Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
ADAMTS8	11095	broad.mit.edu	36	11	129786702	129786702	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:129786702C>T	uc001qgg.2	-	c.1570G>A	c.(1570-1572)GTG>ATG	p.V524M	ADAMTS8_uc001qgf.1_Missense_Mutation_p.V5M	NM_007037	NP_008968	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1	524	Disintegrin.				negative regulation of cell proliferation|proteolysis	proteinaceous extracellular matrix	heparin binding|integrin binding|low affinity phosphate transmembrane transporter activity|metalloendopeptidase activity|zinc ion binding			central_nervous_system(1)	1	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)												0.333333	78.373877	80.439391	28	56	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)	Missense_Mutation	SNP	129786702	129786702	273	11	C	T	T	19	19	ADAMTS8	T	1	1
OR52R1	119695	broad.mit.edu	36	11	4781670	4781670	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:4781670G>T	uc001lzm.1	-	c.754C>A	c.(754-756)CAA>AAA	p.Q252K		NM_001005177	NP_001005177	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R,	173	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)												0.424	154.283275	154.90532	53	72	GG		KEEP	---	---	---	---	capture		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)	Missense_Mutation	SNP	4781670	4781670	11541	11	G	T	T	47	47	OR52R1	T	3	3
SMTNL1	219537	broad.mit.edu	36	11	57066859	57066859	+	Silent	SNP	A	C	C			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:57066859A>C	uc009ymh.1	+	c.222A>C	c.(220-222)GCA>GCC	p.A74A		NM_001105565	NP_001099035	E9PPJ3	E9PPJ3_HUMAN	smoothelin-like 1	56										ovary(1)	1														0.285714	6.605604	7.574931	6	15	AA		KEEP	---	---	---	---	capture			Silent	SNP	57066859	57066859	15315	11	A	C	C	6	6	SMTNL1	C	4	4
APBB1	322	broad.mit.edu	36	11	6381488	6381488	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6381488G>A	uc001mdb.1	-	c.862C>T	c.(862-864)CCC>TCC	p.P288S	APBB1_uc001mcz.1_5'Flank|APBB1_uc001mda.2_Intron|APBB1_uc001mdc.1_Missense_Mutation_p.P288S|APBB1_uc009yey.1_Missense_Mutation_p.P29S|APBB1_uc009yez.1_Missense_Mutation_p.P68S|APBB1_uc009yfa.1_Missense_Mutation_p.P29S|APBB1_uc001mdd.2_Missense_Mutation_p.P68S|APBB1_uc009yfb.1_Missense_Mutation_p.P29S|APBB1_uc001mde.2_Missense_Mutation_p.P29S	NM_001164	NP_001155	O00213	APBB1_HUMAN	amyloid beta A4 precursor protein-binding,	288					apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription activator activity|transcription factor binding			breast(2)	2		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)				GBM(147;1810 2556 5672 39622)								0.389313	152.214533	153.613612	51	80	GG		KEEP	---	---	---	---	capture		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)	Missense_Mutation	SNP	6381488	6381488	769	11	G	A	A	43	43	APBB1	A	2	2
NUMA1	4926	broad.mit.edu	36	11	71394753	71394753	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:71394753C>T	uc001orl.1	-	c.5668G>A	c.(5668-5670)GGG>AGG	p.G1890R	NUMA1_uc001ork.1_Missense_Mutation_p.G754R|NUMA1_uc001orm.1_Missense_Mutation_p.G1876R|NUMA1_uc001orj.2_Missense_Mutation_p.G72R|NUMA1_uc009ysw.1_Missense_Mutation_p.G1457R	NM_006185	NP_006176	Q14980	NUMA1_HUMAN	nuclear mitotic apparatus protein 1	1890					G2/M transition of mitotic cell cycle|mitotic anaphase|nucleus organization	chromosome|cytosol|nucleoplasm|spindle microtubule|spindle pole	protein binding|structural molecule activity			ovary(3)|lung(2)|skin(2)|central_nervous_system(1)	8										525				0.368132	195.378659	198.159544	67	115	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71394753	71394753	11155	11	C	T	T	23	23	NUMA1	T	1	1
AACS	65985	broad.mit.edu	36	12	124157757	124157757	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:124157757A>C	uc001uhc.1	+	c.905A>C	c.(904-906)CAT>CCT	p.H302P	AACS_uc001uhd.1_Missense_Mutation_p.H302P|AACS_uc009zyh.1_Non-coding_Transcript|AACS_uc009zyi.1_5'UTR	NM_023928	NP_076417	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	302					fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)													0.343434	104.825862	106.966769	34	65	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)	Missense_Mutation	SNP	124157757	124157757	10	12	A	C	C	8	8	AACS	C	4	4
MLL2	8085	broad.mit.edu	36	12	47706806	47706806	+	Nonsense_Mutation	SNP	A	T	T			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:47706806A>T	uc001rta.2	-	c.15210T>A	c.(15208-15210)TAT>TAA	p.Y5070*		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	5070					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|promoter binding|protein binding|zinc ion binding			kidney(16)|lung(4)|skin(4)|ovary(3)|pancreas(2)	29														0.333333	84.133396	86.280014	29	58	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	47706806	47706806	10011	12	A	T	T	8	8	MLL2	T	5	4
KRT2	3849	broad.mit.edu	36	12	51331882	51331882	+	Silent	SNP	A	G	G			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51331882A>G	uc001sat.1	-	c.312T>C	c.(310-312)GGT>GGC	p.G104G		NM_000423	NP_000414	P35908	K22E_HUMAN	keratin 2	104	Head.				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton			ovary(2)	2														0.185185	8.767922	11.271006	5	22	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.19)	Silent	SNP	51331882	51331882	8772	12	A	G	G	6	6	KRT2	G	4	4
HOXC13	3229	broad.mit.edu	36	12	52619025	52619025	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:52619025C>T	uc001sei.1	+	c.68C>T	c.(67-69)GCG>GTG	p.A23V		NM_017410	NP_059106	P31276	HXC13_HUMAN	homeobox C13	23					regulation of transcription, DNA-dependent	nucleus	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0										22				0.272727	7.622383	8.133133	3	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52619025	52619025	7604	12	C	T	T	27	27	HOXC13	T	1	1
MMP19	4327	broad.mit.edu	36	12	54517969	54517969	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54517969G>C	uc001sib.1	-	c.985C>G	c.(985-987)CTT>GTT	p.L329V	MMP19_uc001sia.1_Missense_Mutation_p.L43V|MMP19_uc001sid.1_Non-coding_Transcript	NM_002429	NP_002420	Q99542	MMP19_HUMAN	matrix metalloproteinase 19 isoform rasi-1	329	Hemopexin-like 1.				angiogenesis|cell differentiation|collagen catabolic process|proteolysis	proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|zinc ion binding			ovary(1)	1														0.414062	143.310788	144.14467	53	75	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54517969	54517969	10047	12	G	C	C	35	35	MMP19	C	3	3
