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	TCGAscape_Amplification_Peaks	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_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
SORCS3	22986	broad.mit.edu	37	10	106927100	106927100	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:106927100C>A	uc001kyi.1	+	c.1894C>A	c.(1894-1896)CAT>AAT	p.H632N		NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN	VPS10 domain receptor protein SORCS 3 precursor	632	Lumenal (Potential).					integral to membrane	neuropeptide receptor activity			ovary(6)|central_nervous_system(1)	7		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		NSCLC(116;1497 1690 7108 13108 14106)								0.5	72.823203	72.823203	23	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106927100	106927100	15432	10	C	A	A	A	325	25	SORCS3	2	2
HSPA12A	259217	broad.mit.edu	37	10	118434798	118434798	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118434798G>T	uc001lct.2	-	c.1522C>A	c.(1522-1524)CAG>AAG	p.Q508K	HSPA12A_uc001lcu.2_Missense_Mutation_p.Q425K	NM_025015	NP_079291	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	508							ATP binding			ovary(1)	1				all cancers(201;0.0158)										0.666667	24.702722	24.998141	8	4	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118434798	118434798	7703	10	G	T	T	T	611	47	HSPA12A	2	2
KIAA1598	57698	broad.mit.edu	37	10	118719676	118719676	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118719676G>A	uc009xyw.2	-	c.238C>T	c.(238-240)CGA>TGA	p.R80*	KIAA1598_uc001lcz.3_Nonsense_Mutation_p.R80*|KIAA1598_uc010qso.1_Nonsense_Mutation_p.R20*|KIAA1598_uc010qsp.1_Nonsense_Mutation_p.R80*|KIAA1598_uc010qsq.1_Nonsense_Mutation_p.R20*|KIAA1598_uc001lcy.3_Nonsense_Mutation_p.R50*	NM_001127211	NP_001120683	A0MZ66	SHOT1_HUMAN	shootin1 isoform a	80	Potential.				axon guidance	axon					0				all cancers(201;0.00494)										0.235294	10.692755	11.781074	4	13	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	118719676	118719676	8555	10	G	A	A	A	480	37	KIAA1598	5	1
EBF3	253738	broad.mit.edu	37	10	131761676	131761676	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:131761676C>A	uc001lki.1	-	c.246G>T	c.(244-246)GTG>GTT	p.V82V	EBF3_uc010qur.1_Silent_p.V68V	NM_001005463	NP_001005463	Q9H4W6	COE3_HUMAN	early B-cell factor 3	82					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|protein binding|transcription regulator activity			central_nervous_system(1)|pancreas(1)	2		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)										0.214286	7.817166	8.87247	3	11	KEEP	---	---	---	---	capture		Silent	SNP	131761676	131761676	5068	10	C	A	A	A	262	21	EBF3	2	2
NEBL	10529	broad.mit.edu	37	10	21120401	21120401	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:21120401C>A	uc001iqi.2	-	c.1560_splice	c.e15+1	p.Q520_splice	NEBL_uc001iqj.2_Splice_Site_SNP|NEBL_uc001iqk.2_Intron|NEBL_uc001iql.1_Splice_Site_SNP	NM_006393	NP_006384			nebulette sarcomeric isoform						regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2														0.259259	75.151819	80.819914	28	80	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	21120401	21120401	10702	10	C	A	A	A	234	18	NEBL	5	2
MASTL	84930	broad.mit.edu	37	10	27475433	27475433	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:27475433C>T	uc001itm.2	+	c.2608C>T	c.(2608-2610)CAG>TAG	p.Q870*	MASTL_uc001itl.2_Nonsense_Mutation_p.Q869*|MASTL_uc009xkw.1_Nonsense_Mutation_p.Q831*|MASTL_uc009xkx.1_Non-coding_Transcript	NM_032844	NP_116233	Q96GX5	GWL_HUMAN	microtubule associated serine/threonine	870	AGC-kinase C-terminal.				cell division|G2/M transition of mitotic cell cycle|mitosis|negative regulation of protein phosphatase type 2A activity|protein phosphorylation|regulation of cell cycle|response to DNA damage stimulus	centrosome|cleavage furrow|nucleus	ATP binding|protein phosphatase 2A binding|protein serine/threonine kinase activity			stomach(1)|ovary(1)|lung(1)	3										553				0.14557	38.423524	57.511188	23	135	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	27475433	27475433	9712	10	C	T	T	T	377	29	MASTL	5	2
PFKP	5214	broad.mit.edu	37	10	3147690	3147690	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:3147690G>T	uc001igp.2	+	c.771G>T	c.(769-771)TCG>TCT	p.S257S	PFKP_uc001igq.2_Silent_p.S249S|PFKP_uc009xhr.2_Silent_p.S219S|PFKP_uc009xhs.1_Silent_p.S41S|PFKP_uc009xht.2_5'Flank	NM_002627	NP_002618	Q01813	K6PP_HUMAN	phosphofructokinase, platelet	257					glycolysis	6-phosphofructokinase complex	6-phosphofructokinase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)	2				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)										0.263158	12.9669	13.930452	5	14	KEEP	---	---	---	---	capture		Silent	SNP	3147690	3147690	12188	10	G	T	T	T	496	39	PFKP	1	1
NRP1	8829	broad.mit.edu	37	10	33619677	33619677	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:33619677G>C	uc001iwx.3	-	c.207C>G	c.(205-207)ATC>ATG	p.I69M	NRP1_uc001iwv.3_Missense_Mutation_p.I69M|NRP1_uc009xlz.2_Missense_Mutation_p.I69M|NRP1_uc001iww.3_De_novo_Start_OutOfFrame|NRP1_uc001iwy.3_Missense_Mutation_p.I69M|NRP1_uc001iwz.2_Missense_Mutation_p.I69M|NRP1_uc001ixa.2_Missense_Mutation_p.I69M|NRP1_uc001ixb.1_Missense_Mutation_p.I69M|NRP1_uc001ixc.1_Missense_Mutation_p.I69M	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a	69	CUB 1.|Extracellular (Potential).				axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)	3					Palifermin(DB00039)|Pegaptanib(DB04895)	Melanoma(104;886 1489 44640 45944 51153)								0.136364	4.608797	7.426941	3	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33619677	33619677	11065	10	G	C	C	C	577	45	NRP1	3	3
DIP2C	22982	broad.mit.edu	37	10	373024	373024	+	Silent	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:373024C>G	uc001ifp.2	-	c.3846G>C	c.(3844-3846)CTG>CTC	p.L1282L		NM_014974	NP_055789	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C	1282						nucleus	catalytic activity|transcription factor binding			breast(4)|ovary(2)|large_intestine(1)	7		all_cancers(4;0.00336)|all_lung(4;0.00732)|Lung NSC(4;0.00785)|all_epithelial(10;0.0159)|Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.136)	Epithelial(11;0.0123)|all cancers(11;0.0467)|Lung(33;0.0864)|OV - Ovarian serous cystadenocarcinoma(14;0.106)						1018				0.42029	90.926938	91.316598	29	40	KEEP	---	---	---	---	capture		Silent	SNP	373024	373024	4708	10	C	G	G	G	210	17	DIP2C	3	3
CXCL12	6387	broad.mit.edu	37	10	44871411	44871411	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:44871411C>A	uc001jbh.2	-	c.336G>T	c.(334-336)AAG>AAT	p.K112N	CXCL12_uc001jbf.2_Intron	NM_001033886	NP_001029058	P48061	SDF1_HUMAN	chemokine (C-X-C motif) ligand 12 (stromal	Error:Variant_position_missing_in_P48061_after_alignment					blood circulation|cell adhesion|cellular calcium ion homeostasis|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|negative regulation of leukocyte apoptosis|positive regulation of monocyte chemotaxis|regulation of actin polymerization or depolymerization|response to virus	extracellular space	chemokine activity|growth factor activity|signal transducer activity				0					Dexamethasone(DB01234)					379				0.375	74.482386	75.478475	27	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44871411	44871411	4240	10	C	A	A	A	311	24	CXCL12	2	2
CSTF2T	23283	broad.mit.edu	37	10	53458165	53458165	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:53458165C>A	uc001jjp.2	-	c.1145G>T	c.(1144-1146)GGA>GTA	p.G382V	PRKG1_uc001jjm.2_Intron|PRKG1_uc001jjn.2_Intron|PRKG1_uc001jjo.2_Intron	NM_015235	NP_056050	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit	382	Gly-rich.				mRNA processing	nucleus	nucleotide binding|RNA binding			ovary(1)	1				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)										0.217949	34.932967	40.655	17	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53458165	53458165	4126	10	C	A	A	A	390	30	CSTF2T	2	2
PCDH15	65217	broad.mit.edu	37	10	55591282	55591282	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:55591282C>A	uc010qhy.1	-	c.4010G>T	c.(4009-4011)GGC>GTC	p.G1337V	PCDH15_uc010qhq.1_Missense_Mutation_p.G1337V|PCDH15_uc010qhr.1_Missense_Mutation_p.G1332V|PCDH15_uc010qhs.1_Missense_Mutation_p.G1344V|PCDH15_uc010qht.1_Missense_Mutation_p.G1339V|PCDH15_uc010qhu.1_Missense_Mutation_p.G1332V|PCDH15_uc001jjv.1_Intron|PCDH15_uc010qhv.1_Missense_Mutation_p.G1332V|PCDH15_uc010qhw.1_Missense_Mutation_p.G1295V|PCDH15_uc010qhx.1_Missense_Mutation_p.G1261V|PCDH15_uc010qhz.1_Missense_Mutation_p.G1332V|PCDH15_uc010qia.1_Missense_Mutation_p.G1310V|PCDH15_uc001jju.1_Missense_Mutation_p.G1332V|PCDH15_uc010qib.1_Missense_Mutation_p.G1310V	NM_001142763	NP_001136235	Q96QU1	PCD15_HUMAN	protocadherin 15 isoform CD1-1 precursor	1332	Extracellular (Potential).				equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	extracellular region|extracellular space|integral to membrane|photoreceptor outer segment|plasma membrane|stereocilium|synapse	calcium ion binding			pancreas(5)|ovary(4)	9		Melanoma(3;0.117)|Lung SC(717;0.238)								1612				0.272727	31.079664	33.128794	12	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55591282	55591282	11931	10	C	A	A	A	338	26	PCDH15	2	2
SFMBT2	57713	broad.mit.edu	37	10	7247813	7247813	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:7247813T>C	uc009xio.1	-	c.1408A>G	c.(1408-1410)AAT>GAT	p.N470D	SFMBT2_uc001ijn.1_Missense_Mutation_p.N470D|SFMBT2_uc010qay.1_Intron	NM_001029880	NP_001025051	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	470	MBT 4.					nucleus				ovary(4)|large_intestine(1)|central_nervous_system(1)	6														0.156863	16.065868	21.797781	8	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7247813	7247813	14647	10	T	C	C	C	819	63	SFMBT2	4	4
CDH23	64072	broad.mit.edu	37	10	73405688	73405688	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:73405688G>A	uc001jrx.3	+	c.1241G>A	c.(1240-1242)CGG>CAG	p.R414Q	CDH23_uc001jrw.3_Missense_Mutation_p.R414Q|CDH23_uc001jry.2_Missense_Mutation_p.R30Q|CDH23_uc001jrz.2_Missense_Mutation_p.R30Q	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	414	Cadherin 4.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11														0.093023	1.776786	8.933207	4	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73405688	73405688	3237	10	G	A	A	A	507	39	CDH23	1	1
PPIF	10105	broad.mit.edu	37	10	81111255	81111255	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:81111255A>C	uc001kai.2	+	c.328A>C	c.(328-330)ACC>CCC	p.T110P	PPIF_uc001kaj.2_Missense_Mutation_p.T110P	NM_005729	NP_005720	P30405	PPIF_HUMAN	peptidylprolyl isomerase F precursor	110	PPIase cyclophilin-type.				protein folding	membrane fraction|mitochondrial matrix	peptidyl-prolyl cis-trans isomerase activity				0	all_cancers(46;0.0893)|Breast(12;8.52e-05)|all_epithelial(25;0.00449)|Prostate(51;0.00985)		Epithelial(14;0.00242)|all cancers(16;0.0069)|Colorectal(32;0.229)		Dimethyl sulfoxide(DB01093)|L-Proline(DB00172)									0.333333	6.193756	6.429543	3	6	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	81111255	81111255	12758	10	A	C	C	C	78	6	PPIF	4	4
GHITM	27069	broad.mit.edu	37	10	85901331	85901331	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:85901331C>T	uc001kcs.1	+	c.75C>T	c.(73-75)TCC>TCT	p.S25S	GHITM_uc010qma.1_5'UTR|GHITM_uc010qmb.1_5'Flank	NM_014394	NP_055209	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	25					apoptosis	integral to membrane|mitochondrial inner membrane					0														0.072464	-2.580242	10.409445	5	64	KEEP	---	---	---	---	capture		Silent	SNP	85901331	85901331	6638	10	C	T	T	T	275	22	GHITM	2	2
LRIT2	340745	broad.mit.edu	37	10	85984731	85984731	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:85984731G>A	uc010qmc.1	-	c.250C>T	c.(250-252)CTC>TTC	p.L84F	LRIT2_uc001kcy.2_Missense_Mutation_p.L84F	NM_001017924	NP_001017924	A6NDA9	LRIT2_HUMAN	leucine rich repeat containing 22 precursor	84	LRR 1.					integral to membrane				ovary(2)	2														0.203704	53.187114	61.989985	22	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	85984731	85984731	9321	10	G	A	A	A	455	35	LRIT2	2	2
MYOF	26509	broad.mit.edu	37	10	95157206	95157206	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:95157206G>A	uc001kin.2	-	c.1229C>T	c.(1228-1230)ACA>ATA	p.T410I	MYOF_uc001kio.2_Missense_Mutation_p.T410I|MYOF_uc001kip.3_Missense_Mutation_p.T410I|MYOF_uc009xuf.2_Missense_Mutation_p.T392I	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	410	Cytoplasmic (Potential).|C2 3.				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4														0.142857	7.749562	12.053396	5	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95157206	95157206	10484	10	G	A	A	A	624	48	MYOF	2	2
PIK3AP1	118788	broad.mit.edu	37	10	98411325	98411325	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:98411325T>C	uc001kmq.2	-	c.796A>G	c.(796-798)ATG>GTG	p.M266V	PIK3AP1_uc001kmp.2_Missense_Mutation_p.M88V	NM_152309	NP_689522	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	266	DBB.					cytoplasm|plasma membrane				ovary(1)	1		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)										0.071429	-0.907306	7.040563	3	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98411325	98411325	12332	10	T	C	C	C	663	51	PIK3AP1	4	4
ATM	472	broad.mit.edu	37	11	108205807	108205807	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108205807G>A	uc001pkb.1	+	c.8122G>A	c.(8122-8124)GAT>AAT	p.D2708N	ATM_uc009yxr.1_Missense_Mutation_p.D2708N|C11orf65_uc010rvx.1_Intron|C11orf65_uc009yxu.1_Intron|ATM_uc001pke.1_Missense_Mutation_p.D1360N	NM_000051	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated isoform 1	2708					cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding	p.D2708N(1)		haematopoietic_and_lymphoid_tissue(174)|lung(24)|breast(14)|large_intestine(9)|ovary(5)|kidney(5)|central_nervous_system(4)|upper_aerodigestive_tract(1)|stomach(1)|NS(1)	238		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)						1073	TSP Lung(14;0.12)			0.55814	79.918018	80.047974	24	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	108205807	108205807	1128	11	G	A	A	A	481	37	ATM	1	1
PCSK7	9159	broad.mit.edu	37	11	117097897	117097897	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:117097897C>A	uc001pqr.2	-	c.745G>T	c.(745-747)GTG>TTG	p.V249L		NM_004716	NP_004707	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	249	Catalytic.|Extracellular (Potential).				peptide hormone processing	integral to Golgi membrane	serine-type endopeptidase activity				0	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)						435		OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.263158	14.568691	15.530984	5	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	117097897	117097897	12026	11	C	A	A	A	247	19	PCSK7	1	1
USP47	55031	broad.mit.edu	37	11	11926949	11926949	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:11926949G>A	uc001mjs.2	+	c.823G>A	c.(823-825)GAT>AAT	p.D275N	USP47_uc001mjq.1_Missense_Mutation_p.D295N|USP47_uc001mjr.2_Missense_Mutation_p.D207N	NM_017944	NP_060414	Q96K76	UBP47_HUMAN	ubiquitin specific protease 47	295					base-excision repair|cellular response to UV|monoubiquitinated protein deubiquitination|negative regulation of apoptosis|negative regulation of caspase activity|negative regulation of G2/M transition of mitotic cell cycle|negative regulation of gene-specific transcription|positive regulation of cell growth|response to drug|ubiquitin-dependent protein catabolic process	cytoplasm|SCF ubiquitin ligase complex	specific transcriptional repressor activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|WD40-repeat domain binding			ovary(1)|skin(1)	2				Epithelial(150;0.000339)										0.296296	19.286628	20.290503	8	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11926949	11926949	17642	11	G	A	A	A	585	45	USP47	2	2
GRAMD1B	57476	broad.mit.edu	37	11	123480980	123480980	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:123480980A>G	uc001pyw.2	+	c.1445A>G	c.(1444-1446)CAT>CGT	p.H482R	GRAMD1B_uc001pyx.2_Missense_Mutation_p.H475R|GRAMD1B_uc010rzw.1_Missense_Mutation_p.H435R|GRAMD1B_uc010rzx.1_Missense_Mutation_p.H435R|GRAMD1B_uc001pyy.2_Missense_Mutation_p.H166R	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	475						integral to membrane				ovary(1)	1		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)						1503				0.058824	-9.200279	8.17926	5	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123480980	123480980	7024	11	A	G	G	G	104	8	GRAMD1B	4	4
SNX19	399979	broad.mit.edu	37	11	130785334	130785334	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:130785334C>A	uc001qgk.3	-	c.501G>T	c.(499-501)CAG>CAT	p.Q167H	SNX19_uc010sce.1_Intron|SNX19_uc010scf.1_Intron|SNX19_uc010scg.1_Intron|SNX19_uc001qgl.3_Missense_Mutation_p.Q167H|SNX19_uc009zcx.1_Intron	NM_014758	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	167	PXA.				cell communication|protein transport	cytoplasmic vesicle membrane	phosphatidylinositol binding|protein binding			ovary(2)|lung(2)	4	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)						728				0.189189	14.206776	17.548275	7	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130785334	130785334	15390	11	C	A	A	A	415	32	SNX19	2	2
HPS5	11234	broad.mit.edu	37	11	18313428	18313428	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:18313428C>A	uc001mod.1	-	c.2001G>T	c.(1999-2001)ATG>ATT	p.M667I	HPS5_uc001moe.1_Missense_Mutation_p.M553I|HPS5_uc001mof.1_Missense_Mutation_p.M553I	NM_181507	NP_852608	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5 isoform a	667						cytosol				ovary(1)|pancreas(1)	2														0.217822	51.190976	58.608113	22	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18313428	18313428	7634	11	C	A	A	A	377	29	HPS5	2	2
ELP4	26610	broad.mit.edu	37	11	31616420	31616420	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:31616420G>T	uc001mtb.2	+	c.485G>T	c.(484-486)TGG>TTG	p.W162L	ELP4_uc001mta.1_Non-coding_Transcript|ELP4_uc001mtc.2_Missense_Mutation_p.W162L|ELP4_uc010rdz.1_Missense_Mutation_p.W162L	NM_019040	NP_061913	Q96EB1	ELP4_HUMAN	elongation protein 4 homolog	162					histone acetylation|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	cytoplasm|DNA-directed RNA polymerase II, holoenzyme|Elongator holoenzyme complex|transcription elongation factor complex	phosphorylase kinase regulator activity|protein binding			ovary(1)	1	Lung SC(675;0.225)													0.229167	27.901444	31.12901	11	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31616420	31616420	5274	11	G	T	T	T	611	47	ELP4	2	2
RAG2	5897	broad.mit.edu	37	11	36614149	36614149	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:36614149T>A	uc001mwv.3	-	c.1570A>T	c.(1570-1572)AGG>TGG	p.R524W	RAG1_uc001mwt.2_Intron|C11orf74_uc010rfd.1_5'Flank|C11orf74_uc001mww.1_5'Flank|C11orf74_uc001mwx.1_5'Flank|C11orf74_uc001mwy.1_5'Flank|C11orf74_uc001mwz.1_5'Flank|C11orf74_uc010rfe.1_5'Flank	NM_000536	NP_000527	P55895	RAG2_HUMAN	recombination activating gene 2	524					chromatin modification|pre-B cell allelic exclusion|somatic diversification of immunoglobulins|T cell differentiation in thymus|V(D)J recombination	nucleus	chromatin binding|DNA binding|endonuclease activity|methylated histone residue binding|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-4,5-bisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)	2	all_lung(20;0.226)	all_hematologic(20;0.00756)												0.133333	6.778389	10.693281	4	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36614149	36614149	13465	11	T	A	A	A	726	56	RAG2	3	3
LRRC4C	57689	broad.mit.edu	37	11	40137750	40137750	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:40137750C>T	uc001mxa.1	-	c.93G>A	c.(91-93)CTG>CTA	p.L31L	LRRC4C_uc001mxc.1_Silent_p.L27L|LRRC4C_uc001mxd.1_Silent_p.L27L|LRRC4C_uc001mxb.1_Silent_p.L27L	NM_020929	NP_065980	Q9HCJ2	LRC4C_HUMAN	netrin-G1 ligand precursor	31					regulation of axonogenesis	integral to membrane	protein binding			ovary(4)|central_nervous_system(1)	5		all_lung(304;0.0575)|Lung NSC(402;0.138)												0.404762	52.565695	52.898984	17	25	KEEP	---	---	---	---	capture		Silent	SNP	40137750	40137750	9383	11	C	T	T	T	262	21	LRRC4C	2	2
AMBRA1	55626	broad.mit.edu	37	11	46568663	46568663	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:46568663G>A	uc001ncv.2	-	c.378C>T	c.(376-378)CAC>CAT	p.H126H	AMBRA1_uc009ylc.1_Silent_p.H126H|AMBRA1_uc001ncu.1_Silent_p.H126H|AMBRA1_uc010rgu.1_Silent_p.H126H|AMBRA1_uc001ncw.2_Silent_p.H126H|AMBRA1_uc001ncx.2_Silent_p.H126H	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	126	WD 2.				autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)										0.162963	43.678253	58.240674	22	113	KEEP	---	---	---	---	capture		Silent	SNP	46568663	46568663	568	11	G	A	A	A	516	40	AMBRA1	1	1
OR52R1	119695	broad.mit.edu	37	11	4824735	4824735	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4824735G>A	uc010qym.1	-	c.1113C>T	c.(1111-1113)CCC>CCT	p.P371P		NM_001005177	NP_001005177	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R,	292	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.493213	330.259539	330.26844	109	112	KEEP	---	---	---	---	capture		Silent	SNP	4824735	4824735	11541	11	G	A	A	A	600	47	OR52R1	2	2
OR51F2	119694	broad.mit.edu	37	11	4843075	4843075	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4843075C>T	uc010qyn.1	+	c.460C>T	c.(460-462)CGA>TGA	p.R154*		NM_001004753	NP_001004753	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F,	154	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|pancreas(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.081967	8.130107	84.045851	35	392	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	4843075	4843075	11507	11	C	T	T	T	295	23	OR51F2	5	1
