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
CHUK	1147	broad.mit.edu	36	10	101979214	101979214	+	Silent	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:101979214G>C	uc001kqp.1	-	c.66C>G	c.(64-66)GGC>GGG	p.G22G		NM_001278	NP_001269	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	22	ATP (By similarity).|Protein kinase.				I-kappaB phosphorylation|innate immune response|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	CD40 receptor complex|cytosol|internal side of plasma membrane|nucleus	ATP binding|identical protein binding|IkappaB kinase activity			ovary(2)|central_nervous_system(2)|large_intestine(1)|lung(1)|breast(1)	7		Colorectal(252;0.117)				Ovarian(159;52 1904 10536 35305 37148)				415				1	9.002535	8.932306	4	0	GG		KEEP	---	---	---	---	capture		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Silent	SNP	101979214	101979214	3550	10	G	C	C	46	46	CHUK	C	3	3
PLA2G12B	84647	broad.mit.edu	36	10	74384429	74384429	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:74384429G>A	uc001jtf.1	-	c.21C>T	c.(19-21)TTC>TTT	p.F7F	PLA2G12B_uc009xqt.1_5'UTR	NM_032562	NP_115951	Q9BX93	PG12B_HUMAN	phospholipase A2, group XIIB	7					lipid catabolic process	extracellular region	calcium ion binding|phospholipase A2 activity			ovary(1)	1	Prostate(51;0.0198)													0.341463	17.689219	18.670442	14	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	74384429	74384429	12417	10	G	A	A	33	33	PLA2G12B	A	2	2
MYST4	23522	broad.mit.edu	36	10	76460692	76460692	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:76460692A>C	uc001jwn.1	+	c.6104A>C	c.(6103-6105)CAG>CCG	p.Q2035P	MYST4_uc001jwo.1_Missense_Mutation_p.Q1743P|MYST4_uc001jwp.1_Missense_Mutation_p.Q1852P	NM_012330	NP_036462	Q8WYB5	MYST4_HUMAN	MYST histone acetyltransferase (monocytic	2035	Interaction with RUNX1 and RUNX2.|Met-rich.				histone H3 acetylation|negative regulation of transcription, DNA-dependent|nucleosome assembly|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	MOZ/MORF histone acetyltransferase complex|nucleosome	DNA binding|histone acetyltransferase activity|transcription activator activity|transcription factor binding|transcription repressor activity|zinc ion binding			central_nervous_system(5)|ovary(3)|breast(1)	9	all_cancers(46;0.0347)|all_epithelial(25;0.00236)|Prostate(51;0.0112)|Ovarian(15;0.0964)									319				0.209677	9.300745	14.470798	13	49	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	76460692	76460692	10500	10	A	C	C	7	7	MYST4	C	4	4
PTEN	5728	broad.mit.edu	36	10	89682772	89682772	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682772C>A	uc001kfb.1	+	c.276C>A	c.(274-276)GAC>GAA	p.D92E		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	92	Phosphatase tensin-type.			D->A: 700-fold reduction in phosphatase activity towards PtdIns(3,4,5)P3. Loss of protein phosphatase activity. Unable to inhibit focal adhesion formation.	apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.D92H(3)|p.Y27_N212>Y(2)|p.D92E(1)|p.Q87_P96del(1)|p.N82_P95del(1)|p.F90_P95>L(1)|p.F56fs*2(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31	p.D92E(HCC33-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.307692	116.9528	121.237617	40	90	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89682772	89682772	13192	10	C	A	A	18	18	PTEN	A	3	3
FDXACB1	91893	broad.mit.edu	36	11	111254970	111254970	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:111254970T>G	uc001pmc.2	-	c.97A>C	c.(97-99)ACC>CCC	p.T33P	FDXACB1_uc009yyi.1_5'UTR|C11orf1_uc001pmd.1_5'Flank|C11orf1_uc001pme.1_5'Flank	NM_138378	NP_612387	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain	33					phenylalanyl-tRNA aminoacylation|tRNA processing		ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|tRNA binding				0												OREG0021330	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.285714	7.034432	7.98128	6	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111254970	111254970	6043	11	T	G	G	59	59	FDXACB1	G	4	4
MUC5B	727897	broad.mit.edu	36	11	1214956	1214956	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1214956G>C	uc001ltb.2	+	c.3292G>C	c.(3292-3294)GCC>CCC	p.A1098P	MUC5B_uc009yct.1_Missense_Mutation_p.A1095P	NM_002458	NP_002449	Q9HC84	MUC5B_HUMAN	mucin 5, subtype B, tracheobronchial	1095	VWFD 3.				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding				0		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)												0.333333	8.217383	8.613382	5	10	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)	Missense_Mutation	SNP	1214956	1214956	10373	11	G	C	C	38	38	MUC5B	C	3	3
C11orf61	79684	broad.mit.edu	36	11	124175122	124175122	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:124175122A>C	uc001qba.1	-	c.365T>G	c.(364-366)GTG>GGG	p.V122G	C11orf61_uc001qaz.1_Missense_Mutation_p.V122G	NM_024631	NP_078907	Q6P1R3	CK061_HUMAN	hypothetical protein LOC79684	122											0	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)												0.75	11.918304	12.36104	6	2	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0079)	Missense_Mutation	SNP	124175122	124175122	1692	11	A	C	C	6	6	C11orf61	C	4	4
SERPING1	710	broad.mit.edu	36	11	57135833	57135833	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:57135833G>A	uc009ymi.1	+	c.1124G>A	c.(1123-1125)CGT>CAT	p.R375H	SERPING1_uc001nkp.1_Missense_Mutation_p.R366H|SERPING1_uc001nkq.1_Intron|SERPING1_uc001nkr.1_Missense_Mutation_p.R366H|SERPING1_uc009ymj.1_Intron|SERPING1_uc001nks.1_Missense_Mutation_p.R57H	NM_001032295	NP_001027466	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G, member 1	366					blood circulation|blood coagulation, intrinsic pathway|complement activation, classical pathway|innate immune response|negative regulation of complement activation, lectin pathway|platelet activation|platelet degranulation	extracellular space|platelet alpha granule lumen	protein binding|serine-type endopeptidase inhibitor activity			central_nervous_system(1)	1														0.410811	218.919861	220.187954	76	109	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57135833	57135833	14604	11	G	A	A	40	40	SERPING1	A	1	1
OR52B2	255725	broad.mit.edu	36	11	6147330	6147330	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6147330C>T	uc001mch.1	-	c.803G>A	c.(802-804)CGT>CAT	p.R268H		NM_001004052	NP_001004052	Q96RD2	O52B2_HUMAN	olfactory receptor, family 52, subfamily B,	268	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)				NSCLC(5;186 261 1778 7098 14207)								0.291667	55.84547	58.644849	21	51	CC		KEEP	---	---	---	---	capture		Epithelial(150;3.69e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	6147330	6147330	11521	11	C	T	T	19	19	OR52B2	T	1	1
TAF6L	10629	broad.mit.edu	36	11	62306382	62306382	+	Splice_Site_SNP	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62306382G>T	uc001nvc.1	+	c.827_splice	c.e8+1	p.W276_splice	TAF6L_uc009yof.1_Missense_Mutation_p.W276C	NM_006473	NP_006464			TAF6-like RNA polymerase II						chromatin remodeling|histone H3 acetylation|regulation of sequence-specific DNA binding transcription factor activity|regulation of transcription from RNA polymerase II promoter|transcription initiation, DNA-dependent	histone deacetylase complex|STAGA complex	DNA binding|protein binding|RNA polymerase II transcription factor activity|transcription coactivator activity|transcription initiation factor activity			ovary(3)	3														0.190476	12.685232	18.374768	12	51	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	62306382	62306382	16052	11	G	T	T	44	44	TAF6L	T	5	3
DNHD1	144132	broad.mit.edu	36	11	6545610	6545610	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6545610T>C	uc001mea.2	+	c.1102T>C	c.(1102-1104)TCA>CCA	p.S368P	DNHD1_uc001mdw.2_Missense_Mutation_p.S2153P|DNHD1_uc001meb.2_Missense_Mutation_p.S367P|DNHD1_uc001mec.1_Missense_Mutation_p.S367P|DNHD1_uc009yfg.1_5'Flank	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	4099					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)												0.223881	8.857268	13.868414	15	52	TT		KEEP	---	---	---	---	capture		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)	Missense_Mutation	SNP	6545610	6545610	4851	11	T	C	C	54	54	DNHD1	C	4	4
DCHS1	8642	broad.mit.edu	36	11	6605044	6605044	+	Silent	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6605044A>C	uc001mem.1	-	c.5802T>G	c.(5800-5802)GGT>GGG	p.G1934G		NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN	dachsous 1 precursor	1934	Cadherin 18.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|large_intestine(1)|pancreas(1)	5		Medulloblastoma(188;0.00263)|all_neural(188;0.026)												0.4	7.039716	7.225607	6	9	AA		KEEP	---	---	---	---	capture		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Silent	SNP	6605044	6605044	4458	11	A	C	C	6	6	DCHS1	C	4	4
NADSYN1	55191	broad.mit.edu	36	11	70870651	70870651	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:70870651A>G	uc001oqn.1	+	c.1082A>G	c.(1081-1083)GAC>GGC	p.D361G	NADSYN1_uc001oqo.1_Missense_Mutation_p.D101G|NADSYN1_uc001oqp.1_5'UTR	NM_018161	NP_060631	Q6IA69	NADE_HUMAN	NAD synthetase 1	361	ATP (By similarity).|Ligase (By similarity).				NAD biosynthetic process	cytosol	ATP binding|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds|NAD+ synthase (glutamine-hydrolyzing) activity|protein binding			ovary(2)	2					L-Glutamic Acid(DB00142)|L-Glutamine(DB00130)	Ovarian(79;763 1781 6490 50276)								0.6	7.924336	7.967817	3	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70870651	70870651	10534	11	A	G	G	10	10	NADSYN1	G	4	4
PNPLA2	57104	broad.mit.edu	36	11	814736	814736	+	Silent	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:814736A>C	uc001lrt.1	+	c.1389A>C	c.(1387-1389)GCA>GCC	p.A463A	PNPLA2_uc009ycl.1_Missense_Mutation_p.T275P|EFCAB4A_uc009ycm.1_5'Flank	NM_020376	NP_065109	Q96AD5	PLPL2_HUMAN	patatin-like phospholipase domain containing 2	463	Lumenal (Potential).				negative regulation of sequestering of triglyceride|positive regulation of triglyceride catabolic process	integral to membrane|lipid particle|plasma membrane	triglyceride lipase activity				0		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)												0.714286	9.314275	9.588671	5	2	AA		KEEP	---	---	---	---	capture		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Silent	SNP	814736	814736	12592	11	A	C	C	6	6	PNPLA2	C	4	4
SPIC	121599	broad.mit.edu	36	12	100404461	100404461	+	Silent	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:100404461C>T	uc001tid.1	+	c.528C>T	c.(526-528)TAC>TAT	p.Y176Y	SPIC_uc001tie.1_Silent_p.Y176Y|SPIC_uc009zua.1_Silent_p.Y51Y	NM_152323	NP_689536	Q8N5J4	SPIC_HUMAN	Spi-C transcription factor (Spi-1/PU.1 related)	176	ETS.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0														0.240876	78.905599	87.300029	33	104	CC		KEEP	---	---	---	---	capture			Silent	SNP	100404461	100404461	15563	12	C	T	T	19	19	SPIC	T	1	1
ANKRD52	283373	broad.mit.edu	36	12	54932105	54932105	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54932105T>C	uc001skm.2	-	c.1553A>G	c.(1552-1554)GAC>GGC	p.D518G		NM_173595	NP_775866	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	518	ANK 15.						protein binding			ovary(2)	2														0.141414	10.865728	23.231385	14	85	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54932105	54932105	686	12	T	C	C	58	58	ANKRD52	C	4	4
