quinone reductase activity|protein homodimerization activity|quinone binding|zinc ion binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCCGCCACCTTCAGGAGGACT	0.657											OREG0014492	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	66	---	---	---	---	PASS
KHK	3795	broad.mit.edu	37	2	27322321	27322321	+	Silent	SNP	C	T	T	rs142428157	byFrequency	TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:27322321C>T	uc002ril.2	+	7	1204	c.687C>T	c.(685-687)GGC>GGT	p.G229G	KHK_uc002rim.2_Silent_p.G229G|KHK_uc002rin.2_Silent_p.G230G|KHK_uc002rio.2_Silent_p.G145G|CGREF1_uc010ylf.1_3'UTR|CGREF1_uc002rip.1_3'UTR	NM_000221	NP_000212	P50053	KHK_HUMAN	ketohexokinase isoform a	229					fructose catabolic process	cytosol	ATP binding|ketohexokinase activity|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGAGGAGGGCGCCGACGCCC	0.652													32	77	---	---	---	---	PASS
VPS54	51542	broad.mit.edu	37	2	64161068	64161068	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64161068G>A	uc002scq.2	-	12	1641	c.1478C>T	c.(1477-1479)TCA>TTA	p.S493L	VPS54_uc002scp.2_Missense_Mutation_p.S481L|VPS54_uc002sco.2_5'UTR|VPS54_uc010fct.2_Missense_Mutation_p.S340L	NM_016516	NP_057600	Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 isoform 1	493	Potential.				protein transport|retrograde transport, endosome to Golgi						0						CTTCTGTTGTGAAATCTCTTC	0.383													24	92	---	---	---	---	PASS
MEIS1	4211	broad.mit.edu	37	2	66667009	66667009	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:66667009G>T	uc002sdu.2	+	3	731	c.274G>T	c.(274-276)GAG>TAG	p.E92*	MEIS1_uc002sdt.2_Nonsense_Mutation_p.E92*|MEIS1_uc002sdv.2_Nonsense_Mutation_p.E90*|MEIS1_uc010yqh.1_RNA|MEIS1_uc010yqi.1_Nonsense_Mutation_p.E27*|MEIS1_uc002sdw.1_5'Flank	NM_002398	NP_002389	O00470	MEIS1_HUMAN	Meis homeobox 1	92							sequence-specific DNA binding transcription factor activity				0						ACTGATTTTTGAGAAATGTGA	0.502													8	88	---	---	---	---	PASS
FOXD4L1	200350	broad.mit.edu	37	2	114257620	114257620	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:114257620C>T	uc002tjw.3	+	1	960	c.787C>T	c.(787-789)CAC>TAC	p.H263Y		NM_012184	NP_036316	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	263	Pro-rich.				axon extension involved in axon guidance|cartilage development|dichotomous subdivision of terminal units involved in ureteric bud branching|embryo development|enteric nervous system development|iridophore differentiation|lateral line nerve glial cell development|melanocyte differentiation|neural crest cell migration|pattern specification process|peripheral nervous system development|positive regulation of BMP signaling pathway|positive regulation of kidney development|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|sympathetic nervous system development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding				0						CGCTCTGCTGCACCCGCATCC	0.736													22	147	---	---	---	---	PASS
KCNJ3	3760	broad.mit.edu	37	2	155555522	155555522	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:155555522A>C	uc002tyv.1	+	1	430	c.235A>C	c.(235-237)AAG>CAG	p.K79Q	KCNJ3_uc010zce.1_Missense_Mutation_p.K79Q	NM_002239	NP_002230	P48549	IRK3_HUMAN	potassium inwardly-rectifying channel J3	79	Cytoplasmic (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			upper_aerodigestive_tract(1)|pancreas(1)	2					Halothane(DB01159)	GGTGGACCTCAAGTGGCGCTG	0.597													20	84	---	---	---	---	PASS
TTC30B	150737	broad.mit.edu	37	2	178415573	178415573	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178415573T>C	uc002uln.2	-	1	1952	c.1919A>G	c.(1918-1920)CAT>CGT	p.H640R	TTC30B_uc010zfc.1_Missense_Mutation_p.H412R	NM_152517	NP_689730	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	640					cell projection organization	cilium	binding				0			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			CTTTCCAACATGCATTCTTTC	0.358													73	264	---	---	---	---	PASS
NBEAL1	65065	broad.mit.edu	37	2	204039947	204039947	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:204039947T>C	uc002uzt.3	+	41	6647	c.6314T>C	c.(6313-6315)GTC>GCC	p.V2105A	NBEAL1_uc002uzs.3_Missense_Mutation_p.V815A	NM_001114132	NP_001107604	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1 isoform 3	2105	BEACH.						binding			ovary(1)|skin(1)	2						TCTGCGGGGGTCATGCACTAT	0.378													3	138	---	---	---	---	PASS
SEC13	6396	broad.mit.edu	37	3	10354336	10354336	+	Silent	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10354336C>A	uc003bvn.2	-	4	362	c.243G>T	c.(241-243)CGG>CGT	p.R81R	SEC13_uc003bvl.2_Silent_p.R13R|SEC13_uc003bvm.2_Silent_p.R67R|SEC13_uc003bvp.2_Silent_p.R84R|SEC13_uc003bvo.2_Silent_p.R127R|SEC13_uc003bvq.1_Silent_p.R67R|SEC13_uc003bvr.1_Silent_p.R67R|SEC13_uc011aul.1_Silent_p.R81R	NM_183352	NP_899195	P55735	SEC13_HUMAN	SEC13 protein isoform 1	81	WD 2.				COPII vesicle coating|intracellular protein transport|mitotic prometaphase|mRNA transport|post-translational protein modification|protein N-linked glycosylation via asparagine|transmembrane transport	cytosol|endoplasmic reticulum membrane|ER to Golgi transport vesicle membrane|Nup107-160 complex	protein binding			ovary(1)	1						TAATGACTTTCCGGTCATAGG	0.577													9	172	---	---	---	---	PASS
ARHGAP31	57514	broad.mit.edu	37	3	119132967	119132967	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:119132967T>A	uc003ecj.3	+	12	2723	c.2191T>A	c.(2191-2193)TCC>ACC	p.S731T		NM_020754	NP_065805	Q2M1Z3	RHG31_HUMAN	Cdc42 GTPase-activating protein	731	Pro-rich.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|focal adhesion|lamellipodium	GTPase activator activity			ovary(2)	2						ACAGGGGGCTTCCACAGCAGC	0.612													28	103	---	---	---	---	PASS
CCDC48	79825	broad.mit.edu	37	3	128758645	128758645	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128758645C>T	uc011bkt.1	+	8	1751	c.1751C>T	c.(1750-1752)GCC>GTC	p.A584V		NM_024768	NP_079044	Q9HA90	CCD48_HUMAN	coiled-coil domain containing 48	584	Poly-Ala.										0						TCGGCACCAGCCTCTGCAGCA	0.662													22	66	---	---	---	---	PASS
ZBTB38	253461	broad.mit.edu	37	3	141161785	141161785	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141161785G>T	uc003etw.2	+	8	1537	c.555G>T	c.(553-555)TTG>TTT	p.L185F	ZBTB38_uc010hun.2_Missense_Mutation_p.L182F|ZBTB38_uc010huo.2_Missense_Mutation_p.L185F|ZBTB38_uc003ety.2_Missense_Mutation_p.L185F|ZBTB38_uc010hup.2_Missense_Mutation_p.L186F	NM_001080412	NP_001073881	Q8NAP3	ZBT38_HUMAN	zinc finger and BTB domain containing 38	185					positive regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(3)	3						CGCTGGACTTGAGGGCAAGTT	0.498													36	151	---	---	---	---	PASS
PIK3CA	5290	broad.mit.edu	37	3	178952117	178952117	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:178952117A>C	uc003fjk.2	+	21	3329	c.3172A>C	c.(3172-3174)ATC>CTC	p.I1058L		NM_006218	NP_006209	P42336	PK3CA_HUMAN	phosphoinositide-3-kinase, catalytic, alpha	1058	PI3K/PI4K.				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	p.I1058F(2)		breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)			AATGGATTGGATCTTCCACAC	0.393		57	Mis		colorectal|gastric|gliobastoma|breast					HNSCC(19;0.045)|TSP Lung(28;0.18)			3	119	---	---	---	---	PASS
EVC2	132884	broad.mit.edu	37	4	5696064	5696064	+	Silent	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:5696064G>A	uc003gij.2	-	3	502	c.448C>T	c.(448-450)CTG>TTG	p.L150L	EVC2_uc011bwb.1_5'UTR|EVC2_uc003gik.2_Silent_p.L70L	NM_147127	NP_667338	Q86UK5	LBN_HUMAN	limbin	150						integral to membrane				large_intestine(3)|ovary(2)	5						ATACTTACCAGGCGGTGTGTT	0.388													7	176	---	---	---	---	PASS
DHX15	1665	broad.mit.edu	37	4	24534816	24534816	+	Intron	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:24534816G>T	uc003gqx.2	-						DHX15_uc003gqv.2_5'UTR|DHX15_uc003gqw.2_Intron	NM_001358	NP_001349	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 15						mRNA processing	U12-type spliceosomal complex	ATP binding|ATP-dependent helicase activity|nucleic acid binding|RNA helicase activity			ovary(1)	1		Breast(46;0.0503)				TTCTTTAAATGAACTGCAATG	0.318													3	21	---	---	---	---	PASS
UGDH	7358	broad.mit.edu	37	4	39501741	39501741	+	3'UTR	SNP	T	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39501741T>A	uc003guk.1	-	12					UGDH_uc011byp.1_3'UTR|UGDH_uc003gul.1_3'UTR	NM_003359	NP_003350	O60701	UGDH_HUMAN	UDP-glucose dehydrogenase						glycosaminoglycan biosynthetic process|UDP-glucose metabolic process|UDP-glucuronate biosynthetic process|xenobiotic metabolic process	cytosol	electron carrier activity|NAD binding|UDP-glucose 6-dehydrogenase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)|skin(1)	4					NADH(DB00157)	AAAAAAAAAATCACAAATAAA	0.279													4	47	---	---	---	---	PASS
FRAS1	80144	broad.mit.edu	37	4	79458343	79458343	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:79458343T>G	uc003hlb.2	+	72	11727	c.11287T>G	c.(11287-11289)TTC>GTC	p.F3763V		NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	3758	Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5						AAAACACAGATTCCTGCTGTT	0.438													17	64	---	---	---	---	PASS
PITX2	5308	broad.mit.edu	37	4	111553522	111553522	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:111553522G>A	uc003iad.2	-	3	743	c.161C>T	c.(160-162)CCG>CTG	p.P54L	PITX2_uc003iae.2_Intron|PITX2_uc010iml.2_5'UTR|PITX2_uc003iaf.2_Missense_Mutation_p.P54L	NM_153426	NP_700475	Q99697	PITX2_HUMAN	paired-like homeodomain transcription factor 2	54					determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription factor binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		ATGCTGCCGCGGGAAGAACTT	0.627											OREG0016293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	3	74	---	---	---	---	PASS
