Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
AKR7A3	22977	broad.mit.edu	37	1	19609252	19609252	+	Silent	SNP	A	G	G	rs2995181		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:19609252A>G	uc001bbv.1	-	7	1046	c.969T>C	c.(967-969)ACT>ACC	p.T323T		NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3	323					cellular aldehyde metabolic process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GACATTCGTGAGTAACCAAAT	0.522000													4	47					0	0	0.009096	0	0
TCEB3	6924	broad.mit.edu	37	1	24080638	24080638	+	Missense_Mutation	SNP	G	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:24080638G>A	uc001bho.2	+	6	1724	c.1664G>A	c.(1663-1665)AGA>AAA	p.R555K		NM_003198	NP_003189	Q14241	ELOA1_HUMAN	elongin A	555	Activation domain (By similarity).				positive regulation of viral transcription|regulation of transcription from RNA polymerase II promoter|transcription elongation from RNA polymerase II promoter|viral reproduction	integral to membrane	DNA binding			ovary(1)	1		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		ACTGGGCGCAGAATGAATTCC	0.448000													26	12					0	0	0.005443	0	0
ZNF683	257101	broad.mit.edu	37	1	26691295	26691295	+	Missense_Mutation	SNP	C	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:26691295C>T	uc001bmg.1	-	4	860	c.742G>A	c.(742-744)GCT>ACT	p.A248T	ZNF683_uc001bmh.1_Missense_Mutation_p.A248T|ZNF683_uc009vsj.1_Missense_Mutation_p.A248T	NM_173574	NP_775845	Q8IZ20	ZN683_HUMAN	zinc finger protein 683	248					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		TCCCACCGAGCGCTGGGGTGC	0.642000													50	12					0	0	0.014410	0	0
FLG	2312	broad.mit.edu	37	1	152286155	152286155	+	Missense_Mutation	SNP	C	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:152286155C>T	uc001ezu.1	-	3	1243	c.1207G>A	c.(1207-1209)GGG>AGG	p.G403R	uc001ezv.2_RNA	NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	403	Ser-rich.|Filaggrin 2.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAGCTTGCCCGCGCCCAGTG	0.562000									Ichthyosis				98	416					0	0	0.014410	0	0
ARID4B	51742	broad.mit.edu	37	1	235345098	235345098	+	Missense_Mutation	SNP	T	C	C			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr1:235345098T>C	uc001hwq.2	-	20	3634	c.3136A>G	c.(3136-3138)ACA>GCA	p.T1046A	ARID4B_uc001hwr.2_Missense_Mutation_p.T960A|ARID4B_uc001hws.3_Missense_Mutation_p.T960A|ARID4B_uc001hwp.2_RNA|ARID4B_uc001hwt.3_Missense_Mutation_p.T727A	NM_016374	NP_057458	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B isoform 1	1046					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding			ovary(2)|lung(1)	3	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TCTGATACTGTTACAGAAGAC	0.473000													23	42					0	0	0.014323	0	0
CCDC6	8030	broad.mit.edu	37	10	61666054	61666054	+	Silent	SNP	A	C	C			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr10:61666054A>C	uc001jks.3	-	1	765	c.129T>G	c.(127-129)GGT>GGG	p.G43G		NM_005436	NP_005427	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	43	Poly-Gly.					cytoplasm|cytoskeleton	SH3 domain binding|structural constituent of cytoskeleton			ovary(3)|breast(1)	4				Kidney(211;0.0597)		CCGACTTCccaccgccgccgc	0.537000													16	68					0	0	0.010771	0	0
FUT4	2526	broad.mit.edu	37	11	94278274	94278274	+	Silent	SNP	C	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr11:94278274C>T	uc001pez.2	+	1	1258	c.975C>T	c.(973-975)GAC>GAT	p.D325D	PIWIL4_uc010rue.1_Intron|PIWIL4_uc009ywk.1_5'Flank	NM_002033	NP_002024	P22083	FUT4_HUMAN	fucosyltransferase 4	325	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane|membrane fraction	alpha(1,3)-fucosyltransferase activity			skin(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CGGACTCGGACGTCTTTGTGC	0.647000													23	39					0	0	0.005443	0	0