LRP1	4035	broad.mit.edu	36	12	55876248	55876248	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55876248G>C	uc001snd.1	+	c.8813G>C	c.(8812-8814)GGC>GCC	p.G2938A		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	2938	LDL-receptor class A 20.|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)					1456				0.384615	8.859994	9.015189	5	8	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0103)	Missense_Mutation	SNP	55876248	55876248	9324	12	G	C	C	42	42	LRP1	C	3	3
RAB21	23011	broad.mit.edu	36	12	70450651	70450651	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:70450651C>G	uc001swt.1	+	c.232C>G	c.(232-234)CAA>GAA	p.Q78E		NM_014999	NP_055814	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	78	GTP (By similarity).			Q->L: Defects in GTP hydrolysis.	protein transport|small GTPase mediated signal transduction	cleavage furrow|cytoplasmic vesicle membrane|early endosome membrane|endoplasmic reticulum membrane|Golgi membrane	GDP binding|GTP binding|GTPase activity|protein binding				0														0.185185	7.354033	9.870218	5	22	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70450651	70450651	13367	12	C	G	G	29	29	RAB21	G	3	3
KCTD12	115207	broad.mit.edu	36	13	76357643	76357643	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:76357643G>T	uc010aeu.1	-	c.642C>A	c.(640-642)TAC>TAA	p.Y214*	KCTD12_uc001vka.1_Nonsense_Mutation_p.Y214*	NM_138444	NP_612453	Q96CX2	KCD12_HUMAN	potassium channel tetramerisation domain	214						cell junction|postsynaptic membrane|presynaptic membrane|voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			ovary(1)	1		Breast(118;0.212)										OREG0022449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.307692	8.192783	8.623161	4	9	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;0.0499)	Nonsense_Mutation	SNP	76357643	76357643	8405	13	G	T	T	44	44	KCTD12	T	5	3
OR4Q3	441669	broad.mit.edu	36	14	19285931	19285931	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19285931T>C	uc001vwe.1	+	c.505T>C	c.(505-507)TTC>CTC	p.F169L		NM_172194	NP_751944	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q,	169	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(3)	3	all_cancers(95;0.00108)													0.09622	31.378351	78.944824	28	263	TT		KEEP	---	---	---	---	capture	Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)	Missense_Mutation	SNP	19285931	19285931	11491	14	T	C	C	64	64	OR4Q3	C	4	4
JPH4	84502	broad.mit.edu	36	14	23109985	23109985	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23109985C>G	uc001wkr.1	-	c.1795G>C	c.(1795-1797)GCC>CCC	p.A599P	AP1G2_uc001wkm.1_5'Flank|AP1G2_uc001wkn.1_5'Flank|AP1G2_uc001wkl.1_5'Flank|AP1G2_uc010akt.1_5'Flank|JPH4_uc001wkq.1_Missense_Mutation_p.A599P	NM_032452	NP_115828	Q96JJ6	JPH4_HUMAN	junctophilin 4	599	Cytoplasmic (Potential).				calcium ion transport into cytosol|regulation of ryanodine-sensitive calcium-release channel activity	integral to membrane|junctional sarcoplasmic reticulum membrane				ovary(1)|pancreas(1)	2	all_cancers(95;0.000251)													0.25	6.339529	7.00818	3	9	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.00654)	Missense_Mutation	SNP	23109985	23109985	8267	14	C	G	G	25	25	JPH4	G	3	3
DACT1	51339	broad.mit.edu	36	14	58183129	58183129	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:58183129T>G	uc001xdw.1	+	c.2035T>G	c.(2035-2037)TGG>GGG	p.W679G	DACT1_uc001xdx.1_Missense_Mutation_p.W642G	NM_016651	NP_057735	Q9NYF0	DACT1_HUMAN	dapper 1 isoform 1	679					multicellular organismal development|Wnt receptor signaling pathway	cytoplasm|nucleus				large_intestine(2)|lung(2)|ovary(1)	5														0.266667	7.180075	7.929722	4	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58183129	58183129	4388	14	T	G	G	59	59	DACT1	G	4	4
GPR68	8111	broad.mit.edu	36	14	90770466	90770466	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:90770466G>A	uc001xzh.1	-	c.712C>T	c.(712-714)CGG>TGG	p.R238W	GPR68_uc001xzg.1_Missense_Mutation_p.R228W|GPR68_uc010atx.1_Missense_Mutation_p.R238W	NM_003485	NP_003476	Q15743	OGR1_HUMAN	G protein-coupled receptor 68	228	Cytoplasmic (Potential).				inflammatory response	integral to plasma membrane	G-protein coupled receptor activity			kidney(1)	1		all_cancers(154;0.0555)												0.4	29.345406	29.563891	10	15	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(157;0.21)	Missense_Mutation	SNP	90770466	90770466	6982	14	G	A	A	38	38	GPR68	A	1	1
SNX1	6642	broad.mit.edu	36	15	62202777	62202777	+	Silent	SNP	A	G	G			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:62202777A>G	uc002amv.1	+	c.489A>G	c.(487-489)GTA>GTG	p.V163V	SNX1_uc010bgv.1_Intron|SNX1_uc002amw.1_Silent_p.V163V|SNX1_uc002amx.1_Silent_p.V98V|SNX1_uc002amy.1_Silent_p.V92V|SNX1_uc010bgw.1_Silent_p.V65V	NM_003099	NP_003090	Q13596	SNX1_HUMAN	sorting nexin 1 isoform a	163	PX.				cell communication|early endosome to Golgi transport|endocytosis|intracellular protein transport	early endosome membrane|Golgi apparatus	phosphatidylinositol binding|protein binding|protein transporter activity				0														0.30137	143.950695	149.090497	44	102	AA		KEEP	---	---	---	---	capture			Silent	SNP	62202777	62202777	15380	15	A	G	G	15	15	SNX1	G	4	4
HCN4	10021	broad.mit.edu	36	15	71447078	71447078	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:71447078G>C	uc002avp.1	-	c.587C>G	c.(586-588)GCC>GGC	p.A196G		NM_005477	NP_005468	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic	196	Cytoplasmic (Potential).				blood circulation|muscle contraction	integral to membrane	cAMP binding|protein binding|sodium channel activity|voltage-gated potassium channel activity			ovary(5)|liver(1)	6														0.714286	11.712516	11.979475	5	2	GG		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(1;0.142)	Missense_Mutation	SNP	71447078	71447078	7281	15	G	C	C	42	42	HCN4	C	3	3
ANPEP	290	broad.mit.edu	36	15	88141930	88141930	+	Silent	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:88141930C>T	uc002bop.2	-	c.2037G>A	c.(2035-2037)GCG>GCA	p.A679A		NM_001150	NP_001141	P15144	AMPN_HUMAN	membrane alanine aminopeptidase precursor	679	Extracellular.|Metalloprotease.				angiogenesis|cell differentiation|interspecies interaction between organisms	cytosol|ER-Golgi intermediate compartment|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|receptor activity|zinc ion binding			ovary(3)	3	Lung NSC(78;0.0221)|all_lung(78;0.0448)				Ezetimibe(DB00973)	NSCLC(30;827 977 2459 19669 26125)								0.153509	61.902252	88.061734	35	193	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Silent	SNP	88141930	88141930	718	15	C	T	T	27	27	ANPEP	T	1	1
CIITA	4261	broad.mit.edu	36	16	10910411	10910411	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:10910411G>A	uc002daj.2	+	c.2685G>A	c.(2683-2685)GCG>GCA	p.A895A	CIITA_uc010bup.1_Intron|CIITA_uc002dai.2_Silent_p.A894A|CIITA_uc002dak.2_Silent_p.A310A	NM_000246	NP_000237	P33076	C2TA_HUMAN	class II transactivator	894					interferon-gamma-mediated signaling pathway|negative regulation of collagen biosynthetic process|negative regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of MHC class I biosynthetic process|positive regulation of MHC class II biosynthetic process|response to antibiotic|transcription, DNA-dependent	nucleus	activating transcription factor binding|ATP binding|promoter binding|protein C-terminus binding|protein complex binding|RNA polymerase II transcription factor activity|transcription activator activity|transcription coactivator activity|transcription repressor activity			central_nervous_system(1)	1										532				0.322222	73.614343	76.156624	29	61	GG		KEEP	---	---	---	---	capture			Silent	SNP	10910411	10910411	3562	16	G	A	A	38	38	CIITA	A	1	1
ZNF688	146542	broad.mit.edu	36	16	30488865	30488865	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30488865G>A	uc002dyt.1	-	c.704C>T	c.(703-705)TCC>TTC	p.S235F	ZNF688_uc002dys.1_Missense_Mutation_p.S221F	NM_145271	NP_660314	P0C7X2	ZN688_HUMAN	zinc finger protein 688 isoform a	235					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.222222	13.735372	15.652361	6	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30488865	30488865	18688	16	G	A	A	41	41	ZNF688	A	2	2
TRIM72	493829	broad.mit.edu	36	16	31137984	31137984	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31137984T>G	uc002ebn.1	+	c.458T>G	c.(457-459)GTG>GGG	p.V153G	PYDC1_uc002ebo.1_5'Flank|PYDC1_uc010cal.1_5'Flank	NM_001008274	NP_001008275	Q6ZMU5	TRI72_HUMAN	tripartite motif-containing 72	153	Potential.				exocytosis|muscle organ development|muscle system process|plasma membrane repair|protein homooligomerization	cytoplasmic vesicle membrane|sarcolemma	phosphatidylserine binding|zinc ion binding				0														0.32	9.147751	9.950407	8	17	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31137984	31137984	17094	16	T	G	G	59	59	TRIM72	G	4	4
CYLD	1540	broad.mit.edu	36	16	49345790	49345790	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:49345790G>A	uc002egp.1	+	c.867G>A	c.(865-867)GCG>GCA	p.A289A	CYLD_uc002egn.1_Silent_p.A289A|CYLD_uc002ego.2_Silent_p.A289A|CYLD_uc010cbs.1_Silent_p.A289A|CYLD_uc002egq.1_Silent_p.A289A|CYLD_uc002egr.1_Silent_p.A289A|CYLD_uc002egs.1_Silent_p.A289A	NM_015247	NP_056062	Q9NQC7	CYLD_HUMAN	ubiquitin carboxyl-terminal hydrolase CYLD	289	Interaction with TRIP.				cell cycle|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of NF-kappaB import into nucleus|negative regulation of NF-kappaB transcription factor activity|negative regulation of type I interferon production|protein K63-linked deubiquitination|regulation of microtubule cytoskeleton organization|regulation of mitotic cell cycle|translation|ubiquitin-dependent protein catabolic process|Wnt receptor signaling pathway	cytosol|extrinsic to internal side of plasma membrane|microtubule|perinuclear region of cytoplasm|ribosome	proline-rich region binding|protein kinase binding|structural constituent of ribosome|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding	p.A289A(1)		skin(19)|large_intestine(3)|haematopoietic_and_lymphoid_tissue(3)|central_nervous_system(3)	28		all_cancers(37;0.0156)								247				0.261364	59.884678	64.41993	23	65	GG		KEEP	---	---	---	---	capture			Silent	SNP	49345790	49345790	4308	16	G	A	A	40	40	CYLD	A	1	1
MPG	4350	broad.mit.edu	36	16	73088	73088	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:73088G>A	uc002cfn.1	+	c.353G>A	c.(352-354)CGA>CAA	p.R118Q	MPG_uc002cfm.1_Missense_Mutation_p.R101Q|MPG_uc010bqp.1_Missense_Mutation_p.R101Q|MPG_uc002cfo.1_Missense_Mutation_p.R113Q	NM_002434	NP_001015054	P29372	3MG_HUMAN	N-methylpurine-DNA glycosylase isoform a	118					depurination|DNA dealkylation involved in DNA repair	nucleoplasm	alkylbase DNA N-glycosylase activity|damaged DNA binding|identical protein binding			ovary(1)|skin(1)	2		all_cancers(16;9.01e-08)|all_epithelial(16;7.64e-07)|Hepatocellular(780;0.000325)|Lung NSC(18;0.0104)|all_lung(18;0.0239)												0.258389	195.036416	210.800117	77	221	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73088	73088	10116	16	G	A	A	37	37	MPG	A	1	1