UGT3A2	167127	broad.mit.edu	37	5	36035845	36035845	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:36035845C>T	uc003jjz.1	-	7	1620	c.1527G>A	c.(1525-1527)ATG>ATA	p.M509I	UGT3A2_uc011cos.1_Missense_Mutation_p.M475I|UGT3A2_uc011cot.1_Missense_Mutation_p.M207I	NM_174914	NP_777574	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	509	Cytoplasmic (Potential).					integral to membrane	glucuronosyltransferase activity			ovary(2)|skin(2)|large_intestine(1)|pancreas(1)	6	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACCAGACAGCCATGCCCAGCA	0.582													4	80	---	---	---	---	PASS
FBN2	2201	broad.mit.edu	37	5	127685089	127685089	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:127685089C>T	uc003kuu.2	-	23	3378	c.2939G>A	c.(2938-2940)TGC>TAC	p.C980Y	FBN2_uc003kuv.2_Missense_Mutation_p.C947Y	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	980	EGF-like 14; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		AGGGCACTCGCAATGAAAAGA	0.463													12	67	---	---	---	---	PASS
KIF20A	10112	broad.mit.edu	37	5	137522869	137522869	+	Missense_Mutation	SNP	T	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137522869T>C	uc003lcj.2	+	19	2936	c.2440T>C	c.(2440-2442)TAT>CAT	p.Y814H	KIF20A_uc011cyo.1_Missense_Mutation_p.Y796H	NM_005733	NP_005724	O95235	KI20A_HUMAN	kinesin family member 20A	814	Globular (Potential).				cytokinesis|M phase of mitotic cell cycle|microtubule-based movement|protein transport|vesicle-mediated transport	Golgi apparatus|microtubule|nucleoplasm	ATP binding|microtubule motor activity|protein binding|transporter activity				0			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGCTGAGCAGTATCATACTGT	0.473													29	55	---	---	---	---	PASS
HMHB1	57824	broad.mit.edu	37	5	143200170	143200170	+	3'UTR	SNP	T	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:143200170T>A	uc003lnj.2	+	2						NM_021182	NP_067005	O97980	HMHB1_HUMAN	minor histocompatibility antigen HB-1												0		Acute lymphoblastic leukemia(2;0.0236)|all_hematologic(2;0.041)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			CCCAGAGTTTTGGTGTGGATG	0.443													8	232	---	---	---	---	PASS
FABP6	2172	broad.mit.edu	37	5	159656578	159656578	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:159656578G>A	uc003lya.1	+	1	142	c.14G>A	c.(13-15)GGC>GAC	p.G5D	FABP6_uc003lxx.1_Missense_Mutation_p.G54D|FABP6_uc003lxz.1_Missense_Mutation_p.G54D	NM_001445	NP_001436	P51161	FABP6_HUMAN	gastrotropin isoform 2	5					bile acid and bile salt transport|bile acid metabolic process|negative regulation of cell proliferation	cytosol	transporter activity				0	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCTTTCACCGGCAAGTTCGAG	0.537													6	353	---	---	---	---	PASS
ZFP2	80108	broad.mit.edu	37	5	178358703	178358703	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:178358703A>G	uc003mjn.1	+	5	898	c.389A>G	c.(388-390)TAT>TGT	p.Y130C	ZFP2_uc010jky.2_Missense_Mutation_p.Y130C|ZFP2_uc010jkx.1_Missense_Mutation_p.Y130C	NM_030613	NP_085116	Q6ZN57	ZFP2_HUMAN	zinc finger protein 2 homolog	130	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		GAGAAACCCTATAAGTGTAAT	0.393													4	146	---	---	---	---	PASS
TXNDC5	81567	broad.mit.edu	37	6	7904955	7904955	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:7904955A>G	uc003mxv.2	-	2	297	c.265T>C	c.(265-267)TGT>CGT	p.C89R	TXNDC5_uc003mxw.2_Missense_Mutation_p.C46R|TXNDC5_uc010jnz.2_5'UTR|TXNDC5_uc010joa.1_5'UTR	NM_030810	NP_110437	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 isoform 1	89	Thioredoxin 1.				anti-apoptosis|cell redox homeostasis|cellular membrane organization|glycerol ether metabolic process|post-Golgi vesicle-mediated transport	endoplasmic reticulum lumen|lysosomal lumen	electron carrier activity|isomerase activity|protein disulfide oxidoreductase activity				0	Ovarian(93;0.0398)					CAGTGTCCACACCTGGAACAA	0.542													9	51	---	---	---	---	PASS
KIFC1	3833	broad.mit.edu	37	6	33359693	33359693	+	5'UTR	SNP	A	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:33359693A>G	uc003oef.3	+	1					KIFC1_uc011drf.1_5'UTR	NM_002263	NP_002254	Q9BW19	KIFC1_HUMAN	kinesin family member C1						blood coagulation|cell division|microtubule-based movement|mitotic sister chromatid segregation	early endosome|microtubule|microtubule associated complex|microtubule organizing center|nucleus|spindle	ATP binding|microtubule motor activity				0						AGAGAACGCGAGTCCCAGGAT	0.677													3	26	---	---	---	---	PASS
TBCC	6903	broad.mit.edu	37	6	42712716	42712716	+	3'UTR	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42712716G>T	uc003osl.2	-	1						NM_003192	NP_003183	Q15814	TBCC_HUMAN	beta-tubulin cofactor C						'de novo' posttranslational protein folding|post-chaperonin tubulin folding pathway	cytoplasm|microtubule|photoreceptor connecting cilium	chaperone binding|GTPase activity				0	Colorectal(47;0.196)		all cancers(41;0.00122)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.125)			CCAATAAGGGGGAAAGTCCAA	0.413													8	35	---	---	---	---	PASS
GNMT	27232	broad.mit.edu	37	6	42930003	42930003	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42930003C>T	uc003otd.2	+	2	266	c.260C>T	c.(259-261)GCC>GTC	p.A87V	uc003ote.1_5'Flank	NM_018960	NP_061833	Q14749	GNMT_HUMAN	glycine N-methyltransferase	87					protein homotetramerization|protein modification process|S-adenosylmethionine metabolic process		folic acid binding|glycine binding|glycine N-methyltransferase activity				0	Colorectal(47;0.196)		all cancers(41;0.00196)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)	AGTGTGGATGCCAGTGACAAG	0.602													4	154	---	---	---	---	PASS
TFAP2B	7021	broad.mit.edu	37	6	50807923	50807923	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:50807923C>A	uc003pag.2	+	6	1161	c.995C>A	c.(994-996)CCC>CAC	p.P332H		NM_003221	NP_003212	Q92481	AP2B_HUMAN	transcription factor AP-2 beta	332					nervous system development|positive regulation of transcription from RNA polymerase II promoter		protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity				0	Lung NSC(77;0.156)					ACGGAGTTTCCCGCCAAAGCC	0.483													6	272	---	---	---	---	PASS
GCM1	8521	broad.mit.edu	37	6	52993017	52993017	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:52993017C>T	uc003pbp.2	-	6	1507	c.1298G>A	c.(1297-1299)TGT>TAT	p.C433Y		NM_003643	NP_003634	Q9NP62	GCM1_HUMAN	glial cells missing homolog a	433						transcription factor complex	DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding			central_nervous_system(1)	1	Lung NSC(77;0.0755)					TCTCAAAGGACACAGGTTCAG	0.403													78	305	---	---	---	---	PASS
GRM1	2911	broad.mit.edu	37	6	146720058	146720058	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:146720058G>A	uc010khw.1	+	8	2353	c.1883G>A	c.(1882-1884)CGG>CAG	p.R628Q	GRM1_uc010khv.1_Missense_Mutation_p.R628Q|GRM1_uc003qll.2_Missense_Mutation_p.R628Q|GRM1_uc011edz.1_Missense_Mutation_p.R628Q|GRM1_uc011eea.1_Missense_Mutation_p.R628Q	NM_000838	NP_000829	Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1 isoform alpha	628	Cytoplasmic (Potential).				synaptic transmission	integral to plasma membrane	G-protein coupled receptor activity|glutamate receptor activity			lung(8)|ovary(4)|central_nervous_system(3)|large_intestine(2)|breast(2)	19		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)	Acamprosate(DB00659)|L-Glutamic Acid(DB00142)	TCCTCCAGTCGGGAGCTCTGC	0.507													65	261	---	---	---	---	PASS
GHRHR	2692	broad.mit.edu	37	7	31009565	31009565	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:31009565C>A	uc003tbx.2	+	4	400	c.352C>A	c.(352-354)CTG>ATG	p.L118M	GHRHR_uc003tbw.1_Missense_Mutation_p.L118M|GHRHR_uc003tby.2_Missense_Mutation_p.L54M|GHRHR_uc003tbz.2_Translation_Start_Site	NM_000823	NP_000814	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	118	Extracellular (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|positive regulation of cAMP biosynthetic process|positive regulation of cell proliferation|positive regulation of growth hormone secretion|positive regulation of insulin-like growth factor receptor signaling pathway|positive regulation of multicellular organism growth|response to estrogen stimulus|response to glucocorticoid stimulus	cell surface|integral to membrane|nuclear inner membrane|nuclear matrix|nuclear outer membrane|plasma membrane|stored secretory granule	growth factor binding|growth hormone-releasing hormone receptor activity|peptide hormone binding			ovary(2)|lung(1)|breast(1)|large_intestine(1)	5					Sermorelin(DB00010)	GCCTCTGGAGCTGCTGGCTGA	0.408													4	191	---	---	---	---	PASS
GUSB	2990	broad.mit.edu	37	7	65439618	65439618	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:65439618G>A	uc003tun.2	-	7	1215	c.1139C>T	c.(1138-1140)GCT>GTT	p.A380V	GUSB_uc011kdt.1_Missense_Mutation_p.A234V	NM_000181	NP_000172	P08236	BGLR_HUMAN	glucuronidase, beta precursor	380					glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0						GGTACGGAAAGCGTTGGCACC	0.592													20	70	---	---	---	---	PASS
TRRAP	8295	broad.mit.edu	37	7	98503859	98503859	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98503859A>G	uc003upp.2	+	13	1305	c.1096A>G	c.(1096-1098)ACT>GCT	p.T366A	TRRAP_uc011kis.1_Missense_Mutation_p.T366A|TRRAP_uc003upr.2_Missense_Mutation_p.T58A	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	366					histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			CTCAGGATATACTGCCAGAGA	0.403													4	125	---	---	---	---	PASS
STMN4	81551	broad.mit.edu	37	8	27097578	27097578	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:27097578C>A	uc003xfk.2	-	5	534	c.420G>T	c.(418-420)ATG>ATT	p.M140I	STMN4_uc003xfj.2_Missense_Mutation_p.M167I|STMN4_uc011lai.1_Missense_Mutation_p.M167I|STMN4_uc011laj.1_Missense_Mutation_p.M131I|STMN4_uc011lak.1_Missense_Mutation_p.M167I|STMN4_uc010luo.2_Missense_Mutation_p.M140I			Q9H169	STMN4_HUMAN	RecName: Full=Stathmin-4; AltName: Full=Stathmin-like protein B3;          Short=RB3;	140	Potential.				intracellular signal transduction					large_intestine(1)|pancreas(1)	2		Ovarian(32;0.00167)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0214)|Epithelial(17;9.82e-10)|Colorectal(74;0.142)		TTTCCTTAGCCATCTTGATGA	0.522													10	233	---	---	---	---	PASS