OR51G1	79324	broad.mit.edu	37	11	4944782	4944782	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:4944782A>C	uc010qyr.1	-	c.788T>G	c.(787-789)GTG>GGG	p.V263G		NM_001005237	NP_001005237	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G,	263	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)										0.247191	56.94785	62.097583	22	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4944782	4944782	11508	11	A	C	C	C	78	6	OR51G1	4	4
OR52E2	119678	broad.mit.edu	37	11	5080793	5080793	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5080793A>T	uc010qyw.1	-	c.65T>A	c.(64-66)CTA>CAA	p.L22Q		NM_001005164	NP_001005164	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E,	22	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)										0.248	79.965951	87.186317	31	94	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5080793	5080793	11525	11	A	T	T	T	195	15	OR52E2	3	3
OR52D1	390066	broad.mit.edu	37	11	5510137	5510138	+	Nonsense_Mutation	DNP	CC	AA	AA			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:5510137_5510138CC>AA	uc010qzg.1	+	c.201_202CC>AA	c.(199-204)TGCCTT>TGAATT	p.67_68CL>*I	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001005163	NP_001005163	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D,	67_68	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)										0.258065	79.943378	86.520385	32	92	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	5510137	5510138	11524	11	CC	AA	AA	AA	337	26	OR52D1	5	2
OR5M10	390167	broad.mit.edu	37	11	56344538	56344538	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56344538G>T	uc001niz.1	-	c.660C>A	c.(658-660)TTC>TTA	p.F220L		NM_001004741	NP_001004741	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M,	220	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.226087	60.484729	68.41274	26	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56344538	56344538	11583	11	G	T	T	T	581	45	OR5M10	2	2
OR1S2	219958	broad.mit.edu	37	11	57971021	57971021	+	Silent	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:57971021C>G	uc010rkb.1	-	c.633G>C	c.(631-633)GTG>GTC	p.V211V		NM_001004459	NP_001004459	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S,	211	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1		Breast(21;0.0589)												0.130081	23.907797	40.297482	16	107	KEEP	---	---	---	---	capture		Silent	SNP	57971021	57971021	11379	11	C	G	G	G	210	17	OR1S2	3	3
MS4A7	58475	broad.mit.edu	37	11	60161284	60161284	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:60161284C>T	uc001npe.2	+	c.673C>T	c.(673-675)CAA>TAA	p.Q225*	MS4A7_uc001npf.2_Nonsense_Mutation_p.Q225*|MS4A7_uc001npg.2_Nonsense_Mutation_p.Q180*|MS4A7_uc001nph.2_Nonsense_Mutation_p.Q180*|MS4A14_uc001npi.2_Intron	NM_206939	NP_996822	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member	225	Cytoplasmic (Potential).					integral to membrane	receptor activity			ovary(1)|central_nervous_system(1)	2														0.171233	47.978899	62.903866	25	121	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	60161284	60161284	10259	11	C	T	T	T	221	17	MS4A7	5	2
SCGB1D1	10648	broad.mit.edu	37	11	61957767	61957767	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:61957767C>T	uc001nsz.1	+	c.11C>T	c.(10-12)TCG>TTG	p.S4L		NM_006552	NP_006543	O95968	SG1D1_HUMAN	lipophilin A precursor	4						extracellular space	binding				0														0.2	35.562468	42.253509	16	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61957767	61957767	14377	11	C	T	T	T	403	31	SCGB1D1	1	1
SLC22A12	116085	broad.mit.edu	37	11	64359070	64359070	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64359070C>A	uc001oam.1	+	c.42C>A	c.(40-42)GGC>GGA	p.G14G	SLC22A12_uc009ypr.1_Silent_p.G14G|SLC22A12_uc001oal.1_Intron|SLC22A12_uc009yps.1_Silent_p.G14G|SLC22A12_uc001oan.1_Silent_p.G14G|SLC22A12_uc009ypt.2_5'Flank	NM_144585	NP_653186	Q96S37	S22AC_HUMAN	urate anion exchanger 1 isoform a	14	Helical; (Potential).				cellular homeostasis|response to drug|urate metabolic process	apical plasma membrane|brush border membrane|integral to membrane	PDZ domain binding|urate transmembrane transporter activity			ovary(1)	1														0.381818	61.481309	62.147612	21	34	KEEP	---	---	---	---	capture		Silent	SNP	64359070	64359070	14939	11	C	A	A	A	314	25	SLC22A12	2	2
ATG2A	23130	broad.mit.edu	37	11	64664023	64664023	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:64664023G>A	uc001obx.2	-	c.5338C>T	c.(5338-5340)CGG>TGG	p.R1780W	ATG2A_uc001obw.2_Missense_Mutation_p.R545W	NM_015104	NP_055919	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1780							protein binding			ovary(1)|central_nervous_system(1)	2												OREG0004026	type=REGULATORY REGION|Gene=BC027481|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.178571	9.563986	12.282911	5	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64664023	64664023	1112	11	G	A	A	A	493	38	ATG2A	1	1
SPTBN2	6712	broad.mit.edu	37	11	66460730	66460730	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:66460730T>A	uc001ojd.2	-	c.4781A>T	c.(4780-4782)TAC>TTC	p.Y1594F		NM_006946	NP_008877	O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	1594	Spectrin 13.				actin filament capping|axon guidance|cell death|vesicle-mediated transport	cytosol|spectrin	actin binding|structural constituent of cytoskeleton			large_intestine(1)|pancreas(1)|central_nervous_system(1)|skin(1)	4														0.2	31.461279	38.155795	16	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	66460730	66460730	15634	11	T	A	A	A	741	57	SPTBN2	3	3
NLRP10	338322	broad.mit.edu	37	11	7981511	7981511	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7981511C>A	uc001mfv.1	-	c.1648G>T	c.(1648-1650)GAA>TAA	p.E550*		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	550							ATP binding			lung(4)|ovary(2)|kidney(1)|pancreas(1)	8				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)						109				0.555556	75.477775	75.598767	25	20	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	7981511	7981511	10875	11	C	A	A	A	416	32	NLRP10	5	2
NLRP10	338322	broad.mit.edu	37	11	7981770	7981770	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:7981770G>C	uc001mfv.1	-	c.1389C>G	c.(1387-1389)AGC>AGG	p.S463R		NM_176821	NP_789791	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	463	NACHT.						ATP binding			lung(4)|ovary(2)|kidney(1)|pancreas(1)	8				Epithelial(150;1.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)						109				0.2	50.73818	59.510272	21	84	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7981770	7981770	10875	11	G	C	C	C	438	34	NLRP10	3	3
PRCP	5547	broad.mit.edu	37	11	82560238	82560238	+	Silent	SNP	A	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:82560238A>C	uc001ozr.2	-	c.837T>G	c.(835-837)ACT>ACG	p.T279T	PRCP_uc001ozs.2_Silent_p.T258T	NM_199418	NP_955450	P42785	PCP_HUMAN	prolylcarboxypeptidase isoform 2 preproprotein	258	SKS domain.				blood coagulation, intrinsic pathway|proteolysis	lysosome|plasma membrane	protein binding|serine-type carboxypeptidase activity				0														0.349593	105.486569	107.98606	43	80	KEEP	---	---	---	---	capture		Silent	SNP	82560238	82560238	12891	11	A	C	C	C	80	7	PRCP	4	4
TMEM135	65084	broad.mit.edu	37	11	87013349	87013349	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:87013349G>C	uc001pch.2	+	c.563G>C	c.(562-564)GGG>GCG	p.G188A	TMEM135_uc010rtt.1_Missense_Mutation_p.G49A|TMEM135_uc001pci.2_Missense_Mutation_p.G166A	NM_022918	NP_075069	Q86UB9	TM135_HUMAN	transmembrane protein 135	188						integral to membrane					0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)												0.384615	158.408362	159.929209	50	80	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87013349	87013349	16583	11	G	C	C	C	559	43	TMEM135	3	3
PTPN11	5781	broad.mit.edu	37	12	112939970	112939970	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:112939970A>T	uc001ttx.2	+	c.1622A>T	c.(1621-1623)GAA>GTA	p.E541V		NM_002834	NP_002825	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type	545					axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding			haematopoietic_and_lymphoid_tissue(372)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|ovary(1)|NS(1)|kidney(1)	388										372				0.191011	34.822953	42.765165	17	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112939970	112939970	13235	12	A	T	T	T	117	9	PTPN11	3	3
RPH3A	22895	broad.mit.edu	37	12	113307819	113307819	+	Silent	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:113307819T>A	uc010syl.1	+	c.771T>A	c.(769-771)GCT>GCA	p.A257A	RPH3A_uc001ttz.2_Silent_p.A257A|RPH3A_uc001tty.2_Silent_p.A253A|RPH3A_uc009zwe.1_Silent_p.A253A|RPH3A_uc010sym.1_Silent_p.A208A|RPH3A_uc001tua.2_Silent_p.A17A	NM_001143854	NP_001137326	Q9Y2J0	RP3A_HUMAN	rabphilin 3A homolog isoform 1	257	Pro-rich.				intracellular protein transport	cell junction|synaptic vesicle	Rab GTPase binding|transporter activity|zinc ion binding			ovary(3)|central_nervous_system(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(302;0.00453)										0.35	42.658262	43.443048	14	26	KEEP	---	---	---	---	capture		Silent	SNP	113307819	113307819	14030	12	T	A	A	A	704	55	RPH3A	3	3
CLIP1	6249	broad.mit.edu	37	12	122826219	122826219	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:122826219C>A	uc001ucg.1	-	c.1532G>T	c.(1531-1533)CGT>CTT	p.R511L	CLIP1_uc001uch.1_Missense_Mutation_p.R500L|CLIP1_uc001uci.1_Missense_Mutation_p.R465L|CLIP1_uc001ucj.1_Missense_Mutation_p.R201L|CLIP1_uc009zxo.1_Missense_Mutation_p.R67L	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a	511	Potential.				mitotic prometaphase|positive regulation of microtubule polymerization	cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)										0.370968	73.323638	74.224695	23	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122826219	122826219	3670	12	C	A	A	A	247	19	CLIP1	1	1
KRAS	3845	broad.mit.edu	37	12	25380276	25380276	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:25380276T>A	uc001rgp.1	-	c.182A>T	c.(181-183)CAA>CTA	p.Q61L	KRAS_uc001rgq.1_Missense_Mutation_p.Q61L	NM_033360	NP_203524	P01116	RASK_HUMAN	c-K-ras2 protein isoform a precursor	61	GTP.		Q -> R (in a colorectal cancer sample; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.Q61L(47)|p.Q61R(40)|p.Q61H(23)|p.Q61P(11)|p.Q61D(1)		large_intestine(11742)|pancreas(3256)|lung(2694)|biliary_tract(514)|ovary(437)|endometrium(339)|haematopoietic_and_lymphoid_tissue(303)|stomach(179)|thyroid(145)|prostate(85)|soft_tissue(75)|small_intestine(62)|upper_aerodigestive_tract(59)|cervix(49)|urinary_tract(48)|skin(38)|breast(27)|liver(21)|testis(17)|oesophagus(15)|central_nervous_system(8)|peritoneum(5)|kidney(5)|salivary_gland(5)|thymus(5)|eye(4)|gastrointestinal_tract_(site_indeterminate)(4)|autonomic_ganglia(2)|bone(2)|genital_tract(1)|penis(1)|adrenal_gland(1)	20148	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Q61R(PANC0213_PANCREAS)|Q61L(NCIH650_LUNG)|Q61L(SW948_LARGE_INTESTINE)	119		262	TSP Lung(1;<1E-8)|Multiple Myeloma(2;<1E-6)			0.326087	42.608451	43.843214	15	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25380276	25380276	8753	12	T	A	A	A	819	63	KRAS	3	3
CACNA1C	775	broad.mit.edu	37	12	2566852	2566852	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:2566852G>A	uc009zdu.1	+	c.737G>A	c.(736-738)CGG>CAG	p.R246Q	CACNA1C_uc009zdv.1_Missense_Mutation_p.R246Q|CACNA1C_uc001qkb.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkc.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qke.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkf.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qjz.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkd.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkg.2_Missense_Mutation_p.R246Q|CACNA1C_uc009zdw.1_Missense_Mutation_p.R246Q|CACNA1C_uc001qkh.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkl.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkn.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qko.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkp.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkr.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qku.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkq.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qks.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qkt.2_Missense_Mutation_p.R246Q|CACNA1C_uc001qka.1_5'UTR|CACNA1C_uc001qki.1_5'UTR|CACNA1C_uc001qkj.1_5'UTR|CACNA1C_uc001qkk.1_5'UTR|CACNA1C_uc001qkm.1_5'UTR	NM_199460	NP_955630	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type,	246	I.|Helical; Name=S4 of repeat I; (Potential).				axon guidance|calcium ion transport into cytosol|energy reserve metabolic process|regulation of insulin secretion	cytoplasm|postsynaptic density|voltage-gated calcium channel complex	calmodulin binding|voltage-gated calcium channel activity			ovary(10)|central_nervous_system(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Mibefradil(DB01388)|Nicardipine(DB00622)|Verapamil(DB00661)									0.04	-17.617042	10.874257	5	120	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2566852	2566852	2656	12	G	A	A	A	507	39	CACNA1C	1	1
SLC6A12	6539	broad.mit.edu	37	12	301674	301674	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:301674G>T	uc001qhz.2	-	c.1671C>A	c.(1669-1671)ACC>ACA	p.T557T	SLC6A12_uc001qhx.2_Silent_p.T214T|SLC6A12_uc001qhy.2_Silent_p.T113T|SLC6A12_uc001qia.2_Silent_p.T557T|SLC6A12_uc001qib.2_Silent_p.T557T|SLC6A12_uc009zdh.1_Silent_p.T557T	NM_003044	NP_003035	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter	557	Cytoplasmic (Potential).				cellular nitrogen compound metabolic process|neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)											0.285714	33.825	35.847454	14	35	KEEP	---	---	---	---	capture		Silent	SNP	301674	301674	15172	12	G	T	T	T	548	43	SLC6A12	2	2
ADAMTS20	80070	broad.mit.edu	37	12	43837666	43837666	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:43837666T>C	uc010skx.1	-	c.2218A>G	c.(2218-2220)ATT>GTT	p.I740V		NM_025003	NP_079279	P59510	ATS20_HUMAN	a disintegrin-like and metalloprotease with	740	Spacer.					proteinaceous extracellular matrix	zinc ion binding			central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)						2149				0.083333	5.561228	33.076958	13	143	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43837666	43837666	267	12	T	C	C	C	650	50	ADAMTS20	4	4
KRT75	9119	broad.mit.edu	37	12	52824463	52824463	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52824463G>T	uc001saj.2	-	c.897C>A	c.(895-897)GTC>GTA	p.V299V		NM_004693	NP_004684	O95678	K2C75_HUMAN	keratin 75	299	Linker 12.|Rod.					keratin filament	structural molecule activity				0				BRCA - Breast invasive adenocarcinoma(357;0.192)										0.209677	25.944846	30.780374	13	49	KEEP	---	---	---	---	capture		Silent	SNP	52824463	52824463	8803	12	G	T	T	T	470	37	KRT75	1	1
SP1	6667	broad.mit.edu	37	12	53775908	53775908	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53775908C>T	uc001scw.2	+	c.177C>T	c.(175-177)TCC>TCT	p.S59S	SP1_uc010sog.1_Silent_p.S52S	NM_138473	NP_612482	P08047	SP1_HUMAN	Sp1 transcription factor isoform a	59	Ser/Thr-rich.|Repressor domain.			S->E: Some association with chromatin, increased phosphorylation levels and decreased glycosylation.|S->A: Loss of phosphorylation. No effect on activated MAPK8-mediated phosphorylation. Similar loss of phosphorylation as by dephosphorylation by PP2AC. Reduced proteolytic processing.	positive regulation by host of viral transcription|positive regulation of transcription from RNA polymerase II promoter, global	cytoplasm|nucleus	double-stranded DNA binding|histone deacetylase binding|promoter binding|protein C-terminus binding|protein homodimerization activity|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription factor binding|zinc ion binding			ovary(1)|breast(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(357;0.00527)						103		OREG0021870	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.388889	21.633357	21.823587	7	11	KEEP	---	---	---	---	capture		Silent	SNP	53775908	53775908	15459	12	C	T	T	T	275	22	SP1	2	2
ATF7	11016	broad.mit.edu	37	12	53994752	53994752	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:53994752G>A	uc001sdy.2	-	c.33C>T	c.(31-33)GCC>GCT	p.A11A	ATF7_uc010sok.1_Non-coding_Transcript|ATF7_uc001sdz.2_Silent_p.A11A|ATF7_uc010sol.1_Silent_p.A11A|ATF7_uc001sea.3_Silent_p.A11A|ATF7_uc001seb.3_Silent_p.A11A	NM_001130059	NP_001123531	P17544	ATF7_HUMAN	activating transcription factor 7 isoform 1	11	C2H2-type.|Transactivation domain.				interspecies interaction between organisms|regulation of transcription, DNA-dependent	cytoplasm|nuclear periphery|nucleoplasm	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.153846	10.123402	14.593239	6	33	KEEP	---	---	---	---	capture		Silent	SNP	53994752	53994752	1105	12	G	A	A	A	548	43	ATF7	2	2
KIF5A	3798	broad.mit.edu	37	12	57962848	57962848	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:57962848A>T	uc001sor.1	+	c.817A>T	c.(817-819)ACT>TCT	p.T273S	KIF5A_uc010srr.1_Missense_Mutation_p.T184S	NM_004984	NP_004975	Q12840	KIF5A_HUMAN	kinesin family member 5A	273	Kinesin-motor.|Microtubule-binding.				blood coagulation|cell death|microtubule-based movement|synaptic transmission	cytosol|kinesin complex|membrane fraction|microtubule|perinuclear region of cytoplasm	ATP binding|microtubule motor activity			ovary(2)	2														0.3	24.965135	26.036215	9	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57962848	57962848	8616	12	A	T	T	T	78	6	KIF5A	3	3
GDF3	9573	broad.mit.edu	37	12	7842804	7842804	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:7842804G>T	uc001qte.2	-	c.765C>A	c.(763-765)GTC>GTA	p.V255V		NM_020634	NP_065685	Q9NR23	GDF3_HUMAN	growth differentiation factor 3 precursor	255					eye development|growth|skeletal system development	extracellular space	cytokine activity|growth factor activity			skin(2)|ovary(1)|lung(1)|central_nervous_system(1)	5														0.166667	13.835236	19.534082	9	45	KEEP	---	---	---	---	capture		Silent	SNP	7842804	7842804	6583	12	G	T	T	T	522	41	GDF3	2	2
TMTC3	160418	broad.mit.edu	37	12	88589117	88589117	+	Silent	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:88589117T>C	uc001tau.2	+	c.2436T>C	c.(2434-2436)AAT>AAC	p.N812N		NM_181783	NP_861448	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat	813						integral to membrane	binding				0														0.198198	57.791574	67.198634	22	89	KEEP	---	---	---	---	capture		Silent	SNP	88589117	88589117	16803	12	T	C	C	C	634	49	TMTC3	4	4
CDK17	5128	broad.mit.edu	37	12	96694099	96694099	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:96694099A>G	uc001tep.1	-	c.583T>C	c.(583-585)TTG>CTG	p.L195L	CDK17_uc009ztk.2_Silent_p.L195L|CDK17_uc010svb.1_Silent_p.L142L	NM_002595	NP_002586	Q00537	CDK17_HUMAN	PCTAIRE protein kinase 2	195	Protein kinase.				protein phosphorylation		ATP binding|cyclin-dependent protein kinase activity			ovary(3)|lung(2)|kidney(1)|central_nervous_system(1)	7										253				0.195122	19.976918	23.529662	8	33	KEEP	---	---	---	---	capture		Silent	SNP	96694099	96694099	3262	12	A	G	G	G	50	4	CDK17	4	4
NALCN	259232	broad.mit.edu	37	13	102029288	102029288	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:102029288G>A	uc001vox.1	-	c.495C>T	c.(493-495)ACC>ACT	p.T165T	NALCN_uc001voy.2_5'UTR|NALCN_uc001voz.2_Silent_p.T165T|NALCN_uc001vpa.2_Silent_p.T165T	NM_052867	NP_443099	Q8IZF0	NALCN_HUMAN	voltage gated channel like 1	165	Cytoplasmic (Potential).					integral to membrane	sodium channel activity|voltage-gated ion channel activity			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.043103	-15.527735	10.443205	5	111	KEEP	---	---	---	---	capture		Silent	SNP	102029288	102029288	10544	13	G	A	A	A	600	47	NALCN	2	2
TPP2	7174	broad.mit.edu	37	13	103317145	103317145	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:103317145G>T	uc001vpi.3	+	c.3202G>T	c.(3202-3204)GAA>TAA	p.E1068*		NM_003291	NP_003282	P29144	TPP2_HUMAN	tripeptidyl peptidase II	1068					proteolysis	cytoplasm|nucleus	aminopeptidase activity|serine-type endopeptidase activity|tripeptidyl-peptidase activity			ovary(1)	1	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)													0.210526	18.077969	21.024589	8	30	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	103317145	103317145	16956	13	G	T	T	T	533	41	TPP2	5	2
ATP11A	23250	broad.mit.edu	37	13	113473716	113473716	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:113473716C>T	uc001vsj.3	+	c.669C>T	c.(667-669)CTC>CTT	p.L223L	ATP11A_uc001vsi.3_Silent_p.L223L|ATP11A_uc001vsm.1_Silent_p.L99L	NM_032189	NP_115565	P98196	AT11A_HUMAN	ATPase, class VI, type 11A isoform b	223	Cytoplasmic (Potential).				ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)								1064				0.285714	38.128201	40.14835	14	35	KEEP	---	---	---	---	capture		Silent	SNP	113473716	113473716	1138	13	C	T	T	T	405	32	ATP11A	2	2
ATP11A	23250	broad.mit.edu	37	13	113473723	113473723	+	Splice_Site_SNP	SNP	T	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:113473723T>G	uc001vsj.3	+	c.674_splice	c.e7+2	p.K225_splice	ATP11A_uc001vsi.3_Splice_Site_SNP_p.K225_splice|ATP11A_uc001vsm.1_Splice_Site_SNP_p.K101_splice	NM_032189	NP_115565			ATPase, class VI, type 11A isoform b						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			large_intestine(2)|ovary(2)	4	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)								1064				0.355556	53.789604	54.615912	16	29	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	113473723	113473723	1138	13	T	G	G	G	741	57	ATP11A	5	4