LRRC50	123872	broad.mit.edu	36	16	82761118	82761118	+	Missense_Mutation	SNP	A	T	T			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:82761118A>T	uc002fhl.2	+	c.1183A>T	c.(1183-1185)AGT>TGT	p.S395C		NM_178452	NP_848547	Q8NEP3	LRC50_HUMAN	leucine rich repeat containing 50	395	Pro-rich.				axonemal dynein complex assembly|cilium morphogenesis	cilium axoneme|cytoplasm|spindle pole	dynein binding			ovary(4)|pancreas(1)	5														0.282828	68.350118	72.550823	28	71	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	82761118	82761118	9384	16	A	T	T	3	3	LRRC50	T	4	4
MYH8	4626	broad.mit.edu	36	17	10240948	10240948	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10240948G>A	uc002gmm.2	-	c.4259C>T	c.(4258-4260)ACG>ATG	p.T1420M		NM_002472	NP_002463	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle,	1420	Potential.				muscle filament sliding	cytosol|muscle myosin complex|myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity|structural constituent of muscle			ovary(3)|breast(2)	5														0.105691	10.384247	29.387757	13	110	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10240948	10240948	10436	17	G	A	A	40	40	MYH8	A	1	1
PIRT	644139	broad.mit.edu	36	17	10669306	10669306	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:10669306G>A	uc010col.1	-	c.382C>T	c.(382-384)CGC>TGC	p.R128C		NM_001101387	NP_001094857	P0C851	PIRT_HUMAN	phosphoinositide-interacting regulator of	128						integral to membrane				ovary(1)	1														0.179104	19.048835	25.566142	12	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10669306	10669306	12369	17	G	A	A	40	40	PIRT	A	1	1
SMYD4	114826	broad.mit.edu	36	17	1633500	1633500	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:1633500A>C	uc002ftm.2	-	c.2041T>G	c.(2041-2043)TCG>GCG	p.S681A	SMYD4_uc002ftn.1_Missense_Mutation_p.S536A	NM_052928	NP_443160	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	681							zinc ion binding			kidney(2)	2														0.375	8.821659	9.084255	6	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1633500	1633500	15324	17	A	C	C	10	10	SMYD4	C	4	4
NF1	4763	broad.mit.edu	36	17	26610182	26610182	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26610182C>A	uc002hgg.1	+	c.4339C>A	c.(4339-4341)CAG>AAG	p.Q1447K	NF1_uc002hgh.1_Missense_Mutation_p.Q1426K|NF1_uc002hgi.1_Missense_Mutation_p.Q459K	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	1447	Ras-GAP.				actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.Q1447K(1)|p.?(1)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)								847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.352941	32.988462	33.637467	12	22	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	Missense_Mutation	SNP	26610182	26610182	10756	17	C	A	A	29	29	NF1	A	3	3
C17orf102	400591	broad.mit.edu	36	17	29930343	29930343	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:29930343T>C	uc002hie.1	-	c.70A>G	c.(70-72)AGG>GGG	p.R24G	TMEM132E_uc002hif.1_5'Flank	NM_207454	NP_997337	A2RUQ5	CQ102_HUMAN	hypothetical protein LOC400591	24										ovary(1)	1														0.3	7.517507	7.877347	3	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29930343	29930343	1902	17	T	C	C	54	54	C17orf102	C	4	4
ITGA2B	3674	broad.mit.edu	36	17	39813940	39813940	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39813940G>C	uc002igt.1	-	c.1226C>G	c.(1225-1227)GCC>GGC	p.A409G	ITGA2B_uc002igu.1_5'UTR	NM_000419	NP_000410	P08514	ITA2B_HUMAN	integrin alpha 2b preproprotein	409	Extracellular (Potential).|FG-GAP 6.				axon guidance|integrin-mediated signaling pathway|platelet activation|platelet degranulation	integrin complex|platelet alpha granule membrane	identical protein binding|receptor activity			ovary(2)|lung(1)	3		Prostate(33;0.0181)			Tirofiban(DB00775)									0.307692	10.520891	11.982065	12	27	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.191)	Missense_Mutation	SNP	39813940	39813940	8180	17	G	C	C	42	42	ITGA2B	C	3	3
CLDN7	1366	broad.mit.edu	36	17	7104543	7104543	+	Silent	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7104543T>C	uc002gfm.2	-	c.510A>G	c.(508-510)GCA>GCG	p.A170A	CLDN7_uc010cmc.1_Missense_Mutation_p.Q142R|CLDN7_uc002gfn.2_Silent_p.A170A	NM_001307	NP_001298	O95471	CLD7_HUMAN	claudin 7	170	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|lateral plasma membrane|tight junction	identical protein binding|structural molecule activity			ovary(1)	1														0.304348	13.106996	13.898803	7	16	TT		KEEP	---	---	---	---	capture			Silent	SNP	7104543	7104543	3627	17	T	C	C	55	55	CLDN7	C	4	4
UNC13D	201294	broad.mit.edu	36	17	71336558	71336558	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71336558A>G	uc002jpp.1	-	c.3056T>C	c.(3055-3057)TTC>TCC	p.F1019S		NM_199242	NP_954712	Q70J99	UN13D_HUMAN	unc-13 homolog D	1019	C2 2.				positive regulation of exocytosis|regulation of mast cell degranulation	exocytic vesicle|late endosome|lysosome|membrane|recycling endosome	protein binding				0														0.428571	8.954276	9.051629	6	8	AA		KEEP	---	---	---	---	capture	all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)		Missense_Mutation	SNP	71336558	71336558	17545	17	A	G	G	9	9	UNC13D	G	4	4
CD7	924	broad.mit.edu	36	17	77866571	77866571	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77866571T>C	uc002kel.1	-	c.638A>G	c.(637-639)GAT>GGT	p.D213G		NM_006137	NP_006128	P09564	CD7_HUMAN	CD7 antigen precursor	213	Cytoplasmic (Probable).				immune response|T cell activation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to membrane|membrane fraction|plasma membrane	receptor activity				0	Breast(20;0.000675)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.249)					Pancreas(45;804 1068 19702 28207 28798)								0.238095	7.633015	8.983789	5	16	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0667)		Missense_Mutation	SNP	77866571	77866571	3160	17	T	C	C	50	50	CD7	C	4	4
USP43	124739	broad.mit.edu	36	17	9556054	9556054	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:9556054G>C	uc010cod.1	+	c.2215G>C	c.(2215-2217)GGG>CGG	p.G739R	USP43_uc002gma.2_Missense_Mutation_p.G428R|USP43_uc010coe.1_Missense_Mutation_p.G536R|USP43_uc002gmc.2_Missense_Mutation_p.G251R	NM_153210	NP_694942	Q70EL4	UBP43_HUMAN	ubiquitin specific protease 43	739					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|central_nervous_system(1)	2														0.285714	10.394039	10.971051	4	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9556054	9556054	17638	17	G	C	C	39	39	USP43	C	3	3
FECH	2235	broad.mit.edu	36	18	53389741	53389741	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:53389741C>T	uc002lgp.2	-	c.362G>A	c.(361-363)CGA>CAA	p.R121Q	FECH_uc002lgq.2_Missense_Mutation_p.R115Q|FECH_uc002lgr.2_5'UTR	NM_001012515	NP_001012533	P22830	HEMH_HUMAN	ferrochelatase isoform a precursor	115					generation of precursor metabolites and energy|heme biosynthetic process|protoporphyrinogen IX metabolic process|response to light stimulus	mitochondrial inner membrane|mitochondrial matrix	2 iron, 2 sulfur cluster binding|ferrochelatase activity|ferrous iron binding|protein binding			central_nervous_system(1)	1		Colorectal(73;0.227)												0.258065	125.448577	135.291053	48	138	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53389741	53389741	6045	18	C	T	T	31	31	FECH	T	1	1
FAM69C	125704	broad.mit.edu	36	18	70254719	70254719	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:70254719C>A	uc002lll.1	-	c.360G>T	c.(358-360)AAG>AAT	p.K120N	FAM69C_uc002llk.1_Missense_Mutation_p.K419N	NM_001044369	NP_001037834	Q0P6D2	FA69C_HUMAN	hypothetical protein LOC125704	419	Lumenal (Potential).					endoplasmic reticulum membrane|integral to membrane					0														0.375	6.617948	6.729396	3	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70254719	70254719	5827	18	C	A	A	20	20	FAM69C	A	3	3
RGL3	57139	broad.mit.edu	36	19	11373738	11373738	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11373738G>A	uc002mrp.1	-	c.1433C>T	c.(1432-1434)CCG>CTG	p.P478L	RGL3_uc002mrm.1_Missense_Mutation_p.P242L|RGL3_uc002mrn.1_Missense_Mutation_p.P242L|RGL3_uc002mro.1_5'Flank	NM_001035223	NP_001030300	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation	478	Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular				ovary(1)	1						GBM(174;751 2067 17998 27979 33959)				120				0.188679	43.044239	52.653778	20	86	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11373738	11373738	13751	19	G	A	A	39	39	RGL3	A	1	1
CACNA1A	773	broad.mit.edu	36	19	13196580	13196580	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:13196580G>A	uc010dzd.1	-	c.5650C>T	c.(5650-5652)CTG>TTG	p.L1884L	CACNA1A_uc002mwx.2_Silent_p.L584L|CACNA1A_uc010dzc.1_Silent_p.L1404L|CACNA1A_uc002mwz.2_Silent_p.L1884L|CACNA1A_uc002mwy.2_Silent_p.L1878L|CACNA1A_uc010dze.1_Silent_p.L1879L|CACNA1A_uc002mwv.2_Silent_p.L395L	NM_023035	NP_075461	O00555	CAC1A_HUMAN	Voltage-dependent P/Q-type calcium channel subunit alpha-1A (Voltage- gated calcium channel subunit alpha Cav2.1) (Calcium channel, L type, alpha-1 polypeptide isoform 4) (Brain calcium channel I) (BI).	1879	Cytoplasmic (Potential).				cell death|elevation of cytosolic calcium ion concentration|energy reserve metabolic process|membrane depolarization|regulation of insulin secretion	cytoplasm|nucleus	syntaxin binding			large_intestine(2)	2					Bepridil(DB01244)|Cinnarizine(DB00568)|Loperamide(DB00836)|Nisoldipine(DB00401)|Pregabalin(DB00230)									0.5	9.796743	9.796743	4	4	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Silent	SNP	13196580	13196580	2654	19	G	A	A	33	33	CACNA1A	A	2	2
CC2D1A	54862	broad.mit.edu	36	19	13895593	13895593	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:13895593C>T	uc002mxo.1	+	c.1909C>T	c.(1909-1911)CGC>TGC	p.R637C	CC2D1A_uc002mxp.1_Missense_Mutation_p.R637C|CC2D1A_uc010dzh.1_Missense_Mutation_p.R206C|CC2D1A_uc002mxq.1_Missense_Mutation_p.R282C	NM_017721	NP_060191	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	637					positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus|plasma membrane	DNA binding|signal transducer activity				0														0.217949	122.850074	139.974717	51	183	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)		Missense_Mutation	SNP	13895593	13895593	2846	19	C	T	T	23	23	CC2D1A	T	1	1
PKN1	5585	broad.mit.edu	36	19	14422243	14422243	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14422243G>A	uc002myq.1	+	c.742G>A	c.(742-744)GCC>ACC	p.A248T	PKN1_uc002myp.1_Missense_Mutation_p.A242T	NM_213560	NP_998725	Q16512	PKN1_HUMAN	protein kinase N1 isoform 1	242	REM 3.				activation of JUN kinase activity|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|transcription, DNA-dependent	endosome|nucleus|plasma membrane	androgen receptor binding|ATP binding|chromatin binding|GTP-Rho binding|histone binding|histone deacetylase binding|histone kinase activity (H3-T11 specific)|ligand-dependent nuclear receptor transcription coactivator activity|protein kinase C activity|protein kinase C binding|Rac GTPase binding			ovary(2)|breast(2)|skin(2)|large_intestine(1)|central_nervous_system(1)	8						NSCLC(185;2539 2965 10733 52867)				331				0.333333	17.615762	18.133495	7	14	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14422243	14422243	12404	19	G	A	A	46	46	PKN1	A	2	2