HGSNAT	138050	broad.mit.edu	37	8	43002122	43002122	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:43002122G>T	uc003xpx.3	+	2	198	c.150G>T	c.(148-150)AAG>AAT	p.K50N		NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	78	Lumenal, vesicle (Potential).				lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity				0	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			CAGAGCTGAAGATGGATCAGG	0.373													11	43	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68413570	68413570	+	RNA	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68413570G>A	uc004aex.2	+	1		c.125G>A								Homo sapiens mRNA; cDNA DKFZp564N0763 (from clone DKFZp564N0763).																		CCCCAGTGGCGCCGGATCTAG	0.562													4	5	---	---	---	---	PASS
TRPM6	140803	broad.mit.edu	37	9	77416960	77416960	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:77416960C>A	uc004ajl.1	-	16	2101	c.1863G>T	c.(1861-1863)CAG>CAT	p.Q621H	TRPM6_uc004ajk.1_Missense_Mutation_p.Q616H|TRPM6_uc010mpb.1_RNA|TRPM6_uc010mpc.1_Intron|TRPM6_uc010mpd.1_Intron|TRPM6_uc010mpe.1_Intron|TRPM6_uc004ajm.1_5'UTR	NM_017662	NP_060132	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel,	621	Cytoplasmic (Potential).				response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity			lung(3)|stomach(2)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|skin(1)	8						TAGCCATCTTCTGCCTTTTCA	0.483													24	75	---	---	---	---	PASS
FAM22G	441457	broad.mit.edu	37	9	99697651	99697651	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:99697651C>T	uc004awq.1	+	3	1470	c.755C>T	c.(754-756)ACG>ATG	p.T252M	HIATL2_uc004awr.1_Intron	NM_001045477	NP_001038942	Q5VZR2	FA22G_HUMAN	hypothetical protein LOC441457	252										skin(1)	1		Acute lymphoblastic leukemia(62;0.0527)				CCCACCATGACGCTGGAGGAG	0.617													5	63	---	---	---	---	PASS
PKN3	29941	broad.mit.edu	37	9	131469089	131469089	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:131469089G>A	uc004bvw.2	+	4	902	c.509G>A	c.(508-510)GGG>GAG	p.G170E	PKN3_uc010myh.2_Missense_Mutation_p.G170E|PKN3_uc011mbk.1_5'UTR	NM_013355	NP_037487	Q6P5Z2	PKN3_HUMAN	protein kinase PKNbeta	170	REM 2.				signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity			stomach(2)|lung(2)	4						GAGGCCAGTGGGTCCCCGGAG	0.672													3	24	---	---	---	---	PASS
C9orf78	51759	broad.mit.edu	37	9	132595806	132595806	+	Intron	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:132595806G>T	uc004byp.2	-						C9orf78_uc004byo.2_5'Flank|C9orf78_uc004byq.1_Nonsense_Mutation_p.C8*|USP20_uc004bys.2_5'Flank|USP20_uc004byr.2_5'Flank|USP20_uc004byt.1_5'Flank	NM_016520	NP_057604	Q9NZ63	CI078_HUMAN	chromosome 9 open reading frame 78												0		Ovarian(14;0.00556)				CCTGCAGAAAGCAAACACAGT	0.433													24	124	---	---	---	---	PASS
FAM190B	54462	broad.mit.edu	37	10	86130886	86130886	+	Silent	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:86130886A>T	uc001kdh.1	+	2	272	c.78A>T	c.(76-78)ACA>ACT	p.T26T	FAM190B_uc001kdg.1_Silent_p.T26T|FAM190B_uc010qmd.1_Silent_p.T26T	NM_018999	NP_061872	Q9H7U1	F190B_HUMAN	granule cell antiserum positive 14	26										ovary(3)|skin(1)	4						TAAGAAGTACATTGCAGCCAA	0.348													25	82	---	---	---	---	PASS
GRID1	2894	broad.mit.edu	37	10	87407096	87407096	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:87407096C>T	uc001kdl.1	-	13	2157	c.2056G>A	c.(2056-2058)GCT>ACT	p.A686T	GRID1_uc009xsu.1_RNA|GRID1_uc010qmf.1_Missense_Mutation_p.A257T|uc001kdm.1_RNA	NM_017551	NP_060021	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	686	Extracellular (Potential).					cell junction|integral to membrane|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|ionotropic glutamate receptor activity			ovary(5)|upper_aerodigestive_tract(2)|large_intestine(2)|central_nervous_system(1)	10					L-Glutamic Acid(DB00142)	TCATATACAGCAGAATCCCGG	0.542										Multiple Myeloma(13;0.14)			43	516	---	---	---	---	PASS
SLIT1	6585	broad.mit.edu	37	10	98764571	98764571	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98764571C>T	uc001kmw.2	-	33	3841	c.3589G>A	c.(3589-3591)GCA>ACA	p.A1197T		NM_003061	NP_003052	O75093	SLIT1_HUMAN	slit homolog 1 precursor	1197	Laminin G-like.				axon extension involved in axon guidance|forebrain morphogenesis|motor axon guidance|negative chemotaxis|negative regulation of synaptogenesis	cytoplasm|extracellular space	calcium ion binding|Roundabout binding			ovary(4)	4		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TTGTCCTCTGCCGTGGAGACC	0.597													4	63	---	---	---	---	PASS
KCNK18	338567	broad.mit.edu	37	10	118957020	118957020	+	Silent	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:118957020C>T	uc010qsr.1	+	1	21	c.21C>T	c.(19-21)CCC>CCT	p.P7P		NM_181840	NP_862823	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	7	Cytoplasmic (Potential).					integral to membrane|plasma membrane				upper_aerodigestive_tract(1)	1		Colorectal(252;0.19)		all cancers(201;0.0211)		CGGGGCACCCCCAGGCCAGGA	0.632													25	133	---	---	---	---	PASS
MUC5B	727897	broad.mit.edu	37	11	1264193	1264193	+	Missense_Mutation	SNP	C	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:1264193C>G	uc009ycr.1	+	47	8288	c.8162C>G	c.(8161-8163)ACC>AGC	p.T2721S	MUC5B_uc001ltb.2_Missense_Mutation_p.T2031S	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN	SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;	2028	7 X Cys-rich subdomain repeats.|11 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCCACGGCCACCACAACTGGG	0.632													25	114	---	---	---	---	PASS
OR52L1	338751	broad.mit.edu	37	11	6007841	6007841	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:6007841G>A	uc001mcd.2	-	1	375	c.320C>T	c.(319-321)GCC>GTC	p.A107V		NM_001005173	NP_001005173	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L,	107	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)|pancreas(1)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AATCTCGTGGGCATGAACCAG	0.547													3	50	---	---	---	---	PASS
AHNAK	79026	broad.mit.edu	37	11	62295513	62295513	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:62295513A>T	uc001ntl.2	-	5	6676	c.6376T>A	c.(6376-6378)TTG>ATG	p.L2126M	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	AHNAK nucleoprotein isoform 1	2126					nervous system development	nucleus	protein binding			ovary(10)|pancreas(4)|skin(4)|upper_aerodigestive_tract(1)	19		Melanoma(852;0.155)				GGGCCTTTCAAGTGTAAGTCC	0.517													80	348	---	---	---	---	PASS
CCDC88B	283234	broad.mit.edu	37	11	64123150	64123150	+	Intron	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:64123150C>A	uc001nzy.2	+						CCDC88B_uc001oaa.2_Intron|CCDC88B_uc001oab.1_Silent_p.A359A|CCDC88B_uc001oac.2_Intron	NM_032251	NP_115627	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88						microtubule cytoskeleton organization	cytoplasm	microtubule binding			ovary(3)|skin(1)	4						TGCCTGGGGCCCCTGGCAGAA	0.368													7	42	---	---	---	---	PASS
USP35	57558	broad.mit.edu	37	11	77919916	77919916	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:77919916C>A	uc009yva.1	+	9	1745	c.1499C>A	c.(1498-1500)TCC>TAC	p.S500Y	USP35_uc001oze.2_Missense_Mutation_p.S256Y|USP35_uc001ozc.2_Missense_Mutation_p.S68Y|USP35_uc010rsp.1_Intron|USP35_uc001ozd.2_Missense_Mutation_p.S111Y|USP35_uc001ozf.2_Missense_Mutation_p.S231Y	NM_020798	NP_065849	Q9P2H5	UBP35_HUMAN	ubiquitin specific protease 35	500					ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			lung(2)|ovary(1)	3	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			CCTGCCATTTCCCCAGAGAAC	0.612													41	200	---	---	---	---	PASS
AMICA1	120425	broad.mit.edu	37	11	118074350	118074350	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118074350G>T	uc001psk.2	-	6	739	c.565C>A	c.(565-567)CTC>ATC	p.L189I	AMICA1_uc001psg.2_5'UTR|AMICA1_uc001psh.2_Missense_Mutation_p.L150I|AMICA1_uc009yzw.1_RNA|AMICA1_uc001psi.2_Missense_Mutation_p.L179I|AMICA1_uc001psj.2_Missense_Mutation_p.L178I|AMICA1_uc010rxw.1_Missense_Mutation_p.L150I|AMICA1_uc010rxx.1_Missense_Mutation_p.L189I|AMICA1_uc001psl.1_Missense_Mutation_p.L145I	NM_001098526	NP_001091996	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen	189	Ig-like V-type 2.|Extracellular (Potential).				blood coagulation|cell adhesion|leukocyte migration|regulation of immune response	cell junction|integral to membrane				ovary(1)	1	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		GACATCCTGAGTTTGTGGTAG	0.493													34	129	---	---	---	---	PASS
HMBS	3145	broad.mit.edu	37	11	118963206	118963206	+	Silent	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118963206C>A	uc001puz.1	+	11	901	c.744C>A	c.(742-744)ATC>ATA	p.I248I	HMBS_uc009zao.1_3'UTR|HMBS_uc001pvc.1_Silent_p.I193I|HMBS_uc009zap.1_Silent_p.I231I|HMBS_uc001pva.1_Intron|HMBS_uc001pvb.1_Silent_p.I217I|HMBS_uc001pvd.1_Silent_p.I231I|HMBS_uc001pve.1_Intron|HMBS_uc001pvf.1_Silent_p.I231I	NM_000190	NP_000181	P08397	HEM3_HUMAN	hydroxymethylbilane synthase isoform 1	248			I -> IETLLRCI (in AIP).		peptidyl-pyrromethane cofactor linkage	cytosol	hydroxymethylbilane synthase activity				0	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.72e-05)		TTCGCTGCATCGCTGAAAGGG	0.607									Porphyria_Acute_Intermittent				48	204	---	---	---	---	PASS
