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
PRAMEF11	440560	broad.mit.edu	37	1	12885289	12885289	+	Silent	SNP	G	G	T	rs148273194	by1000genomes	TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:12885289G>T	uc001auk.2	-	3	1018	c.822C>A	c.(820-822)ctC>ctA	p.L274L		NM_001146344	NP_001139816	O60813	PRA11_HUMAN	Homo sapiens PRAME family member 11 (PRAMEF11), mRNA.	274								p.L274L(6)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						GGCACTGGGAGAGATGCTTCA	0.458												
KTI12	112970	broad.mit.edu	37	1	52498511	52498511	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:52498511C>T	uc001ctj.1	-	0	962	c.923G>A	c.(922-924)cGg>cAg	p.R308Q	TXNDC12_uc001cti.3_Intron	NM_138417	NP_612426	Q96EK9	KTI12_HUMAN	Homo sapiens KTI12 homolog, chromatin associated (S. cerevisiae) (KTI12), mRNA.	308							ATP binding			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)|urinary_tract(1)	12						CCGGGTAAACCGCAAGTGCTC	0.552												
CACHD1	57685	broad.mit.edu	37	1	65141094	65141094	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:65141094C>T	uc001dbo.1	+	19	2690	c.2585C>T	c.(2584-2586)aCg>aTg	p.T862M	CACHD1_uc001dbp.1_Missense_Mutation_p.T617M|CACHD1_uc001dbq.1_Missense_Mutation_p.T617M|CACHD1_uc010opa.1_Missense_Mutation_p.T106M	NM_020925	NP_065976	Q5VU97	CAHD1_HUMAN	Homo sapiens cache domain containing 1 (CACHD1), mRNA.	913					calcium ion transport	integral to membrane				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GGGGATTTGACGAACCTTGTG	0.463											OREG0013544	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
RPF1	80135	broad.mit.edu	37	1	84961638	84961638	+	Nonsense_Mutation	SNP	C	C	G			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:84961638C>G	uc001djv.4	+	6	818	c.773C>G	c.(772-774)tCa>tGa	p.S258*		NM_025065	NP_079341	Q9H9Y2	RPF1_HUMAN	Homo sapiens ribosome production factor 1 homolog (S. cerevisiae) (RPF1), mRNA.	258	Brix.				rRNA processing|translation	nucleolus	aminoacyl-tRNA ligase activity|ATP binding|rRNA binding			breast(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(2)|prostate(1)	14						CTGGGTCATTCAATTGGACGT	0.373												
ODF2L	57489	broad.mit.edu	37	1	86851250	86851250	+	Missense_Mutation	SNP	T	T	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:86851250T>A	uc001dll.2	-	2	499	c.137A>T	c.(136-138)gAa>gTa	p.E46V	ODF2L_uc001dlp.3_Missense_Mutation_p.E46V|ODF2L_uc010osg.2_Missense_Mutation_p.E46V|ODF2L_uc001dlm.2_Missense_Mutation_p.E46V|ODF2L_uc021opg.1_Intron|ODF2L_uc001dlq.2_Intron|ODF2L_uc009wcr.2_Intron	NM_001007022	NP_001007023	Q9ULJ1	ODF2L_HUMAN	Homo sapiens outer dense fiber of sperm tails 2-like (ODF2L), transcript variant 2, mRNA.	46						centrosome				endometrium(2)|kidney(2)|large_intestine(10)|lung(6)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	24				all cancers(265;0.0313)|Epithelial(280;0.0611)		TTCAGTCTTTTCATTTAGAAT	0.343												
S100A7L2	645922	broad.mit.edu	37	1	153409549	153409549	+	Silent	SNP	G	G	A	rs140750285		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:153409549G>A	uc010pdx.2	-	2	402	c.324C>T	c.(322-324)tcC>tcT	p.S108S		NM_001045479	NP_001038944			Homo sapiens S100 calcium binding protein A7-like 2 (S100A7L2), mRNA.											NS(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	8	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGCTTCCCCCGGAACAGGGTG	0.488												
ZP4	57829	broad.mit.edu	37	1	238048511	238048511	+	Missense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:238048511A>C	uc001hym.3	-	8	1552	c.1265T>G	c.(1264-1266)tTc>tGc	p.F422C	LOC100130331_uc010pyc.2_Intron	NM_021186	NP_067009	Q12836	ZP4_HUMAN	Homo sapiens zona pellucida glycoprotein 4 (ZP4), mRNA.	422	ZP.				acrosomal vesicle exocytosis|negative regulation of binding of sperm to zona pellucida|positive regulation of acrosome reaction|positive regulation of humoral immune response|positive regulation of protein kinase activity|positive regulation of T cell proliferation|protein kinase A signaling cascade|protein kinase C signaling cascade	integral to membrane|intracellular|plasma membrane|proteinaceous extracellular matrix	acrosin binding|receptor activity			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CACAAAGCTGAAGGTGAAGAT	0.537												
OR2G6	391211	broad.mit.edu	37	1	248685273	248685273	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr1:248685273C>T	uc001ien.1	+	0	326	c.326C>T	c.(325-327)tCg>tTg	p.S109L		NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	Homo sapiens olfactory receptor, family 2, subfamily G, member 6 (OR2G6), mRNA.	109					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.S109L(2)		NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGGTTGGGCTCGTCTGAGTGT	0.547												
ZNF37A	7587	broad.mit.edu	37	10	38407548	38407548	+	Missense_Mutation	SNP	T	T	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr10:38407548T>C	uc001izk.3	+	7	2299	c.1469T>C	c.(1468-1470)aTa>aCa	p.I490T	ZNF37A_uc001izl.3_Missense_Mutation_p.I490T|ZNF37A_uc001izm.3_Missense_Mutation_p.I490T	NM_001007094	NP_003412	P17032	ZN37A_HUMAN	Homo sapiens zinc finger protein 37A (ZNF37A), transcript variant 1, mRNA.	490						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						AGAACTCATATAAGACAGAAA	0.413												