BRD4	23476	broad.mit.edu	36	19	15237255	15237255	+	Silent	SNP	C	G	G			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15237255C>G	uc002nar.1	-	c.759G>C	c.(757-759)GTG>GTC	p.V253V	BRD4_uc002nas.1_Silent_p.V253V|BRD4_uc002nat.2_Silent_p.V253V|BRD4_uc002nau.2_Silent_p.V253V	NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long	253					interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of gene-specific transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2										269				0.30303	11.933401	13.21195	10	23	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)		Silent	SNP	15237255	15237255	1535	19	C	G	G	25	25	BRD4	G	3	3
CYP4F3	4051	broad.mit.edu	36	19	15624403	15624403	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15624403G>A	uc002nbj.1	+	c.943G>A	c.(943-945)GAT>AAT	p.D315N	CYP4F3_uc002nbk.1_Missense_Mutation_p.D315N	NM_000896	NP_000887	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F,	315					leukotriene metabolic process|oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	electron carrier activity|heme binding|leukotriene-B4 20-monooxygenase activity|oxygen binding			ovary(3)	3														0.222222	190.715301	216.264952	80	280	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15624403	15624403	4355	19	G	A	A	37	37	CYP4F3	A	1	1
INSL3	3640	broad.mit.edu	36	19	17788847	17788847	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:17788847T>C	uc002nhm.1	-	c.212A>G	c.(211-213)GAG>GGG	p.E71G	INSL3_uc010ebf.1_Missense_Mutation_p.R103G|INSL3_uc010ebg.1_3'UTR	NM_005543	NP_005534	P51460	INSL3_HUMAN	insulin-like 3 precursor	71					cell-cell signaling|spermatogenesis	soluble fraction	hormone activity|insulin receptor binding|signal transducer activity				0														0.535714	21.810977	21.820067	15	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17788847	17788847	8068	19	T	C	C	54	54	INSL3	C	4	4
PIAS4	51588	broad.mit.edu	36	19	3980001	3980001	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:3980001G>A	uc002lzg.1	+	c.874G>A	c.(874-876)GGG>AGG	p.G292R		NM_015897	NP_056981	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	292					positive regulation of protein sumoylation|transcription, DNA-dependent|Wnt receptor signaling pathway	cytoplasm|PML body	DNA binding|SUMO ligase activity|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding			pancreas(1)	1														0.222222	13.52925	15.453274	6	21	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	3980001	3980001	12302	19	G	A	A	47	47	PIAS4	A	2	2
NCCRP1	342897	broad.mit.edu	36	19	44381722	44381722	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:44381722A>C	uc002okq.1	+	c.525A>C	c.(523-525)CAA>CAC	p.Q175H		NM_001001414	NP_001001414	Q6ZVX7	NCRP1_HUMAN	non-specific cytotoxic cell receptor protein 1	175	FBA.				protein catabolic process					ovary(1)	1						Melanoma(107;1207 1556 14956 29427 52130)								0.253968	8.449582	12.51974	16	47	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44381722	44381722	10612	19	A	C	C	2	2	NCCRP1	C	4	4
LTBP4	8425	broad.mit.edu	36	19	45827255	45827255	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45827255A>C	uc002ooh.1	+	c.4835A>C	c.(4834-4836)CAC>CCC	p.H1612P	LTBP4_uc002oog.1_Missense_Mutation_p.H1575P|LTBP4_uc002ooi.1_Missense_Mutation_p.H1545P|LTBP4_uc002ooj.1_Missense_Mutation_p.H485P|LTBP4_uc002ool.1_Missense_Mutation_p.H624P	NM_001042544	NP_001036009	Q8N2S1	LTBP4_HUMAN	latent transforming growth factor beta binding	1612	EGF-like 16.				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														0.636364	23.084959	23.383109	14	8	AA		KEEP	---	---	---	---	capture	Lung(22;0.000158)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Missense_Mutation	SNP	45827255	45827255	9452	19	A	C	C	6	6	LTBP4	C	4	4
LIPE	3991	broad.mit.edu	36	19	47601390	47601390	+	Silent	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47601390C>T	uc002otr.1	-	c.2529G>A	c.(2527-2529)TCG>TCA	p.S843S		NM_005357	NP_005348	Q05469	LIPS_HUMAN	hormone-sensitive lipase	843					cholesterol metabolic process|protein phosphorylation|triglyceride catabolic process	caveola|cytosol	hormone-sensitive lipase activity|protein binding			ovary(1)|breast(1)	2		Prostate(69;0.00682)												0.113924	12.616987	24.229038	9	70	CC		KEEP	---	---	---	---	capture			Silent	SNP	47601390	47601390	9148	19	C	T	T	23	23	LIPE	T	1	1
CEACAM16	388551	broad.mit.edu	36	19	49898711	49898711	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49898711G>C	uc002ozq.1	+	c.467G>C	c.(466-468)GGC>GCC	p.G156A		NM_001039213	NP_001034302	A7LI12	A7LI12_HUMAN	carcinoembryonic antigen-related cell adhesion	97										ovary(1)	1	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)												0.235294	8.202484	9.284892	4	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49898711	49898711	3321	19	G	C	C	42	42	CEACAM16	C	3	3
EML2	24139	broad.mit.edu	36	19	50829560	50829560	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50829560G>T	uc002pcq.1	-	c.792C>A	c.(790-792)TAC>TAA	p.Y264*	EML2_uc002pcn.1_Nonsense_Mutation_p.Y63*|EML2_uc002pco.1_Non-coding_Transcript|EML2_uc002pcp.1_Intron|EML2_uc010ekj.1_Nonsense_Mutation_p.Y63*|EML2_uc010ekk.1_5'Flank	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	63					sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)												0.444444	15.67635	15.726481	8	10	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)	Nonsense_Mutation	SNP	50829560	50829560	5289	19	G	T	T	44	44	EML2	T	5	3
NOVA2	4858	broad.mit.edu	36	19	51135567	51135567	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:51135567G>T	uc002pdv.1	-	c.873C>A	c.(871-873)TAC>TAA	p.Y291*		NM_002516	NP_002507	Q9UNW9	NOVA2_HUMAN	neuro-oncological ventral antigen 2	291	Ala-rich.					nucleus	RNA binding				0		all_neural(266;0.113)|Ovarian(192;0.127)												0.214286	6.817742	7.87281	3	11	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00245)|GBM - Glioblastoma multiforme(486;0.0782)|Epithelial(262;0.179)	Nonsense_Mutation	SNP	51135567	51135567	10959	19	G	T	T	48	48	NOVA2	T	5	3
SIGLEC11	114132	broad.mit.edu	36	19	55153809	55153809	+	Silent	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55153809C>T	uc002pre.1	-	c.1230G>A	c.(1228-1230)GAG>GAA	p.E410E	SIGLEC11_uc010enr.1_Silent_p.E446E	NM_052884	NP_443116	Q96RL6	SIG11_HUMAN	sialic acid binding Ig-like lectin 11 isoform 1	422	Ig-like C2-type 3.|Extracellular (Potential).				cell adhesion	integral to membrane	sugar binding			ovary(3)|central_nervous_system(2)|pancreas(1)	6		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)												0.172414	49.889885	64.588068	25	120	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.00107)|OV - Ovarian serous cystadenocarcinoma(262;0.00517)	Silent	SNP	55153809	55153809	14802	19	C	T	T	28	28	SIGLEC11	T	2	2
NLRP12	91662	broad.mit.edu	36	19	59006249	59006249	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59006249C>T	uc002qcj.2	-	c.476G>A	c.(475-477)CGG>CAG	p.R159Q	NLRP12_uc010eqw.1_5'Flank|NLRP12_uc002qch.2_Missense_Mutation_p.R159Q|NLRP12_uc002qci.2_Missense_Mutation_p.R159Q|NLRP12_uc002qck.2_Non-coding_Transcript|NLRP12_uc010eqx.1_Missense_Mutation_p.R159Q	NM_144687	NP_653288	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12 isoform	159					activation of caspase activity|negative regulation of I-kappaB kinase/NF-kappaB cascade|negative regulation of interleukin-1 secretion|negative regulation of interleukin-6 biosynthetic process|negative regulation of protein autophosphorylation|negative regulation of Toll signaling pathway|positive regulation of inflammatory response|positive regulation of interleukin-1 beta secretion|regulation of interleukin-18 biosynthetic process|release of cytoplasmic sequestered NF-kappaB	cytoplasm	ATP binding|caspase activator activity|protein binding			ovary(4)|lung(1)	5	Ovarian(34;0.19)													0.298578	172.247988	179.897919	63	148	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.026)	Missense_Mutation	SNP	59006249	59006249	10877	19	C	T	T	23	23	NLRP12	T	1	1
FCAR	2204	broad.mit.edu	36	19	60077547	60077547	+	De_novo_Start_OutOfFrame	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60077547G>A	uc002qhr.1	+	c.-10G>A	c.(-12--8)CCGTG>CCATG		FCAR_uc002qhq.1_De_novo_Start_OutOfFrame|FCAR_uc002qhs.1_De_novo_Start_OutOfFrame|FCAR_uc002qht.1_De_novo_Start_OutOfFrame|FCAR_uc010esi.1_De_novo_Start_OutOfFrame|FCAR_uc002qhu.1_De_novo_Start_OutOfFrame|FCAR_uc002qhv.1_De_novo_Start_OutOfFrame|FCAR_uc002qhw.1_De_novo_Start_OutOfFrame|FCAR_uc002qhx.1_De_novo_Start_OutOfFrame|FCAR_uc002qhy.1_De_novo_Start_OutOfFrame|FCAR_uc002qhz.1_De_novo_Start_OutOfFrame|FCAR_uc002qia.1_De_novo_Start_OutOfFrame	NM_002000	NP_001991			Fc alpha receptor isoform a precursor						immune response	extracellular region|integral to plasma membrane	IgA binding|receptor activity			ovary(1)	1														0.201646	105.831578	126.080385	49	194	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0443)	De_novo_Start_OutOfFrame	SNP	60077547	60077547	6010	19	G	A	A	40	40	FCAR	A	5	1
SUV420H2	84787	broad.mit.edu	36	19	60550580	60550580	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:60550580T>G	uc002qkj.2	+	c.1340T>G	c.(1339-1341)GTG>GGG	p.V447G	SUV420H2_uc002qkl.1_Missense_Mutation_p.V332G	NM_032701	NP_116090	Q86Y97	SV422_HUMAN	suppressor of variegation 4-20 homolog 2	447					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding				0	Breast(117;0.191)													0.578947	19.095129	19.163619	11	8	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)	Missense_Mutation	SNP	60550580	60550580	15935	19	T	G	G	59	59	SUV420H2	G	4	4
NLRP8	126205	broad.mit.edu	36	19	61176926	61176926	+	Silent	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61176926C>T	uc002qmh.1	+	c.2631C>T	c.(2629-2631)AAC>AAT	p.N877N	NLRP8_uc010etg.1_Silent_p.N858N	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	877	LRR 4.					cytoplasm	ATP binding			ovary(4)|breast(3)|large_intestine(1)|kidney(1)|skin(1)	10		Colorectal(82;0.000147)|Ovarian(87;0.17)												0.211679	186.208694	217.80477	87	324	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(193;0.0695)	Silent	SNP	61176926	61176926	10886	19	C	T	T	19	19	NLRP8	T	1	1
CELSR2	1952	broad.mit.edu	36	1	109603197	109603197	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:109603197A>C	uc001dxa.2	+	c.3931A>C	c.(3931-3933)ACC>CCC	p.T1311P		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	1311	Extracellular (Potential).|EGF-like 2; calcium-binding.				dendrite morphogenesis|homophilic cell adhesion|neural plate anterior/posterior regionalization|neuropeptide signaling pathway|regulation of cell-cell adhesion|regulation of gene-specific transcription|Wnt receptor signaling pathway	cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(3)	3		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)				NSCLC(158;1285 2011 34800 34852 42084)								0.5	9.819182	9.819182	6	6	AA		KEEP	---	---	---	---	capture		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)	Missense_Mutation	SNP	109603197	109603197	3355	1	A	C	C	6	6	CELSR2	C	4	4