TRPC6	7225	broad.mit.edu	37	11	101342947	101342947	+	Missense_Mutation	SNP	C	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr11:101342947C>A	uc001pgk.3	-	8	2551	c.2126G>T	c.(2125-2127)GGA>GTA	p.G709V	TRPC6_uc009ywy.2_Missense_Mutation_p.G593V|TRPC6_uc009ywz.1_Missense_Mutation_p.G654V	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	709	Helical; (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			skin(2)|ovary(1)|central_nervous_system(1)	4		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)		BRCA - Breast invasive adenocarcinoma(274;0.0442)		ATTATAGACTCCATAAAGAAC	0.328000													6	77					3.59834e-05	3.72918e-05	0.001168	1	0
PRICKLE1	144165	broad.mit.edu	37	12	42860093	42860093	+	Silent	SNP	T	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr12:42860093T>A	uc010skv.1	-	6	965	c.678A>T	c.(676-678)GGA>GGT	p.G226G	PRICKLE1_uc001rnl.2_Silent_p.G226G|PRICKLE1_uc010skw.1_Silent_p.G226G|PRICKLE1_uc001rnm.2_Silent_p.G226G	NM_001144881	NP_001138353	Q96MT3	PRIC1_HUMAN	prickle homolog 1	226	LIM zinc-binding 2.				negative regulation of canonical Wnt receptor signaling pathway|negative regulation of cardiac muscle cell myoblast differentiation|negative regulation of transcription, DNA-dependent|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein import into nucleus	cytosol|nuclear membrane	zinc ion binding			ovary(3)|skin(1)	4	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		ACCTCTGTCCTCCCAGGACCG	0.488000													9	83					0	0	0.006214	0	0
PSPC1	55269	broad.mit.edu	37	13	20279844	20279844	+	Silent	SNP	G	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr13:20279844G>A	uc001uml.2	-	8	1530	c.1344C>T	c.(1342-1344)GCC>GCT	p.A448A	PSPC1_uc001umj.1_Intron|PSPC1_uc001umk.1_Intron	NM_001042414	NP_001035879	Q8WXF1	PSPC1_HUMAN	paraspeckle protein 1	448	Gly-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nuclear matrix|nucleolus	nucleotide binding|protein binding|RNA binding			breast(1)	1		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		CCATATTTGCGGCTCCTTCTG	0.438000													12	29					0	0	0.003954	0	0
GPR68	8111	broad.mit.edu	37	14	91700786	91700786	+	Silent	SNP	C	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr14:91700786C>T	uc001xzg.2	-	2	950	c.609G>A	c.(607-609)GCG>GCA	p.A203A	GPR68_uc001xzh.2_Silent_p.A213A	NM_003485	NP_003476	Q15743	OGR1_HUMAN	G protein-coupled receptor 68	203	Helical; Name=5; (Potential).				inflammatory response	integral to plasma membrane	G-protein coupled receptor activity			kidney(1)	1		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		CCTGGTAGGACGCCAGCAGCA	0.652000													4	23					0	0	0.000602	0	0
ITGAL	3683	broad.mit.edu	37	16	30485546	30485546	+	Missense_Mutation	SNP	C	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr16:30485546C>T	uc002dyi.3	+	2	267	c.91C>T	c.(91-93)CGG>TGG	p.R31W	ITGAL_uc010veu.1_RNA|ITGAL_uc002dyj.3_Missense_Mutation_p.R31W|ITGAL_uc010vev.1_Missense_Mutation_p.R31W	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	31	FG-GAP 1.|Extracellular (Potential).				blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|lung(3)|central_nervous_system(3)|breast(1)	10					Efalizumab(DB00095)	CCTGGACGTGCGGGGCGCGCG	0.706000													13	19					0	0	0.002450	0	0
SCARF1	8578	broad.mit.edu	37	17	1538682	1538682	+	Silent	SNP	C	G	G	rs139029063	byFrequency	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr17:1538682C>G	uc002fsz.1	-	11	1913	c.1863G>C	c.(1861-1863)CGG>CGC	p.R621R	SCARF1_uc002fsy.1_3'UTR|SCARF1_uc002fta.1_RNA|SCARF1_uc010cjv.1_Silent_p.R535R	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1	621	Cytoplasmic (Potential).				cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ACTGCGCCCCCCGGGAGAGCC	0.677000													7	81					0	0	0.001984	0	0
SPNS3	201305	broad.mit.edu	37	17	4348380	4348380	+	Nonsense_Mutation	SNP	C	T	T	rs150923668	byFrequency	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr17:4348380C>T	uc002fxt.2	+	3	363	c.319C>T	c.(319-321)CGA>TGA	p.R107*	SPNS3_uc002fxu.2_Intron	NM_182538	NP_872344	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3	107					lipid transport|transmembrane transport	integral to membrane				large_intestine(1)	1						CCTGGGCGACCGACATAGCCG	0.617000													11	217					0	0	0.008291	0	0