PGR	5241	broad.mit.edu	37	11	100999671	100999671	+	Missense_Mutation	SNP	G	G	T	rs141862537		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr11:100999671G>T	uc001pgh.2	-	0	874	c.131C>A	c.(130-132)aCc>aAc	p.T44N	PGR_uc001pgi.2_Missense_Mutation_p.T44N|PGR_uc009yww.1_Non-coding_Transcript|PGR_uc001pgj.2_Non-coding_Transcript|PGR_uc009ywx.1_Non-coding_Transcript|FJ515873_uc010rum.2_5'Flank	NM_000926	NP_000917	P06401	PRGR_HUMAN	Homo sapiens progesterone receptor (PGR), transcript variant 2, mRNA.	44	Modulating, Pro-Rich.				cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)	TTCAGGCAAGGTGTCCGAGGT	0.692												
COL2A1	1280	broad.mit.edu	37	12	48371798	48371798	+	Nonsense_Mutation	SNP	G	G	A	rs145684327		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr12:48371798G>A	uc001rqu.3	-	43	3287	c.3106C>T	c.(3106-3108)Cga>Tga	p.R1036*	COL2A1_uc001rqt.3_5'Flank|COL2A1_uc009zkw.3_Non-coding_Transcript|COL2A1_uc001rqv.3_Nonsense_Mutation_p.R967*	NM_001844	NP_001835	P02458	CO2A1_HUMAN	Homo sapiens collagen, type II, alpha 1 (COL2A1), transcript variant 1, mRNA.	1036	Triple-helical region.				axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CTCACCTCTCGTCCAGGTTCA	0.662												
GLT8D2	83468	broad.mit.edu	37	12	104390580	104390580	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr12:104390580G>A	uc001tkh.1	-	7	1090	c.533C>T	c.(532-534)gCg>gTg	p.A178V	GLT8D2_uc001tki.1_Missense_Mutation_p.A178V	NM_031302	NP_112592	Q9H1C3	GL8D2_HUMAN	Homo sapiens glycosyltransferase 8 domain containing 2 (GLT8D2), mRNA.	178						integral to membrane	transferase activity, transferring glycosyl groups			kidney(3)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	16						GAAAGCCGCCGCGTGGCCCAG	0.483												
CUX2	23316	broad.mit.edu	37	12	111772341	111772341	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr12:111772341G>A	uc001tsa.2	+	18	3177	c.3023G>A	c.(3022-3024)aGc>aAc	p.S1008N		NM_015267	NP_056082	O14529	CUX2_HUMAN	Homo sapiens cut-like homeobox 2 (CUX2), mRNA.	1008						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	p.E1007D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						TCCCTGGAGAGCAGCAAGGAG	0.647												
ABCC4	10257	broad.mit.edu	37	13	95705392	95705392	+	Missense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr13:95705392A>C	uc001vmd.4	-	26	3532	c.3413T>G	c.(3412-3414)tTt>tGt	p.F1138C	ABCC4_uc010afj.3_Missense_Mutation_p.F22C|ABCC4_uc010afk.3_Missense_Mutation_p.F1091C	NM_005845	NP_005836	O15439	MRP4_HUMAN	Homo sapiens ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), transcript variant 1, mRNA.	1138	ABC transporter 2.				platelet activation|platelet degranulation	integral to membrane|membrane fraction|plasma membrane|platelet dense granule membrane	15-hydroxyprostaglandin dehydrogenase (NAD+) activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|chloride channel activity			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Cefazolin(DB01327)	GTGCTCATTAAAGGGATCCAG	0.373												
TEP1	7011	broad.mit.edu	37	14	20846241	20846241	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr14:20846241G>A	uc001vxe.3	-	38	5703	c.5663C>T	c.(5662-5664)gCt>gTt	p.A1888V	TEP1_uc010ahk.3_Missense_Mutation_p.A1231V|TEP1_uc010tlf.1_Non-coding_Transcript|TEP1_uc010tlg.1_Missense_Mutation_p.A1780V|TEP1_uc010tlh.1_Missense_Mutation_p.A226V	NM_007110	NP_009041	Q99973	TEP1_HUMAN	Homo sapiens telomerase-associated protein 1 (TEP1), mRNA.	1888					telomere maintenance via recombination	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AAGCGCAGCAGCAACAAAGCC	0.632												
MGAT2	4247	broad.mit.edu	37	14	50089072	50089072	+	Nonsense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr14:50089072G>A	uc001wwr.3	+	0	1584	c.1086G>A	c.(1084-1086)tgG>tgA	p.W362*	NEMF_uc010anj.1_Intron|RPL36AL_uc001wwq.1_5'Flank	NM_002408	NP_002399	Q10469	MGAT2_HUMAN	Homo sapiens mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (MGAT2), mRNA.	362					oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|Golgi stack|integral to membrane|membrane fraction	alpha-1,6-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)	11	all_epithelial(31;0.0021)|Breast(41;0.0124)					CAAAATTCTGGAAAGTGCTGG	0.423												
SRSF5	6430	broad.mit.edu	37	14	70237710	70237710	+	Splice_Site	SNP	A	A	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr14:70237710A>T	uc001xll.3	+	8	1892	c.441_splice	c.e8-2	p.G147_splice	SRSF5_uc001xlo.3_Splice_Site_p.G147_splice|SRSF5_uc001xlp.3_Splice_Site_p.G147_splice	NM_006925	NP_008856	Q13243	SRSF5_HUMAN	Homo sapiens serine/arginine-rich splicing factor 5 (SRSF5), transcript variant 2, mRNA.	147	RRM 2.				mRNA 3'-end processing|mRNA export from nucleus|mRNA splice site selection|termination of RNA polymerase II transcription	nuclear speck	nucleotide binding|protein binding|RNA binding			large_intestine(1)|liver(1)	2						TTTCCATTTTAGGGTGGTTGA	0.348												
UBR1	197131	broad.mit.edu	37	15	43269028	43269028	+	Missense_Mutation	SNP	T	T	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr15:43269028T>A	uc001zqq.3	-	38	4322	c.4256A>T	c.(4255-4257)gAt>gTt	p.D1419V		NM_174916	NP_777576	Q8IWV7	UBR1_HUMAN	Homo sapiens ubiquitin protein ligase E3 component n-recognin 1 (UBR1), mRNA.	1419					cellular response to leucine|negative regulation of TOR signaling cascade	cytosol	leucine binding|zinc ion binding			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		AACAGGGTCATCCCAATACAA	0.388												