RBM26	64062	broad.mit.edu	37	13	79942937	79942937	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:79942937G>A	uc001vkz.2	-	c.823C>T	c.(823-825)CAT>TAT	p.H275Y	RBM26_uc001vky.2_Missense_Mutation_p.H275Y|RBM26_uc001vla.2_Missense_Mutation_p.H275Y|RBM26_uc001vkx.2_5'UTR|RBM26_uc001vlb.1_Non-coding_Transcript	NM_022118	NP_071401	Q5T8P6	RBM26_HUMAN	RNA binding motif protein 26	275					mRNA processing		nucleotide binding|protein binding|RNA binding|zinc ion binding			ovary(1)	1		Acute lymphoblastic leukemia(28;0.0279)		GBM - Glioblastoma multiforme(99;0.0188)										0.07	-5.561282	13.53716	7	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79942937	79942937	13588	13	G	A	A	A	585	45	RBM26	2	2
WDR25	79446	broad.mit.edu	37	14	100934399	100934399	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:100934399C>T	uc010avx.2	+	c.864C>T	c.(862-864)TAC>TAT	p.Y288Y	WDR25_uc001yhm.2_Silent_p.Y280Y|WDR25_uc001yhn.2_Silent_p.Y288Y|WDR25_uc010avy.2_Intron|WDR25_uc001yho.2_Silent_p.Y31Y	NM_001161476	NP_001154948	Q64LD2	WDR25_HUMAN	WD repeat domain 25	288											0		Melanoma(154;0.212)												0.132075	10.088676	17.058842	7	46	KEEP	---	---	---	---	capture		Silent	SNP	100934399	100934399	17855	14	C	T	T	T	259	20	WDR25	2	2
AHNAK2	113146	broad.mit.edu	37	14	105410043	105410043	+	Silent	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:105410043T>C	uc010axc.1	-	c.11745A>G	c.(11743-11745)CTA>CTG	p.L3915L	AHNAK2_uc001ypx.2_Silent_p.L3815L	NM_138420	NP_612429	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3915						nucleus				ovary(1)	1		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)											0.076923	1.12734	13.03257	5	60	KEEP	---	---	---	---	capture		Silent	SNP	105410043	105410043	418	14	T	C	C	C	782	61	AHNAK2	4	4
MMP14	4323	broad.mit.edu	37	14	23313044	23313044	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23313044G>A	uc001whc.2	+	c.976G>A	c.(976-978)GTG>ATG	p.V326M		NM_004995	NP_004986	P50281	MMP14_HUMAN	matrix metalloproteinase 14 preproprotein	326	Hemopexin-like 1.|Extracellular (Potential).					extracellular matrix|integral to plasma membrane|melanosome	calcium ion binding|metalloendopeptidase activity|zinc ion binding				0	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)										0.148148	6.612473	9.796572	4	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23313044	23313044	10043	14	G	A	A	A	520	40	MMP14	1	1
REM2	161253	broad.mit.edu	37	14	23354108	23354108	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:23354108A>G	uc001whf.1	+	c.329A>G	c.(328-330)CAA>CGA	p.Q110R	REM2_uc010tnd.1_Missense_Mutation_p.Q102R	NM_173527	NP_775798	Q8IYK8	REM2_HUMAN	rad and gem related GTP binding protein 2	110					regulation of transcription, DNA-dependent|small GTPase mediated signal transduction	intracellular|plasma membrane	ATP binding|GTP binding|transcription factor binding			large_intestine(1)|central_nervous_system(1)	2	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.012)										0.172414	9.955653	12.897816	5	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23354108	23354108	13692	14	A	G	G	G	65	5	REM2	4	4
MDP1	145553	broad.mit.edu	37	14	24683754	24683754	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:24683754G>T	uc001wnl.1	-	c.261C>A	c.(259-261)TTC>TTA	p.F87L	TM9SF1_uc010tob.1_5'Flank|CHMP4A_uc001wni.2_5'Flank|CHMP4A_uc010toc.1_5'Flank|CHMP4A_uc001wnj.2_5'UTR|MDP1_uc001wnk.1_Missense_Mutation_p.F87L|CHMP4A_uc001wnm.1_Missense_Mutation_p.F87L	NM_138476	NP_612485	Q86V88	MGDP1_HUMAN	magnesium-dependent phosphatase 1	87							metal ion binding|protein tyrosine phosphatase activity				0														0.154762	22.516193	32.087522	13	71	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24683754	24683754	9805	14	G	T	T	T	581	45	MDP1	2	2
SYNE2	23224	broad.mit.edu	37	14	64443330	64443330	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:64443330A>G	uc001xgl.2	+	c.1178A>G	c.(1177-1179)CAT>CGT	p.H393R	SYNE2_uc001xgm.2_Missense_Mutation_p.H393R	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	393	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.06278	-16.2077	28.188967	14	209	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64443330	64443330	15967	14	A	G	G	G	104	8	SYNE2	4	4
VASH1	22846	broad.mit.edu	37	14	77236310	77236310	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77236310C>T	uc001xst.2	+	c.314C>T	c.(313-315)CCC>CTC	p.P105L	VASH1_uc001xss.2_Missense_Mutation_p.P105L	NM_014909	NP_055724	Q7L8A9	VASH1_HUMAN	vasohibin 1	105					cell cycle arrest|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|negative regulation of endothelial cell proliferation	endoplasmic reticulum|extracellular space					0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0283)										0.540541	66.114681	66.169623	20	17	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77236310	77236310	17690	14	C	T	T	T	286	22	VASH1	2	2
C14orf174	161394	broad.mit.edu	37	14	77844783	77844783	+	Nonsense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:77844783C>G	uc001xtq.1	+	c.1022C>G	c.(1021-1023)TCA>TGA	p.S341*	TMED8_uc010ast.1_5'Flank|TMED8_uc001xto.1_5'Flank	NM_001010860	NP_001010860	Q9P1V8	SAM15_HUMAN	hypothetical protein LOC161394	341											0			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0278)										0.032491	-45.976499	20.164277	9	268	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	77844783	77844783	1807	14	C	G	G	G	377	29	C14orf174	5	3
NRXN3	9369	broad.mit.edu	37	14	80130240	80130240	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:80130240C>A	uc001xun.2	+	c.2445C>A	c.(2443-2445)GGC>GGA	p.G815G	NRXN3_uc001xum.1_Non-coding_Transcript|NRXN3_uc001xup.2_Non-coding_Transcript|NRXN3_uc001xuq.2_Silent_p.G183G|NRXN3_uc010asw.2_Silent_p.G183G|NRXN3_uc001xur.3_Silent_p.G183G	NM_004796	NP_004787	Q9Y4C0	NRX3A_HUMAN	neurexin 3 isoform 1 precursor	1188	Extracellular (Potential).|Laminin G-like 6.				axon guidance|cell adhesion	integral to plasma membrane	metal ion binding|receptor activity			ovary(3)|pancreas(2)|breast(1)|central_nervous_system(1)	7		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)										0.185185	20.488791	25.453025	10	44	KEEP	---	---	---	---	capture		Silent	SNP	80130240	80130240	11072	14	C	A	A	A	314	25	NRXN3	2	2
SERPINA10	51156	broad.mit.edu	37	14	94756235	94756235	+	Silent	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:94756235A>T	uc001yct.2	-	c.696T>A	c.(694-696)CTT>CTA	p.L232L	SERPINA10_uc001ycu.3_Silent_p.L232L	NM_016186	NP_057270	Q9UK55	ZPI_HUMAN	serine (or cysteine) proteinase inhibitor, clade	232					regulation of proteolysis	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|skin(1)	3		all_cancers(154;0.105)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)										0.234043	27.700858	30.743015	11	36	KEEP	---	---	---	---	capture		Silent	SNP	94756235	94756235	14575	14	A	T	T	T	54	5	SERPINA10	3	3
GABRB3	2562	broad.mit.edu	37	15	26828544	26828544	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:26828544G>A	uc001zbb.2	-	c.647C>T	c.(646-648)GCA>GTA	p.A216V	GABRB3_uc010uae.1_Missense_Mutation_p.A75V|GABRB3_uc001zaz.2_Missense_Mutation_p.A160V|GABRB3_uc001zba.2_Missense_Mutation_p.A160V	NM_021912	NP_068712	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	160	Extracellular (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	4		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.15	14.232788	21.28269	9	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26828544	26828544	6419	15	G	A	A	A	598	46	GABRB3	2	2
RYR3	6263	broad.mit.edu	37	15	33925214	33925214	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:33925214C>A	uc001zhi.2	+	c.2932C>A	c.(2932-2934)CCT>ACT	p.P978T	RYR3_uc010bar.2_Missense_Mutation_p.P978T	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	978	2.|4 X approximate repeats.|Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)										0.255319	57.357594	62.462271	24	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33925214	33925214	14250	15	C	A	A	A	390	30	RYR3	2	2
CHRM5	1133	broad.mit.edu	37	15	34355078	34355078	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:34355078T>A	uc001zhk.1	+	c.160T>A	c.(160-162)TCC>ACC	p.S54T	CHRM5_uc001zhl.1_Missense_Mutation_p.S54T	NM_012125	NP_036257	P08912	ACM5_HUMAN	cholinergic receptor, muscarinic 5	54	Cytoplasmic (By similarity).				cell proliferation|inhibition of adenylate cyclase activity by muscarinic acetylcholine receptor signaling pathway	cell junction|integral to plasma membrane|postsynaptic membrane	muscarinic acetylcholine receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)|central_nervous_system(1)	2		all_lung(180;1.76e-08)		all cancers(64;4.82e-17)|GBM - Glioblastoma multiforme(113;2.58e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0262)	Atropine(DB00572)|Benzquinamide(DB00767)|Cryptenamine(DB00785)|Homatropine Methylbromide(DB00725)|Methotrimeprazine(DB01403)|Metixene(DB00340)|Olanzapine(DB00334)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Thiethylperazine(DB00372)									0.389831	61.416903	62.041692	23	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34355078	34355078	3514	15	T	A	A	A	702	54	CHRM5	3	3
RTF1	23168	broad.mit.edu	37	15	41762554	41762554	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:41762554G>A	uc001zny.2	+	c.989G>A	c.(988-990)CGC>CAC	p.R330H		NM_015138	NP_055953	Q92541	RTF1_HUMAN	Paf1/RNA polymerase II complex component	330	Glu-rich.				histone modification|regulation of transcription, DNA-dependent|transcription initiation, DNA-dependent	nucleoplasm	protein binding|single-stranded DNA binding			ovary(2)	2		all_cancers(109;1.79e-19)|all_epithelial(112;8.18e-17)|Lung NSC(122;3.16e-11)|all_lung(180;8.14e-10)|Melanoma(134;0.0179)|Colorectal(260;0.0946)|Ovarian(310;0.143)		OV - Ovarian serous cystadenocarcinoma(18;1.15e-16)|GBM - Glioblastoma multiforme(113;1.81e-06)|BRCA - Breast invasive adenocarcinoma(123;0.119)										0.043716	-25.585562	15.168344	8	175	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41762554	41762554	14201	15	G	A	A	A	494	38	RTF1	1	1
PTPN9	5780	broad.mit.edu	37	15	75761285	75761285	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75761285T>C	uc002bal.2	-	c.1607A>G	c.(1606-1608)GAG>GGG	p.E536G		NM_002833	NP_002824	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type	536	Tyrosine-protein phosphatase.					cytoplasmic part	non-membrane spanning protein tyrosine phosphatase activity|protein binding			lung(1)|skin(1)	2														0.424242	46.246531	46.411266	14	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75761285	75761285	13251	15	T	C	C	C	702	54	PTPN9	4	4
TXNDC11	51061	broad.mit.edu	37	16	11782158	11782159	+	Splice_Site_DNP	DNP	CC	AA	AA			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:11782158_11782159CC>AA	uc010buu.1	-	c.2124_splice	c.e10+1	p.Q708_splice	TXNDC11_uc002dbg.1_Splice_Site_DNP_p.Q681_splice	NM_015914	NP_056998			thioredoxin domain containing 11						cell redox homeostasis	endoplasmic reticulum membrane|integral to membrane					0														0.119718	22.870407	43.024916	17	125	KEEP	---	---	---	---	capture		Splice_Site_DNP	DNP	11782158	11782159	17348	16	CC	AA	AA	AA	234	18	TXNDC11	5	2
GP2	2813	broad.mit.edu	37	16	20331682	20331682	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:20331682G>A	uc002dgv.2	-	c.769C>T	c.(769-771)CGA>TGA	p.R257*	GP2_uc002dgw.2_Nonsense_Mutation_p.R254*|GP2_uc002dgx.2_Nonsense_Mutation_p.R110*|GP2_uc002dgy.2_Nonsense_Mutation_p.R107*	NM_001007240	NP_001007241	P55259	GP2_HUMAN	zymogen granule membrane glycoprotein 2 isoform	257	ZP.					anchored to membrane|extracellular region|plasma membrane				ovary(3)	3														0.273684	66.213527	70.594804	26	69	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	20331682	20331682	6856	16	G	A	A	A	493	38	GP2	5	1
ABCA3	21	broad.mit.edu	37	16	2334331	2334331	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:2334331G>A	uc002cpy.1	-	c.3811C>T	c.(3811-3813)CGG>TGG	p.R1271W	ABCA3_uc010bsk.1_Missense_Mutation_p.R1213W	NM_001089	NP_001080	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A member 3	1271					response to drug	integral to membrane|lamellar body|membrane fraction|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|breast(3)|central_nervous_system(3)	10		Ovarian(90;0.17)							p.R1271W(RL952-Tumor)	701				0.178571	9.069521	11.785717	5	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2334331	2334331	34	16	G	A	A	A	493	38	ABCA3	1	1
ERN2	10595	broad.mit.edu	37	16	23712306	23712306	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:23712306C>A	uc002dma.3	-	c.1477G>T	c.(1477-1479)GGG>TGG	p.G493W	ERN2_uc010bxp.2_Intron|ERN2_uc010bxq.1_Missense_Mutation_p.G301W	NM_033266	NP_150296	Q76MJ5	ERN2_HUMAN	endoplasmic reticulum to nucleus signalling 2	445	Helical; (Potential).				apoptosis|induction of apoptosis|mRNA processing|negative regulation of transcription, DNA-dependent|protein phosphorylation|rRNA catabolic process|transcription, DNA-dependent	endoplasmic reticulum membrane|integral to membrane	ATP binding|endoribonuclease activity, producing 5'-phosphomonoesters|magnesium ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)						225				0.303797	66.602074	69.298232	24	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23712306	23712306	5431	16	C	A	A	A	312	24	ERN2	2	2
SH2B1	25970	broad.mit.edu	37	16	28883246	28883246	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:28883246G>A	uc002dri.2	+	c.1455G>A	c.(1453-1455)GGG>GGA	p.G485G	SH2B1_uc010vdc.1_Silent_p.G175G|SH2B1_uc002drj.2_Silent_p.G485G|SH2B1_uc002drk.2_Silent_p.G485G|SH2B1_uc002drl.2_Silent_p.G485G|SH2B1_uc010vdd.1_Silent_p.G149G|SH2B1_uc010vde.1_Silent_p.G485G|SH2B1_uc002drm.2_Silent_p.G485G	NM_001145795	NP_001139267	Q9NRF2	SH2B1_HUMAN	SH2B adaptor protein 1 isoform 1	485	Interaction with JAK2 (low-affinity binding; independent of JAK2 phosphorylation) (By similarity).				blood coagulation|intracellular signal transduction	cytosol|membrane|nucleus	signal transducer activity			ovary(2)	2														0.147059	16.446029	24.551385	10	58	KEEP	---	---	---	---	capture		Silent	SNP	28883246	28883246	14718	16	G	A	A	A	522	41	SH2B1	2	2
ITGAL	3683	broad.mit.edu	37	16	30490502	30490502	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30490502A>C	uc002dyi.3	+	c.418A>C	c.(418-420)ATG>CTG	p.M140L	ITGAL_uc010veu.1_Non-coding_Transcript|ITGAL_uc002dyj.3_Intron|ITGAL_uc010vev.1_Intron	NM_002209	NP_002200	P20701	ITAL_HUMAN	integrin alpha L isoform a precursor	140	FG-GAP 2.|Extracellular (Potential).				blood coagulation|heterophilic cell-cell adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|leukocyte migration|regulation of immune response|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell	integrin complex	cell adhesion molecule binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(1)	7					Efalizumab(DB00095)	NSCLC(110;1462 1641 3311 33990 49495)								0.193548	44.009131	52.1502	18	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30490502	30490502	8190	16	A	C	C	C	104	8	ITGAL	4	4
SETD1A	9739	broad.mit.edu	37	16	30975604	30975604	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:30975604G>T	uc002ead.1	+	c.829G>T	c.(829-831)GGC>TGC	p.G277C	SETD1A_uc002eae.1_Missense_Mutation_p.G277C	NM_014712	NP_055527	O15047	SET1A_HUMAN	SET domain containing 1A	277	Ser-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nuclear speck|Set1C/COMPASS complex	histone-lysine N-methyltransferase activity|nucleotide binding|protein binding|RNA binding			ovary(2)	2														0.05102	-10.998076	9.917456	5	93	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30975604	30975604	14618	16	G	T	T	T	559	43	SETD1A	2	2
ALG1	56052	broad.mit.edu	37	16	5129756	5129756	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:5129756A>G	uc002cyn.2	+	c.909A>G	c.(907-909)GAA>GAG	p.E303E	ALG1_uc002cyj.2_Silent_p.E192E|ALG1_uc002cym.2_Silent_p.E303E|ALG1_uc010bue.2_Silent_p.E192E|ALG1_uc010uxy.1_Silent_p.E192E	NM_019109	NP_061982	Q9BT22	ALG1_HUMAN	beta-1,4-mannosyltransferase	303	Lumenal (Potential).				dolichol-linked oligosaccharide biosynthetic process|lipopolysaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	chitobiosyldiphosphodolichol beta-mannosyltransferase activity			ovary(1)	1		Ovarian(90;0.0164)												0.370787	107.253014	108.558364	33	56	KEEP	---	---	---	---	capture		Silent	SNP	5129756	5129756	513	16	A	G	G	G	24	2	ALG1	4	4
MMP2	4313	broad.mit.edu	37	16	55525795	55525796	+	Missense_Mutation	DNP	GG	AT	AT			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:55525795_55525796GG>AT	uc002ehz.3	+	c.1263_1264GG>AT	c.(1261-1266)ATGGCA>ATATCA	p.421_422MA>IS	MMP2_uc010vhd.1_Missense_Mutation_p.345_346MA>IS|MMP2_uc010ccc.2_Missense_Mutation_p.371_372MA>IS|MMP2_uc002eia.3_5'Flank	NM_004530	NP_004521	P08253	MMP2_HUMAN	matrix metalloproteinase 2 isoform a	421_422	Required for inhibitor TIMP2 binding.|Collagenase-like 2.				angiogenesis|collagen catabolic process|proteolysis	extracellular space|membrane|nucleus|proteinaceous extracellular matrix	metalloendopeptidase activity|protein binding|zinc ion binding			ovary(3)|large_intestine(3)|lung(1)|central_nervous_system(1)|kidney(1)	9		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Marimastat(DB00786)|Sulindac(DB00605)					275				0.133333	18.274381	31.981188	14	91	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	55525795	55525796	10048	16	GG	AT	AT	AT	611	47	MMP2	2	2
CDH3	1001	broad.mit.edu	37	16	68712778	68712778	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68712778C>T	uc002ewf.2	+	c.660C>T	c.(658-660)TTC>TTT	p.F220F	CDH3_uc010vli.1_Silent_p.F165F	NM_001793	NP_001784	P22223	CADH3_HUMAN	cadherin 3, type 1 preproprotein	220	Extracellular (Potential).|Cadherin 2.				adherens junction organization|cell junction assembly|homophilic cell adhesion|response to stimulus|visual perception	integral to membrane	calcium ion binding	p.?(1)		ovary(3)	3		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)						243				0.25	7.319349	8.00109	3	9	KEEP	---	---	---	---	capture		Silent	SNP	68712778	68712778	3240	16	C	T	T	T	389	30	CDH3	2	2
NFAT5	10725	broad.mit.edu	37	16	69681331	69681331	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:69681331A>G	uc002exl.1	+	c.654A>G	c.(652-654)AAA>AAG	p.K218K	NFAT5_uc002exh.1_Intron|NFAT5_uc002exi.2_Silent_p.K124K|NFAT5_uc002exj.1_Silent_p.K124K|NFAT5_uc002exk.1_Silent_p.K124K|NFAT5_uc002exn.1_Silent_p.K218K|NFAT5_uc002exm.1_Silent_p.K200K	NM_138713	NP_619727	O94916	NFAT5_HUMAN	nuclear factor of activated T-cells 5 isoform b	200					excretion|regulation of transcription, DNA-dependent|signal transduction|transcription from RNA polymerase II promoter	nucleus	DNA binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding transcription factor activity				0														0.541667	44.577996	44.614397	13	11	KEEP	---	---	---	---	capture		Silent	SNP	69681331	69681331	10760	16	A	G	G	G	50	4	NFAT5	4	4
FTSJD1	55783	broad.mit.edu	37	16	71318473	71318473	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:71318473C>A	uc010cga.2	-	c.1351G>T	c.(1351-1353)GAA>TAA	p.E451*	FTSJD1_uc002ezy.3_Nonsense_Mutation_p.E451*|FTSJD1_uc002ezz.3_Nonsense_Mutation_p.E451*	NM_001099642	NP_001093112	Q8IYT2	FTSJ1_HUMAN	FtsJ methyltransferase domain containing 1	451						integral to membrane	methyltransferase activity|nucleic acid binding				0														0.435897	48.268369	48.408094	17	22	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	71318473	71318473	6341	16	C	A	A	A	416	32	FTSJD1	5	2
DNAH9	1770	broad.mit.edu	37	17	11622753	11622753	+	Silent	SNP	C	G	G	rs111713622		TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:11622753C>G	uc002gne.2	+	c.5655C>G	c.(5653-5655)CGC>CGG	p.R1885R	DNAH9_uc010coo.2_Silent_p.R1179R	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	1885	AAA 1 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(4)|breast(3)|central_nervous_system(2)|pancreas(1)	10		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)										0.140845	19.615181	28.44109	10	61	KEEP	---	---	---	---	capture		Silent	SNP	11622753	11622753	4791	17	C	G	G	G	340	27	DNAH9	3	3
EFCAB5	374786	broad.mit.edu	37	17	28380844	28380844	+	Silent	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:28380844A>T	uc002het.2	+	c.1872A>T	c.(1870-1872)GCA>GCT	p.A624A	EFCAB5_uc010wbi.1_Silent_p.A367A|EFCAB5_uc010wbj.1_Silent_p.A568A|EFCAB5_uc010wbk.1_Silent_p.A281A|EFCAB5_uc010csd.2_Non-coding_Transcript|EFCAB5_uc010cse.2_Silent_p.A503A|EFCAB5_uc010csf.2_Silent_p.A503A	NM_198529	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5 isoform a	624							calcium ion binding			ovary(1)|skin(1)	2														0.181518	122.536503	151.418078	55	248	KEEP	---	---	---	---	capture		Silent	SNP	28380844	28380844	5125	17	A	T	T	T	80	7	EFCAB5	3	3
MRM1	79922	broad.mit.edu	37	17	34964752	34964752	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:34964752A>T	uc002hne.2	+	c.963A>T	c.(961-963)CAA>CAT	p.Q321H	MRM1_uc002hnf.2_Missense_Mutation_p.Q126H	NM_024864	NP_079140	Q6IN84	MRM1_HUMAN	mitochondrial rRNA methyltransferase 1 homolog	321					RNA processing	mitochondrion	RNA binding|RNA methyltransferase activity				0		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0184)										0.056738	-12.917283	16.186052	8	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34964752	34964752	10164	17	A	T	T	T	37	3	MRM1	3	3