MED1	5469	broad.mit.edu	37	17	37565972	37565972	+	Silent	SNP	T	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr17:37565972T>A	uc002hrv.3	-	17	2714	c.2502A>T	c.(2500-2502)CCA>CCT	p.P834P	MED1_uc010wee.1_Silent_p.P662P|MED1_uc002hru.2_Intron	NM_004774	NP_004765	Q15648	MED1_HUMAN	mediator complex subunit 1	834	Interaction with ESR1.				androgen biosynthetic process|androgen receptor signaling pathway|cellular lipid metabolic process|fat cell differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription initiation from RNA polymerase II promoter	mediator complex	DNA binding|estrogen receptor binding|ligand-dependent nuclear receptor binding|ligand-dependent nuclear receptor transcription coactivator activity|peroxisome proliferator activated receptor binding|receptor activity|retinoic acid receptor binding|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			lung(2)|ovary(2)|breast(1)|skin(1)|kidney(1)|pancreas(1)	8		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		GATCAGTGTATGGATTTTCAT	0.433000										HNSCC(31;0.082)			11	64					0	0	0.008291	0	0
KCNH6	81033	broad.mit.edu	37	17	61619698	61619698	+	Missense_Mutation	SNP	A	G	G	rs150234573	byFrequency	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr17:61619698A>G	uc002jay.2	+	9	2131	c.2051A>G	c.(2050-2052)AAG>AGG	p.K684R	KCNH6_uc010wpl.1_Missense_Mutation_p.K561R|KCNH6_uc010wpm.1_Missense_Mutation_p.K684R|KCNH6_uc002jaz.1_Missense_Mutation_p.K631R	NM_030779	NP_110406	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H,	684	cNMP.|Cytoplasmic (Potential).				regulation of transcription, DNA-dependent|signal transduction					skin(1)	1					Ibutilide(DB00308)	GACCTGCACAAGATCCAGCGG	0.602000													7	80					0	0	0.001984	0	0
SMURF2	64750	broad.mit.edu	37	17	62574689	62574689	+	Missense_Mutation	SNP	T	C	C			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr17:62574689T>C	uc002jep.1	-	9	1166	c.778A>G	c.(778-780)AGG>GGG	p.R260G	SMURF2_uc002jeq.1_Missense_Mutation_p.R19G|SMURF2_uc002jer.1_Missense_Mutation_p.R19G	NM_022739	NP_073576	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	260	WW 2.			Missing: Abolishes interaction with SMAD2 and SMAD7.	BMP signaling pathway|negative regulation of transcription, DNA-dependent|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of transforming growth factor beta receptor signaling pathway|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent SMAD protein catabolic process	cytosol|membrane raft|nucleus|plasma membrane|ubiquitin ligase complex	identical protein binding|SMAD binding|ubiquitin-protein ligase activity			skin(3)|lung(1)	4	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			TGCGTTGTCCTCTGTTCTGTA	0.373000													21	13					0	0	0.012319	0	0
Unknown	0	broad.mit.edu	37	19	15881909	15881909	+	RNA	SNP	A	G	G	rs4807985	by1000genomes	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:15881909A>G	uc002nbo.2	-	6		c.989T>C			uc010xor.1_Silent_p.D156D					Homo sapiens cDNA FLJ60024 complete cds, highly similar to Cytochrome P450 4F12 (EC 1.14.14.1).																		GGATGACGGCATCTGTGAAGT	0.537000													6	81					0	0	0.001984	0	0
ZNF99	7652	broad.mit.edu	37	19	22940429	22940429	+	Missense_Mutation	SNP	C	G	G			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:22940429C>G	uc010xrh.1	-	5	2009	c.2009G>C	c.(2008-2010)TGC>TCC	p.C670S		NM_001080409	NP_001073878			zinc finger protein 99											ovary(1)|skin(1)	2		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTCACATTTGCAGGGTTTCTC	0.358000													4	22					0	0	0.001984	0	0
FCGBP	8857	broad.mit.edu	37	19	40430499	40430499	+	Missense_Mutation	SNP	T	G	G			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:40430499T>G	uc002omp.3	-	3	1452	c.1444A>C	c.(1444-1446)ACC>CCC	p.T482P		NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein precursor	482	VWFD 1.					extracellular region	protein binding			ovary(4)|skin(4)|central_nervous_system(1)	9	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCGTCGAAGGTGGTGTAATGG	0.692000													3	8					0	0	0.004672	0	0