LRP1	4035	broad.mit.edu	36	12	55836916	55836916	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55836916A>C	uc001snd.1	+	c.1507A>C	c.(1507-1509)ACC>CCC	p.T503P		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	503	EGF-like 3.|Extracellular (Potential).				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)				p.502_503RT>P(JHH6-Tumor)	1456				0.2	6.607792	8.269001	4	16	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0103)	Missense_Mutation	SNP	55836916	55836916	9324	12	A	C	C	10	10	LRP1	C	4	4
PTPRB	5787	broad.mit.edu	36	12	69270042	69270042	+	Silent	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:69270042C>T	uc001swc.2	-	c.2019G>A	c.(2017-2019)TTG>TTA	p.L673L	PTPRB_uc001swb.2_Silent_p.L455L|PTPRB_uc001swa.2_Silent_p.L673L|PTPRB_uc001swd.2_Silent_p.L672L|PTPRB_uc009zrr.1_Silent_p.L552L	NM_001109754	NP_001103224	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	455	Fibronectin type-III 5.|Extracellular (Potential).				angiogenesis	integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			lung(2)|skin(1)	3	Renal(347;0.236)											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.180617	76.933597	98.712	41	186	CC		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)		Silent	SNP	69270042	69270042	13253	12	C	T	T	29	29	PTPRB	T	2	2
MYF6	4618	broad.mit.edu	36	12	79625698	79625698	+	Silent	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:79625698G>A	uc001szf.1	+	c.69G>A	c.(67-69)CAG>CAA	p.Q23Q		NM_002469	NP_002460	P23409	MYF6_HUMAN	myogenic factor 6	23					muscle cell fate commitment|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of muscle cell differentiation|skeletal muscle tissue development	nucleoplasm	DNA binding|protein heterodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulator activity			central_nervous_system(1)	1														0.412844	131.446543	132.171606	45	64	GG		KEEP	---	---	---	---	capture			Silent	SNP	79625698	79625698	10423	12	G	A	A	34	34	MYF6	A	2	2
C13orf16	121793	broad.mit.edu	36	13	110793234	110793234	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:110793234C>A	uc001vsa.1	+	c.370C>A	c.(370-372)CCA>ACA	p.P124T		NM_152324	NP_689537	Q8N6K0	CM016_HUMAN	hypothetical protein LOC121793	124	Cytoplasmic (Potential).					integral to membrane					0	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)													0.238095	33.713234	37.647956	15	48	CC		KEEP	---	---	---	---	capture	all cancers(43;0.113)|GBM - Glioblastoma multiforme(44;0.174)|BRCA - Breast invasive adenocarcinoma(86;0.188)		Missense_Mutation	SNP	110793234	110793234	1766	13	C	A	A	30	30	C13orf16	A	3	3
ADPRHL1	113622	broad.mit.edu	36	13	113127398	113127398	+	Silent	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:113127398G>A	uc001vtq.1	-	c.744C>T	c.(742-744)CCC>CCT	p.P248P	ADPRHL1_uc001vtp.1_Silent_p.P166P	NM_138430	NP_954631	Q8NDY3	ARHL1_HUMAN	ADP-ribosylhydrolase like 1 isoform 1	248					protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding				0	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0395)|all_epithelial(44;0.011)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)												0.405405	186.980734	188.135419	60	88	GG		KEEP	---	---	---	---	capture	all cancers(43;0.0195)|GBM - Glioblastoma multiforme(44;0.116)		Silent	SNP	113127398	113127398	333	13	G	A	A	39	39	ADPRHL1	A	1	1
CYSLTR2	57105	broad.mit.edu	36	13	48179612	48179612	+	Missense_Mutation	SNP	T	A	A			TCGA-14-1825-01	TCGA-14-1825-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr13:48179612T>A	uc010acw.1	+	c.658T>A	c.(658-660)TGT>AGT	p.C220S	CYSLTR2_uc010acx.1_Missense_Mutation_p.C220S|CYSLTR2_uc010acy.1_Missense_Mutation_p.C220S|CYSLTR2_uc010acz.1_Missense_Mutation_p.C220S|CYSLTR2_uc010ada.1_Missense_Mutation_p.C220S|CYSLTR2_uc010adb.1_Missense_Mutation_p.C220S|CYSLTR2_uc010adc.1_Missense_Mutation_p.C220S|CYSLTR2_uc010add.1_Missense_Mutation_p.C220S|CYSLTR2_uc001vck.2_Missense_Mutation_p.C220S|CYSLTR2_uc010ade.1_Missense_Mutation_p.C220S	NM_020377	NP_065110	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	220	Helical; Name=5; (Potential).				immune response	integral to membrane|plasma membrane				lung(2)	2		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)			Nedocromil(DB00716)					46				0.489796	233.898368	233.911583	72	75	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;1.19e-09)	Missense_Mutation	SNP	48179612	48179612	4367	13	T	A	A	55	55	CYSLTR2	A	4	4
POTEB	339010	broad.mit.edu	36	15	19323980	19323980	+	Missense_Mutation	SNP	T	A	A			TCGA-14-1825-01	TCGA-14-1825-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:19323980T>A	uc001ytu.1	-	c.1120A>T	c.(1120-1122)AAT>TAT	p.N374Y	POTEB_uc010axv.1_Non-coding_Transcript	NM_207355	NP_997238	Q6S5H4	POTEB_HUMAN	protein expressed in prostate, ovary, testis,	374											0														0.148515	26.357341	38.333908	15	86	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19323980	19323980	12691	15	T	A	A	63	63	POTEB	A	4	4
PLA2G4F	255189	broad.mit.edu	36	15	40233913	40233913	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:40233913G>C	uc001zoz.1	-	c.220C>G	c.(220-222)CCC>GCC	p.P74A	PLA2G4F_uc010bcr.1_5'UTR|PLA2G4F_uc001zpa.1_5'UTR|PLA2G4F_uc010bcs.1_5'UTR	NM_213600	NP_998765	Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	74	C2.				phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity			ovary(4)	4		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)												0.204545	6.958804	10.813977	9	35	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(94;8.97e-07)	Missense_Mutation	SNP	40233913	40233913	12432	15	G	C	C	42	42	PLA2G4F	C	3	3
MMP15	4324	broad.mit.edu	36	16	56628900	56628900	+	Nonsense_Mutation	SNP	C	A	A			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56628900C>A	uc002ena.1	+	c.186C>A	c.(184-186)TAC>TAA	p.Y62*		NM_002428	NP_002419	P51511	MMP15_HUMAN	matrix metalloproteinase 15 preproprotein	62					protein modification process|proteolysis	extracellular matrix|integral to plasma membrane	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|protein binding|zinc ion binding			central_nervous_system(2)|breast(1)	3														0.214286	6.51674	7.572641	3	11	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	56628900	56628900	10044	16	C	A	A	18	18	MMP15	A	5	3
AARS	16	broad.mit.edu	36	16	68867972	68867972	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:68867972G>T	uc002eyn.1	-	c.397C>A	c.(397-399)CTT>ATT	p.L133I		NM_001605	NP_001596	P49588	SYAC_HUMAN	alanyl-tRNA synthetase	133					alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)			L-Alanine(DB00160)									0.45	160.483477	160.750799	54	66	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.161)	Missense_Mutation	SNP	68867972	68867972	20	16	G	T	T	36	36	AARS	T	3	3