VWF	7450	broad.mit.edu	37	12	6204730	6204730	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:6204730A>T	uc001qnn.1	-	6	803	c.553T>A	c.(553-555)TAT>AAT	p.Y185N	VWF_uc010set.1_Missense_Mutation_p.Y185N|VWF_uc001qno.1_Missense_Mutation_p.Y222N	NM_000552	NP_000543	P04275	VWF_HUMAN	von Willebrand factor preproprotein	185	VWFD 1.				blood coagulation, intrinsic pathway|cell-substrate adhesion|platelet activation|platelet degranulation|protein homooligomerization	endoplasmic reticulum|platelet alpha granule lumen|proteinaceous extracellular matrix|Weibel-Palade body	chaperone binding|collagen binding|glycoprotein binding|immunoglobulin binding|integrin binding|protease binding|protein homodimerization activity|protein N-terminus binding			skin(4)|ovary(3)|pancreas(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|breast(1)	12					Antihemophilic Factor(DB00025)	GCAAAGTCATAAGGGTCCGAG	0.512													21	200	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9230391	9230391	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9230391G>A	uc001qvk.1	-	26	3295	c.3182C>T	c.(3181-3183)GCA>GTA	p.A1061V	A2M_uc001qvj.1_Missense_Mutation_p.A103V|A2M_uc009zgk.1_Missense_Mutation_p.A911V	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	1061					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	GGTAATGTGTGCTTCATCGAT	0.488													19	108	---	---	---	---	PASS
A2M	2	broad.mit.edu	37	12	9230405	9230405	+	Silent	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9230405G>A	uc001qvk.1	-	26	3281	c.3168C>T	c.(3166-3168)ATC>ATT	p.I1056I	A2M_uc001qvj.1_Silent_p.I98I|A2M_uc009zgk.1_Silent_p.I906I	NM_000014	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin precursor	1056					blood coagulation, intrinsic pathway|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol|extracellular space|platelet alpha granule lumen	enzyme binding|GTPase activator activity|interleukin-1 binding|interleukin-8 binding|serine-type endopeptidase inhibitor activity|tumor necrosis factor binding			central_nervous_system(4)|skin(1)	5					Bacitracin(DB00626)|Becaplermin(DB00102)	CATCGATGAAGATGTAGGCTC	0.473													21	114	---	---	---	---	PASS
LOC642846	642846	broad.mit.edu	37	12	9458891	9458891	+	RNA	SNP	A	G	G	rs140731402	by1000genomes	TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:9458891A>G	uc010sgp.1	+	17		c.1928A>G			LOC642846_uc001qvp.2_RNA	NR_024374				Homo sapiens cDNA FLJ60280 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX11 (EC 3.6.1.-).												0						CTTCCCCACTAATGCACATCG	0.612													4	24	---	---	---	---	PASS
SLCO1A2	6579	broad.mit.edu	37	12	21472329	21472329	+	Intron	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:21472329G>T	uc001rer.2	-						SLCO1A2_uc001res.2_Intron|SLCO1A2_uc010siq.1_Intron|SLCO1A2_uc010sio.1_5'UTR|SLCO1A2_uc010sip.1_Intron|SLCO1A2_uc001ret.2_Missense_Mutation_p.Q11K|SLCO1A2_uc001reu.2_Intron	NM_021094	NP_066580	P46721	SO1A2_HUMAN	organic anion transporting polypeptide A						bile acid metabolic process|sodium-independent organic anion transport	integral to membrane|plasma membrane	bile acid transmembrane transporter activity|organic anion transmembrane transporter activity			large_intestine(1)|pancreas(1)|ovary(1)|skin(1)	4						actctttcctgttcttgcttg	0.075													38	134	---	---	---	---	PASS
ALG10	84920	broad.mit.edu	37	12	34175342	34175342	+	5'UTR	SNP	C	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:34175342C>G	uc001rlm.2	+	1						NM_032834	NP_116223	Q5BKT4	AG10A_HUMAN	asparagine-linked glycosylation 10 homolog						dolichol-linked oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	dolichyl-phosphate-glucose-glycolipid alpha-glucosyltransferase activity			skin(1)	1	Lung NSC(5;3.82e-05)|Acute lymphoblastic leukemia(23;0.0142)|all_hematologic(23;0.0429)	Lung NSC(34;0.204)|all_lung(34;0.235)				GTTATCTAAACCCGTCACTCC	0.602											OREG0021730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	12	---	---	---	---	PASS
P2RX2	22953	broad.mit.edu	37	12	133196058	133196058	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:133196058G>T	uc001ukj.1	+	2	207	c.207G>T	c.(205-207)GAG>GAT	p.E69D	P2RX2_uc001uki.1_Missense_Mutation_p.E69D|P2RX2_uc001ukk.1_Missense_Mutation_p.E69D|P2RX2_uc001ukl.1_Missense_Mutation_p.E69D|P2RX2_uc001ukm.1_Nonsense_Mutation_p.E47*|P2RX2_uc001ukn.1_Intron|P2RX2_uc009zyt.1_Missense_Mutation_p.E69D|P2RX2_uc001uko.1_Missense_Mutation_p.E69D	NM_170682	NP_733782	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X2 isoform A	69	Extracellular (Potential).				positive regulation of calcium ion transport into cytosol|positive regulation of calcium-mediated signaling|protein homooligomerization	integral to membrane	ATP binding|extracellular ATP-gated cation channel activity|identical protein binding|purinergic nucleotide receptor activity				0	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		GCTACCAGGAGAGCGAGACGG	0.662													35	147	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19415641	19415641	+	RNA	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19415641A>T	uc010tcj.1	-	1		c.30469T>A				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						aaaaaaaaaaaaacccaaaca	0.169													5	54	---	---	---	---	PASS
LOC284232	284232	broad.mit.edu	37	13	19415742	19415742	+	RNA	SNP	T	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19415742T>C	uc010tcj.1	-	1		c.30368A>G				NR_027995				Homo sapiens ankyrin repeat domain 20 family, member A2 pseudogene (LOC284232), non-coding RNA.												0						GCTGTTTTCCTAATCTTTCTT	0.313													3	131	---	---	---	---	PASS
N4BP2L2	10443	broad.mit.edu	37	13	33111098	33111098	+	Missense_Mutation	SNP	A	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33111098A>C	uc001uuk.3	-	2	245	c.67T>G	c.(67-69)TGT>GGT	p.C23G	N4BP2L2_uc010abe.1_Intron|N4BP2L2_uc010tdz.1_Intron|N4BP2L2_uc001uul.1_Missense_Mutation_p.C23G|N4BP2L2_uc001uum.2_5'Flank	NM_014887	NP_055702	Q92802	N42L2_HUMAN	phosphonoformate immuno-associated protein 5	23											0		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		AATTTTTTACAGCGTGGCTCA	0.358													13	156	---	---	---	---	PASS
THSD1P1	374500	broad.mit.edu	37	13	52803480	52803480	+	RNA	SNP	G	T	T	rs142077571	by1000genomes	TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:52803480G>T	uc001vgm.1	-	12		c.1013C>A			uc001vgn.2_RNA					Homo sapiens cDNA FLJ14630 fis, clone NT2RP2000459.												0						AATAAATAACGAATCTTTTTA	0.363													3	24	---	---	---	---	PASS
STYX	6815	broad.mit.edu	37	14	53213187	53213187	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:53213187T>A	uc010tqy.1	+	4	196	c.134T>A	c.(133-135)ATG>AAG	p.M45K	STYX_uc001xaa.2_Missense_Mutation_p.M45K	NM_001130701	NP_001124173	Q8WUJ0	STYX_HUMAN	serine/threonine/tyrosine interacting protein	45					protein dephosphorylation|spermatogenesis	cytoplasm	protein tyrosine/serine/threonine phosphatase activity				0	Breast(41;0.176)					TCATCTGCTATGAAAAGCAAG	0.289													31	109	---	---	---	---	PASS
KCNH5	27133	broad.mit.edu	37	14	63417018	63417018	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:63417018C>T	uc001xfx.2	-	7	1253	c.1202G>A	c.(1201-1203)CGC>CAC	p.R401H	KCNH5_uc001xfy.2_Missense_Mutation_p.R401H|KCNH5_uc001xfz.1_Missense_Mutation_p.R343H|KCNH5_uc001xga.2_Missense_Mutation_p.R343H	NM_139318	NP_647479	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H,	401	Extracellular (Potential).				regulation of transcription, DNA-dependent	integral to membrane	calmodulin binding|two-component sensor activity|voltage-gated potassium channel activity			ovary(4)|skin(4)|central_nervous_system(1)	9				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GGTATTGTAGCGATATGGAGT	0.468													10	138	---	---	---	---	PASS
SPTB	6710	broad.mit.edu	37	14	65230548	65230548	+	Intron	SNP	G	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:65230548G>C	uc001xhr.2	-						SPTB_uc001xhs.2_Intron|SPTB_uc010aqi.2_Intron	NM_001024858	NP_001020029	P11277	SPTB1_HUMAN	spectrin beta isoform a						actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton			ovary(7)|skin(2)|lung(1)|central_nervous_system(1)	11		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GAAGGCGGTGGGACCGTGCAG	0.557													40	287	---	---	---	---	PASS
ZFYVE26	23503	broad.mit.edu	37	14	68270865	68270865	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:68270865A>T	uc001xka.2	-	9	1527	c.1388T>A	c.(1387-1389)CTC>CAC	p.L463H	ZFYVE26_uc010tsz.1_Intron|ZFYVE26_uc001xkc.3_Missense_Mutation_p.L463H|ZFYVE26_uc010tta.1_Missense_Mutation_p.L463H	NM_015346	NP_056161	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	463					cell cycle|cell death|cytokinesis|double-strand break repair via homologous recombination	centrosome|midbody	metal ion binding|phosphatidylinositol-3-phosphate binding|protein binding			ovary(9)|breast(2)	11				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		TAAGAGCTTGAGAACATCTTC	0.502													4	159	---	---	---	---	PASS
RTL1	388015	broad.mit.edu	37	14	101347402	101347402	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101347402G>A	uc010txj.1	-	1	3783	c.3724C>T	c.(3724-3726)CGT>TGT	p.R1242C	MIR431_hsa-mir-431|MI0001721_RNA|MIR433_hsa-mir-433|MI0001723_5'Flank|uc001yig.3_5'Flank|MIR127_hsa-mir-127|MI0000472_5'Flank	NM_001134888	NP_001128360	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	1242										pancreas(1)	1						TGACGGTAACGTTGCAGGTCG	0.632													4	17	---	---	---	---	PASS
AHNAK2	113146	broad.mit.edu	37	14	105407363	105407363	+	Missense_Mutation	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:105407363C>A	uc010axc.1	-	7	14545	c.14425G>T	c.(14425-14427)GCT>TCT	p.A4809S	AHNAK2_uc001ypx.2_Missense_Mutation_p.A4709S	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4809						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ATTTCCAGAGCAAGCTCAGGG	0.507													4	93	---	---	---	---	PASS
TUBGCP5	114791	broad.mit.edu	37	15	22846911	22846911	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:22846911G>C	uc001yur.3	+	8	916	c.786G>C	c.(784-786)AGG>AGC	p.R262S	TUBGCP5_uc001yuq.2_Missense_Mutation_p.R262S|TUBGCP5_uc010axz.1_5'Flank	NM_052903	NP_443135	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	262					G2/M transition of mitotic cell cycle|microtubule nucleation	centrosome|cytosol|gamma-tubulin ring complex|microtubule|spindle pole	microtubule binding			skin(1)	1		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		CAGATGACAGGGTTTTGGTTA	0.353													30	129	---	---	---	---	PASS