EDC3	80153	broad.mit.edu	37	15	74925078	74925078	+	Missense_Mutation	SNP	C	C	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr15:74925078C>A	uc002ayn.3	-	9	1890	c.1402G>T	c.(1402-1404)Ggg>Tgg	p.G468W	EDC3_uc002ayo.3_Missense_Mutation_p.G468W|EDC3_uc002aym.3_Missense_Mutation_p.G468W	NM_001142443	NP_079359	Q96F86	EDC3_HUMAN	Homo sapiens enhancer of mRNA decapping 3 homolog (S. cerevisiae) (EDC3), transcript variant 1, mRNA.	468	YjeF N-terminal.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16						GCGTGCTCCCCCAGTGGCAGA	0.577											OREG0023286	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
CSPG4	1464	broad.mit.edu	37	15	75980829	75980829	+	Nonsense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr15:75980829A>C	uc002baw.3	-	2	2670	c.2577T>G	c.(2575-2577)taT>taG	p.Y859*		NM_001897	NP_001888	Q6UVK1	CSPG4_HUMAN	Homo sapiens chondroitin sulfate proteoglycan 4 (CSPG4), mRNA.	859	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1 (By similarity).|Interaction with COL6A2 (By similarity).				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTGTGGCCCCATAGGTCACCC	0.577												
C15orf42	90381	broad.mit.edu	37	15	90142688	90142688	+	Silent	SNP	A	A	G			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr15:90142688A>G	uc002boe.3	+	7	2034	c.2034A>G	c.(2032-2034)aaA>aaG	p.K678K	C15orf42_uc021sug.1_Silent_p.K677K	NM_152259	NP_689472	Q7Z2Z1	TICRR_HUMAN	Homo sapiens chromosome 15 open reading frame 42 (C15orf42), mRNA.	678					cell cycle|DNA repair|DNA replication|formation of translation preinitiation complex|G2/M transition checkpoint|mitotic cell cycle DNA replication checkpoint|regulation of DNA-dependent DNA replication initiation|response to ionizing radiation	nucleus	chromatin binding|protein binding			NS(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(21)|ovary(6)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	59	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			TAAAATCAAAAGGCACCAAGG	0.408												
SPG7	6687	broad.mit.edu	37	16	89598461	89598461	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr16:89598461G>A	uc002fnj.3	+	7	1158	c.1137G>A	c.(1135-1137)gtG>gtA	p.V379V	SPG7_uc002fni.3_Silent_p.V379V	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	Homo sapiens spastic paraplegia 7 (pure and complicated autosomal recessive) (SPG7), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.	379					cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CAGAGTTCGTGGAGGTCATTG	0.647												
CCL2	6347	broad.mit.edu	37	17	32583358	32583358	+	Missense_Mutation	SNP	T	T	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:32583358T>A	uc002hhy.3	+	2	267	c.194_splice	c.e2+1	p.I65_splice		NM_002982	NP_002973	P13500	CCL2_HUMAN	Homo sapiens chemokine (C-C motif) ligand 2 (CCL2), mRNA.	65					angiogenesis|anti-apoptosis|apoptotic cell clearance|astrocyte cell migration|cell adhesion|cellular response to interferon-gamma|cellular response to interleukin-1|cellular response to lipopolysaccharide|cellular response to tumor necrosis factor|G-protein signaling, coupled to cyclic nucleotide second messenger|helper T cell extravasation|humoral immune response|inflammatory response|JAK-STAT cascade|macrophage chemotaxis|monocyte chemotaxis|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of T cell activation|viral genome replication	extracellular space	CCR2 chemokine receptor binding|chemokine activity|protein kinase activity|signal transducer activity			kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	6	Breast(3;0.00224)	Ovarian(249;0.0694)|Breast(31;0.151)|Lung NSC(157;0.153)		UCEC - Uterine corpus endometrioid carcinoma (308;0.000241)|BRCA - Breast invasive adenocarcinoma(366;0.0103)	Atorvastatin(DB01076)|Danazol(DB01406)|Mimosine(DB01055)|Simvastatin(DB00641)	GAAGCTGTGATGTGAGTTCAG	0.478												
TNS4	84951	broad.mit.edu	37	17	38641225	38641225	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:38641225G>A	uc010cxb.3	-	4	1487	c.1323C>T	c.(1321-1323)ttC>ttT	p.F441F		NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	Homo sapiens tensin 4 (TNS4), mRNA.	441					apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			TGTCCATCACGAACTTCATGG	0.547												
KRT39	390792	broad.mit.edu	37	17	39116597	39116597	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:39116597C>T	uc002hvo.1	-	5	1189	c.1153G>A	c.(1153-1155)Gtc>Atc	p.V385I	KRT39_uc010wfm.1_Missense_Mutation_p.V118I	NM_213656	NP_998821	Q6A163	K1C39_HUMAN	Homo sapiens keratin 39 (KRT39), mRNA.	385	Coil 2.|Rod.					intermediate filament	structural molecule activity	p.V385F(2)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				CGGGACTTGACGTCCAGCAGG	0.493												
KRTAP4-11	653240	broad.mit.edu	37	17	39274291	39274291	+	Missense_Mutation	SNP	T	T	C	rs149439944	by1000genomes	TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:39274291T>C	uc002hvz.3	-	0	316	c.277A>G	c.(277-279)Atg>Gtg	p.M93V		NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	Homo sapiens keratin associated protein 4-11 (KRTAP4-11), mRNA.	93	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament		p.M93V(8)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCAGCACATAGACTGGCAG	0.662												
SGCA	6442	broad.mit.edu	37	17	48246591	48246591	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:48246591C>T	uc002iqi.3	+	5	759	c.723C>T	c.(721-723)cgC>cgT	p.R241R	SGCA_uc010wmh.1_Silent_p.R139R|SGCA_uc002iqj.3_Intron|SGCA_uc010wmi.2_Non-coding_Transcript|BC126901_uc010dbn.1_5'Flank	NM_000023	NP_000014	Q16586	SGCA_HUMAN	Homo sapiens sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein) (SGCA), transcript variant 1, mRNA.	241					muscle contraction|muscle organ development	cytoplasm|cytoskeleton|integral to membrane|sarcoglycan complex|sarcolemma	calcium ion binding			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						CCCACTTCCGCGTTGACTGGT	0.662											OREG0024558	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
EPX	8288	broad.mit.edu	37	17	56277732	56277732	+	Nonsense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:56277732C>T	uc002ivq.3	+	9	1803	c.1684C>T	c.(1684-1686)Cga>Tga	p.R562*		NM_000502	NP_000493	P11678	PERE_HUMAN	Homo sapiens eosinophil peroxidase (EPX), mRNA.	562					hydrogen peroxide catabolic process		heme binding|peroxidase activity|protein binding			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48						CAACATGCAACGAAGCCGGGA	0.617											OREG0024608	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)
ENPP7	339221	broad.mit.edu	37	17	77711814	77711814	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr17:77711814G>A	uc002jxa.3	+	4	1366	c.1346G>A	c.(1345-1347)gGg>gAg	p.G449E		NM_178543	NP_848638	Q6UWV6	ENPP7_HUMAN	Homo sapiens ectonucleotide pyrophosphatase/phosphodiesterase 7 (ENPP7), mRNA.	449					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GGACTGCTGGGGACCGTGATT	0.632												
LAMA1	284217	broad.mit.edu	37	18	6977852	6977852	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr18:6977852G>A	uc002knm.3	-	43	6313	c.6219C>T	c.(6217-6219)gaC>gaT	p.D2073D	LAMA1_uc010wzj.2_Silent_p.D1549D	NM_005559	NP_005550	P25391	LAMA1_HUMAN	Homo sapiens laminin, alpha 1 (LAMA1), mRNA.	2073	Domain II and I.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	GAATTTCCACGTCTTTGACTT	0.398												
POTEC	388468	broad.mit.edu	37	18	14542921	14542921	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr18:14542921G>A	uc010dln.3	-	0	679	c.225C>T	c.(223-225)agC>agT	p.S75S	POTEC_uc010xaj.2_Non-coding_Transcript	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN	Homo sapiens POTE ankyrin domain family, member C (POTEC), mRNA.	75								p.S75S(2)|p.S75R(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TGCTCGTGCCGCTCCCCCTGC	0.567												
SERPINB11	89778	broad.mit.edu	37	18	61387390	61387390	+	Splice_Site	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr18:61387390G>A	uc002ljk.4	+	7	786	c.615_splice	c.e7+1	p.E205_splice	SERPINB11_uc010xes.2_Splice_Site_p.E31_splice|SERPINB11_uc010dqd.3_Splice_Site_p.E92_splice|SERPINB11_uc002ljj.4_Splice_Site_p.E92_splice|SERPINB11_uc010dqe.3_Intron|SERPINB11_uc010dqf.3_Intron	NM_080475	NP_536723	Q96P15	SPB11_HUMAN	Homo sapiens serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene) (SERPINB11), mRNA.	206					regulation of proteolysis	cytoplasm	serine-type endopeptidase inhibitor activity			breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				GCTAAGTGAGGTAAGTATTTT	0.313												
PTPRS	5802	broad.mit.edu	37	19	5273496	5273496	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:5273496C>T	uc002mbv.3	-	3	570	c.336G>A	c.(334-336)tcG>tcA	p.S112S	PTPRS_uc002mbu.1_Silent_p.S112S|PTPRS_uc010xin.2_Silent_p.S112S|PTPRS_uc002mbw.3_Silent_p.S112S|PTPRS_uc002mbx.3_Silent_p.S112S|PTPRS_uc002mby.3_Silent_p.S112S|PTPRS_uc002mbz.1_Silent_p.S112S	NM_002850	NP_002841	Q13332	PTPRS_HUMAN	Homo sapiens protein tyrosine phosphatase, receptor type, S (PTPRS), transcript variant 1, mRNA.	112	Ig-like C2-type 1.				cell adhesion	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)		TCTCCCCAACCGAGTTCTGGG	0.587												
KRTDAP	388533	broad.mit.edu	37	19	35979579	35979579	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:35979579G>A	uc002nzh.3	-	2	242	c.153C>T	c.(151-153)atC>atT	p.I51I	KRTDAP_uc021uso.1_Intron	NM_207392	NP_997275	P60985	KTDAP_HUMAN	Homo sapiens keratinocyte differentiation-associated protein (KRTDAP), transcript variant 1, mRNA.	51					cell differentiation	extracellular region				breast(1)|lung(4)|prostate(1)	6	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GCAATTTGTCGATGTTCAGGA	0.512												
SIPA1L3	23094	broad.mit.edu	37	19	38621245	38621245	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:38621245C>T	uc002ohk.3	+	9	3485	c.2976C>T	c.(2974-2976)gaC>gaT	p.D992D		NM_015073	NP_055888	O60292	SI1L3_HUMAN	Homo sapiens signal-induced proliferation-associated 1 like 3 (SIPA1L3), mRNA.	992	PDZ.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGGTTGAGGACTATGGGTTCG	0.662												
LTBP4	8425	broad.mit.edu	37	19	41133127	41133127	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:41133127C>T	uc002ooh.1	+	31	4431	c.4431C>T	c.(4429-4431)gaC>gaT	p.D1477D	LTBP4_uc002oog.1_Silent_p.D1440D|LTBP4_uc002ooi.1_Silent_p.D1410D|LTBP4_uc002ooj.1_Silent_p.D351D|LTBP4_uc002ook.1_Silent_p.D612D|LTBP4_uc002ool.1_Silent_p.D490D|LTBP4_uc010xvp.1_Silent_p.D238D	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	Homo sapiens latent transforming growth factor beta binding protein 4 (LTBP4), transcript variant 1, mRNA.	1478	Pro-rich.				growth hormone secretion|multicellular organismal development|protein folding|regulation of cell differentiation|regulation of cell growth|regulation of proteolysis|regulation of transforming growth factor beta receptor signaling pathway	extracellular space|proteinaceous extracellular matrix	calcium ion binding|glycosaminoglycan binding|integrin binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			central_nervous_system(1)	1			Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)			ACTTTGAGGACGATGGTGGCC	0.701												