MLYCD	23417	broad.mit.edu	36	16	82490677	82490677	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:82490677C>G	uc002fgz.1	+	c.427C>G	c.(427-429)CAC>GAC	p.H143D		NM_012213	NP_036345	O95822	DCMC_HUMAN	malonyl-CoA decarboxylase precursor	143					acyl-CoA metabolic process|fatty acid biosynthetic process	mitochondrion|peroxisome	malonyl-CoA decarboxylase activity|methylmalonyl-CoA decarboxylase activity				0														0.333333	17.543613	17.986618	6	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82490677	82490677	10028	16	C	G	G	21	21	MLYCD	G	3	3
DNAH9	1770	broad.mit.edu	36	17	11749783	11749783	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:11749783G>C	uc002gne.1	+	c.11681G>C	c.(11680-11682)GGA>GCA	p.G3894A	DNAH9_uc010coo.1_Missense_Mutation_p.G3188A|DNAH9_uc002gnf.1_Missense_Mutation_p.G206A	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3894	AAA 6 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)												0.177778	9.51515	14.042698	8	37	GG		KEEP	---	---	---	---	capture		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)	Missense_Mutation	SNP	11749783	11749783	4791	17	G	C	C	41	41	DNAH9	C	3	3
MPP2	4355	broad.mit.edu	36	17	39316233	39316233	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1825-01	TCGA-14-1825-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39316233T>C	uc002ien.1	-	c.218A>G	c.(217-219)GAG>GGG	p.E73G	MPP2_uc002ieo.1_Missense_Mutation_p.E56G|MPP2_uc010czm.1_Missense_Mutation_p.E39G	NM_005374	NP_005365	Q14168	MPP2_HUMAN	palmitoylated membrane protein 2	80				E -> G (in Ref. 4; CAI56746).	signal transduction	cell surface|integral to plasma membrane|membrane fraction	guanylate kinase activity				0		Breast(137;0.00314)												0.192308	6.308065	8.696656	5	21	TT		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.12)	Missense_Mutation	SNP	39316233	39316233	10126	17	T	C	C	54	54	MPP2	C	4	4
PPM1D	8493	broad.mit.edu	36	17	56066053	56066053	+	Silent	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:56066053C>T	uc002iyt.1	+	c.759C>T	c.(757-759)CAC>CAT	p.H253H	PPM1D_uc010ddm.1_Non-coding_Transcript	NM_003620	NP_003611	O15297	PPM1D_HUMAN	protein phosphatase 1D	253	PP2C-like.				negative regulation of cell proliferation|protein dephosphorylation|response to radiation	nucleus|protein serine/threonine phosphatase complex	metal ion binding|protein binding|protein serine/threonine phosphatase activity				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)													0.517241	134.973009	134.995326	45	42	CC		KEEP	---	---	---	---	capture	Epithelial(12;6.75e-12)|all cancers(12;1.96e-10)		Silent	SNP	56066053	56066053	12772	17	C	T	T	17	17	PPM1D	T	2	2
TP53	7157	broad.mit.edu	36	17	7518988	7518988	+	Nonsense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518988G>A	uc002gim.2	-	c.586C>T	c.(586-588)CGA>TGA	p.R196*	TP53_uc002gig.1_Nonsense_Mutation_p.R196*|TP53_uc002gih.1_Nonsense_Mutation_p.R196*|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Nonsense_Mutation_p.R64*|TP53_uc010cng.1_Nonsense_Mutation_p.R64*|TP53_uc002gii.1_Nonsense_Mutation_p.R64*|TP53_uc010cnh.1_Nonsense_Mutation_p.R196*|TP53_uc010cni.1_Nonsense_Mutation_p.R196*|TP53_uc002gij.2_Nonsense_Mutation_p.R196*|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Nonsense_Mutation_p.R103*|TP53_uc002gio.2_Nonsense_Mutation_p.R64*	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	196	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> S (in a sporadic cancer; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.R196*(121)|p.0?(6)|p.R196fs*51(4)|p.A189_V197delAPPQHLIRV(4)|p.I195fs*50(1)|p.P191fs*6(1)|p.I195_G199delIRVEG(1)|p.I195fs*12(1)|p.R196R(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.R196*(P31FUJ-Tumor)|p.R196*(CALU6-Tumor)|p.R196*(HUT78-Tumor)|p.H193fs(59M-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.473684	114.594385	114.640199	36	40	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Nonsense_Mutation	SNP	7518988	7518988	16923	17	G	A	A	39	39	TP53	A	5	1
EMILIN2	84034	broad.mit.edu	36	18	2837912	2837912	+	Silent	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:2837912C>T	uc002kln.1	+	c.240C>T	c.(238-240)CCC>CCT	p.P80P		NM_032048	NP_114437	Q9BXX0	EMIL2_HUMAN	elastin microfibril interfacer 2	80	EMI.				cell adhesion	collagen	extracellular matrix constituent conferring elasticity|protein binding			ovary(1)	1														0.346939	45.238885	46.261622	17	32	CC		KEEP	---	---	---	---	capture		READ - Rectum adenocarcinoma(2;0.1)	Silent	SNP	2837912	2837912	5286	18	C	T	T	24	24	EMILIN2	T	2	2
DUS3L	56931	broad.mit.edu	36	19	5740592	5740592	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1825-01	TCGA-14-1825-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5740592T>G	uc002mdc.1	-	c.526A>C	c.(526-528)ACC>CCC	p.T176P	DUS3L_uc002mdd.1_Intron|DUS3L_uc010duk.1_5'UTR	NM_020175	NP_064560	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like	176	C3H1-type 2.				oxidation-reduction process|tRNA processing		flavin adenine dinucleotide binding|nucleic acid binding|tRNA dihydrouridine synthase activity|zinc ion binding				0														0.266667	7.891632	8.630834	4	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5740592	5740592	4992	19	T	G	G	58	58	DUS3L	G	4	4
CACNG8	59283	broad.mit.edu	36	19	59177250	59177250	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1825-01	TCGA-14-1825-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59177250T>G	uc002qcs.1	+	c.613T>G	c.(613-615)TCC>GCC	p.S205A		NM_031895	NP_114101	Q8WXS5	CCG8_HUMAN	voltage-dependent calcium channel gamma-8	205					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|endocytic vesicle membrane|postsynaptic density|voltage-gated calcium channel complex	voltage-gated calcium channel activity				0	all_cancers(19;0.0385)|all_epithelial(19;0.0207)|all_lung(19;0.145)|Lung NSC(19;0.168)|Ovarian(34;0.19)													0.307692	7.692461	8.12282	4	9	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.162)	Missense_Mutation	SNP	59177250	59177250	2679	19	T	G	G	58	58	CACNG8	G	4	4