MTMR10	54893	broad.mit.edu	37	15	31266655	31266655	+	Missense_Mutation	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:31266655G>T	uc001zfh.1	-	5	434	c.336C>A	c.(334-336)AAC>AAA	p.N112K	MTMR10_uc010azx.1_5'UTR|MTMR10_uc001zfi.1_5'UTR|MTMR10_uc001zfj.2_Missense_Mutation_p.N30K|MTMR10_uc001zfk.2_5'UTR|MTMR10_uc010ubl.1_RNA	NM_017762	NP_060232	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	112							phosphatase activity			ovary(1)	1		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TCTTGTGGTCGTTTACTAAAA	0.303													14	48	---	---	---	---	PASS
RYR3	6263	broad.mit.edu	37	15	34118467	34118467	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:34118467C>T	uc001zhi.2	+	83	11231	c.11161C>T	c.(11161-11163)CGT>TGT	p.R3721C	RYR3_uc010bar.2_Missense_Mutation_p.R3716C	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	3721					cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGTTCGGGAACGTGGTAAGTT	0.378													21	115	---	---	---	---	PASS
TMCO5A	145942	broad.mit.edu	37	15	38229120	38229120	+	Silent	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:38229120G>A	uc001zjw.2	+	3	316	c.213G>A	c.(211-213)ACG>ACA	p.T71T	TMCO5A_uc001zjv.1_Silent_p.T71T|TMCO5A_uc010bbc.1_Silent_p.T71T	NM_152453	NP_689666	Q8N6Q1	TMC5A_HUMAN	transmembrane and coiled-coil domains 5A	71	Potential.					integral to membrane				central_nervous_system(1)	1						ACCGCACCACGATGGAAAGGG	0.512													6	73	---	---	---	---	PASS
AP4E1	23431	broad.mit.edu	37	15	51293254	51293254	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:51293254A>G	uc001zyx.1	+	20	3157	c.3127A>G	c.(3127-3129)AAA>GAA	p.K1043E	AP4E1_uc010bex.1_RNA	NM_007347	NP_031373	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1	1043					intracellular protein transport|vesicle-mediated transport	COPI vesicle coat	binding|structural molecule activity				0				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		CGACTTTGGGAAACTCTGGTT	0.313													47	159	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	85787980	85787980	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:85787980T>G	uc010upj.1	+	6	788	c.723T>G	c.(721-723)CAT>CAG	p.H241Q	uc010upk.1_5'Flank	NM_198181	NP_937824			golgi autoantigen, golgin subfamily a, 6D-like																		TACGTGAACATGAGGAGAGGC	0.562													2	5	---	---	---	---	PASS
AKAP13	11214	broad.mit.edu	37	15	86123644	86123644	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:86123644A>G	uc002blv.1	+	7	2515	c.2345A>G	c.(2344-2346)GAC>GGC	p.D782G	AKAP13_uc002blt.1_Missense_Mutation_p.D782G|AKAP13_uc002blu.1_Missense_Mutation_p.D782G|AKAP13_uc010bne.1_5'Flank	NM_007200	NP_009131	Q12802	AKP13_HUMAN	A-kinase anchor protein 13 isoform 2	782					apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|membrane|membrane fraction|nucleus	cAMP-dependent protein kinase activity|metal ion binding|protein binding|Rho guanyl-nucleotide exchange factor activity|signal transducer activity			central_nervous_system(3)|kidney(2)|urinary_tract(1)|liver(1)|skin(1)|ovary(1)	9						GTAATATCAGACAGTACTTTC	0.443													37	179	---	---	---	---	PASS
ANPEP	290	broad.mit.edu	37	15	90349608	90349608	+	Silent	SNP	T	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:90349608T>C	uc002bop.3	-	2	499	c.207A>G	c.(205-207)AAA>AAG	p.K69K		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	69	Extracellular.|Metalloprotease.				angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)|skin(1)	4	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)	GATTCCACGCTTTACTTTGGT	0.617													41	170	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	102292820	102292820	+	Silent	SNP	G	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:102292820G>C	uc010usj.1	+	4	467	c.408G>C	c.(406-408)ACG>ACC	p.T136T	uc002bxo.2_RNA|uc002bxp.3_5'Flank|uc002bxt.2_5'Flank|uc002bxz.3_5'Flank|uc002byd.2_5'Flank|uc002bye.2_5'Flank|uc002byf.1_5'Flank|uc002byg.2_5'Flank|uc002byi.2_5'Flank|uc002byk.2_5'Flank|uc002bym.2_5'Flank|uc002byn.2_5'Flank|uc010usm.1_5'Flank|uc002byr.2_5'Flank					RecName: Full=Uncharacterized protein C15orf51.; Flags: Fragment;																		GCGTGGGAACGAGAAGACACT	0.592													3	23	---	---	---	---	PASS
PRSS21	10942	broad.mit.edu	37	16	2867459	2867459	+	Splice_Site	SNP	T	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:2867459T>G	uc002crt.2	+	2	197	c.91_splice	c.e2+2	p.G31_splice	PRSS21_uc002crs.2_Splice_Site_p.G31_splice|PRSS21_uc002crr.2_Splice_Site_p.G31_splice	NM_006799	NP_006790	Q9Y6M0	TEST_HUMAN	testisin isoform 1						proteolysis	anchored to membrane|cytoplasm|membrane fraction|plasma membrane	serine-type endopeptidase activity			ovary(1)|skin(1)	2						CGTTATCAGGTAGGGCGCCCA	0.721													5	22	---	---	---	---	PASS
MYH11	4629	broad.mit.edu	37	16	15841458	15841458	+	Missense_Mutation	SNP	G	C	C			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:15841458G>C	uc002ddy.2	-	19	2487	c.2380C>G	c.(2380-2382)CAG>GAG	p.Q794E	MYH11_uc002ddv.2_Missense_Mutation_p.Q801E|MYH11_uc002ddw.2_Missense_Mutation_p.Q794E|MYH11_uc002ddx.2_Missense_Mutation_p.Q801E|MYH11_uc010bvg.2_Missense_Mutation_p.Q626E	NM_002474	NP_002465	P35749	MYH11_HUMAN	smooth muscle myosin heavy chain 11 isoform	794	IQ.				axon guidance|cardiac muscle fiber development|elastic fiber assembly|skeletal muscle myosin thick filament assembly|smooth muscle contraction	cytosol|melanosome|muscle myosin complex|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(6)|skin(3)|lung(2)|breast(2)|upper_aerodigestive_tract(1)|pancreas(1)	15						CACATCGCCTGGAAGGCCATG	0.498			T	CBFB	AML								26	114	---	---	---	---	PASS
ZNF646	9726	broad.mit.edu	37	16	31089296	31089296	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31089296G>A	uc002eap.2	+	2	1940	c.1651G>A	c.(1651-1653)GAT>AAT	p.D551N		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	551					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2						CCCGCACACAGATCAGGACCA	0.597													5	42	---	---	---	---	PASS
MYST1	84148	broad.mit.edu	37	16	31142592	31142592	+	3'UTR	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31142592C>T	uc002eay.2	+	11					MYST1_uc002eax.2_3'UTR|MYST1_uc002eaz.2_3'UTR|MYST1_uc002eba.2_3'UTR|MYST1_uc002ebb.2_RNA	NM_032188	NP_115564	Q9H7Z6	MYST1_HUMAN	MYST histone acetyltransferase 1 isoform 1						histone H4-K16 acetylation|myeloid cell differentiation|negative regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex|MSL complex	histone acetyltransferase activity|metal ion binding|methylated histone residue binding|transcription factor binding			ovary(1)	1						CAGCCTGGCCCCTGCTGTCGG	0.552													6	32	---	---	---	---	PASS
ABCC11	85320	broad.mit.edu	37	16	48244895	48244895	+	Silent	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:48244895G>A	uc002eff.1	-	10	1922	c.1572C>T	c.(1570-1572)GGC>GGT	p.G524G	ABCC11_uc002efg.1_Silent_p.G524G|ABCC11_uc002efh.1_Silent_p.G524G|ABCC11_uc010vgk.1_RNA	NM_033151	NP_149163	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C, member 11	524	ABC transporter 1.|Cytoplasmic (Potential).					integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(3)|skin(2)|central_nervous_system(1)	6		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)				GCAACTCTGGGCCCAGGCTGT	0.617									Cerumen_Type				11	112	---	---	---	---	PASS
KIAA0182	23199	broad.mit.edu	37	16	85696693	85696693	+	Silent	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:85696693C>T	uc002fix.2	+	10	2441	c.2367C>T	c.(2365-2367)TCC>TCT	p.S789S	KIAA0182_uc002fiw.2_Silent_p.S685S|KIAA0182_uc002fiy.2_Silent_p.S716S|KIAA0182_uc002fiz.2_5'UTR|KIAA0182_uc010cho.2_5'Flank	NM_014615	NP_055430	Q14687	GSE1_HUMAN	genetic suppressor element 1 isoform 1	789							protein binding			large_intestine(3)|ovary(1)|skin(1)	5						TGGACACGTCCTCTGAGGTAC	0.627													13	55	---	---	---	---	PASS
NUP88	4927	broad.mit.edu	37	17	5322725	5322725	+	Silent	SNP	G	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:5322725G>T	uc002gbo.1	-	1	272	c.246C>A	c.(244-246)CGC>CGA	p.R82R	NUP88_uc010vsx.1_Silent_p.R82R|NUP88_uc010cle.1_Silent_p.R82R|NUP88_uc010vsy.1_Silent_p.R82R|RPAIN_uc010vsz.1_5'Flank|RPAIN_uc002gbp.1_5'Flank|RPAIN_uc010vta.1_5'Flank|RPAIN_uc002gbq.2_5'Flank|RPAIN_uc010vtb.1_5'Flank|RPAIN_uc002gbs.2_5'Flank|RPAIN_uc002gbt.2_5'Flank|RPAIN_uc002gbu.2_5'Flank|RPAIN_uc002gbv.2_5'Flank|RPAIN_uc002gbr.2_5'Flank|RPAIN_uc002gbw.2_5'Flank	NM_002532	NP_002523	Q99567	NUP88_HUMAN	nucleoporin 88kDa	82					carbohydrate metabolic process|glucose transport|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	transporter activity			kidney(1)	1						GGCCCCGAAGGCGAACGACTA	0.647													16	78	---	---	---	---	PASS
MYH13	8735	broad.mit.edu	37	17	10248602	10248602	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:10248602C>T	uc002gmk.1	-	15	1591	c.1501G>A	c.(1501-1503)GAA>AAA	p.E501K	MYH13_uc010vvf.1_Missense_Mutation_p.E176K	NM_003802	NP_003793	Q9UKX3	MYH13_HUMAN	myosin, heavy polypeptide 13, skeletal muscle	501	Myosin head-like.				muscle contraction	muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(4)|skin(2)	6						TTGTACTCTTCCTGCTCCAGC	0.498													5	244	---	---	---	---	PASS
NF1	4763	broad.mit.edu	37	17	29586101	29586101	+	Missense_Mutation	SNP	C	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:29586101C>T	uc002hgg.2	+	33	4717	c.4384C>T	c.(4384-4386)CGG>TGG	p.R1462W	NF1_uc002hgh.2_Missense_Mutation_p.R1441W|NF1_uc002hgi.1_Missense_Mutation_p.R474W	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1462					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(3)		soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AGAACATATGCGGCCTTTCAA	0.333			D|Mis|N|F|S|O		neurofibroma|glioma	neurofibroma|glioma			Neurofibromatosis_type_1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			4	58	---	---	---	---	PASS