NSF	4905	broad.mit.edu	37	17	44788392	44788392	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:44788392G>T	uc002iku.2	+	c.1534G>T	c.(1534-1536)GAC>TAC	p.D512Y	NSF_uc010wke.1_Missense_Mutation_p.D418Y|NSF_uc010wkf.1_Missense_Mutation_p.D418Y|NSF_uc010wkg.1_Missense_Mutation_p.D507Y	NM_006178	NP_006169	P46459	NSF_HUMAN	vesicle-fusing ATPase	512					protein transport|proteolysis|synaptic transmission	cytosol	ATP binding|ATP-dependent peptidase activity|metal ion binding|serine-type endopeptidase activity			ovary(1)	1		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		Ovarian(25;472 742 1472 36813 50223)								0.102564	6.954155	19.220672	8	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44788392	44788392	11076	17	G	T	T	T	585	45	NSF	2	2
PLD2	5338	broad.mit.edu	37	17	4714202	4714202	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4714202G>A	uc002fzc.2	+	c.966G>A	c.(964-966)CGG>CGA	p.R322R	PLD2_uc010vsj.1_Silent_p.R179R|PLD2_uc002fzd.2_Silent_p.R322R	NM_002663	NP_002654	O14939	PLD2_HUMAN	phospholipase D2	322					cell communication|cytoskeleton organization|small GTPase mediated signal transduction		NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			breast(2)|ovary(1)|central_nervous_system(1)	4					Choline(DB00122)									0.1	1.802905	6.598535	3	27	KEEP	---	---	---	---	capture		Silent	SNP	4714202	4714202	12472	17	G	A	A	A	535	42	PLD2	2	2
KIF1C	10749	broad.mit.edu	37	17	4927272	4927272	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:4927272A>G	uc002gan.1	+	c.3138A>G	c.(3136-3138)GCA>GCG	p.A1046A		NM_006612	NP_006603	O43896	KIF1C_HUMAN	kinesin family member 1C	1046	Pro-rich.				microtubule-based movement|retrograde vesicle-mediated transport, Golgi to ER	endoplasmic reticulum|Golgi apparatus|microtubule	ATP binding|microtubule motor activity			breast(2)	2						Melanoma(96;1023 1447 10250 19259 33730)								0.404762	42.752756	43.088829	17	25	KEEP	---	---	---	---	capture		Silent	SNP	4927272	4927272	8596	17	A	G	G	G	67	6	KIF1C	4	4
USP6	9098	broad.mit.edu	37	17	5042785	5042785	+	Silent	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:5042785T>A	uc002gau.1	+	c.1314T>A	c.(1312-1314)GCT>GCA	p.A438A	USP6_uc002gav.1_Silent_p.A438A|USP6_uc010ckz.1_Silent_p.A121A	NM_004505	NP_004496	P35125	UBP6_HUMAN	ubiquitin specific protease 6	438					protein deubiquitination|regulation of vesicle-mediated transport|ubiquitin-dependent protein catabolic process	lysosome|plasma membrane|recycling endosome	calmodulin binding|cysteine-type endopeptidase activity|nucleic acid binding|protein binding|Rab GTPase activator activity|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			lung(1)	1										464				0.227273	11.763007	13.265283	5	17	KEEP	---	---	---	---	capture		Silent	SNP	5042785	5042785	17650	17	T	A	A	A	691	54	USP6	3	3
C17orf47	284083	broad.mit.edu	37	17	56620020	56620020	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:56620020G>A	uc002iwq.1	-	c.1528C>T	c.(1528-1530)CAA>TAA	p.Q510*	SEPT4_uc010wnx.1_5'Flank|SEPT4_uc010wny.1_5'Flank	NM_001038704	NP_001033793	Q8NEP4	CQ047_HUMAN	hypothetical protein LOC284083	510										breast(1)	1	Medulloblastoma(34;0.127)|all_neural(34;0.237)													0.376404	183.066992	185.458479	67	111	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	56620020	56620020	1914	17	G	A	A	A	624	48	C17orf47	5	2
TUBD1	51174	broad.mit.edu	37	17	57958410	57958410	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:57958410C>A	uc002ixw.1	-	c.382G>T	c.(382-384)GAG>TAG	p.E128*	TUBD1_uc010ddf.1_Nonsense_Mutation_p.E128*|TUBD1_uc010ddg.1_Nonsense_Mutation_p.E93*|TUBD1_uc010ddh.1_Nonsense_Mutation_p.E9*|TUBD1_uc010wok.1_Nonsense_Mutation_p.E128*|TUBD1_uc002ixx.1_Nonsense_Mutation_p.E128*|TUBD1_uc010wol.1_Intron|TUBD1_uc010ddi.1_Intron	NM_016261	NP_057345	Q9UJT1	TBD_HUMAN	delta-tubulin	128					cell differentiation|microtubule-based movement|multicellular organismal development|protein polymerization|spermatogenesis	centriole|microtubule|nucleus	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)											0.175926	33.819844	44.497034	19	89	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	57958410	57958410	17317	17	C	A	A	A	390	30	TUBD1	5	2
LRRC37A3	374819	broad.mit.edu	37	17	62856868	62856868	+	Silent	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:62856868T>A	uc002jey.2	-	c.3396A>T	c.(3394-3396)CTA>CTT	p.L1132L	LRRC37A3_uc010wqg.1_Silent_p.L250L|LRRC37A3_uc002jex.1_Silent_p.L109L|LRRC37A3_uc010wqf.1_Silent_p.L170L|LRRC37A3_uc010dek.1_Silent_p.L138L	NM_199340	NP_955372	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1132	Extracellular (Potential).|LRR 10.					integral to membrane					0														0.132231	49.130637	80.928413	32	210	KEEP	---	---	---	---	capture		Silent	SNP	62856868	62856868	9368	17	T	A	A	A	678	53	LRRC37A3	3	3
XAF1	54739	broad.mit.edu	37	17	6674154	6674154	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:6674154A>G	uc002gdn.2	+	c.700A>G	c.(700-702)AGC>GGC	p.S234G	XAF1_uc002gdm.1_Missense_Mutation_p.S174G|XAF1_uc002gdo.2_Missense_Mutation_p.S215G|XAF1_uc002gdp.2_Missense_Mutation_p.S183G|XAF1_uc002gdq.2_Missense_Mutation_p.S66G|XAF1_uc002gdr.2_Missense_Mutation_p.S164G	NM_017523	NP_059993	Q6GPH4	XAF1_HUMAN	XIAP associated factor 1 isoform 1	234					apoptosis|type I interferon-mediated signaling pathway	mitochondrion|nucleus	zinc ion binding				0														0.171429	28.663705	35.800755	12	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	6674154	6674154	17993	17	A	G	G	G	39	3	XAF1	4	4
ZBTB4	57659	broad.mit.edu	37	17	7366052	7366052	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7366052C>T	uc002ghc.3	-	c.2249G>A	c.(2248-2250)GGG>GAG	p.G750E	ZBTB4_uc002ghd.3_Missense_Mutation_p.G750E	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	750					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)										0.44898	63.829017	63.941806	22	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	7366052	7366052	18127	17	C	T	T	T	286	22	ZBTB4	2	2
MXRA7	439921	broad.mit.edu	37	17	74684255	74684255	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:74684255C>T	uc002jsk.1	-	c.346G>A	c.(346-348)GAG>AAG	p.E116K	MXRA7_uc002jsl.2_Missense_Mutation_p.E116K|MXRA7_uc002jsm.2_Missense_Mutation_p.E116K	NM_001008528	NP_001008528	P84157	MXRA7_HUMAN	transmembrane anchor protein 1 isoform 1	116						integral to membrane					0														0.292683	34.182636	35.761002	12	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	74684255	74684255	10398	17	C	T	T	T	416	32	MXRA7	2	2
CCDC57	284001	broad.mit.edu	37	17	80130706	80130706	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:80130706T>C	uc002kdx.1	-	c.1537A>G	c.(1537-1539)AGT>GGT	p.S513G	CCDC57_uc010dik.1_Missense_Mutation_p.S21G|CCDC57_uc002kdz.1_Missense_Mutation_p.S513G	NM_198082	NP_932348	Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	513										ovary(2)	2	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)											0.192308	11.659845	13.958643	5	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	80130706	80130706	2950	17	T	C	C	C	728	56	CCDC57	4	4
WDR16	146845	broad.mit.edu	37	17	9501582	9501582	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:9501582C>T	uc002gly.2	+	c.568C>T	c.(568-570)CCA>TCA	p.P190S	WDR16_uc002glz.2_Missense_Mutation_p.P122S|WDR16_uc010coc.2_Missense_Mutation_p.P200S	NM_145054	NP_659491	Q8N1V2	WDR16_HUMAN	WD40-repeat protein upregulated in HCC isoform	190	WD 3.					cytoplasm|intracellular membrane-bounded organelle	protein binding			ovary(1)	1														0.111111	5.340681	12.070395	5	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9501582	9501582	17849	17	C	T	T	T	390	30	WDR16	2	2
CEP192	55125	broad.mit.edu	37	18	13049233	13049233	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:13049233A>G	uc010xac.1	+	c.2443A>G	c.(2443-2445)AAA>GAA	p.K815E	CEP192_uc010dlf.1_Non-coding_Transcript|CEP192_uc010xad.1_Missense_Mutation_p.K340E|CEP192_uc002kru.2_Non-coding_Transcript|CEP192_uc002krs.1_Missense_Mutation_p.K556E	NM_032142	NP_115518	E9PF99	E9PF99_HUMAN	centrosomal protein 192kDa	815										ovary(4)|pancreas(1)	5														0.147727	18.41746	28.906392	13	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13049233	13049233	3384	18	A	G	G	G	65	5	CEP192	4	4
LPIN2	9663	broad.mit.edu	37	18	2925289	2925289	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:2925289G>T	uc002klo.2	-	c.1871C>A	c.(1870-1872)ACA>AAA	p.T624K		NM_014646	NP_055461	Q92539	LPIN2_HUMAN	lipin 2	624					fatty acid metabolic process|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent|triglyceride biosynthetic process	cytosol|endoplasmic reticulum membrane|nucleus	phosphatidate phosphatase activity|transcription coactivator activity			ovary(1)|skin(1)	2				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)										0.0625	-2.815542	6.760127	3	45	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2925289	2925289	9292	18	G	T	T	T	624	48	LPIN2	2	2
NOL4	8715	broad.mit.edu	37	18	31599491	31599491	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:31599491T>G	uc010dmi.2	-	c.847A>C	c.(847-849)AGC>CGC	p.S283R	NOL4_uc010xbs.1_5'UTR|NOL4_uc002kxr.3_Missense_Mutation_p.S119R|NOL4_uc010xbt.1_Missense_Mutation_p.S209R|NOL4_uc010dmh.2_Missense_Mutation_p.S209R|NOL4_uc010xbu.1_Missense_Mutation_p.S283R|NOL4_uc002kxt.3_Missense_Mutation_p.S283R|NOL4_uc010xbv.1_Missense_Mutation_p.S32R|NOL4_uc010xbw.1_Missense_Mutation_p.S169R	NM_003787	NP_003778	O94818	NOL4_HUMAN	nucleolar protein 4	283						nucleolus	RNA binding			ovary(3)	3														0.333333	34.056199	35.018529	13	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31599491	31599491	10927	18	T	G	G	G	715	55	NOL4	4	4
NARS	4677	broad.mit.edu	37	18	55282959	55282959	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:55282959C>T	uc002lgs.2	-	c.256G>A	c.(256-258)GAA>AAA	p.E86K	NARS_uc002lgt.2_Missense_Mutation_p.E85K|NARS_uc010xea.1_5'UTR|NARS_uc010xeb.1_Non-coding_Transcript|NARS_uc010xec.1_Missense_Mutation_p.E86K|NARS_uc010xed.1_Missense_Mutation_p.E53K	NM_004539	NP_004530	O43776	SYNC_HUMAN	asparaginyl-tRNA synthetase	86					asparaginyl-tRNA aminoacylation|aspartyl-tRNA aminoacylation	cytosol|soluble fraction	asparagine-tRNA ligase activity|aspartate-tRNA ligase activity|ATP binding|nucleic acid binding|protein binding				0		Colorectal(73;0.227)			L-Asparagine(DB00174)									0.306667	64.0942	66.59536	23	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55282959	55282959	10566	18	C	T	T	T	416	32	NARS	2	2
CDH20	28316	broad.mit.edu	37	18	59174687	59174687	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:59174687G>C	uc010dps.1	+	c.911G>C	c.(910-912)GGC>GCC	p.G304A	CDH20_uc002lif.2_Missense_Mutation_p.G298A	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	304	Extracellular (Potential).|Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)												0.056818	-5.601005	12.551755	5	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59174687	59174687	3235	18	G	C	C	C	546	42	CDH20	3	3
CDH20	28316	broad.mit.edu	37	18	59206373	59206373	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:59206373G>T	uc010dps.1	+	c.1525G>T	c.(1525-1527)GGA>TGA	p.G509*	CDH20_uc002lif.2_Nonsense_Mutation_p.G503*	NM_031891	NP_114097	Q9HBT6	CAD20_HUMAN	cadherin 20, type 2 preproprotein	509	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|ovary(1)|pancreas(1)	5		Colorectal(73;0.186)												0.316667	55.102437	56.896301	19	41	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	59206373	59206373	3235	18	G	T	T	T	455	35	CDH20	5	2
SERPINB5	5268	broad.mit.edu	37	18	61154283	61154283	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61154283G>T	uc002liz.3	+	c.273G>T	c.(271-273)CGG>CGT	p.R91R	SERPINB5_uc002liy.2_Silent_p.R91R	NM_002639	NP_002630	P36952	SPB5_HUMAN	serine (or cysteine) proteinase inhibitor, clade	91					cellular component movement|regulation of proteolysis	cytoplasm|extracellular space	protein binding|serine-type endopeptidase inhibitor activity			ovary(1)	1														0.533333	25.000251	25.014677	8	7	KEEP	---	---	---	---	capture		Silent	SNP	61154283	61154283	14592	18	G	T	T	T	535	42	SERPINB5	2	2
SERPINB2	5055	broad.mit.edu	37	18	61569691	61569691	+	Silent	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:61569691A>T	uc010xeu.1	+	c.732A>T	c.(730-732)GGA>GGT	p.G244G	SERPINB2_uc002ljo.2_Silent_p.G244G|SERPINB2_uc010dqh.2_Silent_p.G174G|SERPINB2_uc002ljp.1_Silent_p.G49G|SERPINB2_uc002ljq.1_Silent_p.G49G	NM_001143818	NP_001137290	P05120	PAI2_HUMAN	serine (or cysteine) proteinase inhibitor, clade	244					anti-apoptosis|blood coagulation|fibrinolysis|regulation of proteolysis	extracellular space|Golgi apparatus|plasma membrane	serine-type endopeptidase inhibitor activity			lung(1)|skin(1)	2		Esophageal squamous(42;0.131)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)									0.149254	17.705693	25.612997	10	57	KEEP	---	---	---	---	capture		Silent	SNP	61569691	61569691	14589	18	A	T	T	T	145	12	SERPINB2	3	3
DNMT1	1786	broad.mit.edu	37	19	10257064	10257064	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10257064C>A	uc010xlc.1	-	c.2857G>T	c.(2857-2859)GAT>TAT	p.D953Y	DNMT1_uc002mnf.2_5'Flank|DNMT1_uc002mng.2_Missense_Mutation_p.D937Y|DNMT1_uc002mnh.2_Missense_Mutation_p.D832Y|DNMT1_uc010xld.1_Missense_Mutation_p.D937Y	NM_001130823	NP_001124295	P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1 isoform a	937					chromatin modification|maintenance of DNA methylation|negative regulation of histone H3-K9 methylation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of gene expression|positive regulation of histone H3-K4 methylation|transcription, DNA-dependent	nucleus	DNA (cytosine-5-)-methyltransferase activity|DNA binding|transcription factor binding			ovary(2)|skin(1)	3			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Ifosfamide(DB01181)|Procainamide(DB01035)					705				0.391304	26.269405	26.507528	9	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10257064	10257064	4858	19	C	A	A	A	377	29	DNMT1	2	2
ICAM5	7087	broad.mit.edu	37	19	10404530	10404530	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10404530G>T	uc002mnu.3	+	c.1622G>T	c.(1621-1623)CGT>CTT	p.R541L	ICAM5_uc002mnv.3_Missense_Mutation_p.R416L	NM_003259	NP_003250	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5 precursor	541	Extracellular (Potential).|Ig-like C2-type 6.				cell-cell adhesion	integral to plasma membrane				breast(3)	3			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)											0.352941	18.446351	18.769916	6	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10404530	10404530	7783	19	G	T	T	T	520	40	ICAM5	1	1
AP1M2	10053	broad.mit.edu	37	19	10692527	10692527	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:10692527C>A	uc002mpd.2	-	c.295G>T	c.(295-297)GAG>TAG	p.E99*	AP1M2_uc002mpc.2_Nonsense_Mutation_p.E99*	NM_005498	NP_005489	Q9Y6Q5	AP1M2_HUMAN	adaptor-related protein complex 1, mu 2 subunit	99					cellular membrane organization|post-Golgi vesicle-mediated transport|protein targeting|regulation of defense response to virus by virus|vesicle targeting|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding			ovary(2)	2			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)											0.214286	12.833509	14.945464	6	22	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	10692527	10692527	745	19	C	A	A	A	390	30	AP1M2	5	2
SYCE2	256126	broad.mit.edu	37	19	13011420	13011420	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:13011420T>C	uc002mvr.2	-	c.349A>G	c.(349-351)ATT>GTT	p.I117V		NM_001105578	NP_001099048	Q6PIF2	SYCE2_HUMAN	synaptonemal complex central element protein 2	117					cell division|meiotic prophase I	central element					0														0.229412	106.341307	117.751082	39	131	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	13011420	13011420	15950	19	T	C	C	C	650	50	SYCE2	4	4
CYP4F12	66002	broad.mit.edu	37	19	15807817	15807817	+	Silent	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:15807817C>G	uc002nbl.2	+	c.1497C>G	c.(1495-1497)CGC>CGG	p.R499R		NM_023944	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F,	499					oxidation-reduction process|xenobiotic metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	aromatase activity|electron carrier activity|heme binding|oxygen binding			ovary(2)|central_nervous_system(2)	4	Acute lymphoblastic leukemia(2;0.0367)													0.101266	7.343473	19.873564	8	71	KEEP	---	---	---	---	capture		Silent	SNP	15807817	15807817	4352	19	C	G	G	G	314	25	CYP4F12	3	3
NDUFA13	51079	broad.mit.edu	37	19	19626829	19626829	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:19626829C>G	uc010xqy.1	+	c.31C>G	c.(31-33)CTG>GTG	p.L11V	TSSK6_uc002nmq.2_5'Flank|TSSK6_uc002nmr.2_5'Flank|NDUFA13_uc002nms.2_Missense_Mutation_p.L11V|NDUFA13_uc010xqx.1_Missense_Mutation_p.L11V	NM_015965	NP_057049	Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha	Error:Variant_position_missing_in_Q9P0J0_after_alignment					apoptotic nuclear change|induction of apoptosis by extracellular signals|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|negative regulation of translation|protein import into nucleus|reactive oxygen species metabolic process|respiratory electron transport chain	integral to membrane|mitochondrial respiratory chain complex I|nucleoplasm	ATP binding|NADH dehydrogenase (ubiquinone) activity|protein binding				0					NADH(DB00157)					42				0.7	127.645838	129.433203	35	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19626829	19626829	10662	19	C	G	G	G	404	32	NDUFA13	3	3
ZNF85	7639	broad.mit.edu	37	19	21132839	21132839	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:21132839G>C	uc002npg.3	+	c.1519G>C	c.(1519-1521)GAG>CAG	p.E507Q	ZNF85_uc010ecn.2_Missense_Mutation_p.E442Q|ZNF85_uc010eco.2_Missense_Mutation_p.E455Q|ZNF85_uc002npi.2_Missense_Mutation_p.E448Q	NM_003429	NP_003420	Q03923	ZNF85_HUMAN	zinc finger protein 85	507					regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			central_nervous_system(1)	1														0.133333	7.478076	11.39298	4	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	21132839	21132839	18795	19	G	C	C	C	429	33	ZNF85	3	3
ZNF492	57615	broad.mit.edu	37	19	22847646	22847646	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:22847646C>A	uc002nqw.3	+	c.1175C>A	c.(1174-1176)CCC>CAC	p.P392H		NM_020855	NP_065906	Q9P255	ZN492_HUMAN	zinc finger protein 492	392					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)												0.135135	7.648813	12.423785	5	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22847646	22847646	18537	19	C	A	A	A	286	22	ZNF492	2	2
SERTAD3	29946	broad.mit.edu	37	19	40947447	40947447	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40947447A>T	uc002onu.3	-	c.541T>A	c.(541-543)TGG>AGG	p.W181R	SERTAD3_uc002onv.3_Missense_Mutation_p.W181R	NM_013368	NP_037500	Q9UJW9	SRTD3_HUMAN	RPA-binding trans-activator	181					negative regulation of cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding				0			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)											0.390476	125.648877	126.752838	41	64	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40947447	40947447	14610	19	A	T	T	T	65	5	SERTAD3	3	3
CEACAM5	1048	broad.mit.edu	37	19	42231194	42231194	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42231194C>T	uc002ork.2	+	c.2067C>T	c.(2065-2067)GTC>GTT	p.V689V	CEACAM5_uc002orj.1_Silent_p.V688V|CEACAM5_uc002orl.2_Silent_p.V689V	NM_004363	NP_004354	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion	689				V -> A (in Ref. 3; AAA62835).		anchored to membrane|basolateral plasma membrane|integral to plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)										0.046472	-73.212237	54.234759	27	554	KEEP	---	---	---	---	capture		Silent	SNP	42231194	42231194	3328	19	C	T	T	T	392	31	CEACAM5	1	1
EBI3	10148	broad.mit.edu	37	19	4234679	4234679	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:4234679C>A	uc002lzu.2	+	c.395C>A	c.(394-396)CCA>CAA	p.P132Q		NM_005755	NP_005746	Q14213	IL27B_HUMAN	Epstein-Barr virus induced 3 precursor	132	Fibronectin type-III 2.				humoral immune response|positive regulation of alpha-beta T cell proliferation|positive regulation of interferon-gamma biosynthetic process|T-helper 1 type immune response	extracellular space|plasma membrane	cytokine activity|cytokine receptor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)										0.076923	-1.912874	12.385395	6	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4234679	4234679	5070	19	C	A	A	A	273	21	EBI3	2	2
ZNF574	64763	broad.mit.edu	37	19	42584008	42584008	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42584008G>T	uc002osk.3	+	c.1520G>T	c.(1519-1521)GGT>GTT	p.G507V	ZNF574_uc002osm.3_Missense_Mutation_p.G417V	NM_022752	NP_073589	Q6ZN55	ZN574_HUMAN	zinc finger protein 574	417					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Prostate(69;0.059)												0.531915	155.8563	155.94003	50	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42584008	42584008	18601	19	G	T	T	T	572	44	ZNF574	2	2