PEX14	5195	broad.mit.edu	36	1	10605691	10605691	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:10605691G>T	uc001arn.1	+	c.413G>T	c.(412-414)GGC>GTC	p.G138V	PEX14_uc009vmu.1_Missense_Mutation_p.G95V|PEX14_uc009vmv.1_Missense_Mutation_p.G74V|PEX14_uc009vmw.1_Missense_Mutation_p.G74V	NM_004565	NP_004556	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	138					negative regulation of gene-specific transcription|negative regulation of sequence-specific DNA binding transcription factor activity|protein homooligomerization|protein import into peroxisome matrix|transmembrane transport	integral to membrane|nucleus|peroxisomal membrane|protein complex	protein N-terminus binding|transcription corepressor activity			breast(1)	1	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)												0.419355	35.970351	36.145938	13	18	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)	Missense_Mutation	SNP	10605691	10605691	12164	1	G	T	T	42	42	PEX14	T	3	3
NUP210L	91181	broad.mit.edu	36	1	152394133	152394133	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152394133A>C	uc001fdw.1	-	c.12T>G	c.(10-12)TGT>TGG	p.C4W		NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	4						integral to membrane				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)													0.416667	7.77368	7.867337	5	7	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)		Missense_Mutation	SNP	152394133	152394133	11166	1	A	C	C	10	10	NUP210L	C	4	4
SH2D2A	9047	broad.mit.edu	36	1	155050694	155050694	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:155050694G>C	uc009wsh.1	-	c.355C>G	c.(355-357)CTG>GTG	p.L119V	NTRK1_uc001fqf.1_5'Flank|NTRK1_uc009wsi.1_5'Flank|SH2D2A_uc001fqc.1_Missense_Mutation_p.L81V|SH2D2A_uc001fqd.1_Missense_Mutation_p.L109V|SH2D2A_uc001fqe.1_Missense_Mutation_p.L91V	NM_003975	NP_003966	Q9NP31	SH22A_HUMAN	SH2 domain protein 2A	109	SH2.				angiogenesis|cell differentiation|signal transduction	cytoplasm|soluble fraction	SH3 domain binding|SH3/SH2 adaptor activity				0	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)									2				0.263158	7.546747	8.528265	5	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	155050694	155050694	14723	1	G	C	C	34	34	SH2D2A	C	3	3
CLCNKB	1188	broad.mit.edu	36	1	16250807	16250807	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:16250807G>A	uc001axw.2	+	c.1313G>A	c.(1312-1314)CGC>CAC	p.R438H	CLCNKB_uc001axx.2_Missense_Mutation_p.R438H|CLCNKB_uc001axy.2_Missense_Mutation_p.R269H	NM_000085	NP_000076	P51801	CLCKB_HUMAN	chloride channel Kb	438			R -> C (in BS3).		excretion	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity				0		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)												0.427313	267.104231	268.131794	97	130	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Missense_Mutation	SNP	16250807	16250807	3606	1	G	A	A	38	38	CLCNKB	A	1	1
PPFIA4	8497	broad.mit.edu	36	1	201296107	201296107	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:201296107G>A	uc001gyz.1	+	c.1205G>A	c.(1204-1206)CGC>CAC	p.R402H	PPFIA4_uc009xaj.1_Missense_Mutation_p.R1033H|PPFIA4_uc001gza.1_Missense_Mutation_p.R298H|PPFIA4_uc001gzb.1_Missense_Mutation_p.R97H|PPFIA4_uc001gzc.1_5'Flank	NM_015053	NP_055868	O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f	402	SAM 1.				cell communication	cell surface|cytoplasm	protein binding			ovary(4)|skin(1)	5														0.189394	50.545467	62.422942	25	107	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	201296107	201296107	12742	1	G	A	A	38	38	PPFIA4	A	1	1
SRRM1	10250	broad.mit.edu	36	1	24869245	24869245	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:24869245G>A	uc001bjm.1	+	c.2252G>A	c.(2251-2253)CGA>CAA	p.R751Q	SRRM1_uc009vri.1_Missense_Mutation_p.R680Q	NM_005839	NP_005830	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	751	Pro-rich.|Ser-rich.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|nuclear matrix|nuclear speck	DNA binding|protein binding|RNA binding			ovary(2)|haematopoietic_and_lymphoid_tissue(1)	3		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)				Ovarian(68;897 1494 3282 17478)								0.39916	271.281397	273.39577	95	143	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)	Missense_Mutation	SNP	24869245	24869245	15682	1	G	A	A	37	37	SRRM1	A	1	1
TAL1	6886	broad.mit.edu	36	1	47458351	47458351	+	Silent	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:47458351G>A	uc001cqx.1	-	c.624C>T	c.(622-624)GCC>GCT	p.A208A	TAL1_uc009vyq.1_5'UTR|TAL1_uc001cqy.1_Silent_p.A208A	NM_003189	NP_003180	P17542	TAL1_HUMAN	T-cell acute lymphocytic leukemia 1	208	Helix-loop-helix motif.				cell fate commitment|cell proliferation|embryonic hemopoiesis|erythrocyte differentiation|positive regulation of cell division|positive regulation of chromatin assembly or disassembly|positive regulation of erythrocyte differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of mitotic cell cycle|positive regulation of protein complex assembly	nuclear chromatin	E-box binding|histone deacetylase binding|sequence-specific DNA binding transcription factor activity|transcription activator activity				0										17				0.229508	31.236497	35.327419	14	47	GG		KEEP	---	---	---	---	capture			Silent	SNP	47458351	47458351	16062	1	G	A	A	39	39	TAL1	A	1	1
L1TD1	54596	broad.mit.edu	36	1	62448181	62448181	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:62448181G>A	uc001dae.2	+	c.1147G>A	c.(1147-1149)GAG>AAG	p.E383K		NM_019079	NP_061952	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	383	Glu-rich.									ovary(1)	1														0.396552	135.727112	136.81282	46	70	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62448181	62448181	8912	1	G	A	A	37	37	L1TD1	A	1	1
TRPC4AP	26133	broad.mit.edu	36	20	33054989	33054989	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33054989C>T	uc002xbk.1	-	c.2141G>A	c.(2140-2142)CGG>CAG	p.R714Q	TRPC4AP_uc002xbj.1_Non-coding_Transcript|TRPC4AP_uc002xbl.1_Missense_Mutation_p.R706Q	NM_015638	NP_056453	Q8TEL6	TP4AP_HUMAN	TRPC4-associated protein isoform a	714					protein ubiquitination|ubiquitin-dependent protein catabolic process	Cul4A-RING ubiquitin ligase complex	protein binding			central_nervous_system(1)	1														0.432432	47.794182	47.941388	16	21	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(18;0.00936)		Missense_Mutation	SNP	33054989	33054989	17132	20	C	T	T	23	23	TRPC4AP	T	1	1
TSHZ2	128553	broad.mit.edu	36	20	51303641	51303641	+	Silent	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:51303641C>T	uc002xwo.2	+	c.237C>T	c.(235-237)GCC>GCT	p.A79A		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	79					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4														0.526316	123.508422	123.555028	40	36	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(23;0.1)		Silent	SNP	51303641	51303641	17175	20	C	T	T	23	23	TSHZ2	T	1	1