CEACAM3	1084	broad.mit.edu	37	19	42301582	42301582	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:42301582G>A	uc002orn.1	+	1	202	c.126G>A	c.(124-126)ccG>ccA	p.P42P	CEACAM3_uc010eia.1_Silent_p.P42P|CEACAM3_uc002oro.1_Non-coding_Transcript	NM_001815	NP_001806	P40198	CEAM3_HUMAN	Homo sapiens carcinoembryonic antigen-related cell adhesion molecule 3 (CEACAM3), mRNA.	42	Ig-like V-type.					integral to membrane		p.P42P(2)		endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						AATCCATGCCGCTCAGTGTCG	0.522												
PSG3	5669	broad.mit.edu	37	19	43383725	43383725	+	Silent	SNP	G	G	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr19:43383725G>T	uc002ovd.1	-	0	147	c.9C>A	c.(7-9)acC>acA	p.T3T	PSG3_uc002ouf.3_Intron|PSG3_uc002oug.1_Silent_p.T3T|PSG3_uc002oun.3_Non-coding_Transcript|PSG3_uc002ovc.3_Silent_p.T3T|PSG3_uc002ova.2_Silent_p.T3T|PSG3_uc002ouz.2_Silent_p.T3T|PSG3_uc002ovb.3_Silent_p.T3T	NM_006905	NP_008836	Q16557	PSG3_HUMAN	Homo sapiens pregnancy specific beta-1-glycoprotein 1 (PSG1), transcript variant 1, mRNA.	3					defense response|female pregnancy	extracellular region				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				GGGCTGAGAGGGTTCCCATGG	0.572												
TRAPPC12	51112	broad.mit.edu	37	2	3392072	3392072	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr2:3392072C>T	uc002qxm.1	+	1	884	c.678C>T	c.(676-678)tcC>tcT	p.S226S	TRAPPC12_uc002qxn.1_Silent_p.S226S|TRAPPC12_uc010ewm.1_Silent_p.S226S	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN	Homo sapiens trafficking protein particle complex 12 (TRAPPC12), mRNA.	226							binding										TCTTCGACTCCTTTACTACCT	0.711												
MAP4K4	9448	broad.mit.edu	37	2	102440436	102440436	+	Missense_Mutation	SNP	A	A	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr2:102440436A>T	uc002tbc.3	+	3	605	c.227A>T	c.(226-228)tAc>tTc	p.Y76F	MAP4K4_uc002tbf.3_Missense_Mutation_p.Y76F|MAP4K4_uc002tbd.3_Missense_Mutation_p.Y76F|MAP4K4_uc010yvy.2_Missense_Mutation_p.Y76F|MAP4K4_uc002tbh.3_Missense_Mutation_p.Y76F|MAP4K4_uc002tbg.3_Missense_Mutation_p.Y76F|MAP4K4_uc002tbi.3_Missense_Mutation_p.Y76F|MAP4K4_uc010yvz.2_Missense_Mutation_p.Y56F|MAP4K4_uc010fiw.1_Intron|MAP4K4_uc002tbj.1_5'Flank	NM_145687	NP_001229488	O95819	M4K4_HUMAN	Homo sapiens mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), transcript variant 3, mRNA.	76	Protein kinase.				intracellular protein kinase cascade|regulation of JNK cascade|response to stress	cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CTAAAGAAATACTCTCATCAC	0.368												
ST6GAL2	84620	broad.mit.edu	37	2	107460197	107460197	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr2:107460197C>T	uc002tdq.3	-	1	356	c.237G>A	c.(235-237)gcG>gcA	p.A79A	ST6GAL2_uc002tdr.3_Silent_p.A79A|ST6GAL2_uc002tds.3_Silent_p.A79A	NM_001142351	NP_115917	Q96JF0	SIAT2_HUMAN	Homo sapiens ST6 beta-galactosamide alpha-2,6-sialyltranferase 2 (ST6GAL2), transcript variant 2, mRNA.	79					growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity	p.A79A(2)|p.A79V(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						CGCGGGGCAGCGCCTGGCGTG	0.657												
GPR149	344758	broad.mit.edu	37	3	154139085	154139085	+	Missense_Mutation	SNP	T	T	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr3:154139085T>C	uc003faa.3	-	2	1466	c.1366A>G	c.(1366-1368)Atc>Gtc	p.I456V		NM_001038705	NP_001033794	Q86SP6	GP149_HUMAN	Homo sapiens G protein-coupled receptor 149 (GPR149), mRNA.	456						integral to membrane|plasma membrane	G-protein coupled receptor activity			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			GTGGTGCTGATTTCTACTTTT	0.393												
SI	6476	broad.mit.edu	37	3	164716358	164716358	+	Nonsense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr3:164716358G>A	uc003fei.3	-	37	4573	c.4510C>T	c.(4510-4512)Cga>Tga	p.R1504*		NM_001041	NP_001032	P14410	SUIS_HUMAN	Homo sapiens sucrase-isomaltase (alpha-glucosidase) (SI), mRNA.	1504	Sucrase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity	p.R1504P(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)	TTGTCCCATCGTGCATAGTTG	0.403										HNSCC(35;0.089)		
TNIK	23043	broad.mit.edu	37	3	170800078	170800078	+	Missense_Mutation	SNP	T	T	G			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr3:170800078T>G	uc003fhh.2	-	26	3620	c.3275A>C	c.(3274-3276)gAt>gCt	p.D1092A	TNIK_uc003fhi.2_Missense_Mutation_p.D1037A|TNIK_uc003fhj.2_Missense_Mutation_p.D1063A|TNIK_uc003fhk.2_Missense_Mutation_p.D1084A|TNIK_uc003fhl.2_Missense_Mutation_p.D1008A|TNIK_uc003fhm.2_Missense_Mutation_p.D1029A|TNIK_uc003fhn.2_Missense_Mutation_p.D1055A|TNIK_uc003fho.2_Missense_Mutation_p.D1000A|TNIK_uc003fhg.2_Missense_Mutation_p.D270A|TNIK_uc003fhp.3_Missense_Mutation_p.D24A	NM_015028	NP_055843	Q9UKE5	TNIK_HUMAN	Homo sapiens TRAF2 and NCK interacting kinase (TNIK), transcript variant 1, mRNA.	1092	CNH.				actin cytoskeleton reorganization|activation of JNKK activity|protein autophosphorylation|regulation of dendrite morphogenesis|Wnt receptor signaling pathway	cytoskeleton|nucleus|recycling endosome	ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(22)|ovary(5)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)	62	all_cancers(22;2.55e-19)|all_lung(20;2.22e-14)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)			CTCTAGCACATCCATCTGCTG	0.483												