PAFAH1B3	5050	broad.mit.edu	37	19	42804211	42804211	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:42804211C>A	uc002otg.2	-	c.319G>T	c.(319-321)GGA>TGA	p.G107*	PAFAH1B3_uc010xwi.1_Nonsense_Mutation_p.G107*|PAFAH1B3_uc010xwj.1_Nonsense_Mutation_p.G107*|PRR19_uc002oth.1_5'Flank|PRR19_uc002oti.2_5'Flank	NM_002573	NP_002564	Q15102	PA1B3_HUMAN	platelet-activating factor acetylhydrolase,	107					lipid catabolic process|nervous system development	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity|protein binding				0		Prostate(69;0.0704)												0.523077	112.460361	112.491255	34	31	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	42804211	42804211	11802	19	C	A	A	A	299	23	PAFAH1B3	5	1
GIPR	2696	broad.mit.edu	37	19	46178075	46178075	+	Silent	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:46178075G>C	uc002pcu.1	+	c.624G>C	c.(622-624)CTG>CTC	p.L208L	GIPR_uc002pct.1_Silent_p.L208L|GIPR_uc010xxp.1_Silent_p.L172L|GIPR_uc010xxq.1_Non-coding_Transcript|MIR642_hsa-mir-642|MI0003657_5'Flank	NM_000164	NP_000155	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	208	Extracellular (Potential).				generation of precursor metabolites and energy|response to nutrient	integral to membrane|plasma membrane					0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)										0.32	24.791322	25.510893	8	17	KEEP	---	---	---	---	capture		Silent	SNP	46178075	46178075	6663	19	G	C	C	C	613	48	GIPR	3	3
SLC17A7	57030	broad.mit.edu	37	19	49934329	49934329	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:49934329C>A	uc002pnp.2	-	c.1332G>T	c.(1330-1332)GTG>GTT	p.V444V	SLC17A7_uc002pno.2_Silent_p.V106V	NM_020309	NP_064705	Q9P2U7	VGLU1_HUMAN	solute carrier family 17, member 7	444	Helical; (Potential).				glutamate secretion|neurotransmitter secretion	cell junction|clathrin sculpted glutamate transport vesicle membrane|integral to membrane|synaptic vesicle membrane|synaptosome	L-glutamate transmembrane transporter activity|sodium-dependent phosphate transmembrane transporter activity|sodium:inorganic phosphate symporter activity			ovary(1)|pancreas(1)	2		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(486;0.0245)										0.27027	52.06647	55.590055	20	54	KEEP	---	---	---	---	capture		Silent	SNP	49934329	49934329	14918	19	C	A	A	A	262	21	SLC17A7	2	2
CPT1C	126129	broad.mit.edu	37	19	50209333	50209333	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:50209333C>A	uc002ppj.2	+	c.1132C>A	c.(1132-1134)CAT>AAT	p.H378N	CPT1C_uc002ppl.3_Missense_Mutation_p.H344N|CPT1C_uc002ppi.2_Missense_Mutation_p.H295N|CPT1C_uc002ppk.2_Missense_Mutation_p.H367N|CPT1C_uc010eng.2_Missense_Mutation_p.H378N|CPT1C_uc010enh.2_Missense_Mutation_p.H378N|CPT1C_uc010ybc.1_Missense_Mutation_p.H249N|CPT1C_uc010eni.1_Missense_Mutation_p.H35N	NM_152359	NP_689572	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C isoform 2	378	Cytoplasmic (Potential).			HEEH -> RTRG (in Ref. 6; CAD38561).	fatty acid metabolic process	integral to membrane|mitochondrial outer membrane	carnitine O-palmitoyltransferase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)										0.151515	9.15351	12.99129	5	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	50209333	50209333	3972	19	C	A	A	A	221	17	CPT1C	2	2
SHANK1	50944	broad.mit.edu	37	19	51165487	51165487	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:51165487C>A	uc002psx.1	-	c.6221G>T	c.(6220-6222)CGC>CTC	p.R2074L	SHANK1_uc002psw.1_Missense_Mutation_p.R1458L	NM_016148	NP_057232	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	2074					cytoskeletal anchoring at plasma membrane	cell junction|cytoplasm|dendrite|membrane fraction|postsynaptic density|postsynaptic membrane	ionotropic glutamate receptor binding			large_intestine(2)	2		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)										0.615385	25.603972	25.757104	8	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51165487	51165487	14756	19	C	A	A	A	351	27	SHANK1	1	1
SIGLEC5	8778	broad.mit.edu	37	19	52132629	52132629	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52132629C>A	uc002pxe.2	-	c.682G>T	c.(682-684)GTC>TTC	p.V228F		NM_003830	NP_003821	O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5 precursor	228	Extracellular (Potential).|Ig-like C2-type 1.				cell adhesion	integral to membrane	sugar binding			breast(1)|central_nervous_system(1)	2		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)										0.428571	167.599055	168.200211	57	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52132629	52132629	14806	19	C	A	A	A	221	17	SIGLEC5	2	2
ZNF610	162963	broad.mit.edu	37	19	52856958	52856958	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:52856958G>T	uc002pyx.3	+	c.87G>T	c.(85-87)GTG>GTT	p.V29V	ZNF610_uc002pyy.3_Silent_p.V29V|ZNF610_uc002pyz.3_Silent_p.V29V|ZNF610_uc002pza.2_Silent_p.V29V	NM_001161426	NP_001154898	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610 isoform a	29	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)										0.273684	67.182813	71.587822	26	69	KEEP	---	---	---	---	capture		Silent	SNP	52856958	52856958	18631	19	G	T	T	T	600	47	ZNF610	2	2
ZNF83	55769	broad.mit.edu	37	19	53117519	53117519	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53117519T>A	uc002pzu.3	-	c.299A>T	c.(298-300)AAG>ATG	p.K100M	ZNF83_uc002pzv.3_Missense_Mutation_p.K100M|ZNF83_uc010eps.2_Missense_Mutation_p.K100M|ZNF83_uc010ept.2_Missense_Mutation_p.K100M|ZNF83_uc010epu.2_Missense_Mutation_p.K100M|ZNF83_uc010epv.2_Missense_Mutation_p.K100M|ZNF83_uc010epw.2_Missense_Mutation_p.K100M|ZNF83_uc010epx.2_Missense_Mutation_p.K100M|ZNF83_uc010epy.2_Missense_Mutation_p.K100M|ZNF83_uc010epz.2_Missense_Mutation_p.K100M|ZNF83_uc010eqb.1_Missense_Mutation_p.K100M	NM_018300	NP_060770	P51522	ZNF83_HUMAN	zinc finger protein 83 isoform a	100	C2H2-type 1; degenerate.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)										0.188679	43.835008	53.450942	20	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53117519	53117519	18782	19	T	A	A	A	728	56	ZNF83	3	3
ZNF28	7576	broad.mit.edu	37	19	53303431	53303431	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:53303431C>A	uc002qad.2	-	c.1667G>T	c.(1666-1668)TGT>TTT	p.C556F	ZNF28_uc002qac.2_Missense_Mutation_p.C503F|ZNF28_uc010eqe.2_Missense_Mutation_p.C502F	NM_006969	NP_008900	P17035	ZNF28_HUMAN	zinc finger protein 28	556	C2H2-type 13.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(1)	1				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)										0.235294	41.084266	45.429016	16	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53303431	53303431	18405	19	C	A	A	A	221	17	ZNF28	2	2
NLRP8	126205	broad.mit.edu	37	19	56466894	56466894	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56466894G>A	uc002qmh.2	+	c.1470G>A	c.(1468-1470)ATG>ATA	p.M490I	NLRP8_uc010etg.2_Missense_Mutation_p.M490I	NM_176811	NP_789781	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	490	NACHT.					cytoplasm	ATP binding			ovary(4)|breast(3)|large_intestine(1)|kidney(1)|skin(1)	10		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)										0.27957	68.713818	72.775149	26	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56466894	56466894	10886	19	G	A	A	A	585	45	NLRP8	2	2
ZSCAN5A	79149	broad.mit.edu	37	19	56733253	56733253	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:56733253C>A	uc002qmq.2	-	c.1182G>T	c.(1180-1182)ATG>ATT	p.M394I	ZSCAN5A_uc010ygi.1_Missense_Mutation_p.M277I|ZSCAN5A_uc002qmr.2_Missense_Mutation_p.M394I|ZSCAN5A_uc002qms.1_Missense_Mutation_p.M393I	NM_024303	NP_077279	Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	394	C2H2-type 2.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			large_intestine(1)|ovary(1)	2														0.068182	-1.711624	6.777223	3	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56733253	56733253	18842	19	C	A	A	A	325	25	ZSCAN5A	2	2
ZNF772	400720	broad.mit.edu	37	19	57985635	57985636	+	Missense_Mutation	DNP	CA	AG	AG			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:57985635_57985636CA>AG	uc002qot.2	-	c.476_477TG>CT	c.(475-477)TTG>TCT	p.L159S	ZNF547_uc002qpm.3_Intron|ZNF772_uc010ygy.1_Missense_Mutation_p.L118S|ZNF772_uc010ygz.1_Missense_Mutation_p.L47S|ZNF772_uc010yha.1_Missense_Mutation_p.L105S|ZNF772_uc002qou.2_Missense_Mutation_p.L47S	NM_001024596	NP_001019767	Q68DY9	ZN772_HUMAN	zinc finger protein 772 isoform 1	159	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)|Lung(386;0.174)		Melanoma(5;289 436 14293 15924 30817)								0.435897	107.937748	108.217381	34	44	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	57985635	57985636	18743	19	CA	AG	AG	AG	272	21	ZNF772	2	2
ZNF418	147686	broad.mit.edu	37	19	58438098	58438098	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:58438098C>A	uc002qqs.1	-	c.1451G>T	c.(1450-1452)TGT>TTT	p.C484F	ZNF418_uc010yhn.1_Non-coding_Transcript|ZNF418_uc010yho.1_Missense_Mutation_p.C399F	NM_133460	NP_597717	Q8TF45	ZN418_HUMAN	zinc finger protein 418	484	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)										0.112069	14.085979	31.336381	13	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	58438098	58438098	18488	19	C	A	A	A	221	17	ZNF418	2	2
MYO1F	4542	broad.mit.edu	37	19	8590441	8590441	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:8590441T>A	uc002mkg.2	-	c.2776A>T	c.(2776-2778)ACG>TCG	p.T926S		NM_012335	NP_036467	O00160	MYO1F_HUMAN	myosin IF	926						unconventional myosin complex	actin binding|ATP binding|calmodulin binding|motor activity			ovary(2)	2														0.2	9.489635	11.162843	4	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8590441	8590441	10468	19	T	A	A	A	741	57	MYO1F	3	3
MUC16	94025	broad.mit.edu	37	19	9089919	9089919	+	Silent	SNP	T	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9089919T>G	uc002mkp.2	-	c.1896A>C	c.(1894-1896)GCA>GCC	p.A632A		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	632	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			ovary(15)|large_intestine(1)|pancreas(1)|breast(1)|skin(1)	19														0.189189	117.538801	140.933136	49	210	KEEP	---	---	---	---	capture		Silent	SNP	9089919	9089919	10367	19	T	G	G	G	652	51	MUC16	4	4
ZNF561	93134	broad.mit.edu	37	19	9721688	9721689	+	Nonsense_Mutation	DNP	CC	AA	AA			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:9721688_9721689CC>AA	uc002mlu.2	-	c.648_649GG>TT	c.(646-651)ATGGGA>ATTTGA	p.216_217MG>I*	ZNF561_uc010dwu.2_Nonsense_Mutation_p.147_148MG>I*|ZNF561_uc010xkr.1_Nonsense_Mutation_p.80_81MG>I*	NM_152289	NP_689502	Q8N587	ZN561_HUMAN	zinc finger protein 561	216_217	C2H2-type 3.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1														0.315789	68.971798	71.266112	24	52	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	9721688	9721689	18587	19	CC	AA	AA	AA	286	22	ZNF561	5	2
NTNG1	22854	broad.mit.edu	37	1	107979286	107979286	+	Splice_Site_SNP	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:107979286G>T	uc001dvh.3	+	c.1256_splice	c.e7-1	p.E419_splice	NTNG1_uc001dvf.3_Intron|NTNG1_uc010out.1_Splice_Site_SNP_p.E385_splice|NTNG1_uc001dvc.3_Intron|NTNG1_uc001dvi.2_Splice_Site_SNP|NTNG1_uc001dve.2_Splice_Site_SNP|NTNG1_uc009wek.2_Splice_Site_SNP|NTNG1_uc001dvg.2_Intron|NTNG1_uc009wem.2_Intron	NM_001113226	NP_001106697			netrin G1 isoform 1						axonogenesis	anchored to plasma membrane	protein binding			large_intestine(2)|ovary(2)	4		all_epithelial(167;1.39e-05)|all_lung(203;0.000115)|Lung NSC(277;0.000238)|Breast(1374;0.243)		Lung(183;0.0946)|BRCA - Breast invasive adenocarcinoma(282;0.237)|Epithelial(280;0.245)										0.202703	30.575909	36.659352	15	59	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	107979286	107979286	11109	1	G	T	T	T	429	33	NTNG1	5	2
CELSR2	1952	broad.mit.edu	37	1	109794679	109794679	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:109794679A>G	uc001dxa.3	+	c.1978A>G	c.(1978-1980)AGC>GGC	p.S660G		NM_001408	NP_001399	Q9HCU4	CELR2_HUMAN	cadherin EGF LAG seven-pass G-type receptor 2	660	Cadherin 5.|Extracellular (Potential).				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)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		NSCLC(158;1285 2011 34800 34852 42084)								0.142857	4.910764	7.49224	3	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109794679	109794679	3355	1	A	G	G	G	91	7	CELSR2	4	4
ZNF697	90874	broad.mit.edu	37	1	120166626	120166626	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:120166626G>A	uc001ehy.1	-	c.340C>T	c.(340-342)CGG>TGG	p.R114W		NM_001080470	NP_001073939	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	114					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)										0.435897	48.253327	48.395096	17	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120166626	120166626	18695	1	G	A	A	A	506	39	ZNF697	1	1
ITGA10	8515	broad.mit.edu	37	1	145528014	145528014	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:145528014C>T	uc001eoa.2	+	c.251C>T	c.(250-252)GCC>GTC	p.A84V	NBPF10_uc001emp.3_Intron|ITGA10_uc001enz.1_Missense_Mutation_p.A84V|ITGA10_uc010oyv.1_Intron|ITGA10_uc009wiw.2_Intron|ITGA10_uc010oyw.1_Missense_Mutation_p.A29V	NM_003637	NP_003628	O75578	ITA10_HUMAN	integrin, alpha 10 precursor	84	Extracellular (Potential).|FG-GAP 1.				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity			lung(2)|ovary(2)|kidney(2)|large_intestine(1)	7	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)									450				0.238095	10.764354	12.080638	5	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	145528014	145528014	8177	1	C	T	T	T	338	26	ITGA10	2	2
FLG	2312	broad.mit.edu	37	1	152279610	152279610	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:152279610A>G	uc001ezu.1	-	c.7752T>C	c.(7750-7752)TCT>TCC	p.S2584S		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2584	Ser-rich.				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)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.108434	10.949352	36.181399	18	148	KEEP	---	---	---	---	capture		Silent	SNP	152279610	152279610	6160	1	A	G	G	G	80	7	FLG	4	4
PKLR	5313	broad.mit.edu	37	1	155264135	155264135	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:155264135G>T	uc001fkb.3	-	c.1007C>A	c.(1006-1008)GCA>GAA	p.A336E	RAG1AP1_uc010pey.1_Intron|PKLR_uc001fka.3_Missense_Mutation_p.A305E	NM_000298	NP_000289	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC isoform 1	336			A -> S (in PKRD).		endocrine pancreas development|energy reserve metabolic process|glycolysis|positive regulation of cellular metabolic process	cytosol	ATP binding|magnesium ion binding|potassium ion binding|pyruvate kinase activity			skin(3)|ovary(1)	4	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)									0.082707	0.748556	24.279331	11	122	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	155264135	155264135	12401	1	G	T	T	T	598	46	PKLR	2	2
SPTA1	6708	broad.mit.edu	37	1	158584094	158584094	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158584094T>A	uc001fst.1	-	c.6791A>T	c.(6790-6792)GAC>GTC	p.D2264V		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2264					actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.095745	4.665319	20.022744	9	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158584094	158584094	15630	1	T	A	A	A	754	58	SPTA1	3	3
SPTA1	6708	broad.mit.edu	37	1	158618310	158618311	+	Missense_Mutation	DNP	GG	CC	CC			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:158618310_158618311GG>CC	uc001fst.1	-	c.3702_3703CC>GG	c.(3700-3705)CCCCTG>CCGGTG	p.L1235V		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1235	Spectrin 12.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.054217	-14.969211	19.814674	9	157	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	158618310	158618311	15630	1	GG	CC	CC	CC	451	35	SPTA1	3	3
VANGL2	57216	broad.mit.edu	37	1	160395114	160395115	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160395114_160395115GG>TT	uc001fwb.1	+	c.1512_1513GG>TT	c.(1510-1515)GTGGAT>GTTTAT	p.D505Y	VANGL2_uc001fwc.1_Missense_Mutation_p.D505Y	NM_020335	NP_065068	Q9ULK5	VANG2_HUMAN	vang-like 2	505	Cytoplasmic (Potential).				apical protein localization|heart looping|sensory cilium assembly	apical plasma membrane|integral to membrane				ovary(1)	1	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)											0.221774	133.01225	150.671329	55	193	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	160395114	160395115	17685	1	GG	TT	TT	TT	600	47	VANGL2	2	2
C1orf114	57821	broad.mit.edu	37	1	169366528	169366528	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:169366528C>A	uc001gga.1	-	c.1317G>T	c.(1315-1317)GAG>GAT	p.E439D	C1orf114_uc001gfz.1_Missense_Mutation_p.E438D|C1orf114_uc009wvq.1_Missense_Mutation_p.E438D	NM_021179	NP_067002	Q5TID7	CA114_HUMAN	hypothetical protein LOC57821	439											0	all_hematologic(923;0.208)													0.238806	40.964972	45.13993	16	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169366528	169366528	2054	1	C	A	A	A	311	24	C1orf114	2	2
MR1	3140	broad.mit.edu	37	1	181018211	181018211	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181018211C>T	uc001goq.1	+	c.91C>T	c.(91-93)CGC>TGC	p.R31C	MR1_uc001gop.2_Missense_Mutation_p.R31C|MR1_uc001gor.1_Missense_Mutation_p.R31C|MR1_uc001gos.1_Missense_Mutation_p.R31C|MR1_uc010pns.1_Missense_Mutation_p.R31C	NM_001531	NP_001522	Q95460	HMR1_HUMAN	major histocompatibility complex, class	31	Extracellular (Potential).|Ligand-binding.|Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I|immune response	endoplasmic reticulum|extracellular region|integral to membrane|MHC class I protein complex	MHC class I receptor activity				0						Colon(174;1412 1962 45296 46549 47110)								0.070175	-2.73551	8.125936	4	53	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	181018211	181018211	10144	1	C	T	T	T	403	31	MR1	1	1
CACNA1E	777	broad.mit.edu	37	1	181546994	181546994	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181546994C>A	uc001gow.2	+	c.605C>A	c.(604-606)TCA>TAA	p.S202*	CACNA1E_uc009wxr.2_Nonsense_Mutation_p.S109*|CACNA1E_uc009wxs.2_Nonsense_Mutation_p.S109*	NM_000721	NP_000712	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type,	202	Helical; Name=S4 of repeat I.|I.				energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6														0.107143	6.608064	15.183779	6	50	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	181546994	181546994	2658	1	C	A	A	A	377	29	CACNA1E	5	2
CACNA1E	777	broad.mit.edu	37	1	181705572	181705572	+	Splice_Site_SNP	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:181705572T>A	uc001gow.2	+	c.3422_splice	c.e22+2	p.P1141_splice	CACNA1E_uc009wxs.2_Splice_Site_SNP_p.P1029_splice|CACNA1E_uc001gox.1_Splice_Site_SNP_p.P367_splice|CACNA1E_uc009wxt.2_Splice_Site_SNP_p.P367_splice	NM_000721	NP_000712			calcium channel, voltage-dependent, R type,						energy reserve metabolic process|membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	voltage-gated calcium channel activity			ovary(3)|central_nervous_system(2)|pancreas(1)	6														0.276596	32.854484	34.966361	13	34	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	181705572	181705572	2658	1	T	A	A	A	741	57	CACNA1E	5	3
HMCN1	83872	broad.mit.edu	37	1	186062355	186062355	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186062355G>C	uc001grq.1	+	c.9977G>C	c.(9976-9978)GGA>GCA	p.G3326A		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	3326	Ig-like C2-type 31.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.145985	39.803043	56.319767	20	117	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	186062355	186062355	7511	1	G	C	C	C	533	41	HMCN1	3	3
HMCN1	83872	broad.mit.edu	37	1	186077690	186077690	+	Silent	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:186077690A>T	uc001grq.1	+	c.10950A>T	c.(10948-10950)CCA>CCT	p.P3650P		NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	3650	Ig-like C2-type 35.				bioluminescence|protein-chromophore linkage|response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)	22														0.218487	62.790068	71.477879	26	93	KEEP	---	---	---	---	capture		Silent	SNP	186077690	186077690	7511	1	A	T	T	T	67	6	HMCN1	3	3
AKR7A3	22977	broad.mit.edu	37	1	19612451	19612451	+	Silent	SNP	T	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:19612451T>G	uc001bbv.1	-	c.438A>C	c.(436-438)GCA>GCC	p.A146A		NM_012067	NP_036199	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3	146					cellular aldehyde metabolic process|oxidation-reduction process	cytosol	aldo-keto reductase (NADP) activity|electron carrier activity				0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)										0.166667	7.113646	9.009567	3	15	KEEP	---	---	---	---	capture		Silent	SNP	19612451	19612451	479	1	T	G	G	G	704	55	AKR7A3	4	4
CFH	3075	broad.mit.edu	37	1	196684731	196684731	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:196684731G>C	uc001gtj.3	+	c.1528G>C	c.(1528-1530)GAT>CAT	p.D510H		NM_000186	NP_000177	P08603	CFAH_HUMAN	complement factor H isoform a precursor	510					complement activation, alternative pathway	extracellular space				ovary(1)|breast(1)|skin(1)	3														0.20202	53.144369	61.309881	20	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	196684731	196684731	3416	1	G	C	C	C	585	45	CFH	3	3
ASPM	259266	broad.mit.edu	37	1	197071122	197071122	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:197071122G>A	uc001gtu.2	-	c.7259C>T	c.(7258-7260)TCA>TTA	p.S2420L	ASPM_uc001gtv.2_Intron|ASPM_uc001gtw.3_Missense_Mutation_p.S268L	NM_018136	NP_060606	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle)-like, microcephaly	2420	IQ 25.				mitosis	cytoplasm|nucleus	calmodulin binding			ovary(4)|central_nervous_system(2)	6														0.095238	8.064931	35.69942	16	152	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	197071122	197071122	1075	1	G	A	A	A	585	45	ASPM	2	2