CIC	23152	broad.mit.edu	37	19	42796331	42796331	+	Nonsense_Mutation	SNP	C	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:42796331C>T	uc002otf.1	+	12	3020	c.2980C>T	c.(2980-2982)CAG>TAG	p.Q994*		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	994	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)|lung(1)|central_nervous_system(1)|skin(1)	11		Prostate(69;0.00682)				CTCTCAGCCTCAGAAGGTCCT	0.662000			T	DUX4	soft tissue sarcoma								23	42					0	0	0.003954	0	0
TPO	7173	broad.mit.edu	37	2	1491722	1491722	+	Missense_Mutation	SNP	C	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:1491722C>A	uc002qww.2	+	10	1818	c.1727C>A	c.(1726-1728)GCG>GAG	p.A576E	TPO_uc010ewj.2_Intron|TPO_uc002qwu.2_Intron|TPO_uc002qwr.2_Missense_Mutation_p.A576E|TPO_uc002qwx.2_Intron|TPO_uc010yio.1_Missense_Mutation_p.A403E|TPO_uc010yip.1_Missense_Mutation_p.A576E|TPO_uc002qwy.1_Intron|TPO_uc002qwz.2_Intron	NM_000547	NP_000538	P07202	PERT_HUMAN	thyroid peroxidase isoform a	576	Extracellular (Potential).				cellular nitrogen compound metabolic process|hormone biosynthetic process|hydrogen peroxide catabolic process	cell surface|cytoplasm|integral to plasma membrane	calcium ion binding|heme binding|iodide peroxidase activity	p.A576E(1)		ovary(7)|pancreas(6)|skin(5)|lung(1)|kidney(1)	20	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TTGGATCTGGCGTCCATCAAC	0.592000													33	52					1.45844e-13	1.56851e-13	0.013726	1	0
LOC401010	401010	broad.mit.edu	37	2	132201718	132201718	+	Missense_Mutation	SNP	T	C	C	rs2001215	by1000genomes	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:132201718T>C	uc002tst.2	-	1	750	c.284A>G	c.(283-285)CAT>CGT	p.H95R		NR_002826				SubName: Full=cDNA FLJ12694 fis, clone NT2RP1000358, highly similar to Homo sapiens mRNA; cDNA DKFZp564C186 (from clone DKFZp564C186);												0						GATGTCCACATGGAGCTTCCC	0.597000													4	17					0	0	0.009096	0	0
MBD5	55777	broad.mit.edu	37	2	149227787	149227787	+	Missense_Mutation	SNP	G	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:149227787G>A	uc002twm.3	+	9	3263	c.2275G>A	c.(2275-2277)GTG>ATG	p.V759M	MBD5_uc010zbs.1_RNA|MBD5_uc010fns.2_Missense_Mutation_p.V759M|MBD5_uc002twn.1_Missense_Mutation_p.V200M	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	759						chromosome|nucleus	chromatin binding|DNA binding			skin(3)|ovary(2)	5				BRCA - Breast invasive adenocarcinoma(221;0.0569)		AGGGGAAGCCGTGCACTGCCA	0.448000													35	40					0	0	0.003271	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	T	T	rs121913500		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:209113112C>T	uc002vcs.2	-	4	641	c.395G>A	c.(394-396)CGT>CAT	p.R132H	IDH1_uc002vct.2_Missense_Mutation_p.R132H|IDH1_uc002vcu.2_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	132		Substrate.	R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).		2-oxoglutarate metabolic process|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(2023)|p.R132C(344)|p.R132?(210)|p.R132G(117)|p.R132S(79)|p.R132L(58)|p.R132V(1)|p.G131_R132>VL(1)		central_nervous_system(2156)|haematopoietic_and_lymphoid_tissue(606)|bone(74)|thyroid(22)|large_intestine(4)|skin(2)|prostate(2)|autonomic_ganglia(1)|soft_tissue(1)	2868				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma 								27	36					0	0	0.005443	0	0
FAM124B	79843	broad.mit.edu	37	2	225266211	225266211	+	Missense_Mutation	SNP	G	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr2:225266211G>A	uc002vnx.2	-	1	501	c.275C>T	c.(274-276)TCG>TTG	p.S92L	FAM124B_uc002vnw.2_Missense_Mutation_p.S92L	NM_001122779	NP_001116251	Q9H5Z6	F124B_HUMAN	hypothetical protein LOC79843 isoform a	92							protein binding			ovary(2)	2		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		CTGCCATGGCGAATGCTGGAG	0.582000													14	19					0	0	0.002450	0	0