MC3R	4159	broad.mit.edu	36	20	54257825	54257825	+	Silent	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:54257825C>T	uc002xxb.2	+	c.630C>T	c.(628-630)GGC>GGT	p.G210G		NM_019888	NP_063941	P41968	MC3R_HUMAN	melanocortin 3 receptor	210	Helical; Name=4; (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|positive regulation of cAMP biosynthetic process	integral to plasma membrane	melanocyte-stimulating hormone receptor activity|neuropeptide binding|protein binding			ovary(2)	2														0.410256	178.785277	179.877505	64	92	CC		KEEP	---	---	---	---	capture	Colorectal(105;0.202)		Silent	SNP	54257825	54257825	9754	20	C	T	T	27	27	MC3R	T	1	1
SMCR7L	54471	broad.mit.edu	36	22	38239698	38239698	+	Silent	SNP	C	G	G			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:38239698C>G	uc003axw.2	+	c.816C>G	c.(814-816)GGC>GGG	p.G272G	SMCR7L_uc010gxz.1_Silent_p.G94G|SMCR7L_uc003axx.1_Silent_p.G272G|SMCR7L_uc003axy.1_Silent_p.G94G	NM_019008	NP_061881	Q9NQG6	SMC7L_HUMAN	hypothetical protein LOC54471	272						integral to membrane|mitochondrion				central_nervous_system(1)	1	Melanoma(58;0.04)											OREG0026577	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.333333	26.449811	27.415447	13	26	CC		KEEP	---	---	---	---	capture			Silent	SNP	38239698	38239698	15289	22	C	G	G	28	28	SMCR7L	G	3	3
ACR	49	broad.mit.edu	36	22	49530158	49530158	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49530158G>A	uc003bnh.2	+	c.923G>A	c.(922-924)CGA>CAA	p.R308Q		NM_001097	NP_001088	P10323	ACRO_HUMAN	acrosin precursor	308					acrosome matrix dispersal|activation of adenylate cyclase activity	acrosomal matrix|protein complex	amidase activity|copper ion binding|DNA binding|drug binding|fucose binding|mannose binding|protein binding|serine-type endopeptidase activity|zinc ion binding				0		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.5	17.448678	17.448678	6	6	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;1.1e-06)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49530158	49530158	170	22	G	A	A	37	37	ACR	A	1	1
FAM123C	205147	broad.mit.edu	36	2	131237665	131237665	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:131237665C>T	uc002trw.2	+	c.1550C>T	c.(1549-1551)ACG>ATG	p.T517M	FAM123C_uc010fms.1_Missense_Mutation_p.T517M|FAM123C_uc010fmt.1_Missense_Mutation_p.T517M|FAM123C_uc010fmu.1_Missense_Mutation_p.T517M|FAM123C_uc010fmv.1_Missense_Mutation_p.T517M	NM_152698	NP_689911	Q8N944	F123C_HUMAN	hypothetical protein LOC205147	517										pancreas(2)|ovary(1)	3	Colorectal(110;0.1)													0.444444	12.100124	12.124065	4	5	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.13)	Missense_Mutation	SNP	131237665	131237665	5621	2	C	T	T	19	19	FAM123C	T	1	1
THSD7B	80731	broad.mit.edu	36	2	137705183	137705183	+	Missense_Mutation	SNP	C	T	T	rs61741154	unknown	TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:137705183C>T	uc002tva.1	+	c.1730C>T	c.(1729-1731)ACG>ATG	p.T577M	THSD7B_uc002tvb.2_Missense_Mutation_p.T467M	NM_001080427	NP_001073896			thrombospondin, type I, domain containing 7B											ovary(4)|central_nervous_system(2)|pancreas(1)	7														0.482759	85.800161	85.814946	28	30	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.19)	Missense_Mutation	SNP	137705183	137705183	16408	2	C	T	T	19	19	THSD7B	T	1	1
XIRP2	129446	broad.mit.edu	36	2	167809481	167809481	+	Silent	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:167809481G>A	uc002udx.1	+	c.3333G>A	c.(3331-3333)TCG>TCA	p.S1111S	XIRP2_uc010fpn.1_Intron|XIRP2_uc010fpo.1_Intron|XIRP2_uc010fpp.1_Intron|XIRP2_uc002udy.2_Silent_p.S936S|XIRP2_uc010fpq.1_Silent_p.S889S|XIRP2_uc010fpr.1_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	936					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.379747	87.032492	88.034076	30	49	GG		KEEP	---	---	---	---	capture			Silent	SNP	167809481	167809481	18011	2	G	A	A	40	40	XIRP2	A	1	1
TTN	7273	broad.mit.edu	36	2	179355246	179355246	+	Silent	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179355246G>A	uc002umr.1	-	c.3318C>T	c.(3316-3318)GGC>GGT	p.G1106G	TTN_uc002ums.1_Silent_p.G1060G|TTN_uc010frc.1_Silent_p.G1060G|TTN_uc010frd.1_Silent_p.G1060G|TTN_uc002unb.1_Silent_p.G1106G	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1106										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153									p.G1106G(SIMA-Tumor)|p.G1106G(CFPAC1-Tumor)	8722				0.418803	138.848432	139.522717	49	68	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Silent	SNP	179355246	179355246	17290	2	G	A	A	38	38	TTN	A	1	1
CYP1B1	1545	broad.mit.edu	36	2	38155511	38155511	+	Silent	SNP	G	C	C			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:38155511G>C	uc002rqo.2	-	c.525C>G	c.(523-525)CGC>CGG	p.R175R		NM_000104	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B,	175					oxidation-reduction process|visual perception|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding|protein binding			ovary(1)|central_nervous_system(1)	2		all_hematologic(82;0.21)			Estrone(DB00655)					68				0.428571	8.222622	8.253987	3	4	GG		KEEP	---	---	---	---	capture			Silent	SNP	38155511	38155511	4316	2	G	C	C	38	38	CYP1B1	C	3	3
TET3	200424	broad.mit.edu	36	2	74128047	74128047	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:74128047C>T	uc002skb.2	+	c.1090C>T	c.(1090-1092)CCG>TCG	p.P364S	TET3_uc010fez.1_Missense_Mutation_p.P364S	NM_144993	NP_659430	O43151	TET3_HUMAN	tet oncogene family member 3	364					oxidation-reduction process		metal ion binding|methylcytosine dioxygenase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen				0														0.6	56.151509	56.413193	18	12	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74128047	74128047	16298	2	C	T	T	22	22	TET3	T	2	2
TIPARP	25976	broad.mit.edu	36	3	157905312	157905312	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:157905312A>G	uc003fav.1	+	c.1672A>G	c.(1672-1674)ATG>GTG	p.M558V	TIPARP_uc003faw.1_Missense_Mutation_p.M558V	NM_015508	NP_056323	Q7Z3E1	PARPT_HUMAN	TCDD-inducible poly(ADP-ribose) polymerase	558	PARP catalytic.						NAD+ ADP-ribosyltransferase activity|nucleic acid binding|protein binding|zinc ion binding			ovary(1)	1						Ovarian(171;276 1987 3319 6837 11197)								0.216561	274.99212	309.902567	102	369	AA		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)		Missense_Mutation	SNP	157905312	157905312	16453	3	A	G	G	4	4	TIPARP	G	4	4
VPS8	23355	broad.mit.edu	36	3	186130994	186130994	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:186130994G>A	uc003fpb.1	+	c.2836G>A	c.(2836-2838)GGA>AGA	p.G946R	VPS8_uc010hyd.1_Missense_Mutation_p.G856R|VPS8_uc010hye.1_Missense_Mutation_p.G375R	NM_015303	NP_056118	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog isoform b	948							zinc ion binding			ovary(1)	1	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)													0.638889	384.679829	387.742371	115	65	GG		KEEP	---	---	---	---	capture	Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)		Missense_Mutation	SNP	186130994	186130994	17785	3	G	A	A	39	39	VPS8	A	1	1