MXRA8	54587	broad.mit.edu	36	1	1279952	1279952	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1279952A>G	uc001aex.2	-	c.922T>C	c.(922-924)TCC>CCC	p.S308P	MXRA8_uc001aev.1_5'Flank|MXRA8_uc001aew.1_Missense_Mutation_p.S308P|MXRA8_uc001aez.1_Missense_Mutation_p.S207P|MXRA8_uc001afa.1_Missense_Mutation_p.S299P|MXRA8_uc001aey.2_Missense_Mutation_p.S308P	NM_032348	NP_115724	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8	308	Extracellular (Potential).					integral to membrane					0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)												1	9.747233	9.685559	4	0	AA		KEEP	---	---	---	---	capture		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)	Missense_Mutation	SNP	1279952	1279952	10399	1	A	G	G	11	11	MXRA8	G	4	4
FLG	2312	broad.mit.edu	36	1	150546346	150546346	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150546346G>A	uc001ezu.1	-	c.7640C>T	c.(7639-7641)TCG>TTG	p.S2547L		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2547	Ser-rich.|Filaggrin 15.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.284264	447.261955	471.952788	168	423	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150546346	150546346	6160	1	G	A	A	37	37	FLG	A	1	1
PLEKHM2	23207	broad.mit.edu	36	1	15927761	15927761	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:15927761G>A	uc001axa.2	+	c.2241G>A	c.(2239-2241)GAG>GAA	p.E747E		NM_015164	NP_055979	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M	644					Golgi organization	cytoplasm	kinesin binding			ovary(1)	1		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)												0.222222	6.779902	8.070226	4	14	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)	Silent	SNP	15927761	15927761	12507	1	G	A	A	33	33	PLEKHM2	A	2	2
DUSP27	92235	broad.mit.edu	36	1	165330810	165330810	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:165330810T>C	uc001geb.1	+	c.100T>C	c.(100-102)TCC>CCC	p.S34P		NM_001080426	NP_001073895	Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	34					protein dephosphorylation		protein tyrosine/serine/threonine phosphatase activity			ovary(3)	3														0.4	7.520571	7.684606	6	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	165330810	165330810	5009	1	T	C	C	54	54	DUSP27	C	4	4
F5	2153	broad.mit.edu	36	1	167785674	167785674	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:167785674G>A	uc001ggg.1	-	c.1600C>T	c.(1600-1602)CGA>TGA	p.R534*		NM_000130	NP_000121	P12259	FA5_HUMAN	coagulation factor V precursor	534	F5/8 type A 2.	Cleavage; by activated protein C.			cell adhesion|oxidation-reduction process|platelet activation|platelet degranulation	plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity			ovary(3)|large_intestine(1)|central_nervous_system(1)	5	all_hematologic(923;0.208)				Drotrecogin alfa(DB00055)									0.254717	67.806078	73.572274	27	79	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	167785674	167785674	5542	1	G	A	A	46	46	F5	A	5	2
ZNF648	127665	broad.mit.edu	36	1	180293126	180293126	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:180293126T>G	uc001goz.1	-	c.643A>C	c.(643-645)ACC>CCC	p.T215P	ZNF648_uc009wxu.1_Missense_Mutation_p.T215P	NM_001009992	NP_001009992	Q5T619	ZN648_HUMAN	zinc finger protein 648	215					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1						NSCLC(71;908 1374 5429 20458 35642)								0.47619	13.84269	13.863789	10	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	180293126	180293126	18658	1	T	G	G	59	59	ZNF648	G	4	4
TMCC2	9911	broad.mit.edu	36	1	203477541	203477541	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:203477541G>C	uc001hbz.1	+	c.493G>C	c.(493-495)GCC>CCC	p.A165P		NM_014858	NP_055673	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	165						integral to membrane				pancreas(1)	1	Breast(84;0.0871)													0.388889	14.045556	14.26222	7	11	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(75;0.117)		Missense_Mutation	SNP	203477541	203477541	16523	1	G	C	C	38	38	TMCC2	C	3	3
OR2AK2	391191	broad.mit.edu	36	1	246195796	246195796	+	Missense_Mutation	SNP	G	T	T	rs74153217	unknown	TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246195796G>T	uc001idu.1	+	c.540G>T	c.(538-540)CAG>CAT	p.Q180H	OR2L13_uc001ids.1_Intron	NM_001004491	NP_001004491	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK,	180	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|breast(1)	2	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)					Melanoma(45;390 1181 23848 28461 41504)								0.257053	210.936105	227.9813	82	237	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0152)		Missense_Mutation	SNP	246195796	246195796	11392	1	G	T	T	34	34	OR2AK2	T	3	3
ACTRT2	140625	broad.mit.edu	36	1	2928933	2928933	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:2928933G>A	uc001ajz.1	+	c.823G>A	c.(823-825)GGG>AGG	p.G275R		NM_080431	NP_536356	Q8TDY3	ACTT2_HUMAN	actin-related protein M2	275						cytoplasm|cytoskeleton					0	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)												0.263158	128.291874	137.850519	50	140	GG		KEEP	---	---	---	---	capture		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)	Missense_Mutation	SNP	2928933	2928933	220	1	G	A	A	39	39	ACTRT2	A	1	1
SLC24A3	57419	broad.mit.edu	36	20	19612921	19612921	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:19612921A>C	uc002wrl.1	+	c.1003A>C	c.(1003-1005)ACC>CCC	p.T335P		NM_020689	NP_065740	Q9HC58	NCKX3_HUMAN	solute carrier family 24	335	Cytoplasmic (Potential).					integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1														0.333333	13.419983	14.443886	12	24	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	19612921	19612921	14964	20	A	C	C	2	2	SLC24A3	C	4	4
ZNF335	63925	broad.mit.edu	36	20	44024144	44024144	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:44024144G>A	uc002xqw.1	-	c.1618C>T	c.(1618-1620)CGG>TGG	p.R540W		NM_022095	NP_071378	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	540	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Myeloproliferative disorder(115;0.0122)												0.306748	133.79534	139.220178	50	113	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44024144	44024144	18444	20	G	A	A	37	37	ZNF335	A	1	1
KCNG1	3755	broad.mit.edu	36	20	49054393	49054393	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:49054393C>T	uc002xwa.2	-	c.1132G>A	c.(1132-1134)GGG>AGG	p.G378R		NM_002237	NP_002228	Q9UIX4	KCNG1_HUMAN	potassium voltage-gated channel, subfamily G,	378	Helical; Name=Segment S5; (Potential).					voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|central_nervous_system(1)	2														0.291667	18.317036	19.249058	7	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49054393	49054393	8332	20	C	T	T	23	23	KCNG1	T	1	1
DSCAM	1826	broad.mit.edu	36	21	40387535	40387535	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:40387535A>C	uc002yyq.1	-	c.3833T>G	c.(3832-3834)GTC>GGC	p.V1278G	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1278	Fibronectin type-III 4.|Extracellular (Potential).				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.181818	9.840607	12.97698	6	27	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40387535	40387535	4952	21	A	C	C	10	10	DSCAM	C	4	4
ZNF295	49854	broad.mit.edu	36	21	42285029	42285029	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42285029C>T	uc002zab.2	-	c.2245G>A	c.(2245-2247)GTC>ATC	p.V749I	ZNF295_uc002yzz.2_Missense_Mutation_p.V548I|ZNF295_uc002yzy.2_Missense_Mutation_p.V749I|ZNF295_uc002zaa.2_Missense_Mutation_p.V749I|ZNF295_uc010gou.1_Missense_Mutation_p.V749I	NM_001098402	NP_065778	Q9ULJ3	ZN295_HUMAN	zinc finger protein 295 isoform L	749	C2H2-type 4; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	methyl-CpG binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2														0.2603	316.851053	344.678187	139	395	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42285029	42285029	18419	21	C	T	T	19	19	ZNF295	T	1	1
PCNT	5116	broad.mit.edu	36	21	46642417	46642417	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:46642417A>G	uc002zji.2	+	c.4508A>G	c.(4507-4509)GAG>GGG	p.E1503G	PCNT_uc002zjj.1_Missense_Mutation_p.E1385G	NM_006031	NP_006022	O95613	PCNT_HUMAN	pericentrin	1503	Potential.				cilium assembly|G2/M transition of mitotic cell cycle	cytosol|microtubule	calmodulin binding			ovary(4)|breast(2)|pancreas(2)	8	Breast(49;0.112)													0.428571	8.058055	8.135658	6	8	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	46642417	46642417	12010	21	A	G	G	11	11	PCNT	G	4	4
BID	637	broad.mit.edu	36	22	16606602	16606602	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:16606602T>G	uc002znc.1	-	c.328A>C	c.(328-330)AGC>CGC	p.S110R	BID_uc002znd.1_Missense_Mutation_p.S64R|BID_uc002zne.1_5'UTR|BID_uc010gra.1_Non-coding_Transcript|BID_uc002znf.1_Intron|BID_uc010grb.1_Missense_Mutation_p.S64R|BID_uc010grc.1_Intron	NM_197966	NP_001187	P55957	BID_HUMAN	BH3 interacting domain death agonist isoform 1	64					activation of pro-apoptotic gene products|establishment of protein localization in membrane|induction of apoptosis by intracellular signals|induction of apoptosis via death domain receptors|neuron apoptosis|positive regulation of protein homooligomerization|positive regulation of release of cytochrome c from mitochondria|release of cytochrome c from mitochondria	cytosol|membrane fraction|mitochondrial outer membrane	death receptor binding				0		all_epithelial(15;0.198)								1081				0.46875	25.769769	25.814989	15	17	TT		KEEP	---	---	---	---	capture		Lung(27;0.0419)	Missense_Mutation	SNP	16606602	16606602	1455	22	T	G	G	55	55	BID	G	4	4
ELFN2	114794	broad.mit.edu	36	22	36099206	36099206	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36099206C>T	uc003asq.2	-	c.2315G>A	c.(2314-2316)CGC>CAC	p.R772H	ELFN2_uc010gxg.1_Missense_Mutation_p.R772H	NM_052906	NP_443138	Q5R3F8	LRFN6_HUMAN	leucine rich repeat containing 62	772	Cytoplasmic (Potential).					cell surface|integral to membrane				ovary(1)	1	Melanoma(58;0.0574)													0.26087	90.944274	98.082702	36	102	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36099206	36099206	5250	22	C	T	T	27	27	ELFN2	T	1	1
C22orf32	91689	broad.mit.edu	36	22	40805738	40805738	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:40805738G>C	uc003bca.1	+	c.20G>C	c.(19-21)CGC>CCC	p.R7P		NM_033318	NP_201575	Q9H4I9	CV032_HUMAN	hypothetical protein LOC91689	7						integral to membrane|mitochondrion				ovary(1)	1														0.375	16.535489	17.060912	12	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40805738	40805738	2225	22	G	C	C	38	38	C22orf32	C	3	3
TTLL12	23170	broad.mit.edu	36	22	41900169	41900169	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:41900169G>A	uc003bdq.1	-	c.1219C>T	c.(1219-1221)CGG>TGG	p.R407W	TTLL12_uc003bdr.1_Missense_Mutation_p.R407W	NM_015140	NP_055955	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	407	TTL.				protein modification process		tubulin-tyrosine ligase activity			central_nervous_system(1)	1		Ovarian(80;0.221)|Glioma(61;0.222)												0.274247	203.607309	217.34605	82	217	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41900169	41900169	17280	22	G	A	A	38	38	TTLL12	A	1	1
PLXNB2	23654	broad.mit.edu	36	22	49063290	49063290	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49063290G>C	uc003bkv.2	-	c.2964C>G	c.(2962-2964)TTC>TTG	p.F988L	PLXNB2_uc003bkt.1_5'Flank|PLXNB2_uc003bku.1_5'Flank	NM_012401	NP_036533	O15031	PLXB2_HUMAN	plexin B2	988	IPT/TIG 3.|Extracellular (Potential).				regulation of small GTPase mediated signal transduction	integral to membrane|intracellular	GTPase activator activity|protein binding|receptor activity			ovary(4)|central_nervous_system(1)	5		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.428571	14.286058	14.359174	6	8	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49063290	49063290	12550	22	G	C	C	37	37	PLXNB2	C	3	3