CYP2D7P1	1564	broad.mit.edu	37	22	42537597	42537597	+	Missense_Mutation	SNP	A	G	G	rs1800754	by1000genomes	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr22:42537597A>G	uc003bci.2	-	6	1043	c.662T>C	c.(661-663)TTG>TCG	p.L221S	CYP2D7P1_uc003bcg.2_5'UTR|CYP2D7P1_uc003bch.2_Intron|CYP2D7P1_uc010gyv.2_Missense_Mutation_p.L5S|CYP2D7P1_uc010gyw.2_RNA|CYP2D7P1_uc010gyx.1_Missense_Mutation_p.L221S	NR_002570				SubName: Full=Cytochrome P450 2D6;          EC=1.14.14.1;												0						CAGCGTGGTCAAGGTGGTCAC	0.627000													3	26					0	0	0.009096	0	0
COL7A1	1294	broad.mit.edu	37	3	48609570	48609570	+	Missense_Mutation	SNP	C	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr3:48609570C>T	uc003ctz.2	-	90	7014	c.7013G>A	c.(7012-7014)CGA>CAA	p.R2338Q		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	2338	Triple-helical region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(3)|central_nervous_system(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CTTCTCGCCTCGCGGCCCTGG	0.612000													15	26					0	0	0.004007	0	0
UBA7	7318	broad.mit.edu	37	3	49848836	49848836	+	Missense_Mutation	SNP	C	T	T	rs12486358		TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr3:49848836C>T	uc003cxr.2	-	9	1163	c.992G>A	c.(991-993)CGG>CAG	p.R331Q		NM_003335	NP_003326	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	331	2 approximate repeats.				ISG15-protein conjugation|negative regulation of type I interferon production	cytosol	ATP binding|ISG15 activating enzyme activity|ligase activity			ovary(1)|pancreas(1)	2				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		ttccTCTGTCCGCTTCAGTGG	0.522000													5	23					0	0	0.000602	0	0
TLR1	7096	broad.mit.edu	37	4	38799099	38799099	+	Missense_Mutation	SNP	G	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr4:38799099G>A	uc003gtl.2	-	4	1628	c.1354C>T	c.(1354-1356)CTT>TTT	p.L452F		NM_003263	NP_003254	Q15399	TLR1_HUMAN	toll-like receptor 1 precursor	452	Extracellular (Potential).|LRR 10.				cellular response to triacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|inflammatory response|innate immune response|macrophage activation|positive regulation of interleukin-6 biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	integral to plasma membrane|phagocytic vesicle membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	protein heterodimerization activity|transmembrane receptor activity			lung(2)|skin(2)|prostate(1)	5						TTGCTGTGAAGATCAAGTACC	0.338000													6	62					0	0	0.001168	0	0
GABRA4	2557	broad.mit.edu	37	4	46979112	46979112	+	Missense_Mutation	SNP	C	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr4:46979112C>T	uc003gxg.2	-	5	682	c.543G>A	c.(541-543)ATG>ATA	p.M181I		NM_000809	NP_000800	P48169	GBRA4_HUMAN	gamma-aminobutyric acid A receptor, alpha 4	181	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|upper_aerodigestive_tract(1)|breast(1)	4					Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	CATGACCATCCATGGGAAAAT	0.333000													10	34					0	0	0.013537	0	0
CLOCK	9575	broad.mit.edu	37	4	56301648	56301648	+	Silent	SNP	T	C	C			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr4:56301648T>C	uc003haz.1	-	24	3401	c.2475A>G	c.(2473-2475)CAA>CAG	p.Q825Q	CLOCK_uc003hba.1_Silent_p.Q825Q|CLOCK_uc010igu.1_RNA	NM_004898	NP_004889	O15516	CLOCK_HUMAN	clock	825	Poly-Gln.				circadian rhythm|photoperiodism|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|transcription factor complex	DNA binding|histone acetyltransferase activity|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(2)|ovary(1)	3	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			GTTGCTGCTGTTGCTGAGACT	0.527000													43	62					0	0	0.009718	0	0