JUP	3728	broad.mit.edu	37	17	39680198	39680198	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39680198G>A	uc010wfs.1	-	9	1497	c.1489C>T	c.(1489-1491)CAG>TAG	p.Q497*	KRT15_uc002hxb.1_5'Flank|uc002hxc.1_5'Flank|KRT19_uc002hxd.3_Nonsense_Mutation_p.Q334*	NM_021991	NP_068831	P14923	PLAK_HUMAN	junction plakoglobin	Error:Variant_position_missing_in_P14923_after_alignment					adherens junction organization|atrioventricular valve morphogenesis|cell migration|cell morphogenesis|cellular response to indole-3-methanol|cytoskeletal anchoring at plasma membrane|detection of mechanical stimulus|ectoderm development|endothelial cell-cell adhesion|gastrulation|morphogenesis of embryonic epithelium|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of Wnt receptor signaling pathway involved in heart development|nervous system development|oocyte development|positive regulation of protein import into nucleus|positive regulation of sequence-specific DNA binding transcription factor activity|skin development	actin cytoskeleton|Axin-APC-beta-catenin-GSK3B complex|basolateral plasma membrane|catenin complex|desmosome|fascia adherens|gamma-catenin-TCF7L2 complex|internal side of plasma membrane|nucleus|protein-DNA complex|Z disc|zonula adherens	alpha-catenin binding|cadherin binding|protein homodimerization activity|protein kinase binding|protein phosphatase binding|RPTP-like protein binding|specific RNA polymerase II transcription factor activity|transcription coactivator activity			ovary(2)|lung(2)|breast(1)	5		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		TGCGCCAGCTGGGCTCCAAAG	0.597													17	84	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	45128685	45128685	+	5'Flank	SNP	T	C	C	rs145089594	by1000genomes	TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:45128685T>C	uc010wkl.1	-						uc010wkm.1_RNA					Homo sapiens cDNA FLJ38031 fis, clone CTONG2013348.																		TTCCAGGATATGGCTATACTG	0.289													5	197	---	---	---	---	PASS
PLEKHM1P	440456	broad.mit.edu	37	17	62788499	62788499	+	Silent	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:62788499G>A	uc002jew.3	-	8	2141	c.1230C>T	c.(1228-1230)TGC>TGT	p.C410C	PLEKHM1P_uc002jev.3_RNA	NR_024386				RecName: Full=Putative pleckstrin homology domain-containing family M member 1P;												0						CGCCACTCCGGCACAGGCCCA	0.527													3	72	---	---	---	---	PASS
FADS6	283985	broad.mit.edu	37	17	72888762	72888762	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72888762A>T	uc002jmd.1	-	2	257	c.245T>A	c.(244-246)ATC>AAC	p.I82N		NM_178128	NP_835229	Q8N9I5	FADS6_HUMAN	fatty acid desaturase domain family, member 6	88	Helical; (Potential).				fatty acid biosynthetic process	integral to membrane	oxidoreductase activity				0	all_lung(278;0.172)|Lung NSC(278;0.207)					CACACCCAAGATGGTGATGCC	0.597													7	23	---	---	---	---	PASS
SLC38A10	124565	broad.mit.edu	37	17	79257257	79257257	+	Silent	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79257257C>A	uc002jzz.1	-	4	684	c.309G>T	c.(307-309)GTG>GTT	p.V103V	SLC38A10_uc002jzy.1_Silent_p.V21V|SLC38A10_uc002kab.2_Silent_p.V103V	NM_001037984	NP_001033073	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10 isoform a	103	Helical; (Potential).				amino acid transport|sodium ion transport	integral to membrane				pancreas(1)|skin(1)	2	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			AGTCGCCGATCACGACGTAGA	0.587													13	31	---	---	---	---	PASS
ALPK2	115701	broad.mit.edu	37	18	56205106	56205106	+	Silent	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:56205106A>T	uc002lhj.3	-	5	2527	c.2313T>A	c.(2311-2313)CCT>CCA	p.P771P	ALPK2_uc002lhk.1_Silent_p.P102P	NM_052947	NP_443179	Q86TB3	ALPK2_HUMAN	heart alpha-kinase	771							ATP binding|protein serine/threonine kinase activity			ovary(7)|skin(5)|lung(1)|central_nervous_system(1)	14						AGACAGCCACAGGCTCCCTGA	0.527													39	176	---	---	---	---	PASS
CCNE1	898	broad.mit.edu	37	19	30314751	30314751	+	3'UTR	SNP	C	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:30314751C>A	uc002nsn.2	+	12					CCNE1_uc002nso.2_3'UTR|CCNE1_uc002nsp.2_3'UTR	NM_001238	NP_001229	P24864	CCNE1_HUMAN	cyclin E1 isoform 1						androgen receptor signaling pathway|cell division|positive regulation of transcription, DNA-dependent|regulation of cyclin-dependent protein kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle	cytosol|nucleoplasm	androgen receptor binding|protein kinase binding|transcription coactivator activity			lung(2)	2	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			TCTGTTGCAGCGGAGGCGTGC	0.502													3	64	---	---	---	---	PASS
FAM113A	64773	broad.mit.edu	37	20	2819279	2819279	+	Missense_Mutation	SNP	A	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:2819279A>G	uc002wgz.1	-	5	1054	c.557T>C	c.(556-558)CTC>CCC	p.L186P	FAM113A_uc002whb.1_Missense_Mutation_p.S38P|FAM113A_uc002wha.1_Missense_Mutation_p.S38P|FAM113A_uc010zqa.1_Missense_Mutation_p.L33P|FAM113A_uc002whc.1_Missense_Mutation_p.L135P|VPS16_uc002whe.2_5'Flank|VPS16_uc002whf.2_5'Flank|VPS16_uc002whd.2_5'Flank	NM_022760	NP_073597	Q9H1Q7	F113A_HUMAN	hypothetical protein LOC64773	186							hydrolase activity|protein binding			ovary(2)	2						ACGTTCCCCGAGGGGCATCGC	0.577													35	195	---	---	---	---	PASS
ZNFX1	57169	broad.mit.edu	37	20	47887117	47887117	+	Missense_Mutation	SNP	T	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47887117T>A	uc002xui.2	-	3	1479	c.1232A>T	c.(1231-1233)TAC>TTC	p.Y411F		NM_021035	NP_066363	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	411							metal ion binding			ovary(2)	2			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GGTGTCAAAGTAGATTCGGAT	0.443													66	266	---	---	---	---	PASS
PCK1	5105	broad.mit.edu	37	20	56138156	56138156	+	Missense_Mutation	SNP	T	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:56138156T>G	uc002xyn.3	+	5	846	c.683T>G	c.(682-684)ATC>AGC	p.I228S	PCK1_uc010zzm.1_Intron	NM_002591	NP_002582	P35558	PCKGC_HUMAN	cytosolic phosphoenolpyruvate carboxykinase 1	228					gluconeogenesis|glucose homeostasis|glycerol biosynthetic process from pyruvate|response to insulin stimulus	cytosol|nucleus	carboxylic acid binding|GTP binding|magnesium ion binding|manganese ion binding|phosphoenolpyruvate carboxykinase (GTP) activity			skin(1)	1	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CGCAGAGAGATCATCTCCTTT	0.617													27	137	---	---	---	---	PASS
POM121L9P	29774	broad.mit.edu	37	22	24659691	24659691	+	RNA	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:24659691G>A	uc002zzs.3	+	7		c.3423G>A			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						TCTCCTCCACGCACTGGCGCA	0.622													7	52	---	---	---	---	PASS
TOB2	10766	broad.mit.edu	37	22	41832248	41832248	+	3'UTR	SNP	T	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41832248T>G	uc003azz.1	-	2						NM_016272	NP_057356	Q14106	TOB2_HUMAN	transducer of ERBB2, 2						female gamete generation|negative regulation of cell proliferation	cytoplasm|nucleus				ovary(1)	1						TTTTCCTCTTTTTTTTGGCCT	0.498													5	29	---	---	---	---	PASS
ZDHHC9	51114	broad.mit.edu	37	X	128975882	128975882	+	Missense_Mutation	SNP	A	T	T			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:128975882A>T	uc004euv.2	-	2	409	c.40T>A	c.(40-42)TGG>AGG	p.W14R	ZDHHC9_uc004euw.2_Missense_Mutation_p.W14R|ZDHHC9_uc004eux.1_Missense_Mutation_p.W14R|ZDHHC9_uc004euy.1_Intron	NM_001008222	NP_001008223	Q9Y397	ZDHC9_HUMAN	zinc finger, DHHC domain containing 9	14	Cytoplasmic (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)	1						AGTTTCTCCCATTTCCGTGTC	0.502													115	95	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	14423	14423	+	RNA	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:14423G>A	uc004cox.3	+	1		c.2087G>A			uc004coy.2_5'Flank|uc004coz.1_5'Flank					Homo sapiens NADH dehydrogenase subunit 5 (MTND5) mRNA, RNA 5, complete cds; mitochondrial gene for mitochondrial product.																		CCTCAACCCCTGACCCCCATG	0.453													16	21	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15356	15356	+	Missense_Mutation	SNP	G	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15356G>A	uc004coy.2	+	1	596	c.521G>A	c.(520-522)GGG>GAG	p.G174E	uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		TGCACGAAACGGGATCAAACA	0.478											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	3	41	---	---	---	---	PASS
HP1BP3	50809	broad.mit.edu	37	1	21094272	21094272	+	Intron	DEL	A	-	-	rs138055687		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:21094272delA	uc001bdw.1	-						HP1BP3_uc001bdv.1_Intron|HP1BP3_uc010odh.1_Intron|HP1BP3_uc001bdy.1_Intron|HP1BP3_uc001bdz.2_Intron|HP1BP3_uc001bea.2_Intron|HP1BP3_uc010odf.1_5'Flank|HP1BP3_uc010odg.1_Intron	NM_016287	NP_057371	Q5SSJ5	HP1B3_HUMAN	HP1-BP74						nucleosome assembly	nucleosome|nucleus	DNA binding			central_nervous_system(1)|skin(1)	2		all_lung(284;6.55e-06)|Lung NSC(340;6.59e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.26e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00015)|GBM - Glioblastoma multiforme(114;0.000521)|Kidney(64;0.000529)|STAD - Stomach adenocarcinoma(196;0.00311)|KIRC - Kidney renal clear cell carcinoma(64;0.00687)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.201)		TTCTTCAGAGAAAAAAAaaaa	0.169													9	4	---	---	---	---	
TMEM182	130827	broad.mit.edu	37	2	103378582	103378582	+	5'UTR	DEL	T	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103378582delT	uc010fjb.2	+	1					TMEM182_uc002tcc.3_Intron|TMEM182_uc002tcd.3_Intron	NM_144632	NP_653233	Q6ZP80	TM182_HUMAN	transmembrane protein 182 precursor							integral to membrane					0						aatattattcttttttttttt	0.343													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	241579567	241579574	+	IGR	DEL	TCCTTCCC	-	-	rs142912596	by1000genomes	TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:241579567_241579574delTCCTTCCC								GPR35 (8892 upstream) : AQP12B (36262 downstream)																							cctccctccttccttccctccttccctg	0.000													4	2	---	---	---	---	