FYB	2533	broad.mit.edu	37	5	39153687	39153687	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr5:39153687C>T	uc003jls.3	-	1	1222	c.1155G>A	c.(1153-1155)acG>acA	p.T385T	FYB_uc003jlt.3_Silent_p.T385T|FYB_uc003jlu.3_Silent_p.T385T|FYB_uc011cpl.2_Silent_p.T395T	NM_199335	NP_955367	O15117	FYB_HUMAN	Homo sapiens FYN binding protein (FYB), transcript variant 2, mRNA.	385	Interaction with SKAP1.				cell junction assembly|immune response|intracellular protein kinase cascade|NLS-bearing substrate import into nucleus|protein phosphorylation|T cell receptor signaling pathway	cytosol|nucleus	protein binding			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			TTGAGTAAGACGTCTGGCCTT	0.468												
IQGAP2	10788	broad.mit.edu	37	5	75998408	75998408	+	Missense_Mutation	SNP	A	A	G			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr5:75998408A>G	uc003kek.3	+	34	4829	c.4607A>G	c.(4606-4608)aAt>aGt	p.N1536S	IQGAP2_uc011csv.2_Missense_Mutation_p.N1032S|IQGAP2_uc003kel.3_Missense_Mutation_p.N1032S	NM_006633	NP_006624	Q13576	IQGA2_HUMAN	Homo sapiens IQ motif containing GTPase activating protein 2 (IQGAP2), mRNA.	1536					small GTPase mediated signal transduction	actin cytoskeleton	actin binding|calmodulin binding|GTPase inhibitor activity|Ras GTPase activator activity			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		GTGCAACTCAATATTCAGGTA	0.353												
CEP120	153241	broad.mit.edu	37	5	122754205	122754205	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr5:122754205C>T	uc003ktk.3	-	2	170	c.54G>A	c.(52-54)cgG>cgA	p.R18R	CEP120_uc010jcz.2_5'UTR|CEP120_uc011cwq.2_5'UTR	NM_153223	NP_001159698	Q8N960	CE120_HUMAN	Homo sapiens centrosomal protein 120kDa (CEP120), transcript variant 1, mRNA.	18						centrosome				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						TGGGGAAATGCCGACCTGGAG	0.383												
DSP	1832	broad.mit.edu	37	6	7565623	7565623	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr6:7565623G>A	uc003mxp.1	+	6	1088	c.809G>A	c.(808-810)cGa>cAa	p.R270Q	DSP_uc003mxq.1_Missense_Mutation_p.R270Q|DSP_uc021yle.1_Missense_Mutation_p.R270Q	NM_004415	NP_004406	P15924	DESP_HUMAN	Homo sapiens desmoplakin (DSP), transcript variant 1, mRNA.	270	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				cellular component disassembly involved in apoptosis|keratinocyte differentiation|peptide cross-linking	cornified envelope|cytoplasm|desmosome	protein binding, bridging|structural constituent of cytoskeleton			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GATCACCTGCGACAGCTGCAG	0.502												
DNAH8	1769	broad.mit.edu	37	6	38957817	38957817	+	Silent	SNP	G	G	A	rs143472136	byFrequency	TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr6:38957817G>A	uc021yzh.1	+	87	13192	c.13083G>A	c.(13081-13083)ccG>ccA	p.P4361P	DNAH8_uc003ooe.2_Silent_p.P4144P	NM_001206927	NP_001193856			Homo sapiens dynein, axonemal, heavy chain 8 (DNAH8), mRNA.											NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TGTTTGAACCGTCATTCTGCT	0.368												
GSTA1	2938	broad.mit.edu	37	6	52658945	52658945	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr6:52658945C>T	uc003paz.3	-	4	504	c.392G>A	c.(391-393)cGc>cAc	p.R131H	GSTA1_uc021zan.1_Missense_Mutation_p.R131H	NM_145740	NP_665683	P08263	GSTA1_HUMAN	Homo sapiens glutathione S-transferase alpha 1 (GSTA1), mRNA.	131	GST C-terminal.				glutathione metabolic process|xenobiotic metabolic process	cytosol	glutathione transferase activity			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Amsacrine(DB00276)|Busulfan(DB01008)|Glutathione(DB00143)	AGGGAAGTAGCGATTTTTTAT	0.438												
AKD1	221264	broad.mit.edu	37	6	109827537	109827537	+	Missense_Mutation	SNP	T	T	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr6:109827537T>C	uc003ptn.2	-	34	4919	c.4842A>G	c.(4840-4842)atA>atG	p.I1614M	AKD1_uc011eas.1_Missense_Mutation_p.I13M	NM_001145128	NP_001138600	Q5TCS8	AKD1_HUMAN	Homo sapiens adenylate kinase domain containing 1 (AKD1), transcript variant 1, mRNA.	1614					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process		ATP binding|nucleobase, nucleoside, nucleotide kinase activity|nucleoside-triphosphatase activity			endometrium(2)|large_intestine(6)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(2)	20						TACCTGCTTTTATTCTTTCCA	0.323												
MIOS	54468	broad.mit.edu	37	7	7612689	7612689	+	Nonsense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:7612689C>T	uc003srf.3	+	3	891	c.583C>T	c.(583-585)Cga>Tga	p.R195*	MIOS_uc010ktp.1_Nonsense_Mutation_p.R195*	NM_019005	NP_061878	Q9NXC5	MIO_HUMAN	Homo sapiens missing oocyte, meiosis regulator, homolog (Drosophila) (MIOS), mRNA.	195										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TTGGCTTCCACGAGACCAGAA	0.383												
ABCA13	154664	broad.mit.edu	37	7	48450229	48450229	+	Silent	SNP	G	G	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:48450229G>T	uc003toq.2	+	39	12207	c.12183G>T	c.(12181-12183)ctG>ctT	p.L4061L	ABCA13_uc010kys.1_Silent_p.L1135L|ABCA13_uc010kyt.1_Non-coding_Transcript	NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 13 (ABCA13), mRNA.	4061	ABC transporter 1.				transport	integral to membrane	ATP binding|ATPase activity	p.T4060S(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CCTTCTGCCTGAAGGAGGCAT	0.582												