NPFFR2	10886	broad.mit.edu	37	4	72994632	72994632	+	Silent	SNP	A	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr4:72994632A>T	uc003hgg.2	+	2	728	c.630A>T	c.(628-630)ATA>ATT	p.I210I	NPFFR2_uc010iig.1_Intron|NPFFR2_uc003hgi.2_Silent_p.I111I|NPFFR2_uc003hgh.2_Silent_p.I108I	NM_004885	NP_004876	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2 isoform 1	210	Extracellular (Potential).				detection of abiotic stimulus	actin cytoskeleton|integral to plasma membrane	neuropeptide receptor activity			ovary(2)|central_nervous_system(1)	3			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			ACAATATTATAGCAGGTATGT	0.368000													29	31					0	0	0.005443	0	0
MARCH6	10299	broad.mit.edu	37	5	10426541	10426541	+	Missense_Mutation	SNP	A	T	T			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr5:10426541A>T	uc003jet.1	+	24	2596	c.2413A>T	c.(2413-2415)ATT>TTT	p.I805F	MARCH6_uc011cmu.1_Missense_Mutation_p.I757F|MARCH6_uc003jeu.1_Missense_Mutation_p.I503F|MARCH6_uc011cmv.1_Missense_Mutation_p.I700F	NM_005885	NP_005876	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6	805	Cytoplasmic (Potential).				protein K48-linked ubiquitination	integral to endoplasmic reticulum membrane	ubiquitin conjugating enzyme binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(1)|breast(1)	2						CCTTCACTATATTGTTCGTAA	0.403000													10	152					0	0	0.008291	0	0
SYNE1	23345	broad.mit.edu	37	6	152665261	152665261	+	Missense_Mutation	SNP	C	A	A	rs4645434	byFrequency	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr6:152665261C>A	uc010kiw.2	-	74	12782	c.12180G>T	c.(12178-12180)GAG>GAT	p.E4060D	SYNE1_uc003qot.3_Missense_Mutation_p.E3989D|SYNE1_uc003qou.3_Missense_Mutation_p.E4060D|SYNE1_uc010kja.1_Missense_Mutation_p.E765D	NM_182961	NP_892006	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4060	Cytoplasmic (Potential).				cell death|cytoskeletal anchoring at nuclear membrane|Golgi organization|muscle cell differentiation|nuclear matrix anchoring at nuclear membrane	cytoskeleton|Golgi apparatus|integral to membrane|nuclear outer membrane|postsynaptic membrane|sarcomere|SUN-KASH complex	actin binding|lamin binding	p.E4060D(1)		central_nervous_system(15)|upper_aerodigestive_tract(9)|ovary(8)|skin(6)|large_intestine(5)|pancreas(2)	45		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GAGGACTTGGCTCTAAATCCG	0.453000										HNSCC(10;0.0054)			7	100					5.18039e-06	5.46819e-06	0.003080	1	0
MUC17	140453	broad.mit.edu	37	7	100678653	100678653	+	Missense_Mutation	SNP	C	T	T	rs144372503	byFrequency	TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr7:100678653C>T	uc003uxp.1	+	3	4009	c.3956C>T	c.(3955-3957)CCT>CTT	p.P1319L	MUC17_uc010lho.1_RNA	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17 precursor	1319	Extracellular (Potential).|20.|59 X approximate tandem repeats.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|skin(8)|breast(3)|lung(2)	27	Lung NSC(181;0.136)|all_lung(186;0.182)					AGTTCATCTCCTACACCTGCT	0.478000													24	300					0	0	0.014323	0	0
CLU	1191	broad.mit.edu	37	8	27472227	27472227	+	Silent	SNP	A	G	G			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr8:27472227A>G	uc003xfz.1	-	1	101	c.72T>C	c.(70-72)AGT>AGC	p.S24S		NM_001831	NP_001822	P10909	CLUS_HUMAN	clusterin isoform 1	Error:Variant_position_missing_in_P10909_after_alignment					chaperone-mediated protein folding|complement activation, classical pathway|innate immune response|lipid metabolic process|negative regulation of apoptosis|negative regulation of protein homooligomerization|platelet activation|platelet degranulation|positive regulation of NF-kappaB transcription factor activity|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|protein stabilization|response to misfolded protein|response to virus|reverse cholesterol transport	chromaffin granule|cytosol|endoplasmic reticulum|microsome|mitochondrial membrane|nucleus|perinuclear region of cytoplasm|platelet alpha granule lumen|spherical high-density lipoprotein particle	misfolded protein binding|ubiquitin protein ligase binding			ovary(2)	2		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		CGTTGTGGGCACTGGGAGGCG	0.652000											OREG0018671	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	60	72					0	0	0.014410	0	0