PTPRC	5788	broad.mit.edu	37	1	198675924	198675924	+	Silent	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:198675924A>T	uc001gur.1	+	c.741A>T	c.(739-741)ACA>ACT	p.T247T	PTPRC_uc001gus.1_Silent_p.T199T|PTPRC_uc001gut.1_Silent_p.T86T|PTPRC_uc009wzf.1_Silent_p.T135T|PTPRC_uc010ppg.1_Silent_p.T183T	NM_002838	NP_002829	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	247	Extracellular (Potential).				axon guidance|B cell proliferation|B cell receptor signaling pathway|defense response to virus|immunoglobulin biosynthetic process|negative regulation of cytokine-mediated signaling pathway|negative regulation of protein kinase activity|negative regulation of T cell mediated cytotoxicity|positive regulation of antigen receptor-mediated signaling pathway|positive regulation of B cell proliferation|positive regulation of protein kinase activity|positive regulation of T cell proliferation|regulation of S phase|release of sequestered calcium ion into cytosol|T cell differentiation|T cell receptor signaling pathway	focal adhesion|integral to plasma membrane|membrane raft	protein kinase binding|transmembrane receptor protein tyrosine phosphatase activity			breast(4)|skin(2)|ovary(2)|lung(1)|kidney(1)|pancreas(1)	11										815				0.084677	6.57298	49.999689	21	227	KEEP	---	---	---	---	capture		Silent	SNP	198675924	198675924	13254	1	A	T	T	T	80	7	PTPRC	3	3
LAX1	54900	broad.mit.edu	37	1	203743159	203743159	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:203743159G>A	uc001haa.2	+	c.547G>A	c.(547-549)GCA>ACA	p.A183T	LAX1_uc010pql.1_Missense_Mutation_p.A167T|LAX1_uc001hab.2_Missense_Mutation_p.A107T	NM_017773	NP_060243	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1 isoform a	183	Cytoplasmic (Potential).				B cell activation|immune response|inactivation of MAPK activity|negative regulation of T cell activation	Golgi apparatus|integral to membrane|plasma membrane	protein kinase binding|SH2 domain binding			central_nervous_system(2)	2	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)											0.111111	14.115514	31.587082	13	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	203743159	203743159	8971	1	G	A	A	A	494	38	LAX1	1	1
IKBKE	9641	broad.mit.edu	37	1	206648289	206648289	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:206648289G>A	uc001hdz.1	+	c.310G>A	c.(310-312)GCC>ACC	p.A104T	IKBKE_uc009xbu.1_Missense_Mutation_p.A104T|IKBKE_uc009xbv.1_Missense_Mutation_p.A104T|IKBKE_uc001hea.1_Missense_Mutation_p.A19T	NM_014002	NP_054721	Q14164	IKKE_HUMAN	IKK-related kinase epsilon	104	Protein kinase.				DNA damage response, signal transduction resulting in induction of apoptosis|innate immune response|MyD88-independent toll-like receptor signaling pathway|negative regulation of type I interferon production|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein phosphorylation|Toll signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane|PML body	ATP binding|IkappaB kinase activity|NF-kappaB-inducing kinase activity|protein binding			ovary(3)|lung(1)|central_nervous_system(1)|skin(1)	6	Breast(84;0.137)									537				0.08642	-0.018993	14.002399	7	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	206648289	206648289	7913	1	G	A	A	A	598	46	IKBKE	2	2
C1orf107	27042	broad.mit.edu	37	1	210010463	210010463	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:210010463C>A	uc001hhr.1	+	c.969C>A	c.(967-969)GCC>GCA	p.A323A	C1orf107_uc009xcu.1_Silent_p.A38A	NM_014388	NP_055203	Q68CQ4	DIEXF_HUMAN	digestive-organ expansion factor homolog	323					multicellular organismal development	nucleus					0				OV - Ovarian serous cystadenocarcinoma(81;0.0367)										0.322034	107.3411	110.643062	38	80	KEEP	---	---	---	---	capture		Silent	SNP	210010463	210010463	2048	1	C	A	A	A	275	22	C1orf107	2	2
PRKCZ	5590	broad.mit.edu	37	1	2106259	2106259	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:2106259G>C	uc001aiq.2	+	c.1472G>C	c.(1471-1473)GGA>GCA	p.G491A	PRKCZ_uc001air.2_Missense_Mutation_p.G308A|PRKCZ_uc010nyw.1_Missense_Mutation_p.G387A|PRKCZ_uc001ais.2_Missense_Mutation_p.G308A|PRKCZ_uc009vla.2_Missense_Mutation_p.G315A|PRKCZ_uc010nyx.1_Non-coding_Transcript|PRKCZ_uc001ait.2_Missense_Mutation_p.G339A	NM_002744	NP_002735	Q05513	KPCZ_HUMAN	protein kinase C, zeta isoform 1	491	Protein kinase.				anti-apoptosis|intracellular signal transduction|negative regulation of insulin receptor signaling pathway|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein complex assembly|peptidyl-serine phosphorylation|platelet activation	endosome	ATP binding|insulin receptor substrate binding|protein kinase C activity|zinc ion binding			central_nervous_system(4)|large_intestine(2)	6	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)						2432		OREG0013007	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.25	30.187709	32.704065	11	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2106259	2106259	12960	1	G	C	C	C	533	41	PRKCZ	3	3
CENPF	1063	broad.mit.edu	37	1	214819597	214819597	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:214819597A>G	uc001hkm.2	+	c.6684A>G	c.(6682-6684)GAA>GAG	p.E2228E		NM_016343	NP_057427	P49454	CENPF_HUMAN	centromere protein F	2324	Potential.|2-1.|2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation|cell division|cell proliferation|DNA replication|G2 phase of mitotic cell cycle|kinetochore assembly|metaphase plate congression|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|muscle organ development|negative regulation of transcription, DNA-dependent|protein transport|regulation of G2/M transition of mitotic cell cycle|regulation of striated muscle tissue development|response to drug	condensed chromosome outer kinetochore|cytosol|midbody|nuclear envelope|nuclear matrix|perinuclear region of cytoplasm|spindle pole	chromatin binding|dynein binding|protein C-terminus binding|protein homodimerization activity|transcription factor binding			ovary(6)|central_nervous_system(4)|large_intestine(2)	12				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		Colon(80;575 1284 11000 14801 43496)								0.115942	41.238828	81.514235	32	244	KEEP	---	---	---	---	capture		Silent	SNP	214819597	214819597	3364	1	A	G	G	G	24	2	CENPF	4	4
KCNK2	3776	broad.mit.edu	37	1	215342563	215342563	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:215342563G>T	uc001hkq.2	+	c.497G>T	c.(496-498)CGC>CTC	p.R166L	KCNK2_uc001hko.2_Missense_Mutation_p.R162L|KCNK2_uc009xdm.2_Non-coding_Transcript|KCNK2_uc001hkp.2_Non-coding_Transcript|KCNK2_uc010pua.1_Non-coding_Transcript|KCNK2_uc001hkr.3_Missense_Mutation_p.R151L	NM_001017425	NP_001017425	O95069	KCNK2_HUMAN	potassium channel, subfamily K, member 2 isoform	166							outward rectifier potassium channel activity				0				OV - Ovarian serous cystadenocarcinoma(81;0.0399)|all cancers(67;0.0556)|GBM - Glioblastoma multiforme(131;0.068)	Dofetilide(DB00204)									0.076389	0.637941	53.557569	22	266	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	215342563	215342563	8371	1	G	T	T	T	494	38	KCNK2	1	1
USH2A	7399	broad.mit.edu	37	1	216595416	216595416	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:216595416C>A	uc001hku.1	-	c.263G>T	c.(262-264)TGC>TTC	p.C88F	USH2A_uc001hkv.2_Missense_Mutation_p.C88F	NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	88	Extracellular (Potential).				maintenance of organ identity|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	basement membrane|cytoplasm|integral to membrane|stereocilium membrane	collagen binding			ovary(20)|kidney(1)|central_nervous_system(1)	22				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)										0.097222	9.163864	32.548646	14	130	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	216595416	216595416	17598	1	C	A	A	A	325	25	USH2A	2	2
CDC42BPA	8476	broad.mit.edu	37	1	227333438	227333438	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:227333438C>G	uc001hqr.2	-	c.895G>C	c.(895-897)GAG>CAG	p.E299Q	CDC42BPA_uc001hqs.2_Missense_Mutation_p.E299Q|CDC42BPA_uc009xes.2_Missense_Mutation_p.E299Q|CDC42BPA_uc010pvs.1_Missense_Mutation_p.E299Q	NM_003607	NP_003598	Q5VT25	MRCKA_HUMAN	CDC42-binding protein kinase alpha isoform B	299	Protein kinase.				actin cytoskeleton reorganization|intracellular signal transduction|protein phosphorylation	cell leading edge|cell-cell junction|cytoplasm	ATP binding|identical protein binding|magnesium ion binding|protein serine/threonine kinase activity|small GTPase regulator activity	p.E299Q(1)		lung(6)|breast(2)|ovary(1)|pancreas(1)	10		all_cancers(173;0.156)|Prostate(94;0.0792)								1574				0.264706	78.079748	83.183309	27	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	227333438	227333438	3200	1	C	G	G	G	390	30	CDC42BPA	3	3
EPHB2	2048	broad.mit.edu	37	1	23239017	23239017	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:23239017A>G	uc009vqj.1	+	c.2777A>G	c.(2776-2778)AAG>AGG	p.K926R	EPHB2_uc001bge.2_Missense_Mutation_p.K927R|EPHB2_uc001bgf.2_Missense_Mutation_p.K926R|EPHB2_uc010odu.1_Missense_Mutation_p.K868R	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	926	Cytoplasmic (Potential).|SAM.				axon guidance|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)						437				0.113208	5.508692	13.343476	6	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23239017	23239017	5368	1	A	G	G	G	39	3	EPHB2	4	4
EPHB2	2048	broad.mit.edu	37	1	23239019	23239019	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:23239019A>G	uc009vqj.1	+	c.2779A>G	c.(2779-2781)ATG>GTG	p.M927V	EPHB2_uc001bge.2_Missense_Mutation_p.M928V|EPHB2_uc001bgf.2_Missense_Mutation_p.M927V|EPHB2_uc010odu.1_Missense_Mutation_p.M869V	NM_017449	NP_059145	P29323	EPHB2_HUMAN	ephrin receptor EphB2 isoform 1 precursor	927	Cytoplasmic (Potential).|SAM.				axon guidance|protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|transmembrane-ephrin receptor activity			ovary(3)|lung(1)|pancreas(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)						437				0.111111	6.814151	14.88584	6	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	23239019	23239019	5368	1	A	G	G	G	156	12	EPHB2	4	4
RBM34	23029	broad.mit.edu	37	1	235295246	235295246	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:235295246C>T	uc001hwn.2	-	c.1075G>A	c.(1075-1077)GTC>ATC	p.V359I	TOMM20_uc001hwl.2_5'Flank|RBM34_uc001hwo.2_Non-coding_Transcript|ARID4B_uc001hwp.2_Non-coding_Transcript	NM_015014	NP_055829	P42696	RBM34_HUMAN	RNA binding motif protein 34 isoform 1	359	RRM 2.					nucleolus	nucleotide binding|RNA binding			central_nervous_system(1)	1	Ovarian(103;0.0398)	all_cancers(173;0.177)|Prostate(94;0.0166)	OV - Ovarian serous cystadenocarcinoma(106;5.43e-05)|Epithelial(3;0.000121)											0.152542	17.23444	24.052467	9	50	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	235295246	235295246	13593	1	C	T	T	T	260	20	RBM34	2	2
RYR2	6262	broad.mit.edu	37	1	237947067	237947067	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237947067A>T	uc001hyl.1	+	c.12055A>T	c.(12055-12057)ATG>TTG	p.M4019L	RYR2_uc010pya.1_Missense_Mutation_p.M434L	NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4019					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.095238	2.200529	12.565637	6	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237947067	237947067	14249	1	A	T	T	T	104	8	RYR2	3	3
OR2L2	26246	broad.mit.edu	37	1	248202413	248202413	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248202413C>A	uc001idw.2	+	c.844C>A	c.(844-846)CCA>ACA	p.P282T	OR2L13_uc001ids.2_Intron	NM_001004686	NP_001004686	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L,	282	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)											0.081181	-4.204932	44.201588	22	249	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248202413	248202413	11413	1	C	A	A	A	286	22	OR2L2	2	2
OR2T27	403239	broad.mit.edu	37	1	248814014	248814014	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:248814014G>T	uc010pzo.1	-	c.172C>A	c.(172-174)CCC>ACC	p.P58T		NM_001001824	NP_001001824	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T,	58	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)											0.277108	57.884599	61.599081	23	60	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	248814014	248814014	11427	1	G	T	T	T	559	43	OR2T27	2	2
GJB4	127534	broad.mit.edu	37	1	35226919	35226919	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:35226919C>A	uc001bxv.1	+	c.64C>A	c.(64-66)CGC>AGC	p.R22S	GJB4_uc001bxw.3_Missense_Mutation_p.R22S	NM_153212	NP_694944	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4	22	Helical; (Potential).				cell communication	connexon complex|integral to membrane	gap junction channel activity			ovary(2)|central_nervous_system(1)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)												0.494118	135.549063	135.551556	42	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35226919	35226919	6678	1	C	A	A	A	299	23	GJB4	1	1
THRAP3	9967	broad.mit.edu	37	1	36748202	36748202	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:36748202C>G	uc001cae.3	+	c.38C>G	c.(37-39)TCT>TGT	p.S13C	THRAP3_uc001caf.3_Missense_Mutation_p.S13C|THRAP3_uc001cag.1_Missense_Mutation_p.S13C	NM_005119	NP_005110	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	13	Arg-rich.|Ser-rich.				androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ATP binding|ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(5)|lung(1)	6		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				Pancreas(129;785 1795 20938 23278 32581)				199				0.139535	12.422966	17.817312	6	37	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36748202	36748202	16402	1	C	G	G	G	416	32	THRAP3	3	3
CTPS	1503	broad.mit.edu	37	1	41457512	41457512	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:41457512G>C	uc001cgk.3	+	c.715G>C	c.(715-717)GAA>CAA	p.E239Q	CTPS_uc010ojo.1_Missense_Mutation_p.E8Q|CTPS_uc010ojp.1_Missense_Mutation_p.E246Q|CTPS_uc001cgl.3_Missense_Mutation_p.E239Q|CTPS_uc010ojq.1_Missense_Mutation_p.E83Q	NM_001905	NP_001896	P17812	PYRG1_HUMAN	CTP synthase	239					CTP biosynthetic process|glutamine metabolic process|nucleobase, nucleoside and nucleotide interconversion|response to drug	cytosol	ATP binding|CTP synthase activity|protein binding				0	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)			L-Glutamine(DB00130)									0.134328	16.926431	25.615803	9	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41457512	41457512	4181	1	G	C	C	C	585	45	CTPS	3	3
KIAA0467	23334	broad.mit.edu	37	1	43894141	43894141	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:43894141C>A	uc001cjk.1	+	c.1453C>A	c.(1453-1455)CTA>ATA	p.L485I		NM_015284	NP_056099	Q5T011	SZT2_HUMAN	hypothetical protein LOC23334	1384						peroxisome				breast(6)|ovary(4)|pancreas(1)	11	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)												0.061728	-5.888556	10.341309	5	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43894141	43894141	8485	1	C	A	A	A	311	24	KIAA0467	2	2
TMEM48	55706	broad.mit.edu	37	1	54262454	54262454	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:54262454T>A	uc001cvs.2	-	c.1492A>T	c.(1492-1494)AAT>TAT	p.N498Y	TMEM48_uc010onu.1_Missense_Mutation_p.N458Y|TMEM48_uc001cvt.2_Missense_Mutation_p.N375Y|TMEM48_uc009vzk.2_Non-coding_Transcript|TMEM48_uc010onv.1_Missense_Mutation_p.N163Y	NM_018087	NP_060557	Q9BTX1	NDC1_HUMAN	transmembrane protein 48	498	Cytoplasmic (Potential).				mRNA transport|nuclear pore complex assembly|nuclear pore distribution|protein transport|transmembrane transport	nuclear membrane|nuclear pore	protein binding|structural constituent of nuclear pore			ovary(1)|pancreas(1)	2						Ovarian(178;223 2720 6667 9715)								0.56	91.005433	91.162235	28	22	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54262454	54262454	16711	1	T	A	A	A	793	61	TMEM48	3	3
SGIP1	84251	broad.mit.edu	37	1	67105479	67105479	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:67105479C>A	uc001dcr.2	+	c.191C>A	c.(190-192)CCA>CAA	p.P64Q		NM_032291	NP_115667	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting	64					intracellular protein transport|positive regulation of energy homeostasis|positive regulation of feeding behavior|positive regulation of receptor-mediated endocytosis|response to dietary excess|vesicle-mediated transport	AP-2 adaptor complex	microtubule binding|phospholipid binding|SH3 domain binding			ovary(3)	3														0.445783	116.709202	116.913361	37	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	67105479	67105479	14697	1	C	A	A	A	273	21	SGIP1	2	2
LRRC7	57554	broad.mit.edu	37	1	70477610	70477610	+	Splice_Site_SNP	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:70477610G>A	uc001dep.2	+	c.1020_splice	c.e10+1	p.E340_splice	LRRC7_uc009wbg.2_Splice_Site_SNP	NM_020794	NP_065845			leucine rich repeat containing 7							centrosome|focal adhesion|nucleolus	protein binding			ovary(8)|breast(2)|central_nervous_system(2)|liver(1)	13										783				0.318182	20.016571	20.663358	7	15	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	70477610	70477610	9396	1	G	A	A	A	468	36	LRRC7	5	2
C1orf173	127254	broad.mit.edu	37	1	75078352	75078352	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:75078352C>A	uc001dgg.2	-	c.1142G>T	c.(1141-1143)GGC>GTC	p.G381V	C1orf173_uc001dgi.3_Missense_Mutation_p.G175V	NM_001002912	NP_001002912	Q5RHP9	CA173_HUMAN	hypothetical protein LOC127254	381										ovary(3)|central_nervous_system(1)	4														0.158537	21.917456	31.037692	13	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	75078352	75078352	2081	1	C	A	A	A	338	26	C1orf173	2	2
OVOL2	58495	broad.mit.edu	37	20	18005403	18005403	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:18005403A>T	uc002wqi.1	-	c.705T>A	c.(703-705)AGT>AGA	p.S235R		NM_021220	NP_067043	Q9BRP0	OVOL2_HUMAN	zinc finger protein 339	235	C2H2-type 4.				negative regulation of keratinocyte differentiation|negative regulation of Notch signaling pathway|negative regulation of transcription by competitive promoter binding|regulation of cell cycle|regulation of keratinocyte proliferation|transcription, DNA-dependent	nucleus|nucleus	DNA binding|promoter binding|zinc ion binding			central_nervous_system(1)	1														0.363636	24.595624	24.954874	8	14	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18005403	18005403	11740	20	A	T	T	T	76	6	OVOL2	3	3
ZNF341	84905	broad.mit.edu	37	20	32332941	32332941	+	Nonsense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:32332941A>T	uc002wzy.2	+	c.175A>T	c.(175-177)AAG>TAG	p.K59*	ZNF341_uc002wzx.2_Nonsense_Mutation_p.K59*|ZNF341_uc010geq.2_Intron|ZNF341_uc010ger.2_Non-coding_Transcript	NM_032819	NP_116208	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	59	C2H2-type 1; atypical.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.202703	30.18398	36.260506	15	59	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	32332941	32332941	18449	20	A	T	T	T	169	13	ZNF341	5	3
MAVS	57506	broad.mit.edu	37	20	3838457	3838457	+	Splice_Site_SNP	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:3838457G>C	uc002wjw.3	+	c.292_splice	c.e3+1	p.R98_splice	MAVS_uc002wjv.2_Missense_Mutation_p.R98P|MAVS_uc010zqn.1_Splice_Site_SNP_p.Q98_splice|MAVS_uc002wjx.3_Intron|MAVS_uc002wjy.3_Splice_Site_SNP	NM_020746	NP_065797			virus-induced signaling adapter						activation of innate immune response|cellular response to exogenous dsRNA|defense response to bacterium|innate immune response|interspecies interaction between organisms|negative regulation of type I interferon production|positive regulation of chemokine (C-C motif) ligand 5 production|positive regulation of defense response to virus by host|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interferon-alpha production|positive regulation of interferon-beta production|positive regulation of interleukin-8 production|positive regulation of IP-10 production|positive regulation of protein import into nucleus, translocation|positive regulation of protein phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription factor import into nucleus|positive regulation of tumor necrosis factor production|positive regulation of type I interferon-mediated signaling pathway|response to virus	integral to membrane|mitochondrial outer membrane	CARD domain binding|protein kinase binding|signal transducer activity				0														0.172414	24.631943	30.496876	10	48	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	3838457	3838457	9722	20	G	C	C	C	520	40	MAVS	5	3
CHD6	84181	broad.mit.edu	37	20	40050438	40050438	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:40050438T>C	uc002xka.1	-	c.4837A>G	c.(4837-4839)AGA>GGA	p.R1613G		NM_032221	NP_115597	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1613					chromatin assembly or disassembly|chromatin remodeling|nervous system development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding			ovary(6)|lung(2)|central_nervous_system(1)|skin(1)	10		Myeloproliferative disorder(115;0.00425)												0.127273	11.087908	18.537932	7	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40050438	40050438	3463	20	T	C	C	C	687	53	CHD6	4	4
PTPRT	11122	broad.mit.edu	37	20	40730771	40730771	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:40730771A>T	uc010ggj.2	-	c.3764T>A	c.(3763-3765)CTG>CAG	p.L1255Q	PTPRT_uc002xkg.2_Missense_Mutation_p.L1236Q|PTPRT_uc010ggi.2_Missense_Mutation_p.L439Q	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1236	Cytoplasmic (Potential).|Tyrosine-protein phosphatase 2.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.060241	-5.492215	11.284667	5	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	40730771	40730771	13270	20	A	T	T	T	91	7	PTPRT	3	3