POM121L12	285877	broad.mit.edu	37	7	53104048	53104048	+	Silent	SNP	C	C	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:53104048C>A	uc003tpz.3	+	0	700	c.684C>A	c.(682-684)tcC>tcA	p.S228S		NM_182595	NP_872401	Q8N7R1	P1L12_HUMAN	Homo sapiens POM121 membrane glycoprotein-like 12 (POM121L12), mRNA.	228								p.A227S(1)		endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CGGTTGCTTCCTTCGTGCCCA	0.637												
NSUN5	55695	broad.mit.edu	37	7	72717906	72717906	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:72717906G>A	uc003txw.3	-	7	1139	c.1062C>T	c.(1060-1062)ctC>ctT	p.L354L	FKBP6_uc003twz.2_Intron|NSUN5_uc011kev.2_Silent_p.L354L|NSUN5_uc003txv.3_Silent_p.L354L|NSUN5_uc003txx.3_Silent_p.L316L	NM_018044	NP_060514	Q96P11	NSUN5_HUMAN	Homo sapiens NOP2/Sun domain family, member 5 (NSUN5), transcript variant 2, mRNA.	354							methyltransferase activity			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				TGGAGTAGACGAGCCGCTGCA	0.677												
EPHB6	2051	broad.mit.edu	37	7	142566033	142566033	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr7:142566033C>T	uc011kst.2	+	13	2740	c.1953C>T	c.(1951-1953)taC>taT	p.Y651Y	EPHB6_uc011ksu.2_Silent_p.Y651Y|EPHB6_uc003wbs.3_Silent_p.Y359Y|EPHB6_uc003wbt.3_Silent_p.Y125Y|EPHB6_uc003wbu.3_Silent_p.Y359Y|EPHB6_uc003wbv.3_Silent_p.Y35Y	NM_004445	NP_004436	O15197	EPHB6_HUMAN	Homo sapiens EPH receptor B6 (EPHB6), mRNA.	651						extracellular region|integral to plasma membrane	ATP binding|ephrin receptor activity			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					CCTCCACCTACGAGGACCCCT	0.577												
FAM110B	90362	broad.mit.edu	37	8	59059474	59059474	+	Missense_Mutation	SNP	A	A	C	rs139483735		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr8:59059474A>C	uc022auu.1	+	0	685	c.685A>C	c.(685-687)Aaa>Caa	p.K229Q	FAM110B_uc003xtj.1_Missense_Mutation_p.K229Q	NM_147189	NP_671722	Q8TC76	F110B_HUMAN	Homo sapiens family with sequence similarity 110, member B (FAM110B), mRNA.	229						microtubule organizing center|mitochondrion|nucleus				breast(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)	26		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				TCCCAAGCCCAAAATCGCAGC	0.632												
MYBL1	4603	broad.mit.edu	37	8	67507922	67507922	+	Nonsense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr8:67507922G>A	uc003xwj.3	-	5	990	c.583C>T	c.(583-585)Caa>Taa	p.Q195*	MYBL1_uc003xwl.3_Nonsense_Mutation_p.Q195*|MYBL1_uc003xwk.3_Nonsense_Mutation_p.Q195*	NM_001080416	NP_001073885	P10243	MYBA_HUMAN	Homo sapiens v-myb myeloblastosis viral oncogene homolog (avian)-like 1 (MYBL1), transcript variant 1, mRNA.	195					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			ATTCCATCTTGTAAATAGCCC	0.343												
NOL8	55035	broad.mit.edu	37	9	95077750	95077750	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr9:95077750G>A	uc022bjx.1	-	6	1494	c.1157C>T	c.(1156-1158)gCg>gTg	p.A386V	NOL8_uc010mqw.3_Non-coding_Transcript|NOL8_uc022bjw.1_Missense_Mutation_p.A318V	NM_017948	NP_060418	Q76FK4	NOL8_HUMAN	Homo sapiens nucleolar protein 8 (NOL8), transcript variant 1, mRNA.	386					DNA replication|positive regulation of cell growth	nucleolus	nucleotide binding|protein binding|RNA binding			endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTTTTTCATCGCAATAATTTC	0.323												
PALM2-AKAP2	445815	broad.mit.edu	37	9	112687347	112687347	+	Missense_Mutation	SNP	T	T	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr9:112687347T>C	uc004bei.2	+	4	571	c.379T>C	c.(379-381)Tcc>Ccc	p.S127P	PALM2-AKAP2_uc004beg.3_Missense_Mutation_p.S129P|PALM2-AKAP2_uc004beh.4_Missense_Mutation_p.S127P|PALM2-AKAP2_uc004bej.4_Missense_Mutation_p.S127P|PALM2-AKAP2_uc004bek.4_Missense_Mutation_p.S127P|PALM2-AKAP2_uc004bel.1_5'UTR	NM_001136562	NP_001130034	Q9Y2D5	AKAP2_HUMAN	Homo sapiens A kinase (PRKA) anchor protein 2 (AKAP2), transcript variant 2, mRNA.	0							enzyme binding	p.S127Y(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	44						ACAGGGTTTCTCCAGTACGGA	0.463												
CEL	1056	broad.mit.edu	37	9	135945919	135945919	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chr9:135945919C>T	uc010naa.1	+	9	1383	c.1367C>T	c.(1366-1368)gCc>gTc	p.A456V		NM_001807	NP_001798	P19835	CEL_HUMAN	Homo sapiens carboxyl ester lipase (bile salt-stimulated lipase) (CEL), mRNA.	453					cholesterol catabolic process|fatty acid catabolic process|intestinal cholesterol absorption|intestinal lipid catabolic process|pancreatic juice secretion|protein esterification	cytosol|extracellular space	acylglycerol lipase activity|carboxylesterase activity|heparin binding|sterol esterase activity|triglyceride lipase activity			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		TGGGTGGGGGCCGACCATGCA	0.607												
MAP7D2	256714	broad.mit.edu	37	X	20074865	20074865	+	Silent	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:20074865C>T	uc010nfo.2	-	3	534	c.417G>A	c.(415-417)caG>caA	p.Q139Q	MAP7D2_uc004czq.2_Silent_p.Q10Q|MAP7D2_uc011mji.2_Silent_p.Q95Q|MAP7D2_uc004czr.2_Silent_p.Q139Q|MAP7D2_uc011mjj.2_Silent_p.Q139Q|MAP7D2_uc004czs.1_Silent_p.Q95Q	NM_001168465	NP_001161937	Q96T17	MA7D2_HUMAN	Homo sapiens MAP7 domain containing 2 (MAP7D2), transcript variant 1, mRNA.	139										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						GCTCCAGCTGCTGTGTGCGCT	0.557												