ZNF618	114991	broad.mit.edu	37	9	116811917	116811917	+	Missense_Mutation	SNP	G	A	A			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr9:116811917G>A	uc004bid.2	+	15	2434	c.2335G>A	c.(2335-2337)GGC>AGC	p.G779S	ZNF618_uc004bic.2_Missense_Mutation_p.G686S|ZNF618_uc011lxi.1_Missense_Mutation_p.G746S|ZNF618_uc011lxj.1_Missense_Mutation_p.G747S|ZNF618_uc010mvb.2_Missense_Mutation_p.G369S	NM_133374	NP_588615	Q5T7W0	ZN618_HUMAN	zinc finger protein 618	779					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						CAACGACGCAGGCACTGTCAG	0.627000													6	81					0	0	0.001984	0	0
MAGEA12	4111	broad.mit.edu	37	X	151896231	151896231	+	RNA	SNP	A	G	G			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chrX:151896231A>G	uc004fgb.2	-	4		c.536T>C						P43365	MAGAC_HUMAN	Homo sapiens melanoma antigen family A, 12, mRNA (cDNA clone MGC:4914 IMAGE:3450217), complete cds.											skin(1)	1	Acute lymphoblastic leukemia(192;6.56e-05)					GAGTGGCTGGATAGTGTTGGC	0.517000													3	12					0	0	0.002450	0	0
PRPF18	8559	broad.mit.edu	37	10	13655742	13655744	+	In_Frame_Del	DEL	TTC	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr10:13655742_13655744delTTC	uc001imp.2	+	7	729_731	c.581_583delTTC	c.(580-585)TTTCTT>TTT	p.L196del	PRPF18_uc001imq.2_Intron	NM_003675	NP_003666	Q99633	PRP18_HUMAN	PRP18 pre-mRNA processing factor 18 homolog	196					mRNA processing|RNA splicing	nuclear speck|spliceosomal complex				central_nervous_system(1)	1						TTTCAACAGTTTCTTCTTGGCGT	0.429													10	55	---	---	---	---					
NCAM1	4684	broad.mit.edu	37	11	113126648	113126649	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr11:113126648_113126649delCT	uc001pns.2	+	1	50_51	c.18_19delCT	c.(16-21)AACTCTfs	p.N6fs				P13591	NCAM1_HUMAN	SubName: Full=cDNA FLJ52974, highly similar to Neural cell adhesion molecule 1, 140 kDa isoform;	626_627	Extracellular (Potential).|Fibronectin type-III 2.				axon guidance|interferon-gamma-mediated signaling pathway	anchored to membrane|extracellular region|Golgi membrane|integral to membrane				ovary(1)	1		all_cancers(61;5.82e-19)|all_epithelial(67;6.87e-12)|Melanoma(852;1.99e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;0.00119)|Breast(348;0.0109)|all_neural(223;0.0299)|Medulloblastoma(222;0.0458)|Renal(330;0.198)|Prostate(24;0.207)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.000114)|all cancers(92;0.000467)|OV - Ovarian serous cystadenocarcinoma(223;0.212)		AGGATGGAAACTCTATTAAAGT	0.500													8	16	---	---	---	---					
MON2	23041	broad.mit.edu	37	12	62965290	62965292	+	In_Frame_Del	DEL	CTT	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr12:62965290_62965292delCTT	uc001sre.2	+	30	4833_4835	c.4442_4444delCTT	c.(4441-4446)GCTTCT>GCT	p.S1483del	MON2_uc009zqj.2_In_Frame_Del_p.S1483del|MON2_uc010ssl.1_In_Frame_Del_p.S1411del|MON2_uc010ssm.1_In_Frame_Del_p.S1454del|MON2_uc010ssn.1_In_Frame_Del_p.S1477del|MON2_uc001srf.2_In_Frame_Del_p.S1246del|MON2_uc001srg.2_In_Frame_Del_p.S352del	NM_015026	NP_055841	Q7Z3U7	MON2_HUMAN	MON2 homolog	1484					Golgi to endosome transport|protein transport	cytoplasm	ARF guanyl-nucleotide exchange factor activity|binding			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		CGGCAGCATGCTTCTTCTGGAAA	0.399													7	84	---	---	---	---					
ZMYM2	7750	broad.mit.edu	37	13	20577051	20577052	+	Frame_Shift_Del	DEL	TT	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr13:20577051_20577052delTT	uc001umr.2	+	5	1207_1208	c.909_910delTT	c.(907-912)TCTTTAfs	p.S303fs	ZMYM2_uc001umq.2_Frame_Shift_Del_p.S216fs|ZMYM2_uc001ums.2_Frame_Shift_Del_p.S303fs|ZMYM2_uc001umt.2_Frame_Shift_Del_p.S303fs|ZMYM2_uc009zzn.1_Frame_Shift_Del_p.S238fs	NM_003453	NP_003444	Q9UBW7	ZMYM2_HUMAN	zinc finger protein 198	303_304				L -> V (in Ref. 4; CAB66556).	regulation of transcription, DNA-dependent|transcription, DNA-dependent	PML body	ubiquitin conjugating enzyme binding|zinc ion binding			lung(3)|ovary(2)|prostate(1)	6		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		GGGTGGACTCTTTATCACCAGT	0.421													76	82	---	---	---	---					