HOXD13	3239	broad.mit.edu	36	2	176666269	176666269	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:176666269C>A	uc002ukf.1	+	c.405C>A	c.(403-405)TAC>TAA	p.Y135*		NM_000523	NP_000514	P35453	HXD13_HUMAN	homeobox D13	135					skeletal system development|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding|transcription regulator activity				0										34				0.2	7.987887	9.663038	4	16	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0526)|READ - Rectum adenocarcinoma(9;0.0678)	Nonsense_Mutation	SNP	176666269	176666269	7614	2	C	A	A	20	20	HOXD13	A	5	3
TTN	7273	broad.mit.edu	36	2	179255750	179255750	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179255750G>A	uc002umr.1	-	c.29281C>T	c.(29281-29283)CCA>TCA	p.P9761S	TTN_uc002ums.1_Intron|TTN_uc010frc.1_Intron|TTN_uc010frd.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.P6422S|TTN_uc010fre.1_Missense_Mutation_p.P608S	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	10688										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										8722				0.237458	170.564995	189.403484	71	228	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179255750	179255750	17290	2	G	A	A	44	44	TTN	A	2	2
CCDC108	255101	broad.mit.edu	36	2	219579007	219579007	+	Silent	SNP	A	G	G			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219579007A>G	uc002vjl.1	-	c.4902T>C	c.(4900-4902)TTT>TTC	p.F1634F		NM_194302	NP_919278	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108 isoform 1	1634						integral to membrane	structural molecule activity			ovary(2)|pancreas(1)	3		Renal(207;0.0915)												0.255814	8.882109	11.525552	11	32	AA		KEEP	---	---	---	---	capture		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Silent	SNP	219579007	219579007	2863	2	A	G	G	9	9	CCDC108	G	4	4
SLC3A1	6519	broad.mit.edu	36	2	44393364	44393364	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:44393364G>T	uc002ruc.2	+	c.1468G>T	c.(1468-1470)GTA>TTA	p.V490L	SLC3A1_uc002rtz.2_Missense_Mutation_p.V490L|SLC3A1_uc002rua.2_Missense_Mutation_p.V490L|SLC3A1_uc002rub.2_Missense_Mutation_p.V490L|SLC3A1_uc002rud.2_Missense_Mutation_p.V212L|SLC3A1_uc002rue.2_Missense_Mutation_p.V110L	NM_000341	NP_000332	Q07837	SLC31_HUMAN	solute carrier family 3, member 1	490	Extracellular (Potential).				carbohydrate metabolic process|cellular amino acid metabolic process|ion transport	integral to plasma membrane|membrane fraction	basic amino acid transmembrane transporter activity|catalytic activity|cation binding|L-cystine transmembrane transporter activity				0		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)									0.233333	24.274603	30.240034	21	69	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44393364	44393364	15123	2	G	T	T	48	48	SLC3A1	T	3	3
BBX	56987	broad.mit.edu	36	3	108980057	108980057	+	Splice_Site_SNP	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:108980057G>T	uc010hpr.1	+	c.2203_splice	c.e13+1	p.G735_splice	BBX_uc003dwk.2_Splice_Site_SNP_p.G735_splice|BBX_uc003dwl.2_Splice_Site_SNP_p.K398_splice|BBX_uc003dwm.2_Splice_Site_SNP_p.G735_splice|BBX_uc003dwo.2_Splice_Site_SNP_p.K84_splice	NM_020235	NP_064620			HMG-BOX transcription factor BBX isoform 2						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(3)	3														0.222222	66.894667	75.19397	26	91	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(3;0.112)		Splice_Site_SNP	SNP	108980057	108980057	1364	3	G	T	T	44	44	BBX	T	5	3
CNTN6	27255	broad.mit.edu	36	3	1237380	1237380	+	Missense_Mutation	SNP	T	A	A			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:1237380T>A	uc003boz.1	+	c.65T>A	c.(64-66)CTT>CAT	p.L22H	CNTN6_uc010hbo.1_Missense_Mutation_p.L17H|CNTN6_uc003bpa.1_Missense_Mutation_p.L22H	NM_014461	NP_055276	Q9UQ52	CNTN6_HUMAN	contactin 6	22					axon guidance|cell adhesion|central nervous system development|Notch signaling pathway	anchored to membrane|plasma membrane				lung(2)|breast(2)|pancreas(1)	5		all_cancers(2;0.000164)|all_epithelial(2;0.107)								1038				0.280488	121.474405	128.582125	46	118	TT		KEEP	---	---	---	---	capture		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)	Missense_Mutation	SNP	1237380	1237380	3783	3	T	A	A	56	56	CNTN6	A	4	4
ZBTB47	92999	broad.mit.edu	36	3	42680821	42680821	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:42680821G>A	uc003clu.1	+	c.843G>A	c.(841-843)GAG>GAA	p.E281E		NM_145166	NP_660149	Q9UFB7	ZBT47_HUMAN	zinc finger protein 651	281					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.545455	11.473963	11.486892	6	5	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.216)	Silent	SNP	42680821	42680821	18135	3	G	A	A	33	33	ZBTB47	A	2	2
CCDC72	51372	broad.mit.edu	36	3	48456827	48456827	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48456827G>A	uc003cte.1	+	c.27G>A	c.(25-27)AAG>AAA	p.K9K	CCDC51_uc003csz.1_5'Flank|CCDC51_uc003cta.1_5'Flank|CCDC51_uc003ctb.1_5'Flank|CCDC51_uc003ctc.1_5'Flank|CCDC51_uc003ctd.1_5'Flank	NM_015933	NP_057017	Q9Y2S6	CCD72_HUMAN	coiled-coil domain containing 72	9											0														0.307692	9.781811	10.709469	8	18	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)	Silent	SNP	48456827	48456827	2968	3	G	A	A	33	33	CCDC72	A	2	2
BSN	8927	broad.mit.edu	36	3	49665710	49665710	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49665710G>A	uc003cxe.2	+	c.3717G>A	c.(3715-3717)CAG>CAA	p.Q1239Q		NM_003458	NP_003449	Q9UPA5	BSN_HUMAN	bassoon protein	1239					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	zinc ion binding			ovary(5)|central_nervous_system(1)|pancreas(1)	7														0.235294	9.399166	10.483382	4	13	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)	Silent	SNP	49665710	49665710	1561	3	G	A	A	35	35	BSN	A	2	2
DCHS2	54798	broad.mit.edu	36	4	155506903	155506903	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155506903G>A	uc003inw.1	-	c.603C>T	c.(601-603)GCC>GCT	p.A201A	DCHS2_uc003inx.1_Silent_p.A795A	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN	dachsous 2 isoform 1	201	Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|pancreas(1)	4	all_hematologic(180;0.208)	Renal(120;0.0854)												0.319328	108.606423	112.059071	38	81	GG		KEEP	---	---	---	---	capture		LUSC - Lung squamous cell carcinoma(193;0.107)	Silent	SNP	155506903	155506903	4459	4	G	A	A	47	47	DCHS2	A	2	2
ZCCHC4	29063	broad.mit.edu	36	4	24975826	24975826	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:24975826G>A	uc003grl.2	+	c.1346G>A	c.(1345-1347)GGT>GAT	p.G449D	ZCCHC4_uc003grn.2_Intron	NM_024936	NP_079212	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	449	CCHC-type.						methyltransferase activity|nucleic acid binding|zinc ion binding			ovary(2)	2		Breast(46;0.0503)												0.330882	117.415531	120.92269	45	91	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24975826	24975826	18178	4	G	A	A	44	44	ZCCHC4	A	2	2
GABRA4	2557	broad.mit.edu	36	4	46625437	46625437	+	Silent	SNP	A	G	G			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:46625437A>G	uc003gxg.1	-	c.1227T>C	c.(1225-1227)CAT>CAC	p.H409H		NM_000809	NP_000800	P48169	GBRA4_HUMAN	gamma-aminobutyric acid A receptor, alpha 4	409	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)|breast(1)	3					Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)	Ovarian(6;283 369 8234 12290 33402)								0.285714	111.554752	116.742036	36	90	AA		KEEP	---	---	---	---	capture			Silent	SNP	46625437	46625437	6414	4	A	G	G	4	4	GABRA4	G	4	4
SLC12A7	10723	broad.mit.edu	36	5	1110736	1110736	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1110736G>A	uc003jbu.1	-	c.2876C>T	c.(2875-2877)GCG>GTG	p.A959V		NM_006598	NP_006589	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride	959	Cytoplasmic (Potential).				potassium ion transport|sodium ion transport	integral to plasma membrane	potassium:chloride symporter activity			large_intestine(1)	1	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)				Potassium Chloride(DB00761)									0.287736	149.278643	157.851955	61	151	GG		KEEP	---	---	---	---	capture	Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Missense_Mutation	SNP	1110736	1110736	14883	5	G	A	A	38	38	SLC12A7	A	1	1
FLT4	2324	broad.mit.edu	36	5	179991368	179991368	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:179991368G>T	uc003mlz.2	-	c.75C>A	c.(73-75)TAC>TAA	p.Y25*	FLT4_uc003mma.2_Nonsense_Mutation_p.Y25*|FLT4_uc003mmb.1_5'Flank	NM_182925	NP_891555	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4 isoform 1	25	Extracellular (Potential).				positive regulation of cell proliferation|protein phosphorylation	integral to plasma membrane	ATP binding|protein binding|vascular endothelial growth factor receptor activity			lung(3)|ovary(1)|central_nervous_system(1)|kidney(1)|skin(1)	7	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)			Sorafenib(DB00398)|Sunitinib(DB01268)	Colon(97;1075 1466 27033 27547 35871)				2638				0.545455	29.568185	29.605211	12	10	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Nonsense_Mutation	SNP	179991368	179991368	6186	5	G	T	T	36	36	FLT4	T	5	3
MGC42105	167359	broad.mit.edu	36	5	43316092	43316092	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:43316092G>A	uc003jno.1	+	c.815G>A	c.(814-816)CGG>CAG	p.R272Q		NM_153361	NP_699192	Q8IY84	NIM1_HUMAN	serine/threonine-protein kinase NIM1	272	Protein kinase.				protein phosphorylation		ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(4)|ovary(2)|stomach(1)|large_intestine(1)|breast(1)	9										94				0.235714	81.800787	90.747432	33	107	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43316092	43316092	9942	5	G	A	A	39	39	MGC42105	A	1	1
NDUFS4	4724	broad.mit.edu	36	5	53014794	53014794	+	Missense_Mutation	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:53014794G>T	uc003jpe.2	+	c.514G>T	c.(514-516)GTA>TTA	p.V172L		NM_002495	NP_002486	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4	172					brain development|cAMP-mediated signaling|mitochondrial electron transport, NADH to ubiquinone|mitochondrial respiratory chain complex I assembly|positive regulation of fibroblast proliferation|reactive oxygen species metabolic process|regulation of protein phosphorylation|response to cAMP|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity				0		Lung NSC(810;8.27e-05)|Breast(144;0.0848)			NADH(DB00157)									0.225352	12.473697	17.715254	16	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53014794	53014794	10693	5	G	T	T	36	36	NDUFS4	T	3	3
ADCY2	108	broad.mit.edu	36	5	7743813	7743813	+	Silent	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:7743813C>T	uc003jdz.1	+	c.730C>T	c.(730-732)CTG>TTG	p.L244L		NM_020546	NP_065433	Q08462	ADCY2_HUMAN	adenylate cyclase 2	244	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|dendrite|integral to membrane|plasma membrane	ATP binding|metal ion binding			ovary(5)|pancreas(1)	6														0.52	20.381018	20.38298	13	12	CC		KEEP	---	---	---	---	capture			Silent	SNP	7743813	7743813	295	5	C	T	T	32	32	ADCY2	T	2	2