FGG	2266	broad.mit.edu	36	4	155747470	155747470	+	Silent	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155747470G>A	uc003iok.1	-	c.990C>T	c.(988-990)GGC>GGT	p.G330G	FGG_uc003iog.1_Silent_p.G322G|FGG_uc003ioh.1_Silent_p.G330G|FGG_uc010ipx.1_Silent_p.G150G|FGG_uc010ipy.1_Silent_p.G33G|FGG_uc003ioi.1_Silent_p.G33G|FGG_uc003ioj.1_Silent_p.G322G	NM_021870	NP_068656	P02679	FIBG_HUMAN	fibrinogen, gamma chain isoform gamma-B	322	Fibrinogen C-terminal.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding				0	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)									0.40625	180.257553	181.480832	65	95	GG		KEEP	---	---	---	---	capture			Silent	SNP	155747470	155747470	6107	4	G	A	A	38	38	FGG	A	1	1
C4orf35	85438	broad.mit.edu	36	4	71235870	71235870	+	Silent	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71235870C>T	uc003hff.1	+	c.525C>T	c.(523-525)GAC>GAT	p.D175D	C4orf35_uc010ihx.1_Silent_p.D175D	NM_033122	NP_149113	Q96KC9	CABS1_HUMAN	testis development protein NYD-SP26	175						flagellum	calcium ion binding				0		all_hematologic(202;0.196)												0.463415	114.445917	114.54092	38	44	CC		KEEP	---	---	---	---	capture			Silent	SNP	71235870	71235870	2360	4	C	T	T	19	19	C4orf35	T	1	1
NKD2	85409	broad.mit.edu	36	5	1086572	1086572	+	Silent	SNP	C	G	G			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1086572C>G	uc003jbt.1	+	c.288C>G	c.(286-288)CGC>CGG	p.R96R	NKD2_uc010itf.1_Silent_p.R96R	NM_033120	NP_149111	Q969F2	NKD2_HUMAN	naked cuticle homolog 2	96	Targeting to the basolateral cell membrane.				exocytosis|Wnt receptor signaling pathway	cytoplasmic membrane-bounded vesicle|plasma membrane	calcium ion binding|ubiquitin protein ligase binding				0	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)									126				0.428571	9.022989	9.054247	3	4	CC		KEEP	---	---	---	---	capture	Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)		Silent	SNP	1086572	1086572	10843	5	C	G	G	27	27	NKD2	G	3	3
PCDHGB2	56103	broad.mit.edu	36	5	140721808	140721808	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140721808G>A	uc003ljs.1	+	c.1922G>A	c.(1921-1923)CGC>CAC	p.R641H	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGA5_uc003lju.1_5'Flank|PCDHGB2_uc003ljr.1_Missense_Mutation_p.R641H|PCDHGA5_uc003ljt.1_5'Flank	NM_018923	NP_061746	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2 isoform 1	641	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0														0.47619	29.350946	29.361057	10	11	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140721808	140721808	11983	5	G	A	A	38	38	PCDHGB2	A	1	1
KIF4B	285643	broad.mit.edu	36	5	154377169	154377169	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:154377169C>A	uc010jih.1	+	c.3557C>A	c.(3556-3558)GCT>GAT	p.A1186D		NM_001099293	NP_001092763	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	1186	Interaction with PRC1 (By similarity).|Globular (By similarity).				axon guidance|blood coagulation|microtubule-based movement	cytosol|microtubule|nuclear matrix	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1	Renal(175;0.00488)	Medulloblastoma(196;0.0523)												0.47541	84.683246	84.714086	29	32	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)		Missense_Mutation	SNP	154377169	154377169	8615	5	C	A	A	28	28	KIF4B	A	3	3
C6orf170	221322	broad.mit.edu	36	6	121667267	121667267	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:121667267C>T	uc003pyo.1	-	c.878G>A	c.(877-879)CGT>CAT	p.R293H	C6orf170_uc003pyq.1_Non-coding_Transcript	NM_152730	NP_689943	Q96NH3	BROMI_HUMAN	hypothetical protein LOC221322	293					multicellular organismal development	cilium|cytoplasm	Rab GTPase activator activity			central_nervous_system(2)|ovary(1)	3														0.457447	129.411863	129.560233	43	51	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(226;0.00521)	Missense_Mutation	SNP	121667267	121667267	2449	6	C	T	T	19	19	C6orf170	T	1	1
HFE	3077	broad.mit.edu	36	6	26199194	26199194	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:26199194G>A	uc003nfx.1	+	c.223G>A	c.(223-225)GTT>ATT	p.V75I	HFE_uc010jqe.1_Missense_Mutation_p.V75I|HFE_uc003nfy.1_Missense_Mutation_p.V52I|HFE_uc003nfz.1_Intron|HFE_uc003nga.1_Missense_Mutation_p.V75I|HFE_uc003ngc.1_Missense_Mutation_p.V75I|HFE_uc003ngb.1_Missense_Mutation_p.V75I|HFE_uc003ngd.1_Intron|HFE_uc003nge.1_Intron|HFE_uc003ngf.1_Intron	NM_000410	NP_000401	Q30201	HFE_HUMAN	hemochromatosis protein isoform 1 precursor	75	Extracellular (Potential).|Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I|cellular iron ion homeostasis|immune response|iron ion transport|protein complex assembly|receptor-mediated endocytosis	apical part of cell|basal part of cell|cytoplasmic vesicle|early endosome|integral to plasma membrane|MHC class I protein complex|perinuclear region of cytoplasm|recycling endosome	protein binding				0														0.432	153.751895	154.250511	54	71	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26199194	26199194	7364	6	G	A	A	44	44	HFE	A	2	2
DUSP22	56940	broad.mit.edu	36	6	280117	280117	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:280117G>T	uc003msx.1	+	c.142G>T	c.(142-144)GTT>TTT	p.V48F	DUSP22_uc003msy.1_Missense_Mutation_p.V5F	NM_020185	NP_064570	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	48					apoptosis|cell proliferation|inactivation of MAPK activity|multicellular organismal development|positive regulation of JNK cascade|regulation of cell proliferation|transforming growth factor beta receptor signaling pathway	cytoplasm|nucleus	protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(1)|kidney(1)|central_nervous_system(1)	3	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)												0.132075	20.073929	34.01699	14	92	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)	Missense_Mutation	SNP	280117	280117	5006	6	G	T	T	36	36	DUSP22	T	3	3