BCOR	54880	broad.mit.edu	37	X	39933293	39933293	+	Missense_Mutation	SNP	C	C	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:39933293C>T	uc004den.4	-	3	1598	c.1306G>A	c.(1306-1308)Gtc>Atc	p.V436I	BCOR_uc004dep.4_Missense_Mutation_p.V436I|BCOR_uc004deo.4_Missense_Mutation_p.V436I|BCOR_uc004dem.4_Missense_Mutation_p.V436I|BCOR_uc004deq.4_Missense_Mutation_p.V436I	NM_001123385	NP_001116857	Q6W2J9	BCOR_HUMAN	Homo sapiens BCL6 corepressor (BCOR), transcript variant 5, mRNA.	436					heart development|histone H2A monoubiquitination|negative regulation of bone mineralization|negative regulation of histone H3-K36 methylation|negative regulation of histone H3-K4 methylation|negative regulation of tooth mineralization|negative regulation of transcription from RNA polymerase II promoter|odontogenesis|palate development|specification of axis polarity|transcription, DNA-dependent	nucleus	heat shock protein binding|histone deacetylase binding|transcription corepressor activity|transcription factor binding|transcription regulatory region DNA binding			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						TTATCTGTGACGTCTTTGGTA	0.527			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic					
ITIH6	347365	broad.mit.edu	37	X	54783873	54783873	+	Missense_Mutation	SNP	G	G	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:54783873G>T	uc004dtj.2	-	7	2664	c.2634C>A	c.(2632-2634)aaC>aaA	p.N878K		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	Homo sapiens inter-alpha-trypsin inhibitor heavy chain family, member 6 (ITIH6), mRNA.	878	Pro-rich.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity										GCATATGGGGGTTTGGGGTCT	0.483												
ZXDA	7789	broad.mit.edu	37	X	57935325	57935325	+	Silent	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:57935325G>A	uc004dve.3	-	0	1743	c.1530C>T	c.(1528-1530)ttC>ttT	p.F510F		NM_007156	NP_009087	P98168	ZXDA_HUMAN	Homo sapiens zinc finger, X-linked, duplicated A (ZXDA), mRNA.	510	Required for interaction with ZXDC.				positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.F510F(2)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(13)|ovary(2)|prostate(2)|skin(1)	37						CAGGACACACGAAAGGCTTTG	0.552												
MAGT1	84061	broad.mit.edu	37	X	77112989	77112989	+	Missense_Mutation	SNP	G	G	T			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:77112989G>T	uc004fof.3	-	3	554	c.492C>A	c.(490-492)aaC>aaA	p.N164K	MAGT1_uc004fog.4_Non-coding_Transcript	NM_032121	NP_115497	Q9H0U3	MAGT1_HUMAN	Homo sapiens magnesium transporter 1 (MAGT1), mRNA.	132					protein N-linked glycosylation via asparagine	integral to membrane|oligosaccharyltransferase complex				cervix(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	17						CTGAATTCATGTTTAGCTGAA	0.368												
RHOXF1	158800	broad.mit.edu	37	X	119243159	119243159	+	Silent	SNP	G	G	A	rs145568775		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:119243159G>A	uc004esk.1	-	2	621	c.546C>T	c.(544-546)gtC>gtT	p.V182V	AK123976_uc004esi.1_Intron	NM_139282	NP_644811	Q8NHV9	RHXF1_HUMAN	Homo sapiens Rhox homeobox family, member 1 (RHOXF1), mRNA.	182					gamete generation|multicellular organismal development|steroid hormone receptor signaling pathway	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			NS(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10						GCTAGTCCACGACGATGTAGA	0.507												
RAP2C	57826	broad.mit.edu	37	X	131348336	131348336	+	Missense_Mutation	SNP	A	A	C			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:131348336A>C	uc004ewp.3	-	2	1196	c.412T>G	c.(412-414)Tgg>Ggg	p.W138G	RAP2C_uc004ewo.3_Missense_Mutation_p.W72G|RAP2C_uc010nrk.3_Non-coding_Transcript|RAP2C_uc004ewq.4_Missense_Mutation_p.W138G	NM_021183	NP_067006	Q9Y3L5	RAP2C_HUMAN	Homo sapiens RAP2C, member of RAS oncogene family (RAP2C), mRNA.	138					negative regulation of cell migration|positive regulation of protein autophosphorylation|Rap protein signal transduction|regulation of protein tyrosine kinase activity	recycling endosome membrane	GTP binding|GTPase activity			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	8	Acute lymphoblastic leukemia(192;0.000127)					GGACAGCCCCATTCTTGAGCC	0.438												
F9	2158	broad.mit.edu	37	X	138643011	138643011	+	Missense_Mutation	SNP	G	G	A	rs137852247		TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:138643011G>A	uc004fas.1	+	6	864	c.835G>A	c.(835-837)Gca>Aca	p.A279T	F9_uc004fat.1_Missense_Mutation_p.A241T	NM_000133	NP_000124	P00740	FA9_HUMAN	Homo sapiens coagulation factor IX (F9), mRNA.	279	Peptidase S1.		A -> T (in HEMB; mild).		blood coagulation, extrinsic pathway|blood coagulation, intrinsic pathway|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen|plasma membrane	calcium ion binding|serine-type endopeptidase activity			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Heparin(DB01109)|Menadione(DB00170)	TACAGTTGTCGCAGGTAAATA	0.353												
FATE1	89885	broad.mit.edu	37	X	150891145	150891145	+	Missense_Mutation	SNP	G	G	A			TCGA-87-5896-01A-01D-1696-08	TCGA-87-5896-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	640c33a6-a7df-4dba-9c21-367a9a839f0f	6de80c2c-8a7e-4ec4-9efa-9d43c101306b	g.chrX:150891145G>A	uc004fex.3	+	4	550	c.466G>A	c.(466-468)Gcc>Acc	p.A156T		NM_033085	NP_149076	Q969F0	FATE1_HUMAN	Homo sapiens fetal and adult testis expressed 1 (FATE1), mRNA.	156						endoplasmic reticulum|integral to membrane				NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|lung(6)|ovary(1)	15	Acute lymphoblastic leukemia(192;6.56e-05)					GGAACAGGGCGCCACCTGGCG	0.652