PASK	23178	broad.mit.edu	37	2	242058385	242058385	+	Intron	DEL	C	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:242058385delC	uc002wao.1	-						PASK_uc010zol.1_Intron|PASK_uc010zom.1_Intron|PASK_uc010fzl.1_Intron|PASK_uc010zon.1_Intron|PASK_uc002wap.2_Intron|PASK_uc002waq.2_Intron	NM_015148	NP_055963	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase						regulation of transcription, DNA-dependent	Golgi apparatus	ATP binding|identical protein binding|protein serine/threonine kinase activity|signal transducer activity			ovary(4)|lung(1)|skin(1)	6		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		AAGGGCAGCACCCCCAGCCTC	0.662													4	2	---	---	---	---	
LOC728323	728323	broad.mit.edu	37	2	243056967	243056967	+	Intron	DEL	T	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:243056967delT	uc010zpd.1	+						LOC728323_uc010zpe.1_Intron|LOC728323_uc010zpf.1_Intron|LOC728323_uc010zpg.1_Intron	NR_024437				Homo sapiens cDNA FLJ60027 complete cds, moderately similar to F-box only protein 25.												0						CAGTGCTATCTTATGAAATAA	0.299													9	4	---	---	---	---	
C3orf64	285203	broad.mit.edu	37	3	69059081	69059084	+	Intron	DEL	CAAC	-	-	rs66913571		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69059081_69059084delCAAC	uc003dnl.2	-						C3orf64_uc003dnk.2_Intron|C3orf64_uc011bfw.1_Intron|C3orf64_uc003dnm.1_Intron	NM_173654	NP_775925	Q5NDL2	AER61_HUMAN	AER61 glycosyltransferase							extracellular region	transferase activity, transferring glycosyl groups			ovary(1)	1		Lung NSC(201;0.126)		BRCA - Breast invasive adenocarcinoma(55;4.61e-05)|Epithelial(33;0.000291)|LUSC - Lung squamous cell carcinoma(21;0.0127)|KIRC - Kidney renal clear cell carcinoma(39;0.216)		acaacaacaacaacaaaaaaaaaa	0.216													4	2	---	---	---	---	
PLS1	5357	broad.mit.edu	37	3	142402698	142402698	+	Intron	DEL	T	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142402698delT	uc010huv.2	+						PLS1_uc003euz.2_Intron|PLS1_uc003eva.2_Intron	NM_001145319	NP_001138791	Q14651	PLSI_HUMAN	plastin 1							cytoplasm	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(1)	1						aaaccatgTGTTTTTTTTTTT	0.109													4	2	---	---	---	---	
BDH1	622	broad.mit.edu	37	3	197273010	197273011	+	Intron	INS	-	A	A	rs71623360		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:197273010_197273011insA	uc003fxr.2	-						BDH1_uc003fxs.2_Intron|BDH1_uc003fxt.2_Intron|BDH1_uc003fxu.2_Intron	NM_203314	NP_976059	Q02338	BDH_HUMAN	3-hydroxybutyrate dehydrogenase, type 1						cellular lipid metabolic process|ketone body biosynthetic process|ketone body catabolic process	mitochondrial matrix	3-hydroxybutyrate dehydrogenase activity			ovary(1)	1	all_cancers(143;3.35e-10)|Ovarian(172;0.0418)|Breast(254;0.0437)	Lung NSC(153;0.118)	Epithelial(36;3.52e-24)|all cancers(36;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-19)|LUSC - Lung squamous cell carcinoma(58;1.02e-06)|Lung(62;1.34e-06)	GBM - Glioblastoma multiforme(93;0.0977)	NADH(DB00157)	ccatcaaaaagaaaaaaaaata	0.218													4	2	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7726580	7726581	+	Intron	INS	-	TTA	TTA	rs147507704	by1000genomes	TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7726580_7726581insTTA	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						gatggtggtagtggtgatggtg	0.000													1	5	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	95332244	95332245	+	IGR	INS	-	AAGG	AAGG	rs141921585	by1000genomes	TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:95332244_95332245insAAGG								HPGDS (68217 upstream) : PDLIM5 (40793 downstream)																							aaagaaagaaaaaggaaggaag	0.074													7	4	---	---	---	---	
HMGCS1	3157	broad.mit.edu	37	5	43297956	43297956	+	Intron	DEL	G	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:43297956delG	uc003jnr.3	-						HMGCS1_uc003jnp.3_5'Flank|HMGCS1_uc003jnq.3_Intron	NM_001098272	NP_001091742	Q01581	HMCS1_HUMAN	hydroxymethylglutaryl-CoA synthase 1						cholesterol biosynthetic process|isoprenoid biosynthetic process	cytosol|soluble fraction	hydroxymethylglutaryl-CoA synthase activity				0						aaaaaaaaaagaaaaaaaaac	0.020													4	2	---	---	---	---	
TUBE1	51175	broad.mit.edu	37	6	112400624	112400625	+	Intron	INS	-	A	A	rs111683493		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:112400624_112400625insA	uc003pvq.2	-						TUBE1_uc003pvr.2_Intron	NM_016262	NP_057346	Q9UJT0	TBE_HUMAN	tubulin, epsilon 1						centrosome cycle|microtubule-based movement|protein polymerization	microtubule|pericentriolar material	GTP binding|GTPase activity|structural constituent of cytoskeleton			ovary(1)	1		all_cancers(87;0.0101)|all_hematologic(75;0.000258)|Colorectal(196;0.0466)|all_epithelial(87;0.1)		all cancers(137;0.0217)|OV - Ovarian serous cystadenocarcinoma(136;0.0613)|Epithelial(106;0.0636)|GBM - Glioblastoma multiforme(226;0.0972)|BRCA - Breast invasive adenocarcinoma(108;0.246)		GGGCTTACATTAaaaaaaaaaa	0.262													4	2	---	---	---	---	
SEMA3A	10371	broad.mit.edu	37	7	83764433	83764434	+	Intron	DEL	TT	-	-	rs147767556		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:83764433_83764434delTT	uc003uhz.2	-							NM_006080	NP_006071	Q14563	SEM3A_HUMAN	semaphorin 3A precursor						axon guidance	extracellular region|membrane	receptor activity			ovary(2)|breast(1)|kidney(1)	4						TGCAttttactttttttttttt	0.163													6	3	---	---	---	---	
CDK14	5218	broad.mit.edu	37	7	90721001	90721004	+	Intron	DEL	GAAG	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:90721001_90721004delGAAG	uc003uky.2	+						CDK14_uc003ukz.1_Intron|CDK14_uc010les.1_Intron|CDK14_uc011khl.1_Intron	NM_012395	NP_036527	O94921	CDK14_HUMAN	PFTAIRE protein kinase 1						cell division|G2/M transition of mitotic cell cycle|regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	cytoplasmic cyclin-dependent protein kinase holoenzyme complex|nucleus|plasma membrane	ATP binding|cyclin binding|cyclin-dependent protein kinase activity			lung(3)|ovary(1)	4						gagaaaGGGAgaaggaaggaagga	0.044													5	4	---	---	---	---	
AKAP9	10142	broad.mit.edu	37	7	91706403	91706403	+	Intron	DEL	T	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:91706403delT	uc003ulg.2	+						AKAP9_uc003ulf.2_Intron|AKAP9_uc003uli.2_Intron|AKAP9_uc003ulj.2_Intron	NM_005751	NP_005742	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 isoform 2						G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			breast(7)|ovary(6)|lung(5)|skin(3)|large_intestine(2)|prostate(2)|central_nervous_system(1)	26	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			attattattattTCtttcttt	0.100			T	BRAF	papillary thyroid								4	2	---	---	---	---	
GLDC	2731	broad.mit.edu	37	9	6602378	6602378	+	Intron	DEL	T	-	-	rs10975676		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:6602378delT	uc003zkc.2	-							NM_000170	NP_000161	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)						glycine catabolic process	mitochondrion	electron carrier activity|glycine dehydrogenase (decarboxylating) activity|lyase activity|pyridoxal phosphate binding			ovary(2)	2		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	TGATTACTGAttttttttttt	0.174													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	70182344	70182346	+	RNA	DEL	TTG	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:70182344_70182346delTTG	uc004afw.2	-	3		c.1766_1768delCAA								Homo sapiens COBW domain containing 5, mRNA (cDNA clone IMAGE:5287337), complete cds.																		TTTCTGTGTATTGTTTTTTTTTT	0.236													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	10	42387645	42387647	+	IGR	DEL	GGA	-	-	rs112453866		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:42387645_42387647delGGA								None (None upstream) : LOC441666 (439668 downstream)																							atcgtcgaatggaggaaacaaat	0.000													1	7	---	---	---	---	
EXOC6	54536	broad.mit.edu	37	10	94675322	94675323	+	Intron	INS	-	T	T	rs72254411		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:94675322_94675323insT	uc001kig.2	+						EXOC6_uc010qnr.1_Intron|EXOC6_uc001kie.2_Intron|EXOC6_uc009xub.2_Intron|EXOC6_uc009xuc.2_Intron	NM_019053	NP_061926	Q8TAG9	EXOC6_HUMAN	SEC15-like 1 isoform a						protein transport|vesicle docking involved in exocytosis	exocyst				skin(1)	1		Colorectal(252;0.123)				tgagaccctgAttttttttttt	0.000													2	4	---	---	---	---	
NAALAD2	10003	broad.mit.edu	37	11	89868965	89868965	+	Intron	DEL	T	-	-	rs34639551		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:89868965delT	uc001pdf.3	+						NAALAD2_uc009yvx.2_Intron|NAALAD2_uc009yvy.2_Intron|NAALAD2_uc001pdd.2_Intron|NAALAD2_uc001pde.2_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2						proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)|skin(1)	2		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)				AGTCATCAACTTTTTTTTTTT	0.308													6	4	---	---	---	---	
PIP4K2C	79837	broad.mit.edu	37	12	57989486	57989486	+	Intron	DEL	A	-	-	rs72197760		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:57989486delA	uc001sou.2	+						PIP4K2C_uc001sot.2_Intron|PIP4K2C_uc010srs.1_Intron|PIP4K2C_uc010srt.1_Intron	NM_001146258	NP_001139730	Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type							cytoplasm|membrane	1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|identical protein binding			central_nervous_system(2)|lung(1)	3	Melanoma(17;0.122)					actccttgtcaaaaaaaaaaa	0.184													6	3	---	---	---	---	