LST1	7940	broad.mit.edu	36	6	31663462	31663462	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:31663462G>C	uc003num.1	+	c.85G>C	c.(85-87)GCC>CCC	p.A29P	LST1_uc003nun.1_Intron|LST1_uc003nuo.1_Intron|LST1_uc003nup.1_Intron|LST1_uc010jss.1_Non-coding_Transcript|LST1_uc003nuq.1_Intron|LST1_uc010jst.1_Intron|LST1_uc010jsu.1_Missense_Mutation_p.A29P|LST1_uc003nus.2_Intron|LST1_uc003nuu.1_Non-coding_Transcript|LST1_uc010jsv.1_Missense_Mutation_p.R21P|LST1_uc003nut.1_Intron|LST1_uc010jsw.1_Missense_Mutation_p.R21P|LST1_uc010jsx.1_5'Flank	NM_007161	NP_009092	O00453	LST1_HUMAN	leukocyte specific transcript 1 isoform 1	29					cell morphogenesis|dendrite development|immune response|negative regulation of lymphocyte proliferation|regulation of cell shape	Golgi membrane|integral to membrane	protein binding				0														0.944444	36.948469	38.164756	17	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31663462	31663462	9443	6	G	C	C	38	38	LST1	C	3	3
TAP1	6890	broad.mit.edu	36	6	32923768	32923768	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32923768G>C	uc003ocg.1	-	c.1826C>G	c.(1825-1827)GCC>GGC	p.A609G		NM_000593	NP_000584	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family	609	Cytoplasmic (Potential).|ABC transporter.				antigen processing and presentation of endogenous peptide antigen via MHC class I|cytosol to ER transport|intracellular transport of viral proteins in host cell|positive regulation of T cell mediated cytotoxicity	cytosol|plasma membrane|TAP complex	ADP binding|ATP binding|MHC class I protein binding|oligopeptide-transporting ATPase activity|peptide antigen binding|protein homodimerization activity|TAP1 binding|TAP2 binding|tapasin binding				0														0.404255	28.532016	28.975568	19	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32923768	32923768	16071	6	G	C	C	42	42	TAP1	C	3	3
USP49	25862	broad.mit.edu	36	6	41882335	41882335	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:41882335G>A	uc003ori.1	-	c.365C>T	c.(364-366)TCG>TTG	p.S122L		NM_018561	NP_061031	Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	122					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0919)|Colorectal(47;0.121)													0.372549	49.005312	49.734466	19	32	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)		Missense_Mutation	SNP	41882335	41882335	17644	6	G	A	A	37	37	USP49	A	1	1
TRAM2	9697	broad.mit.edu	36	6	52477428	52477428	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:52477428T>C	uc003paq.1	-	c.959A>G	c.(958-960)GAA>GGA	p.E320G		NM_012288	NP_036420	Q15035	TRAM2_HUMAN	translocation-associated membrane protein 2	320	TLC.				collagen biosynthetic process|protein transport|transmembrane transport	integral to membrane	protein binding				0	Lung NSC(77;0.109)													0.277778	8.54789	9.364701	5	13	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52477428	52477428	16997	6	T	C	C	62	62	TRAM2	C	4	4
ANKRD6	22881	broad.mit.edu	36	6	90378746	90378746	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:90378746A>C	uc003pni.2	+	c.452A>C	c.(451-453)AAC>ACC	p.N151T	ANKRD6_uc003pne.2_Missense_Mutation_p.N151T|ANKRD6_uc003pnf.2_Missense_Mutation_p.N151T|ANKRD6_uc010kcd.1_Missense_Mutation_p.N118T|LYRM2_uc010kce.1_Intron|LYRM2_uc003png.2_Intron|ANKRD6_uc003pnh.2_5'UTR	NM_014942	NP_055757	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	151	ANK 5.						protein binding			ovary(2)|pancreas(1)	3		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)												0.333333	7.620668	7.84274	3	6	AA		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(108;0.0209)	Missense_Mutation	SNP	90378746	90378746	693	6	A	C	C	2	2	ANKRD6	C	4	4
ORAI2	80228	broad.mit.edu	36	7	101874382	101874382	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:101874382A>C	uc010lhz.1	+	c.643A>C	c.(643-645)ACC>CCC	p.T215P	ORAI2_uc003uzj.2_Missense_Mutation_p.T215P|ORAI2_uc003uzk.2_Missense_Mutation_p.T215P	NM_001126340	NP_001119812	Q96SN7	ORAI2_HUMAN	ORAI calcium release-activated calcium modulator	215	Helical; (Potential).					integral to membrane	protein binding			ovary(1)|kidney(1)	2														0.275	7.291971	9.463199	11	29	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101874382	101874382	11669	7	A	C	C	6	6	ORAI2	C	4	4
PIK3CG	5294	broad.mit.edu	36	7	106295735	106295735	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106295735G>A	uc003vdv.2	+	c.493G>A	c.(493-495)GTC>ATC	p.V165I	PIK3CG_uc003vdu.1_Missense_Mutation_p.V165I|PIK3CG_uc003vdw.1_Missense_Mutation_p.V165I	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	165					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.205479	31.888979	37.759018	15	58	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106295735	106295735	12340	7	G	A	A	40	40	PIK3CG	A	1	1
CADPS2	93664	broad.mit.edu	36	7	122048898	122048898	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:122048898G>A	uc010lkp.1	-	c.977C>T	c.(976-978)TCG>TTG	p.S326L	CADPS2_uc003vkg.2_Missense_Mutation_p.S26L|CADPS2_uc010lkq.1_Missense_Mutation_p.S326L	NM_017954	NP_060424	Q86UW7	CAPS2_HUMAN	Ca2+-dependent activator protein for secretion 2	326					exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|synapse	lipid binding|metal ion binding			ovary(1)|central_nervous_system(1)	2														0.182266	77.949552	97.200188	37	166	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122048898	122048898	2687	7	G	A	A	37	37	CADPS2	A	1	1
ABCB5	340273	broad.mit.edu	36	7	20745211	20745211	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:20745211C>T	uc010kuh.1	+	c.2948C>T	c.(2947-2949)TCG>TTG	p.S983L	ABCB5_uc003suw.2_Missense_Mutation_p.S538L|ABCB5_uc010kui.1_Missense_Mutation_p.S538L	NM_178559	NP_848654	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	538	Cytoplasmic (Potential).				regulation of membrane potential	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus	ATP binding|ATPase activity, coupled to transmembrane movement of substances|efflux transmembrane transporter activity			large_intestine(1)|ovary(1)|pancreas(1)	3														0.130952	14.669013	25.79274	11	73	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20745211	20745211	45	7	C	T	T	31	31	ABCB5	T	1	1
COBL	23242	broad.mit.edu	36	7	51078783	51078783	+	Silent	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:51078783C>T	uc003tpr.2	-	c.1197G>A	c.(1195-1197)GCG>GCA	p.A399A	COBL_uc003tpp.2_Silent_p.A185A|COBL_uc003tpq.2_Silent_p.A340A|COBL_uc003tps.1_Silent_p.A372A|COBL_uc010kzc.1_Silent_p.A399A	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	399										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.234848	74.47439	82.952369	31	101	CC		KEEP	---	---	---	---	capture			Silent	SNP	51078783	51078783	3791	7	C	T	T	19	19	COBL	T	1	1
FZD9	8326	broad.mit.edu	36	7	72486429	72486429	+	Nonsense_Mutation	SNP	C	A	A			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72486429C>A	uc003tyb.1	+	c.156C>A	c.(154-156)TAC>TAA	p.Y52*		NM_003508	NP_003499	O00144	FZD9_HUMAN	frizzled 9	52	FZ.|Extracellular (Potential).				B cell differentiation|brain development|canonical Wnt receptor signaling pathway|embryo development|gonad development|neuroblast proliferation|regulation of gene-specific transcription from RNA polymerase II promoter|vasculature development	cell surface|filopodium membrane|integral to membrane|perinuclear region of cytoplasm	G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				Pancreas(144;909 1878 36867 38226 39554)								0.357143	7.545663	7.807046	5	9	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	72486429	72486429	6388	7	C	A	A	17	17	FZD9	A	5	3
FZD9	8326	broad.mit.edu	36	7	72486521	72486521	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:72486521G>C	uc003tyb.1	+	c.248G>C	c.(247-249)GGC>GCC	p.G83A		NM_003508	NP_003499	O00144	FZD9_HUMAN	frizzled 9	83	FZ.|Extracellular (Potential).				B cell differentiation|brain development|canonical Wnt receptor signaling pathway|embryo development|gonad development|neuroblast proliferation|regulation of gene-specific transcription from RNA polymerase II promoter|vasculature development	cell surface|filopodium membrane|integral to membrane|perinuclear region of cytoplasm	G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			central_nervous_system(1)	1		Lung NSC(55;0.0659)|all_lung(88;0.152)				Pancreas(144;909 1878 36867 38226 39554)								0.333333	6.821129	7.042971	3	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72486521	72486521	6388	7	G	C	C	42	42	FZD9	C	3	3
PTCD1	26024	broad.mit.edu	36	7	98861174	98861174	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:98861174A>C	uc003uqh.1	-	c.917T>G	c.(916-918)GTG>GGG	p.V306G	PDAP1_uc010lfv.1_Intron	NM_015545	NP_056360	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	306	PPR 5.									ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)													0.583333	9.91666	9.957493	7	5	AA		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.215)		Missense_Mutation	SNP	98861174	98861174	13181	7	A	C	C	6	6	PTCD1	C	4	4
KCNV1	27012	broad.mit.edu	36	8	111054088	111054088	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:111054088C>T	uc003ynr.2	-	c.566G>A	c.(565-567)TGT>TAT	p.C189Y	KCNV1_uc010mcw.1_Missense_Mutation_p.C189Y	NM_014379	NP_055194	Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	189	Cytoplasmic (Potential).					voltage-gated potassium channel complex	ion channel inhibitor activity|potassium channel regulator activity|voltage-gated potassium channel activity			lung(1)|kidney(1)	2	all_neural(195;0.219)													0.263158	117.753004	127.400937	50	140	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)		Missense_Mutation	SNP	111054088	111054088	8399	8	C	T	T	17	17	KCNV1	T	2	2
SLURP1	57152	broad.mit.edu	36	8	143820795	143820795	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143820795C>T	uc003ywy.1	-	c.11G>A	c.(10-12)CGC>CAC	p.R4H		NM_020427	NP_065160	P55000	SLUR1_HUMAN	ARS component B precursor	4					cell activation|cell adhesion	extracellular space	cytokine activity				0	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)													0.188679	21.925959	26.727396	10	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143820795	143820795	15254	8	C	T	T	27	27	SLURP1	T	1	1
PUF60	22827	broad.mit.edu	36	8	144971776	144971776	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144971776C>G	uc003yzs.1	-	c.982G>C	c.(982-984)GCA>CCA	p.A328P	SCRIB_uc003yzo.1_5'Flank|SCRIB_uc003yzp.1_5'Flank|PUF60_uc003yzq.1_Missense_Mutation_p.A285P|PUF60_uc003yzr.1_Missense_Mutation_p.A268P|PUF60_uc003yzt.1_Missense_Mutation_p.A311P|PUF60_uc003yzu.1_Missense_Mutation_p.A317P	NM_078480	NP_510965	Q9UHX1	PUF60_HUMAN	poly-U binding splicing factor 60KDa isoform a	328	Ala-rich.|Inhibits homodimerization.|Inhibits transcriptional repression, interaction with ERCC3 and apoptosis induction.				apoptosis|mRNA processing|regulation of transcription, DNA-dependent|RNA splicing|transcription, DNA-dependent	nucleus|ribonucleoprotein complex	DNA binding|nucleotide binding|protein binding|RNA binding				0	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.5	9.289663	9.289663	5	5	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)		Missense_Mutation	SNP	144971776	144971776	13282	8	C	G	G	25	25	PUF60	G	3	3