SULF2	55959	broad.mit.edu	37	20	46295154	46295154	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:46295154C>G	uc002xto.2	-	c.1655G>C	c.(1654-1656)GGC>GCC	p.G552A	SULF2_uc002xtr.2_Missense_Mutation_p.G552A|SULF2_uc002xtq.2_Missense_Mutation_p.G552A|SULF2_uc010zyd.1_5'Flank	NM_018837	NP_061325	Q8IWU5	SULF2_HUMAN	sulfatase 2 isoform a precursor	552					bone development|heparan sulfate proteoglycan metabolic process|kidney development|negative regulation of fibroblast growth factor receptor signaling pathway	cell surface|endoplasmic reticulum|extracellular space|Golgi stack	arylsulfatase activity|calcium ion binding			ovary(2)|breast(2)|pancreas(1)	5										709				0.1875	6.215402	7.67961	3	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46295154	46295154	15891	20	C	G	G	G	338	26	SULF2	3	3
PREX1	57580	broad.mit.edu	37	20	47269935	47269935	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47269935G>T	uc002xtw.1	-	c.2310C>A	c.(2308-2310)CAC>CAA	p.H770Q	PREX1_uc002xtv.1_Missense_Mutation_p.H67Q	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	770					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)											0.063492	-9.175653	15.798303	8	118	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47269935	47269935	12919	20	G	T	T	T	464	36	PREX1	2	2
PREX1	57580	broad.mit.edu	37	20	47269937	47269937	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:47269937G>T	uc002xtw.1	-	c.2308C>A	c.(2308-2310)CAC>AAC	p.H770N	PREX1_uc002xtv.1_Missense_Mutation_p.H67N	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	770					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)											0.065574	-8.424398	15.427739	8	114	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47269937	47269937	12919	20	G	T	T	T	598	46	PREX1	2	2
MOCS3	27304	broad.mit.edu	37	20	49575858	49575858	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:49575858C>A	uc002xvy.1	+	c.479C>A	c.(478-480)GCC>GAC	p.A160D	DPM1_uc002xvw.1_5'Flank|DPM1_uc002xvx.1_5'Flank	NM_014484	NP_055299	O95396	MOCS3_HUMAN	molybdenum cofactor synthesis 3	160					enzyme active site formation via L-cysteine persulfide|Mo-molybdopterin cofactor biosynthetic process|tRNA thio-modification|tRNA wobble uridine modification|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|nucleotidyltransferase activity|protein binding|thiosulfate sulfurtransferase activity|URM1 activating enzyme activity			ovary(1)|skin(1)	2														0.069767	-1.856032	6.31326	3	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	49575858	49575858	10083	20	C	A	A	A	338	26	MOCS3	2	2
SALL4	57167	broad.mit.edu	37	20	50407375	50407375	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:50407375C>T	uc002xwh.3	-	c.1647G>A	c.(1645-1647)CTG>CTA	p.L549L	SALL4_uc010gii.2_Intron|SALL4_uc002xwi.3_Intron	NM_020436	NP_065169	Q9UJQ4	SALL4_HUMAN	sal-like 4	549					transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2														0.0625	-5.983853	9.974044	5	75	KEEP	---	---	---	---	capture		Silent	SNP	50407375	50407375	14293	20	C	T	T	T	366	29	SALL4	2	2
TSHZ2	128553	broad.mit.edu	37	20	51872217	51872217	+	Silent	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:51872217G>C	uc002xwo.2	+	c.2220G>C	c.(2218-2220)CCG>CCC	p.P740P		NM_173485	NP_775756	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	740					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4			STAD - Stomach adenocarcinoma(23;0.1)											0.419753	104.50557	104.966067	34	47	KEEP	---	---	---	---	capture		Silent	SNP	51872217	51872217	17175	20	G	C	C	C	496	39	TSHZ2	3	3
CASS4	57091	broad.mit.edu	37	20	55012273	55012273	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:55012273G>T	uc002xxp.2	+	c.90G>T	c.(88-90)CTG>CTT	p.L30L	CASS4_uc002xxq.3_Silent_p.L30L|CASS4_uc002xxr.2_Silent_p.L30L|CASS4_uc010zze.1_Silent_p.L30L|CASS4_uc010gio.2_Silent_p.L30L	NM_001164116	NP_001157588	Q9NQ75	CASS4_HUMAN	HEF-like protein isoform a	30	SH3.				cell adhesion	cytoplasm|cytoskeleton|focal adhesion	two-component sensor activity			ovary(2)	2														0.196721	109.553349	130.468388	48	196	KEEP	---	---	---	---	capture		Silent	SNP	55012273	55012273	2802	20	G	T	T	T	600	47	CASS4	2	2
PLCB1	23236	broad.mit.edu	37	20	8630053	8630053	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:8630053G>T	uc002wnb.2	+	c.551G>T	c.(550-552)CGA>CTA	p.R184L	PLCB1_uc010zrb.1_Missense_Mutation_p.R83L|PLCB1_uc010gbv.1_Missense_Mutation_p.R184L|PLCB1_uc002wmz.1_Missense_Mutation_p.R184L|PLCB1_uc002wna.2_Missense_Mutation_p.R184L|PLCB1_uc002wnc.1_Missense_Mutation_p.R83L	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	184					activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of gene-specific transcription|negative regulation of monocyte extravasation|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of gene-specific transcription|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity|transcription repressor activity			ovary(4)|breast(3)|lung(1)	8														0.464286	40.673849	40.704728	13	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	8630053	8630053	12453	20	G	T	T	T	481	37	PLCB1	1	1
TPTE	7179	broad.mit.edu	37	21	10941970	10941970	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:10941970G>T	uc002yip.1	-	c.733C>A	c.(733-735)CGT>AGT	p.R245S	TPTE_uc002yis.1_Non-coding_Transcript|TPTE_uc002yiq.1_Missense_Mutation_p.R227S|TPTE_uc002yir.1_Missense_Mutation_p.R207S|TPTE_uc010gkv.1_Missense_Mutation_p.R107S	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	245	Phosphatase tensin-type.				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)										0.067568	-4.470818	24.181633	10	138	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10941970	10941970	16974	21	G	T	T	T	520	40	TPTE	1	1
KRTAP24-1	643803	broad.mit.edu	37	21	31654973	31654973	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:31654973A>C	uc002ynv.2	-	c.278T>G	c.(277-279)GTG>GGG	p.V93G		NM_001085455	NP_001078924	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	93						keratin filament	structural molecule activity				0														0.515152	109.747212	109.76028	34	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31654973	31654973	8863	21	A	C	C	C	78	6	KRTAP24-1	4	4
C2CD2	25966	broad.mit.edu	37	21	43327262	43327262	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:43327262T>C	uc002yzw.2	-	c.1157A>G	c.(1156-1158)GAA>GGA	p.E386G	C2CD2_uc002yzt.2_Missense_Mutation_p.E2G|C2CD2_uc002yzu.2_Missense_Mutation_p.E218G|C2CD2_uc002yzv.2_Missense_Mutation_p.E231G|C2CD2_uc002yzx.1_Missense_Mutation_p.E231G	NM_015500	NP_056315	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2 isoform	386						cytosol|extracellular region|nucleus				ovary(1)	1														0.184211	14.10092	17.658779	7	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43327262	43327262	2235	21	T	C	C	C	806	62	C2CD2	4	4
PACSIN2	11252	broad.mit.edu	37	22	43272936	43272936	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:43272936G>A	uc010gzg.2	-	c.1109C>T	c.(1108-1110)ACG>ATG	p.T370M	PACSIN2_uc003bdg.3_Missense_Mutation_p.T370M|PACSIN2_uc003bde.3_Missense_Mutation_p.T370M|PACSIN2_uc003bdf.3_Intron	NM_007229	NP_009160	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in	370					actin cytoskeleton organization|endocytosis	cytoplasmic membrane-bounded vesicle	transporter activity				0		Glioma(61;0.222)												0.307692	31.683324	32.970374	12	27	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43272936	43272936	11791	22	G	A	A	A	520	40	PACSIN2	1	1
EFCAB6	64800	broad.mit.edu	37	22	43950875	43950875	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:43950875C>T	uc003bdy.1	-	c.3522G>A	c.(3520-3522)GTG>GTA	p.V1174V	EFCAB6_uc003bdz.1_Silent_p.V1022V|EFCAB6_uc010gzi.1_Silent_p.V1022V|EFCAB6_uc010gzj.1_Silent_p.V400V	NM_022785	NP_073622	Q5THR3	EFCB6_HUMAN	CAP-binding protein complex interacting protein	1174					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	calcium ion binding			ovary(3)|pancreas(1)	4		Ovarian(80;0.0247)|all_neural(38;0.025)												0.894737	107.271454	113.159012	34	4	KEEP	---	---	---	---	capture		Silent	SNP	43950875	43950875	5126	22	C	T	T	T	366	29	EFCAB6	2	2
ERCC3	2071	broad.mit.edu	37	2	128016978	128016978	+	Missense_Mutation	SNP	G	A	A	rs4150521	byFrequency	TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128016978G>A	uc002toh.1	-	c.2111C>T	c.(2110-2112)TCG>TTG	p.S704L	ERCC3_uc002toe.1_Missense_Mutation_p.S459L|ERCC3_uc002tof.1_Missense_Mutation_p.S640L|ERCC3_uc002tog.1_Missense_Mutation_p.S640L	NM_000122	NP_000113	P19447	ERCC3_HUMAN	excision repair cross-complementing rodent	704					cell cycle checkpoint|DNA topological change|hair cell differentiation|induction of apoptosis|interspecies interaction between organisms|mRNA capping|nucleotide-excision repair, DNA damage removal|nucleotide-excision repair, DNA duplex unwinding|nucleotide-excision repair, DNA incision|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|protein localization|response to oxidative stress|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex	3'-5' DNA helicase activity|ATP binding|damaged DNA binding|protein C-terminus binding|protein N-terminus binding|transcription factor binding			ovary(1)|lung(1)|breast(1)|kidney(1)	4	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)						281				0.040404	-14.571741	7.939693	4	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	128016978	128016978	5407	2	G	A	A	A	481	37	ERCC3	1	1
GPR17	2840	broad.mit.edu	37	2	128408864	128408864	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:128408864C>A	uc010yzn.1	+	c.639C>A	c.(637-639)TAC>TAA	p.Y213*	LIMS2_uc002tox.2_Intron|LIMS2_uc010fmb.2_Intron|LIMS2_uc002toy.2_Intron|LIMS2_uc010yzm.1_Intron|LIMS2_uc002tpa.2_Intron|LIMS2_uc002toz.2_Intron|LIMS2_uc002tpb.2_Intron|GPR17_uc002tpc.2_Nonsense_Mutation_p.Y213*|GPR17_uc010yzo.1_Nonsense_Mutation_p.Y185*|GPR17_uc002tpd.2_Nonsense_Mutation_p.Y185*	NM_001161415	NP_001154887	Q13304	GPR17_HUMAN	G protein-coupled receptor 17 isoform a	213	Extracellular (Potential).					integral to plasma membrane	chemokine receptor activity|purinergic nucleotide receptor activity, G-protein coupled				0	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)										0.2	6.416239	7.672061	3	12	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	128408864	128408864	6942	2	C	A	A	A	233	18	GPR17	5	2
CCDC115	84317	broad.mit.edu	37	2	131098596	131098596	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131098596C>G	uc002tqy.1	-	c.315G>C	c.(313-315)AAG>AAC	p.K105N	CCDC115_uc002tqw.1_Missense_Mutation_p.K97N|CCDC115_uc010zaf.1_Missense_Mutation_p.K100N|CCDC115_uc002tqx.2_Missense_Mutation_p.K100N|CCDC115_uc002tqz.1_Missense_Mutation_p.K105N|IMP4_uc002tra.1_5'Flank	NM_032357	NP_115733	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	105						endosome|lysosome					0	Colorectal(110;0.1)													0.266667	10.693209	11.430886	4	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131098596	131098596	2872	2	C	G	G	G	311	24	CCDC115	3	3
ARHGEF4	50649	broad.mit.edu	37	2	131785526	131785526	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:131785526G>A	uc002tsa.1	+	c.436G>A	c.(436-438)GAT>AAT	p.D146N	ARHGEF4_uc010fmw.1_Intron|ARHGEF4_uc002tsb.1_Missense_Mutation_p.D146N|ARHGEF4_uc010fmx.1_Missense_Mutation_p.D146N	NM_015320	NP_056135	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor 4 isoform	146					apoptosis|filopodium assembly|induction of apoptosis by extracellular signals|lamellipodium assembly|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|ruffle membrane	protein domain specific binding|Rac guanyl-nucleotide exchange factor activity			breast(3)|ovary(2)|skin(1)	6		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)										0.3125	12.165509	12.668459	5	11	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131785526	131785526	923	2	G	A	A	A	585	45	ARHGEF4	2	2
LCT	3938	broad.mit.edu	37	2	136558283	136558283	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:136558283C>A	uc002tuu.1	-	c.4760G>T	c.(4759-4761)CGC>CTC	p.R1587L		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	1587	Extracellular (Potential).|4.|4 X approximate repeats.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|lung(1)|pancreas(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.169)										0.230769	15.641948	17.365058	6	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136558283	136558283	9017	2	C	A	A	A	351	27	LCT	1	1
LCT	3938	broad.mit.edu	37	2	136566189	136566189	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:136566189G>T	uc002tuu.1	-	c.3728C>A	c.(3727-3729)ACG>AAG	p.T1243K		NM_002299	NP_002290	P09848	LPH_HUMAN	lactase-phlorizin hydrolase preproprotein	1243	3.|Extracellular (Potential).|4 X approximate repeats.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			ovary(7)|central_nervous_system(2)|lung(1)|pancreas(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.169)										0.377049	70.610901	71.419863	23	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	136566189	136566189	9017	2	G	T	T	T	520	40	LCT	1	1
KCNJ3	3760	broad.mit.edu	37	2	155711582	155711582	+	Silent	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:155711582T>C	uc002tyv.1	+	c.1263T>C	c.(1261-1263)TCT>TCC	p.S421S	KCNJ3_uc010zce.1_3'UTR	NM_002239	NP_002230	P48549	IRK3_HUMAN	potassium inwardly-rectifying channel J3	421	Cytoplasmic (By similarity).				synaptic transmission	voltage-gated potassium channel complex	G-protein activated inward rectifier potassium channel activity|protein binding			pancreas(1)	1					Halothane(DB01159)									0.030612	-34.419229	12.922177	6	190	KEEP	---	---	---	---	capture		Silent	SNP	155711582	155711582	8357	2	T	C	C	C	678	53	KCNJ3	4	4
GRB14	2888	broad.mit.edu	37	2	165404188	165404188	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:165404188G>A	uc002ucl.2	-	c.463C>T	c.(463-465)CTG>TTG	p.L155L	GRB14_uc010zcv.1_Silent_p.L68L|GRB14_uc002ucm.2_Non-coding_Transcript	NM_004490	NP_004481	Q14449	GRB14_HUMAN	growth factor receptor-bound protein 14	155	Ras-associating.				blood coagulation|leukocyte migration	cytosol|endosome membrane|Golgi membrane|microsome|plasma membrane	SH3/SH2 adaptor activity			ovary(5)|lung(1)	6														0.17284	30.597746	38.787311	14	67	KEEP	---	---	---	---	capture		Silent	SNP	165404188	165404188	7034	2	G	A	A	A	451	35	GRB14	2	2
XIRP2	129446	broad.mit.edu	37	2	168103121	168103121	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168103121G>A	uc002udx.2	+	c.5219G>A	c.(5218-5220)AGA>AAA	p.R1740K	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.R1565K|XIRP2_uc010fpq.2_Missense_Mutation_p.R1518K|XIRP2_uc010fpr.2_Intron|XIRP2_uc010fps.1_5'Flank	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	1565					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.058065	-12.357378	19.386751	9	146	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168103121	168103121	18011	2	G	A	A	A	429	33	XIRP2	2	2
MAP1D	254042	broad.mit.edu	37	2	172945095	172945095	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:172945095G>T	uc002uhk.2	+	c.969G>T	c.(967-969)AGG>AGT	p.R323S	MAP1D_uc010zdw.1_Missense_Mutation_p.R205S	NM_199227	NP_954697	Q6UB28	AMP1D_HUMAN	methionine aminopeptidase 1D precursor	323					N-terminal protein amino acid modification|peptidyl-methionine modification|proteolysis	mitochondrion	aminopeptidase activity|metal ion binding|metalloexopeptidase activity				0			OV - Ovarian serous cystadenocarcinoma(117;0.216)											0.395604	100.59916	101.457412	36	55	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	172945095	172945095	9612	2	G	T	T	T	555	43	MAP1D	2	2
TTN	7273	broad.mit.edu	37	2	179594622	179594622	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:179594622C>T	uc010zfg.1	-	c.14626G>A	c.(14626-14628)GGA>AGA	p.G4876R	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.G1537R	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	1855										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			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)							8722				0.125	10.420356	20.320097	9	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179594622	179594622	17290	2	C	T	T	T	273	21	TTN	2	2
MDH1B	130752	broad.mit.edu	37	2	207615683	207615683	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:207615683G>T	uc002vbs.2	-	c.1027C>A	c.(1027-1029)CCT>ACT	p.P343T	MDH1B_uc010ziw.1_Intron|MDH1B_uc010fui.2_Missense_Mutation_p.P343T|MDH1B_uc010fuj.2_Missense_Mutation_p.P245T|MDH1B_uc002vbt.2_Intron	NM_001039845	NP_001034934	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	343					carbohydrate metabolic process|malate metabolic process|tricarboxylic acid cycle		binding|malate dehydrogenase activity			ovary(3)|kidney(1)	4				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		Pancreas(76;29 1355 28675 37177 51207)								0.069444	-3.284052	10.504936	5	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	207615683	207615683	9798	2	G	T	T	T	559	43	MDH1B	2	2
FAM119A	151194	broad.mit.edu	37	2	208478080	208478080	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:208478080G>C	uc002vcf.2	-	c.347C>G	c.(346-348)ACT>AGT	p.T116S	FAM119A_uc002vce.2_Intron|FAM119A_uc010fuk.1_Missense_Mutation_p.T116S|FAM119A_uc002vcg.3_Missense_Mutation_p.T116S	NM_145280	NP_660323	Q8WXB1	MT21A_HUMAN	hypothetical protein LOC151194	116						integral to membrane	methyltransferase activity				0				LUSC - Lung squamous cell carcinoma(261;0.0705)|Epithelial(149;0.131)|Lung(261;0.135)						1				0.368421	68.160907	69.028036	21	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	208478080	208478080	5610	2	G	C	C	C	468	36	FAM119A	3	3
CPS1	1373	broad.mit.edu	37	2	211464237	211464237	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:211464237C>A	uc010fur.2	+	c.1519C>A	c.(1519-1521)CCA>ACA	p.P507T	CPS1_uc002vee.3_Missense_Mutation_p.P501T|CPS1_uc010fus.2_Missense_Mutation_p.P50T	NM_001122633	NP_001116105	P31327	CPSM_HUMAN	carbamoyl-phosphate synthetase 1 isoform a	501					carbamoyl phosphate biosynthetic process|citrulline biosynthetic process|glutamine metabolic process|glycogen catabolic process|nitric oxide metabolic process|positive regulation of vasodilation|response to lipopolysaccharide|triglyceride catabolic process|urea cycle	mitochondrial nucleoid	ATP binding|carbamoyl-phosphate synthase (ammonia) activity			ovary(8)|central_nervous_system(3)|breast(1)	12				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)										0.136364	21.764165	35.838132	15	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	211464237	211464237	3961	2	C	A	A	A	338	26	CPS1	2	2
FARSB	10056	broad.mit.edu	37	2	223507723	223507723	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:223507723G>A	uc010zlq.1	-	c.176C>T	c.(175-177)ACA>ATA	p.T59I	FARSB_uc002vne.1_Missense_Mutation_p.T39I|FARSB_uc002vnf.1_5'UTR	NM_005687	NP_005678	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	39					phenylalanyl-tRNA aminoacylation	cytosol|soluble fraction	ATP binding|magnesium ion binding|phenylalanine-tRNA ligase activity|RNA binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)									0.272727	13.657747	14.671862	6	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	223507723	223507723	5916	2	G	A	A	A	624	48	FARSB	2	2
SERPINE2	5270	broad.mit.edu	37	2	224866446	224866446	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:224866446T>A	uc010zlr.1	-	c.208A>T	c.(208-210)ATT>TTT	p.I70F	SERPINE2_uc002vnt.2_Missense_Mutation_p.I58F|SERPINE2_uc002vnu.2_Missense_Mutation_p.I58F|SERPINE2_uc002vnv.2_Missense_Mutation_p.I58F	NM_001136530	NP_001130002	P07093	GDN_HUMAN	plasminogen activator inhibitor type 1, member 2	58					negative regulation of blood coagulation|negative regulation of plasminogen activation|negative regulation of platelet aggregation|positive regulation of astrocyte differentiation|regulation of cell migration	cytosol|extracellular matrix|extracellular space|extrinsic to external side of plasma membrane|neuromuscular junction|platelet alpha granule	heparin binding|receptor binding|serine-type endopeptidase inhibitor activity			breast(2)|ovary(1)|central_nervous_system(1)	4		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)										0.098361	8.530138	28.203176	12	110	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	224866446	224866446	14600	2	T	A	A	A	650	50	SERPINE2	3	3
SPHKAP	80309	broad.mit.edu	37	2	228881213	228881213	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:228881213G>A	uc002vpq.2	-	c.4357C>T	c.(4357-4359)CTA>TTA	p.L1453L	SPHKAP_uc002vpp.2_Silent_p.L1453L|SPHKAP_uc010zlx.1_Silent_p.L1453L	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1453						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)										0.169811	19.474698	24.916358	9	44	KEEP	---	---	---	---	capture		Silent	SNP	228881213	228881213	15560	2	G	A	A	A	451	35	SPHKAP	2	2