RIMS1	22999	broad.mit.edu	36	6	73100131	73100131	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:73100131G>C	uc003pga.1	+	c.4238G>C	c.(4237-4239)GGC>GCC	p.G1413A	RIMS1_uc003pgc.1_Missense_Mutation_p.G862A|RIMS1_uc010kar.1_Intron|RIMS1_uc003pgh.1_Intron|RIMS1_uc003pgi.1_Intron|RIMS1_uc003pgd.1_Missense_Mutation_p.G479A|RIMS1_uc003pge.1_Missense_Mutation_p.G453A|RIMS1_uc003pgf.1_Missense_Mutation_p.G413A|RIMS1_uc003pgg.1_Intron	NM_014989	NP_055804	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1413					calcium ion-dependent exocytosis|cellular membrane fusion|glutamate secretion|intracellular protein transport|protein complex assembly|regulated secretory pathway|response to stimulus|synaptic vesicle exocytosis|visual perception	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(7)|pancreas(2)|breast(1)	10		all_epithelial(107;0.179)|all_hematologic(105;0.212)												0.5	7.018725	7.018725	3	3	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73100131	73100131	13844	6	G	C	C	42	42	RIMS1	C	3	3
RBAK	57786	broad.mit.edu	36	7	5063561	5063561	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:5063561G>A	uc010kss.1	+	c.125G>A	c.(124-126)AGC>AAC	p.S42N	LOC389458_uc003snr.1_Missense_Mutation_p.S42N|RBAK_uc003sns.1_Missense_Mutation_p.S42N	NM_021163	NP_066986	Q9NYW8	RBAK_HUMAN	RB-associated KRAB repressor	42	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription repressor activity|zinc ion binding			ovary(3)|kidney(1)|skin(1)	5		Ovarian(82;0.0175)												0.255556	177.437753	192.078185	69	201	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)	Missense_Mutation	SNP	5063561	5063561	13561	7	G	A	A	34	34	RBAK	A	2	2
DLGAP2	9228	broad.mit.edu	36	8	1485199	1485199	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:1485199C>A	uc003wpl.1	+	c.933C>A	c.(931-933)GAC>GAA	p.D311E	DLGAP2_uc003wpm.1_Missense_Mutation_p.D311E	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	390					nerve-nerve synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)												0.428571	6.920138	6.951917	3	4	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)	Missense_Mutation	SNP	1485199	1485199	4740	8	C	A	A	17	17	DLGAP2	A	3	3
PDGFRL	5157	broad.mit.edu	36	8	17491535	17491535	+	Splice_Site_SNP	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:17491535G>A	uc003wxr.2	+	c.353_splice	c.e2+1	p.S118_splice		NM_006207	NP_006198			platelet-derived growth factor receptor-like							extracellular region	platelet activating factor receptor activity|platelet-derived growth factor beta-receptor activity				0														0.330275	96.160398	98.944579	36	73	GG		KEEP	---	---	---	---	capture		Colorectal(111;0.0752)	Splice_Site_SNP	SNP	17491535	17491535	12084	8	G	A	A	44	44	PDGFRL	A	5	2
SLC44A1	23446	broad.mit.edu	36	9	107150504	107150504	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:107150504A>G	uc004bcn.1	+	c.451A>G	c.(451-453)ACA>GCA	p.T151A	SLC44A1_uc010mtk.1_Missense_Mutation_p.T151A	NM_080546	NP_536856	Q8WWI5	CTL1_HUMAN	CDW92 antigen	151	Mitochondrial intermembrane (Potential).					integral to membrane|mitochondrial outer membrane|plasma membrane	choline transmembrane transporter activity			breast(3)|ovary(1)	4					Choline(DB00122)									0.342342	122.415173	124.853308	38	73	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107150504	107150504	15132	9	A	G	G	14	14	SLC44A1	G	4	4
MED22	6837	broad.mit.edu	36	9	135200921	135200921	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1825-01	TCGA-14-1825-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135200921A>G	uc004cdc.1	-	c.293T>C	c.(292-294)ATT>ACT	p.I98T	MED22_uc004cdd.1_Missense_Mutation_p.I98T	NM_133640	NP_598395	Q15528	MED22_HUMAN	mediator complex subunit 22 isoform b	98	Potential.				regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|mediator complex|soluble fraction	protein binding|RNA polymerase II transcription mediator activity			ovary(1)	1														0.467153	214.389761	214.51815	64	73	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.14e-06)|Epithelial(140;8.2e-06)|all cancers(34;6.94e-05)	Missense_Mutation	SNP	135200921	135200921	9829	9	A	G	G	4	4	MED22	G	4	4
PLIN2	123	broad.mit.edu	36	9	19110899	19110899	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:19110899G>A	uc003zno.1	-	c.574C>T	c.(574-576)CCT>TCT	p.P192S		NM_001122	NP_001113	Q99541	PLIN2_HUMAN	adipose differentiation-related protein	192					cellular lipid metabolic process	endoplasmic reticulum|extracellular region|lipid particle				ovary(1)	1														0.414815	169.073312	169.928942	56	79	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19110899	19110899	12516	9	G	A	A	43	43	PLIN2	A	2	2
RANBP6	26953	broad.mit.edu	36	9	6004248	6004248	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:6004248G>T	uc003zjr.1	-	c.1360C>A	c.(1360-1362)CTG>ATG	p.L454M	RANBP6_uc003zjs.1_Missense_Mutation_p.L42M	NM_012416	NP_036548	O60518	RNBP6_HUMAN	RAN binding protein 6	454	HEAT 4.				protein transport	cytoplasm|nucleus	binding			ovary(3)	3		Acute lymphoblastic leukemia(23;0.158)												0.356164	71.425582	72.757806	26	47	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)	Missense_Mutation	SNP	6004248	6004248	13491	9	G	T	T	33	33	RANBP6	T	3	3
DCAF12L1	139170	broad.mit.edu	36	X	125513269	125513269	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:125513269C>T	uc004eul.1	-	c.1004G>A	c.(1003-1005)CGC>CAC	p.R335H	DCAF12L1_uc010nqz.1_Missense_Mutation_p.R335H	NM_178470	NP_848565	Q5VU92	DC121_HUMAN	WD repeat domain 40B	335										skin(3)	3														0.876923	183.714153	192.75592	57	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	125513269	125513269	4435	23	C	T	T	27	27	DCAF12L1	T	1	1
MAGEA10	4109	broad.mit.edu	36	X	151054036	151054036	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:151054036C>T	uc004ffk.1	-	c.713G>A	c.(712-714)GGC>GAC	p.G238D	MAGEA10_uc004ffl.1_Missense_Mutation_p.G238D|MAGEA10_uc010ntj.1_Missense_Mutation_p.G238D	NM_001011543	NP_066386	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	238	MAGE.										0	Acute lymphoblastic leukemia(192;6.56e-05)													0.851852	151.682613	158.098008	46	8	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151054036	151054036	9541	23	C	T	T	26	26	MAGEA10	T	2	2
CFP	5199	broad.mit.edu	36	X	47371223	47371223	+	Missense_Mutation	SNP	G	T	T			TCGA-14-1825-01	TCGA-14-1825-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:47371223G>T	uc004dig.2	-	c.833C>A	c.(832-834)ACC>AAC	p.T278N	CFP_uc004dih.1_Missense_Mutation_p.T278N|CFP_uc004dii.1_Missense_Mutation_p.T214N|CFP_uc010nhu.1_Missense_Mutation_p.T278N	NM_002621	NP_002612	P27918	PROP_HUMAN	complement factor properdin precursor	278	TSP type-1 4.				complement activation, alternative pathway|defense response to bacterium	extracellular space				breast(2)|lung(1)	3														0.923077	41.030849	42.891199	12	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47371223	47371223	3426	23	G	T	T	44	44	CFP	T	3	3