FGF20	26281	broad.mit.edu	36	8	16895072	16895072	+	Silent	SNP	G	A	A			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:16895072G>A	uc003wxc.1	-	c.516C>T	c.(514-516)GAC>GAT	p.D172D	FGF20_uc010lsv.1_Non-coding_Transcript|FGF20_uc010lsw.1_3'UTR	NM_019851	NP_062825	Q9NP95	FGF20_HUMAN	fibroblast growth factor 20	172					cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway	extracellular region|soluble fraction	growth factor activity				0									(IM95-Tumor)	153				0.087542	6.843255	57.966259	26	271	GG		KEEP	---	---	---	---	capture		Colorectal(111;0.0511)|COAD - Colon adenocarcinoma(73;0.207)	Silent	SNP	16895072	16895072	6086	8	G	A	A	40	40	FGF20	A	1	1
DOCK5	80005	broad.mit.edu	36	8	25272413	25272413	+	Silent	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25272413C>T	uc003xeg.1	+	c.2868C>T	c.(2866-2868)TGC>TGT	p.C956C	DOCK5_uc010luf.1_Non-coding_Transcript|DOCK5_uc003xei.1_Silent_p.C526C|DOCK5_uc003xej.1_Non-coding_Transcript|DOCK5_uc003xeh.1_Silent_p.C670C	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	956						cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity			ovary(3)	3		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)				Pancreas(145;34 1887 3271 10937 30165)								0.162791	8.696139	13.355412	7	36	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	Silent	SNP	25272413	25272413	4874	8	C	T	T	25	25	DOCK5	T	2	2
ANK1	286	broad.mit.edu	36	8	41685642	41685642	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:41685642G>T	uc003xom.1	-	c.1908C>A	c.(1906-1908)TAC>TAA	p.Y636*	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.1_5'Flank|ANK1_uc003xoi.1_Nonsense_Mutation_p.Y603*|ANK1_uc003xoj.1_Nonsense_Mutation_p.Y603*|ANK1_uc003xok.1_Nonsense_Mutation_p.Y603*|ANK1_uc003xol.1_Nonsense_Mutation_p.Y603*	NM_020475	NP_065208	P16157	ANK1_HUMAN	ankyrin 1 isoform 4	603	ANK 18.|89 kDa domain.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)|breast(1)	8	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)												0.197531	16.424682	23.432717	16	65	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)		Nonsense_Mutation	SNP	41685642	41685642	623	8	G	T	T	48	48	ANK1	T	5	3
ZNF704	619279	broad.mit.edu	36	8	81762184	81762184	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:81762184G>T	uc003yby.1	-	c.390C>A	c.(388-390)TAC>TAA	p.Y130*		NM_001033723	NP_001028895	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	130						intracellular	zinc ion binding				0	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)											OREG0018841	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.272727	6.831489	7.336791	3	8	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)		Nonsense_Mutation	SNP	81762184	81762184	18702	8	G	T	T	36	36	ZNF704	T	5	3
OR1L8	138881	broad.mit.edu	36	9	124369946	124369946	+	Missense_Mutation	SNP	C	T	T	rs10739614	by-cluster,by-frequency,by-2hit-2allele,by-hapmap,by-1000genomes	TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:124369946C>T	uc004bmp.1	-	c.632G>A	c.(631-633)CGT>CAT	p.R211H		NM_001004454	NP_001004454	Q8NGR8	OR1L8_HUMAN	olfactory receptor, family 1, subfamily L,	211	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3														0.220779	39.734152	45.260479	17	60	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124369946	124369946	11373	9	C	T	T	19	19	OR1L8	T	1	1
MPDZ	8777	broad.mit.edu	36	9	13098980	13098980	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:13098980G>C	uc010mhy.1	-	c.5934C>G	c.(5932-5934)AGC>AGG	p.S1978R	MPDZ_uc003zkx.2_Missense_Mutation_p.S202R|MPDZ_uc003zky.2_Missense_Mutation_p.S541R|MPDZ_uc010mhx.1_Missense_Mutation_p.S829R|MPDZ_uc003zkz.2_Missense_Mutation_p.S700R|MPDZ_uc010mhz.1_Missense_Mutation_p.S1974R|MPDZ_uc003zlb.2_Missense_Mutation_p.S1978R	NM_003829	NP_003820	O75970	MPDZ_HUMAN	multiple PDZ domain protein	2007	PDZ 13.				interspecies interaction between organisms	apical plasma membrane|dendrite|postsynaptic density|postsynaptic membrane|synaptosome|tight junction	protein C-terminus binding			ovary(5)|central_nervous_system(1)	6														0.315789	7.156009	7.783464	6	13	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(50;2.03e-06)	Missense_Mutation	SNP	13098980	13098980	10114	9	G	C	C	42	42	MPDZ	C	3	3
NTNG2	84628	broad.mit.edu	36	9	134063717	134063717	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:134063717C>T	uc004cbh.2	+	c.757C>T	c.(757-759)CGC>TGC	p.R253C		NM_032536	NP_115925	Q96CW9	NTNG2_HUMAN	netrin G2	253	Laminin N-terminal.				axonogenesis	anchored to plasma membrane					0														0.169811	50.038078	66.433721	27	132	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)	Missense_Mutation	SNP	134063717	134063717	11110	9	C	T	T	27	27	NTNG2	T	1	1
FUT7	2529	broad.mit.edu	36	9	139045459	139045459	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139045459G>C	uc004ckq.2	-	c.553C>G	c.(553-555)CTG>GTG	p.L185V	ABCA2_uc010nby.1_5'Flank|ABCA2_uc010nbz.1_5'Flank|ABCA2_uc004ckl.1_5'Flank|ABCA2_uc004ckm.1_5'Flank|C9orf139_uc004ckp.1_Intron	NM_004479	NP_004470	Q11130	FUT7_HUMAN	fucosyltransferase 7	185	Lumenal (Potential).				L-fucose catabolic process|protein glycosylation	Golgi cisterna membrane|integral to membrane	alpha(1,3)-fucosyltransferase activity				0	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)												0.333333	24.484027	25.656044	15	30	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)	Missense_Mutation	SNP	139045459	139045459	6360	9	G	C	C	34	34	FUT7	C	3	3
EXD3	54932	broad.mit.edu	36	9	139362498	139362498	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:139362498A>C	uc004cmp.2	-	c.1844T>G	c.(1843-1845)GTG>GGG	p.V615G	EXD3_uc010ncf.1_Intron|EXD3_uc004cmq.1_Non-coding_Transcript	NM_017820	NP_060290	Q8N9H8	MUT7_HUMAN	hypothetical protein LOC54932	615					nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding				0														0.304348	6.824077	7.737589	7	16	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139362498	139362498	5492	9	A	C	C	6	6	EXD3	C	4	4
CDKN2A	1029	broad.mit.edu	36	9	21961137	21961137	+	Silent	SNP	T	G	G			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:21961137T>G	uc003zpl.1	-	c.387A>C	c.(385-387)CGA>CGC	p.R129R	MTAP_uc003zpi.1_Intron|CDKN2A_uc003zpk.1_Missense_Mutation_p.D74A|CDKN2A_uc003zpj.1_3'UTR|CDKN2A_uc010miu.1_Non-coding_Transcript	NM_058195	NP_478102	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A isoform 4	144			R -> C (in squamous cell carcinoma).		cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein binding|protein kinase binding	p.0?(425)|p.D74V(2)|p.L65fs*38(1)|p.V59fs*45(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.C72fs*71(1)		haematopoietic_and_lymphoid_tissue(647)|skin(417)|upper_aerodigestive_tract(405)|central_nervous_system(380)|lung(319)|pancreas(237)|oesophagus(230)|urinary_tract(225)|pleura(94)|liver(91)|ovary(76)|soft_tissue(73)|biliary_tract(71)|bone(70)|breast(46)|stomach(44)|kidney(39)|NS(28)|thyroid(24)|cervix(23)|meninges(18)|genital_tract(15)|endometrium(13)|prostate(11)|autonomic_ganglia(10)|large_intestine(9)|salivary_gland(8)|adrenal_gland(6)|eye(4)|vulva(2)|small_intestine(1)	3636		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)						17		76	TSP Lung(5;3.83e-07)			0.285714	9.591926	10.170555	4	10	TT		KEEP	---	---	---	---	capture		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)	Silent	SNP	21961137	21961137	3290	9	T	G	G	58	58	CDKN2A	G	4	4
SUSD3	203328	broad.mit.edu	36	9	94877910	94877910	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0190-01	TCGA-06-0190-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:94877910C>A	uc004atb.1	+	c.112C>A	c.(112-114)CCC>ACC	p.P38T	SUSD3_uc004atc.1_Missense_Mutation_p.P25T	NM_145006	NP_659443	Q96L08	SUSD3_HUMAN	sushi domain containing 3	38	Sushi.|Extracellular (Potential).					integral to membrane				breast(2)|skin(2)|ovary(1)|lung(1)	6														0.253968	12.535107	16.172849	16	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94877910	94877910	15929	9	C	A	A	18	18	SUSD3	A	3	3
AMELX	265	broad.mit.edu	36	X	11226788	11226788	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:11226788A>C	uc004cus.1	+	c.386A>C	c.(385-387)CAC>CCC	p.H129P	ARHGAP6_uc004cup.1_Intron|ARHGAP6_uc004cuo.1_Intron|ARHGAP6_uc004cur.1_Intron|ARHGAP6_uc004cun.1_Intron|AMELX_uc004cut.1_Missense_Mutation_p.H115P|AMELX_uc004cuu.1_Missense_Mutation_p.H99P	NM_182680	NP_872621	Q99217	AMELX_HUMAN	amelogenin (X chromosome) isoform 3 precursor	115					cell adhesion|cell proliferation|chondrocyte differentiation|enamel mineralization|epithelial to mesenchymal transition|ion homeostasis|odontogenesis of dentine-containing tooth|osteoblast differentiation|positive regulation of collagen biosynthetic process|positive regulation of tooth mineralization|signal transduction	extracellular matrix part|proteinaceous extracellular matrix	cell surface binding|growth factor activity|hydroxyapatite binding|identical protein binding|structural constituent of tooth enamel				0														0.255814	7.158919	9.817704	11	32	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11226788	11226788	572	23	A	C	C	6	6	AMELX	C	4	4
PLXNB3	5365	broad.mit.edu	36	X	152688508	152688508	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0190-01	TCGA-06-0190-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152688508T>G	uc004fii.1	+	c.1549T>G	c.(1549-1551)TGG>GGG	p.W517G	PLXNB3_uc010nuk.1_Missense_Mutation_p.W540G	NM_005393	NP_005384	Q9ULL4	PLXB3_HUMAN	plexin B3	517	Extracellular (Potential).				axon guidance	integral to membrane|intracellular|plasma membrane	protein binding|receptor activity			lung(1)	1	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)													0.636364	11.136852	11.297717	7	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152688508	152688508	12551	23	T	G	G	59	59	PLXNB3	G	4	4
KLHL34	257240	broad.mit.edu	36	X	21585595	21585595	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0190-01	TCGA-06-0190-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:21585595G>C	uc004czz.1	-	c.233C>G	c.(232-234)GCC>GGC	p.A78G		NM_153270	NP_695002	Q8N239	KLH34_HUMAN	kelch-like 34	78	BTB.									ovary(1)	1														0.272727	6.318565	6.832062	3	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21585595	21585595	8701	23	G	C	C	42	42	KLHL34	C	3	3
NLGN4Y	22829	broad.mit.edu	36	Y	15451591	15451591	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0190-01	TCGA-06-0190-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrY:15451591A>C	uc004ftg.1	+	c.1399A>C	c.(1399-1401)ACC>CCC	p.T467P	NLGN4Y_uc004fte.1_Missense_Mutation_p.T299P|NLGN4Y_uc004ftf.1_Missense_Mutation_p.T160P|NLGN4Y_uc004fth.1_Missense_Mutation_p.T467P	NM_014893	NP_055708	Q8NFZ3	NLGNY_HUMAN	neuroligin 4, Y-linked	467	Extracellular (Potential).				brainstem development|cell adhesion|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of synaptic transmission|social behavior|territorial aggressive behavior|vocalization behavior	integral to membrane|plasma membrane|synapse	carboxylesterase activity|protein binding				0														0.217391	10.374154	13.972651	10	36	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15451591	15451591	10868	24	A	C	C	6	6	NLGN4Y	C	4	4