MYL2	4633	broad.mit.edu	37	12	111349075	111349075	+	Intron	DEL	G	-	-	rs72145780		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:111349075delG	uc001try.3	-						MYL2_uc001trx.3_Intron	NM_000432	NP_000423	P10916	MLRV_HUMAN	slow cardiac myosin regulatory light chain 2						cardiac myofibril assembly|heart contraction|muscle filament sliding|negative regulation of cell growth|regulation of striated muscle contraction|ventricular cardiac muscle tissue morphogenesis	cytosol|myosin complex|sarcomere	actin monomer binding|calcium ion binding|myosin heavy chain binding|structural constituent of muscle			ovary(1)	1						ACGGATAGCTGGGGGGTGGGG	0.488													6	6	---	---	---	---	
TMEM120B	144404	broad.mit.edu	37	12	122186093	122186094	+	Intron	INS	-	CA	CA			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122186093_122186094insCA	uc001ubc.3	+						TMEM120B_uc009zxh.2_Intron	NM_001080825	NP_001074294	A0PK00	T120B_HUMAN	transmembrane protein 120B							integral to membrane					0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		aaggtgggaggctggggtagaa	0.203													5	3	---	---	---	---	
VPS33A	65082	broad.mit.edu	37	12	122743734	122743735	+	Intron	INS	-	TGTA	TGTA			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122743734_122743735insTGTA	uc001ucd.2	-						VPS33A_uc001ucc.2_Intron|VPS33A_uc001uce.2_Intron	NM_022916	NP_075067	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33A						lysosome localization|melanosome localization|platelet formation|protein transport|regulation of developmental pigmentation|vesicle docking involved in exocytosis	early endosome|late endosome membrane|lysosomal membrane|perinuclear region of cytoplasm	protein binding			skin(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		gtatgtatgtgtgtatgtatgt	0.000													3	3	---	---	---	---	
KL	9365	broad.mit.edu	37	13	33637746	33637746	+	Intron	DEL	A	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:33637746delA	uc001uus.2	+							NM_004795	NP_004786	Q9UEF7	KLOT_HUMAN	klotho precursor						aging|carbohydrate metabolic process|insulin receptor signaling pathway|positive regulation of bone mineralization	extracellular space|extracellular space|integral to membrane|integral to plasma membrane|membrane fraction|soluble fraction	beta-glucosidase activity|beta-glucuronidase activity|cation binding|fibroblast growth factor binding|hormone activity|signal transducer activity|vitamin D binding			large_intestine(1)|ovary(1)|skin(1)	3	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		catctctactaaaaaaaaaaa	0.000													4	2	---	---	---	---	
DHRS4	10901	broad.mit.edu	37	14	24473479	24473479	+	Intron	DEL	A	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24473479delA	uc001wlc.3	+						DHRS4L2_uc001wld.3_Intron|DHRS4L2_uc001wle.3_Intron|DHRS4L2_uc001wlg.3_Intron|DHRS4L2_uc001wlh.3_Intron|DHRS4L2_uc010tnt.1_Intron|DHRS4L2_uc001wli.3_Intron|DHRS4L2_uc010alb.2_Intron	NM_021004	NP_066284	Q9BTZ2	DHRS4_HUMAN	peroxisomal short-chain alcohol dehydrogenase							mitochondrion|nuclear membrane|peroxisome	binding|carbonyl reductase (NADPH) activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	ctccgtctctaaaaaaaaaaa	0.134													6	4	---	---	---	---	
PLD2	5338	broad.mit.edu	37	17	4719678	4719678	+	Intron	DEL	A	-	-	rs113078659		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:4719678delA	uc002fzc.2	+						PLD2_uc010vsj.1_Intron|PLD2_uc002fzd.2_Intron	NM_002663	NP_002654	O14939	PLD2_HUMAN	phospholipase D2						cell communication|cytoskeleton organization|small GTPase mediated signal transduction		NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	5					Choline(DB00122)	actctgtctcaaaaaaaaaaa	0.224													6	5	---	---	---	---	
ULK2	9706	broad.mit.edu	37	17	19752508	19752510	+	Intron	DEL	AAC	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:19752508_19752510delAAC	uc002gwm.3	-						ULK2_uc002gwn.2_Intron	NM_001142610	NP_001136082	Q8IYT8	ULK2_HUMAN	unc-51-like kinase 2						signal transduction		ATP binding|protein binding|protein serine/threonine kinase activity			skin(2)|large_intestine(1)|stomach(1)	4	all_cancers(12;4.97e-05)|all_epithelial(12;0.00362)|Breast(13;0.186)					CAAAACCACAAACAACAACAACA	0.360													4	2	---	---	---	---	
TMEM106A	113277	broad.mit.edu	37	17	41370072	41370073	+	3'UTR	INS	-	G	G			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41370072_41370073insG	uc002idn.1	+	9					TMEM106A_uc010why.1_3'UTR|TMEM106A_uc010cze.1_3'UTR|TMEM106A_uc010whz.1_3'UTR	NM_145041	NP_659478	Q96A25	T106A_HUMAN	transmembrane protein 106A							integral to membrane					0		Breast(137;0.0164)		BRCA - Breast invasive adenocarcinoma(366;0.0917)		GTTAGTTttttgtttttttttt	0.218													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	41381913	41381914	+	Intron	INS	-	T	T	rs71220402		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:41381913_41381914insT	uc002ido.2	-						uc010wia.1_RNA					Homo sapiens cDNA clone IMAGE:5169062, partial cds.																		accctgatctatcatcgggagg	0.000													4	2	---	---	---	---	
NFE2L1	4779	broad.mit.edu	37	17	46134236	46134237	+	Intron	INS	-	CT	CT	rs140826056	by1000genomes	TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:46134236_46134237insCT	uc002imz.3	+						NFE2L1_uc002ina.3_Intron|NFE2L1_uc002inb.3_Intron|NFE2L1_uc010wle.1_Intron|NFE2L1_uc010wlf.1_Intron	NM_003204	NP_003195	Q14494	NF2L1_HUMAN	nuclear factor erythroid 2-like 1						anatomical structure morphogenesis|heme biosynthetic process|inflammatory response|transcription from RNA polymerase II promoter	nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription cofactor activity			skin(1)	1						GGACTCTTTCACTCTCTTCTGT	0.550													7	4	---	---	---	---	
SPOP	8405	broad.mit.edu	37	17	47700373	47700373	+	Intron	DEL	T	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:47700373delT	uc010dbk.2	-						SPOP_uc002ipb.2_Intron|SPOP_uc002ipc.2_Intron|SPOP_uc002ipd.2_Intron|SPOP_uc002ipe.2_Intron|SPOP_uc002ipf.2_Intron|SPOP_uc002ipg.2_Intron|SPOP_uc010wlx.1_Intron	NM_003563	NP_003554	O43791	SPOP_HUMAN	speckle-type POZ protein						mRNA processing	nucleus	protein binding			prostate(2)|ovary(2)|lung(2)	6						GGTCCTAAAAttttttttttt	0.194										Prostate(2;0.17)			4	2	---	---	---	---	
ACSF2	80221	broad.mit.edu	37	17	48521998	48521999	+	Intron	DEL	AC	-	-	rs113837683		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48521998_48521999delAC	uc002iqu.2	+						ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron	NM_025149	NP_079425	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2 precursor						fatty acid metabolic process	mitochondrion	ATP binding|ligase activity				0	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CTCTCTGCAAacacacacacac	0.223													4	2	---	---	---	---	
CA10	56934	broad.mit.edu	37	17	50234899	50234899	+	Intron	DEL	G	-	-	rs67822192		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:50234899delG	uc002itw.3	-						CA10_uc002itv.3_Intron|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)			ACCCCCCCCCGCAAAACACAC	0.522													8	4	---	---	---	---	
KIAA1328	57536	broad.mit.edu	37	18	34465500	34465500	+	Intron	DEL	T	-	-	rs33942453		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:34465500delT	uc002kzz.2	+							NM_020776	NP_065827	Q86T90	K1328_HUMAN	hypothetical protein LOC57536											central_nervous_system(1)	1				COAD - Colon adenocarcinoma(74;0.195)		ATGTTAAAGGTTTTTTTTTTT	0.373													4	2	---	---	---	---	
TPRX1	284355	broad.mit.edu	37	19	48305584	48305584	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:48305584delT	uc002php.1	-	2	755	c.684delA	c.(682-684)CCAfs	p.P228fs		NM_198479	NP_940881	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox	228	Gly-rich.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		agattgggcctgggattgggc	0.000													4	2	---	---	---	---	
HSD17B14	51171	broad.mit.edu	37	19	49337748	49337749	+	Intron	INS	-	A	A			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49337748_49337749insA	uc002pkv.1	-						HSD17B14_uc010emk.1_Intron	NM_016246	NP_057330	Q9BPX1	DHB14_HUMAN	dehydrogenase/reductase (SDR family) member 10						steroid catabolic process	centrosome|cytosol	estradiol 17-beta-dehydrogenase activity|protein binding|testosterone 17-beta-dehydrogenase (NADP+) activity				0		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		gaggggctgaggtctggactcc	0.000													4	2	---	---	---	---	
TTLL12	23170	broad.mit.edu	37	22	43568707	43568708	+	Intron	INS	-	T	T	rs76577202		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:43568707_43568708insT	uc003bdq.2	-						TTLL12_uc003bdp.2_5'Flank|TTLL12_uc003bdr.1_Intron	NM_015140	NP_055955	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12						protein modification process		tubulin-tyrosine ligase activity			central_nervous_system(1)	1		Ovarian(80;0.221)|Glioma(61;0.222)				GCTGCAAAGtcttttttttttt	0.277													4	2	---	---	---	---	
TBL1X	6907	broad.mit.edu	37	X	9622195	9622195	+	Intron	DEL	A	-	-			TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:9622195delA	uc010ndq.2	+						TBL1X_uc004csq.3_Intron|TBL1X_uc010ndr.2_Intron|TBL1X_uc004csr.2_Intron	NM_001139466	NP_001132938	O60907	TBL1X_HUMAN	transducin beta-like 1X isoform a						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|sensory perception of sound|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein C-terminus binding|protein domain specific binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			ovary(1)	1		Hepatocellular(5;0.000888)				TAGTCATCTCAAAAAAAAAAA	0.308													10	5	---	---	---	---	
DOCK11	139818	broad.mit.edu	37	X	117761299	117761299	+	Intron	DEL	T	-	-	rs78788801		TCGA-CJ-4902-01A-01D-1429-08	TCGA-CJ-4902-11A-01D-1429-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:117761299delT	uc004eqp.2	+						DOCK11_uc004eqq.2_Intron	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11						blood coagulation	cytosol	GTP binding			ovary(3)	3						TGCTAGTAGCTTTTTTTTTTT	0.318													6	3	---	---	---	---	