ITIH5L	347365	broad.mit.edu	36	X	54794495	54794495	+	Silent	SNP	C	T	T			TCGA-14-1825-01	TCGA-14-1825-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:54794495C>T	uc004dtj.1	-	c.3396G>A	c.(3394-3396)CCG>CCA	p.P1132P		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	inter-alpha (globulin) inhibitor H5-like	1132					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5										249				0.815789	106.647688	110.203353	31	7	CC		KEEP	---	---	---	---	capture			Silent	SNP	54794495	54794495	8212	23	C	T	T	23	23	ITIH5L	T	1	1
PLCE1	51196	broad.mit.edu	36	10	96029587	96029588	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-14-1825-01	TCGA-14-1825-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:96029587_96029588delGA	uc001kjk.1	+	c.4724_4725delGA	c.(4723-4725)CGAfs	p.R1575fs	PLCE1_uc001kjm.2_Frame_Shift_Del_p.R1267fs	NM_016341	NP_057425	Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1575				R -> Q (in Ref. 2; AAG28341).	activation of MAPK activity|activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger|activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|calcium-mediated signaling|cell proliferation|cytoskeleton organization|diacylglycerol biosynthetic process|elevation of cytosolic calcium ion concentration|epidermal growth factor receptor signaling pathway|glomerulus development|heart development|lipid catabolic process|phospholipid metabolic process|Ras protein signal transduction|regulation of cell growth|regulation of G-protein coupled receptor protein signaling pathway|regulation of Ras protein signal transduction|regulation of smooth muscle contraction	cytosol|Golgi membrane|membrane fraction|plasma membrane	calcium ion binding|guanyl-nucleotide exchange factor activity|phosphatidylinositol phospholipase C activity|Ras GTPase binding|receptor signaling protein activity			ovary(2)|skin(1)	3		Colorectal(252;0.0458)										OREG0020383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.33			20	40				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	96029587	96029588	12460	10	GA	-	-	37	37	PLCE1	-	5	5
MICALCL	84953	broad.mit.edu	36	11	12272963	12272965	+	In_Frame_Del	DEL	CTA	-	-			TCGA-14-1825-01	TCGA-14-1825-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:12272963_12272965delCTA	uc001mkg.1	+	c.1409_1411delCTA	c.(1408-1413)CCTACA>CCA	p.T471del		NM_032867	NP_116256	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	471					cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm	mitogen-activated protein kinase binding				0				Epithelial(150;0.00177)										0.80			12	3				---	---	---	---	capture_indel			In_Frame_Del	DEL	12272963	12272965	9962	11	CTA	-	-	24	24	MICALCL	-	5	5
CACNA1G	8913	broad.mit.edu	36	17	46058852	46058853	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-1825-01	TCGA-14-1825-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:46058852_46058853insC	uc002irk.1	+	c.6875_6876insC	c.(6874-6876)GGCfs	p.G2292fs	CACNA1G_uc002irj.1_Frame_Shift_Ins_p.G2086fs|CACNA1G_uc002irl.1_Frame_Shift_Ins_p.G2176fs|CACNA1G_uc002irm.1_Frame_Shift_Ins_p.G2213fs|CACNA1G_uc002irn.1_Frame_Shift_Ins_p.G2158fs|CACNA1G_uc002iro.1_Frame_Shift_Ins_p.G2165fs|CACNA1G_uc002irp.1_Frame_Shift_Ins_p.G2247fs|CACNA1G_uc002irq.1_Frame_Shift_Ins_p.G2269fs|CACNA1G_uc002irr.1_Frame_Shift_Ins_p.G2199fs|CACNA1G_uc002irs.1_Frame_Shift_Ins_p.G2236fs|CACNA1G_uc002irt.1_Frame_Shift_Ins_p.G2181fs|CACNA1G_uc002irv.1_Frame_Shift_Ins_p.G2188fs|CACNA1G_uc002irw.1_Frame_Shift_Ins_p.G2221fs|CACNA1G_uc002iru.1_Frame_Shift_Ins_p.G2258fs|CACNA1G_uc002irx.1_Frame_Shift_Ins_p.G2033fs|CACNA1G_uc002iry.1_Frame_Shift_Ins_p.G2022fs|CACNA1G_uc002irz.1_Frame_Shift_Ins_p.G2105fs|CACNA1G_uc002isa.1_Frame_Shift_Ins_p.G2078fs|CACNA1G_uc002isb.1_Frame_Shift_Ins_p.G2119fs|CACNA1G_uc002isc.1_Frame_Shift_Ins_p.G2194fs|CACNA1G_uc002isd.1_Frame_Shift_Ins_p.G2087fs|CACNA1G_uc002ise.1_Frame_Shift_Ins_p.G2115fs|CACNA1G_uc002isf.1_Frame_Shift_Ins_p.G2142fs|CACNA1G_uc002isg.1_Frame_Shift_Ins_p.G2060fs|CACNA1G_uc002ish.1_Frame_Shift_Ins_p.G2067fs|CACNA1G_uc002isi.1_Frame_Shift_Ins_p.G2055fs	NM_018896	NP_061496	O43497	CAC1G_HUMAN	voltage-dependent calcium channel alpha 1G	2292	Cytoplasmic (Potential).				axon guidance	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(1)	1	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Ethosuximide(DB00593)|Flunarizine(DB04841)|Levetiracetam(DB01202)|Mibefradil(DB01388)|Pimozide(DB01100)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)							OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.33			3	6				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	46058852	46058853	2660	17	-	C	C	42	42	CACNA1G	C	5	5
PRIM2	5558	broad.mit.edu	36	6	57620875	57620876	+	Splice_Site_Ins	INS	-	T	T			TCGA-14-1825-01	TCGA-14-1825-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:57620875_57620876insT	uc003pdx.1	+	c.e16_splice_site				NM_000947	NP_000938			DNA primase polypeptide 2						DNA replication, synthesis of RNA primer|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0				Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)										0.43			3	4				---	---	---	---	capture_indel			Splice_Site_Ins	INS	57620875	57620876	12934	6	-	T	T	4	4	PRIM2	T	5	5
MAMDC4	158056	broad.mit.edu	36	9	138873365	138873366	+	Frame_Shift_Ins	INS	-	G	G			TCGA-14-1825-01	TCGA-14-1825-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:138873365_138873366insG	uc004cjs.1	+	c.3044_3045insG	c.(3043-3045)CTGfs	p.L1015fs		NM_206920	NP_996803	Q6UXC1	AEGP_HUMAN	apical early endosomal glycoprotein precursor	1094	Extracellular (Potential).|MAM 6.				protein transport	integral to membrane				breast(4)	4	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)						290				0.38			3	5				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	138873365	138873366	9587	9	-	G	G	55	55	MAMDC4	G	5	5
SLC35A2	7355	broad.mit.edu	36	X	48647495	48647496	+	Frame_Shift_Del	DEL	GA	-	-			TCGA-14-1825-01	TCGA-14-1825-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48647495_48647496delGA	uc004dlo.1	-	c.634_635delTC	c.(634-636)TCCfs	p.S212fs	SLC35A2_uc004dlp.1_Frame_Shift_Del_p.S212fs|SLC35A2_uc004dlq.1_Intron|SLC35A2_uc004dlr.1_Intron	NM_005660	NP_005651	P78381	S35A2_HUMAN	solute carrier family 35, member A2 isoform a	212	Helical; (Potential).				galactose metabolic process	Golgi membrane|integral to membrane|nucleus	sugar:hydrogen symporter activity|UDP-galactose transmembrane transporter activity			breast(1)	1														0.67			4	2				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	48647495	48647496	15068	23	GA	-	-	41	41	SLC35A2	-	5	5