TCF12	6938	broad.mit.edu	37	15	57526268	57526269	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr15:57526268_57526269delCA	uc002aec.2	+	12	1282_1283	c.998_999delCA	c.(997-999)TCAfs	p.S333fs	TCF12_uc010ugm.1_Frame_Shift_Del_p.S385fs|TCF12_uc010ugn.1_Frame_Shift_Del_p.S329fs|TCF12_uc002aea.2_Frame_Shift_Del_p.S333fs|TCF12_uc010bfs.2_Intron|TCF12_uc002aeb.2_Frame_Shift_Del_p.S333fs|TCF12_uc002aed.2_Frame_Shift_Del_p.S333fs|TCF12_uc002aee.2_Frame_Shift_Del_p.S163fs|TCF12_uc010bft.2_Frame_Shift_Del_p.S163fs|TCF12_uc010ugo.1_Frame_Shift_Del_p.S97fs	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b	333					immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GCTGGAAGCTCACAGACAGGTG	0.356			T	TEC	extraskeletal myxoid chondrosarcoma								7	42	---	---	---	---					
TCF12	6938	broad.mit.edu	37	15	57565414	57565416	+	In_Frame_Del	DEL	TCA	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr15:57565414_57565416delTCA	uc002aec.2	+	18	2144_2146	c.1860_1862delTCA	c.(1858-1863)CTTCAT>CTT	p.H621del	TCF12_uc010ugm.1_In_Frame_Del_p.H673del|TCF12_uc010ugn.1_In_Frame_Del_p.H641del|TCF12_uc002aea.2_In_Frame_Del_p.H645del|TCF12_uc010bfs.2_In_Frame_Del_p.H42del|TCF12_uc002aeb.2_In_Frame_Del_p.H645del|TCF12_uc002aed.2_In_Frame_Del_p.H621del|TCF12_uc002aee.2_In_Frame_Del_p.H451del|TCF12_uc010bft.2_In_Frame_Del_p.H475del|TCF12_uc010ugo.1_In_Frame_Del_p.H385del|TCF12_uc010ugp.1_In_Frame_Del_p.H278del|TCF12_uc010ugq.1_In_Frame_Del_p.H255del|TCF12_uc010ugr.1_In_Frame_Del_p.H234del	NM_207038	NP_996921	Q99081	HTF4_HUMAN	transcription factor 12 isoform b	621	Helix-loop-helix motif.				immune response|muscle organ development|regulation of transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(5)|ovary(2)|lung(1)	8		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		TCCTTATTCTTCATCAAGCCGTG	0.448			T	TEC	extraskeletal myxoid chondrosarcoma								19	22	---	---	---	---					
DOCK6	57572	broad.mit.edu	37	19	11364342	11364342	+	Frame_Shift_Del	DEL	G	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:11364342delG	uc002mqs.3	-	2	146	c.105delC	c.(103-105)TCCfs	p.S35fs		NM_020812	NP_065863	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	35					blood coagulation	cytosol	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(2)|skin(1)	3						AGCGCCTGCTGGAGTGGGGGG	0.662													2	4	---	---	---	---					
CCDC123	84902	broad.mit.edu	37	19	33392289	33392292	+	Frame_Shift_Del	DEL	CTTT	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr19:33392289_33392292delCTTT	uc002nty.2	-	15	1681_1684	c.1592_1595delAAAG	c.(1591-1596)GAAAGGfs	p.E531fs	CCDC123_uc002ntx.2_Frame_Shift_Del_p.E284fs|CCDC123_uc010edg.2_RNA	NM_032816	NP_116205	Q96ST8	CEP89_HUMAN	coiled-coil domain containing 123	531_532	Potential.					centrosome|spindle pole					0	Esophageal squamous(110;0.137)					CATCTCAGCCCTTTCTTTCTCTTC	0.451													35	58	---	---	---	---					
SYCP2L	221711	broad.mit.edu	37	6	10955433	10955436	+	Frame_Shift_Del	DEL	AAGA	-	-			TCGA-HT-7875-01A-11D-2395-08	TCGA-HT-7875-10A-01D-2396-08									Somatic	Phase_I	Capture				Illumina GAIIx	e4c82b3e-cb3a-4e3b-8805-09887d6cf639	3b415304-5b67-40c9-96a3-45e5731b194c	g.chr6:10955433_10955436delAAGA	uc003mzo.2	+	24	2335_2338	c.2039_2042delAAGA	c.(2038-2043)GAAGAAfs	p.E680fs	SYCP2L_uc010jow.2_Frame_Shift_Del_p.E300fs	NM_001040274	NP_001035364	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	680_681						nucleus				ovary(1)|skin(1)	2	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TCAATAACAGAAGAAAGAGAGTTG	0.451											OREG0017189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	15	67	---	---	---	---					