SP100	6672	broad.mit.edu	37	2	231338154	231338154	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:231338154G>C	uc002vqu.1	+	c.1545G>C	c.(1543-1545)ATG>ATC	p.M515I	SP100_uc002vqs.2_Missense_Mutation_p.M515I|SP100_uc002vqt.2_Missense_Mutation_p.M515I	NM_001080391	NP_001073860	P23497	SP100_HUMAN	nuclear antigen Sp100 isoform 1	515					DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|negative regulation of cellular component movement|negative regulation of DNA binding|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|negative regulation of viral transcription|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|positive regulation of transcription, DNA-dependent|response to cytokine stimulus|response to retinoic acid|response to type I interferon|retinoic acid receptor signaling pathway|type I interferon-mediated signaling pathway	cytoplasm|nuclear periphery|nucleolus|PML body	chromo shadow domain binding|DNA binding|general transcriptional repressor activity|identical protein binding|kinase binding|protein homodimerization activity|transcription coactivator activity|transcription corepressor activity|transcription factor binding			ovary(4)|central_nervous_system(1)	5		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)										0.20603	88.555174	104.51265	41	158	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	231338154	231338154	15460	2	G	C	C	C	611	47	SP100	3	3
CIB4	130106	broad.mit.edu	37	2	26852375	26852375	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:26852375C>T	uc002rhm.2	-	c.90_splice	c.e3-1	p.C30_splice		NM_001029881	NP_001025052			calcium and integrin binding family member 4								calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.285714	6.047042	6.335492	2	5	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	26852375	26852375	3557	2	C	T	T	T	364	28	CIB4	5	2
GCKR	2646	broad.mit.edu	37	2	27746241	27746241	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:27746241C>A	uc002rky.2	+	c.1813C>A	c.(1813-1815)CTT>ATT	p.L605I	GCKR_uc010ezd.2_Missense_Mutation_p.L603I|GCKR_uc010ylu.1_Missense_Mutation_p.L415I	NM_001486	NP_001477	Q14397	GCKR_HUMAN	glucokinase regulatory protein	605					carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			ovary(2)	2	Acute lymphoblastic leukemia(172;0.155)													0.423077	57.11197	57.385265	22	30	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27746241	27746241	6560	2	C	A	A	A	416	32	GCKR	2	2
GALNT14	79623	broad.mit.edu	37	2	31178601	31178601	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:31178601C>T	uc002rns.2	-	c.552G>A	c.(550-552)CTG>CTA	p.L184L	GALNT14_uc002rnq.2_Silent_p.L159L|GALNT14_uc002rnr.2_Silent_p.L179L|GALNT14_uc010ymr.1_Silent_p.L144L|GALNT14_uc010ezo.1_Silent_p.L146L|GALNT14_uc010ezp.1_Silent_p.L150L	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	N-acetylgalactosaminyltransferase 14	179	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	Acute lymphoblastic leukemia(172;0.155)													0.170732	53.590304	70.422679	28	136	KEEP	---	---	---	---	capture		Silent	SNP	31178601	31178601	6476	2	C	T	T	T	262	21	GALNT14	2	2
PRKD3	23683	broad.mit.edu	37	2	37516516	37516516	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:37516516C>A	uc002rqd.2	-	c.700G>T	c.(700-702)GCC>TCC	p.A234S	PRKD3_uc002rqf.1_Missense_Mutation_p.A234S	NM_005813	NP_005804	O94806	KPCD3_HUMAN	protein kinase D3	234					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|protein phosphorylation	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_hematologic(82;0.21)				Melanoma(80;621 1355 8613 11814 51767)				569				0.050633	-9.169511	7.740584	4	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37516516	37516516	12963	2	C	A	A	A	364	28	PRKD3	2	2
MAP4K3	8491	broad.mit.edu	37	2	39514070	39514070	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:39514070G>A	uc002rro.2	-	c.1510C>T	c.(1510-1512)CGA>TGA	p.R504*	MAP4K3_uc002rrp.2_Nonsense_Mutation_p.R483*|MAP4K3_uc010yns.1_Nonsense_Mutation_p.R57*	NM_003618	NP_003609	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase	504					JNK cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity|small GTPase regulator activity			ovary(3)|lung(3)|pancreas(1)	7		all_hematologic(82;0.211)								525				0.122449	8.916314	15.753063	6	43	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	39514070	39514070	9644	2	G	A	A	A	519	40	MAP4K3	5	1
SOX11	6664	broad.mit.edu	37	2	5833048	5833048	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:5833048G>A	uc002qyj.2	+	c.195G>A	c.(193-195)AGG>AGA	p.R65R		NM_003108	NP_003099	P35716	SOX11_HUMAN	SRY-box 11	65	HMG box.					cytoplasm|nucleolus	DNA binding|translation factor activity, nucleic acid binding			central_nervous_system(3)	3	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			OV - Ovarian serous cystadenocarcinoma(76;0.132)						14				0.185185	10.366853	12.869959	5	22	KEEP	---	---	---	---	capture		Silent	SNP	5833048	5833048	15442	2	G	A	A	A	529	41	SOX11	2	2
AFTPH	54812	broad.mit.edu	37	2	64800103	64800103	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:64800103A>G	uc002sdc.2	+	c.2295A>G	c.(2293-2295)GAA>GAG	p.E765E	AFTPH_uc002scz.2_Silent_p.E765E|AFTPH_uc002sda.2_Silent_p.E765E|AFTPH_uc002sdb.2_Silent_p.E765E	NM_203437	NP_982261	Q6ULP2	AFTIN_HUMAN	aftiphilin protein isoform a	765					protein transport	AP-1 adaptor complex|cytosol|nucleus	clathrin binding			ovary(2)	2														0.041916	-43.130582	32.153906	14	320	KEEP	---	---	---	---	capture		Silent	SNP	64800103	64800103	365	2	A	G	G	G	24	2	AFTPH	4	4
ANXA4	307	broad.mit.edu	37	2	70043264	70043264	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:70043264G>A	uc002sfr.3	+	c.566G>A	c.(565-567)GGG>GAG	p.G189E	ANXA4_uc010yqn.1_Non-coding_Transcript|ANXA4_uc002sfs.3_Missense_Mutation_p.G167E|ANXA4_uc010yqo.1_Missense_Mutation_p.G105E	NM_001153	NP_001144	P09525	ANXA4_HUMAN	annexin IV	187	Annexin 3.				anti-apoptosis|signal transduction	cytoplasm	calcium ion binding|calcium-dependent phospholipid binding|phospholipase inhibitor activity				0														0.098901	6.002702	20.648513	9	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70043264	70043264	728	2	G	A	A	A	559	43	ANXA4	2	2
SFTPB	6439	broad.mit.edu	37	2	85892885	85892885	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:85892885C>A	uc002sqi.2	-	c.462G>T	c.(460-462)CTG>CTT	p.L154L	SFTPB_uc002sqh.2_Silent_p.L142L|SFTPB_uc002sqj.2_Silent_p.L142L	NM_198843	NP_942140	P07988	PSPB_HUMAN	surfactant, pulmonary-associated protein B	142	Saposin B-type 1.				organ morphogenesis|respiratory gaseous exchange|sphingolipid metabolic process	extracellular space|lysosome				ovary(1)|central_nervous_system(1)	2														0.228571	20.48216	22.846981	8	27	KEEP	---	---	---	---	capture		Silent	SNP	85892885	85892885	14682	2	C	A	A	A	210	17	SFTPB	2	2
RNF103	7844	broad.mit.edu	37	2	86847581	86847582	+	Nonsense_Mutation	DNP	CC	AA	AA			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:86847581_86847582CC>AA	uc002srn.2	-	c.237_238GG>TT	c.(235-240)ATGGAG>ATTTAG	p.79_80ME>I*	VPS24_uc010ytl.1_Nonsense_Mutation_p.1_2ME>I*|RNF103_uc002srp.2_Nonsense_Mutation_p.79_80ME>I*	NM_005667	NP_005658	O00237	RN103_HUMAN	ring finger protein 103	79_80					central nervous system development|ER-associated protein catabolic process	endoplasmic reticulum membrane|integral to membrane	protein binding|ubiquitin-protein ligase activity|zinc ion binding			central_nervous_system(1)	1														0.195122	17.576708	21.130152	8	33	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	86847581	86847582	13900	2	CC	AA	AA	AA	390	30	RNF103	5	2
CNNM4	26504	broad.mit.edu	37	2	97474331	97474331	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:97474331G>T	uc002swx.2	+	c.1982G>T	c.(1981-1983)CGC>CTC	p.R661L	CNNM4_uc010yuy.1_Missense_Mutation_p.R148L	NM_020184	NP_064569	Q6P4Q7	CNNM4_HUMAN	cyclin M4	661					biomineral tissue development|ion transport|response to stimulus|visual perception	integral to membrane|plasma membrane				breast(2)|ovary(1)	3														0.333333	31.063136	31.961354	12	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97474331	97474331	3753	2	G	T	T	T	494	38	CNNM4	1	1
TBC1D23	55773	broad.mit.edu	37	3	100014011	100014011	+	Silent	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:100014011A>T	uc003dtt.2	+	c.681A>T	c.(679-681)CCA>CCT	p.P227P	TBC1D23_uc003dts.2_Silent_p.P227P	NM_018309	NP_060779	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	227						intracellular	Rab GTPase activator activity			ovary(1)|liver(1)	2														0.3	43.40501	45.192227	15	35	KEEP	---	---	---	---	capture		Silent	SNP	100014011	100014011	16135	3	A	T	T	T	93	8	TBC1D23	3	3
ATP2B2	491	broad.mit.edu	37	3	10417176	10417176	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:10417176C>T	uc003bvt.2	-	c.1354G>A	c.(1354-1356)GTG>ATG	p.V452M	ATP2B2_uc003bvv.2_Missense_Mutation_p.V407M|ATP2B2_uc003bvw.2_Missense_Mutation_p.V407M|ATP2B2_uc010hdo.2_Missense_Mutation_p.V157M	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	452	Helical; (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|central_nervous_system(1)	4						Ovarian(125;1619 1709 15675 19819 38835)								0.583333	19.207174	19.277007	7	5	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10417176	10417176	1159	3	C	T	T	T	234	18	ATP2B2	2	2
MYH15	22989	broad.mit.edu	37	3	108220687	108220688	+	Nonsense_Mutation	DNP	CC	AA	AA			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:108220687_108220688CC>AA	uc003dxa.1	-	c.270_271GG>TT	c.(268-273)AAGGAG>AATTAG	p.90_91KE>N*		NM_014981	NP_055796	Q9Y2K3	MYH15_HUMAN	myosin, heavy polypeptide 15	90_91	Myosin head-like.					myofibril|myosin filament	actin binding|ATP binding|calmodulin binding|motor activity			ovary(5)|central_nervous_system(2)	7														0.165217	74.945094	99.376225	38	192	KEEP	---	---	---	---	capture		Nonsense_Mutation	DNP	108220687	108220688	10429	3	CC	AA	AA	AA	390	30	MYH15	5	2
ADPRH	141	broad.mit.edu	37	3	119301158	119301158	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:119301158G>T	uc003ecs.2	+	c.142G>T	c.(142-144)GTG>TTG	p.V48L	ADPRH_uc010hqv.2_Missense_Mutation_p.V48L|ADPRH_uc011bjb.1_Intron|ADPRH_uc003ect.2_Missense_Mutation_p.V48L	NM_001125	NP_001116	P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	48					protein de-ADP-ribosylation		ADP-ribosylarginine hydrolase activity|magnesium ion binding			ovary(1)	1		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		GBM(133;579 1804 5989 9967 40052)								0.487805	63.697662	63.702905	20	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	119301158	119301158	332	3	G	T	T	T	520	40	ADPRH	1	1
ADCY5	111	broad.mit.edu	37	3	123166724	123166724	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:123166724C>T	uc003egh.1	-	c.669G>A	c.(667-669)TCG>TCA	p.S223S		NM_183357	NP_899200	O95622	ADCY5_HUMAN	adenylate cyclase 5	223					activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding			ovary(4)	4				GBM - Glioblastoma multiforme(114;0.0342)										0.214286	7.521774	8.573804	3	11	KEEP	---	---	---	---	capture		Silent	SNP	123166724	123166724	298	3	C	T	T	T	288	23	ADCY5	1	1
KALRN	8997	broad.mit.edu	37	3	123946896	123946896	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:123946896G>T	uc003ehg.2	+	c.127G>T	c.(127-129)GTG>TTG	p.V43L	KALRN_uc010hrv.1_Missense_Mutation_p.V43L|KALRN_uc003ehf.1_Missense_Mutation_p.V43L|KALRN_uc011bjy.1_Missense_Mutation_p.V43L	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	43	CRAL-TRIO.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)	5										1865				0.395455	265.29902	267.39626	87	133	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123946896	123946896	8279	3	G	T	T	T	572	44	KALRN	2	2
DZIP1L	199221	broad.mit.edu	37	3	137799408	137799408	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:137799408C>A	uc003erq.2	-	c.1288_splice	c.e10+1	p.E430_splice	DZIP1L_uc003err.1_Splice_Site_SNP_p.E430_splice	NM_173543	NP_775814			DAZ interacting protein 1-like							intracellular	zinc ion binding			ovary(1)|pancreas(1)	2														0.222222	31.878132	36.31083	14	49	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	137799408	137799408	5050	3	C	A	A	A	234	18	DZIP1L	5	2
GPR87	53836	broad.mit.edu	37	3	151012910	151012910	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:151012910T>A	uc003eyt.2	-	c.124A>T	c.(124-126)ACA>TCA	p.T42S	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_023915	NP_076404	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	42	Extracellular (Potential).					integral to membrane|plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			large_intestine(1)	1			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)							39				0.102041	8.978021	24.453176	10	88	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151012910	151012910	6991	3	T	A	A	A	767	59	GPR87	3	3
SI	6476	broad.mit.edu	37	3	164758884	164758884	+	Splice_Site_SNP	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:164758884T>A	uc003fei.2	-	c.2005_splice	c.e18-1	p.H669_splice		NM_001041	NP_001032			sucrase-isomaltase						carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|pancreas(1)	8		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)									0.469388	307.590567	307.750021	92	104	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	164758884	164758884	14792	3	T	A	A	A	715	55	SI	5	3
NAALADL2	254827	broad.mit.edu	37	3	175520847	175520847	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:175520847G>T	uc003fit.2	+	c.2244G>T	c.(2242-2244)GAG>GAT	p.E748D		NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	748	Extracellular (Potential).				proteolysis	integral to membrane	peptidase activity			pancreas(1)	1	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)										0.285714	37.029467	39.048759	14	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	175520847	175520847	10525	3	G	T	T	T	451	35	NAALADL2	2	2
SATB1	6304	broad.mit.edu	37	3	18390907	18390907	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:18390907C>A	uc003cbi.2	-	c.2143G>T	c.(2143-2145)GAC>TAC	p.D715Y	SATB1_uc003cbh.2_Missense_Mutation_p.D683Y|SATB1_uc003cbj.2_Missense_Mutation_p.D683Y	NM_002971	NP_002962	Q01826	SATB1_HUMAN	special AT-rich sequence binding protein 1	683	Homeobox.				cellular component disassembly involved in apoptosis|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter	nuclear matrix|PML body	double-stranded DNA binding|sequence-specific DNA binding			ovary(1)|lung(1)|skin(1)	3														0.073333	-2.844691	25.186362	11	139	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18390907	18390907	14334	3	C	A	A	A	403	31	SATB1	1	1
ATP13A3	79572	broad.mit.edu	37	3	194175080	194175080	+	Silent	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:194175080T>A	uc003fty.3	-	c.672A>T	c.(670-672)ATA>ATT	p.I224I	ATP13A3_uc003ftz.1_5'Flank	NM_024524	NP_078800	Q9H7F0	AT133_HUMAN	ATPase type 13A3	224	Helical; (Potential).				ATP biosynthetic process|cation transport	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|metal ion binding			ovary(1)	1	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)										0.275	29.910196	31.732258	11	29	KEEP	---	---	---	---	capture		Silent	SNP	194175080	194175080	1144	3	T	A	A	A	732	57	ATP13A3	3	3
NEK10	152110	broad.mit.edu	37	3	27387648	27387648	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:27387648G>A	uc003cdt.1	-	c.192C>T	c.(190-192)ATC>ATT	p.I64I		NM_199347	NP_955379	Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10 isoform 3	64					protein phosphorylation		ATP binding|metal ion binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(5)|lung(2)|central_nervous_system(2)|pancreas(1)|skin(1)	11										332				0.163043	26.165604	36.096488	15	77	KEEP	---	---	---	---	capture		Silent	SNP	27387648	27387648	10721	3	G	A	A	A	577	45	NEK10	2	2
SCN10A	6336	broad.mit.edu	37	3	38770317	38770317	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:38770317C>A	uc003ciq.2	-	c.2356G>T	c.(2356-2358)GCA>TCA	p.A786S		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha	786	II.				sensory perception	voltage-gated sodium channel complex				ovary(5)|large_intestine(1)|kidney(1)|skin(1)	8				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)									0.197674	30.194223	37.56865	17	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38770317	38770317	14394	3	C	A	A	A	338	26	SCN10A	2	2
SETD2	29072	broad.mit.edu	37	3	47098503	47098503	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:47098503C>T	uc003cqv.2	-	c.6972G>A	c.(6970-6972)TTG>TTA	p.L2324L	SETD2_uc003cqs.2_Silent_p.L2257L|SETD2_uc003cqt.1_Intron	NM_014159	NP_054878	Q9BYW2	SETD2_HUMAN	SET domain containing 2	2257	Low charge region.				oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	DNA binding|histone-lysine N-methyltransferase activity|oxidoreductase activity|transition metal ion binding			kidney(24)|ovary(5)|skin(1)|central_nervous_system(1)|breast(1)	32		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)										0.217391	10.961973	12.656328	5	18	KEEP	---	---	---	---	capture		Silent	SNP	47098503	47098503	14620	3	C	T	T	T	324	25	SETD2	2	2
VPRBP	9730	broad.mit.edu	37	3	51477789	51477789	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:51477789G>T	uc003dbe.1	-	c.506C>A	c.(505-507)TCA>TAA	p.S169*	VPRBP_uc003dbg.1_Nonsense_Mutation_p.S169*	NM_014703	NP_055518	Q9Y4B6	VPRBP_HUMAN	HIV-1 Vpr binding protein	169					interspecies interaction between organisms	cytoplasm|nucleus	protein binding			ovary(1)|skin(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)										0.24	15.737515	17.279915	6	19	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	51477789	51477789	17752	3	G	T	T	T	585	45	VPRBP	5	2
DNAH1	25981	broad.mit.edu	37	3	52433737	52433737	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52433737C>T	uc011bef.1	+	c.12618C>T	c.(12616-12618)CGC>CGT	p.R4206R	DNAH1_uc003ddv.2_Missense_Mutation_p.A1039V	NM_015512	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	4271					ciliary or flagellar motility|microtubule-based movement|response to mechanical stimulus	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			large_intestine(3)	3				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)										0.30303	26.136198	27.279737	10	23	KEEP	---	---	---	---	capture		Silent	SNP	52433737	52433737	4779	3	C	T	T	T	314	25	DNAH1	2	2
ITIH3	3699	broad.mit.edu	37	3	52840934	52840934	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:52840934C>T	uc003dfv.2	+	c.2074C>T	c.(2074-2076)CAG>TAG	p.Q692*	ITIH3_uc011bek.1_Intron	NM_002217	NP_002208	Q06033	ITIH3_HUMAN	inter-alpha (globulin) inhibitor H3	692					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)										0.5	10.597635	10.597635	4	4	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	52840934	52840934	8209	3	C	T	T	T	325	25	ITIH3	5	2
MAGI1	9223	broad.mit.edu	37	3	65479268	65479268	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:65479268C>T	uc003dmn.2	-	c.469G>A	c.(469-471)GTG>ATG	p.V157M	MAGI1_uc003dmm.2_Missense_Mutation_p.V157M|MAGI1_uc003dmo.2_Missense_Mutation_p.V157M|MAGI1_uc003dmp.2_Missense_Mutation_p.V157M|MAGI1_uc010hny.2_Missense_Mutation_p.V41M|MAGI1_uc003dmr.2_Missense_Mutation_p.V157M	NM_001033057	NP_001028229	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ	157	Guanylate kinase-like.				cell adhesion|cell surface receptor linked signaling pathway|protein complex assembly	tight junction	ATP binding|protein C-terminus binding			kidney(1)|pancreas(1)	2		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)										0.078947	0.097855	6.975501	3	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65479268	65479268	9573	3	C	T	T	T	247	19	MAGI1	1	1
ZNF654	55279	broad.mit.edu	37	3	88188579	88188579	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:88188579T>C	uc003dqv.2	+	c.119T>C	c.(118-120)ATG>ACG	p.M40T	CGGBP1_uc003dqu.2_Intron	NM_018293	NP_060763	Q8IZM8	ZN654_HUMAN	zinc finger protein 654	40	C2H2-type 1.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Lung NSC(201;0.0283)		UCEC - Uterine corpus endometrioid carcinoma (27;0.194)|LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00661)										0.139535	17.640311	28.439299	12	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88188579	88188579	18662	3	T	C	C	C	663	51	ZNF654	4	4
IL17RC	84818	broad.mit.edu	37	3	9959148	9959148	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:9959148A>T	uc003bua.2	+	c.149A>T	c.(148-150)CAG>CTG	p.Q50L	CIDEC_uc003bto.2_Intron|IL17RC_uc010hcr.2_Intron|IL17RC_uc011ato.1_Intron|IL17RC_uc010hcs.2_Intron|IL17RC_uc003btz.2_Intron|IL17RC_uc011atp.1_Intron|IL17RC_uc003bud.2_Intron|IL17RC_uc003bub.2_Intron|IL17RC_uc010hct.2_Intron|IL17RC_uc010hcu.2_Intron|IL17RC_uc010hcv.2_Intron|IL17RC_uc011atq.1_Intron|IL17RC_uc003buc.2_Intron	NM_153461	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C isoform 1 precursor	50	Extracellular (Potential).					integral to membrane|plasma membrane	receptor activity			ovary(1)|pancreas(1)	2														0.192308	11.867465	14.160272	5	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	9959148	9959148	7942	3	A	T	T	T	91	7	IL17RC	3	3
NPNT	255743	broad.mit.edu	37	4	106888393	106888393	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:106888393C>T	uc011cfd.1	+	c.1484C>T	c.(1483-1485)GCT>GTT	p.A495V	NPNT_uc003hya.2_Missense_Mutation_p.A465V|NPNT_uc011cfc.1_Missense_Mutation_p.A482V|NPNT_uc011cfe.1_Missense_Mutation_p.A466V|NPNT_uc010ilt.1_Missense_Mutation_p.A436V|NPNT_uc011cff.1_Missense_Mutation_p.A436V|NPNT_uc010ilu.1_Intron	NM_001033047	NP_001028219	Q6UXI9	NPNT_HUMAN	nephronectin precursor	465	MAM.				cell differentiation	membrane	calcium ion binding				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)										0.513514	55.593858	55.59891	19	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	106888393	106888393	10995	4	C	T	T	T	364	28	NPNT	2	2
DKK2	27123	broad.mit.edu	37	4	107956733	107956733	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:107956733G>T	uc003hyi.2	-	c.16C>A	c.(16-18)CGG>AGG	p.R6R	DKK2_uc010ilw.1_Intron|DKK2_uc003hyj.1_Silent_p.R6R	NM_014421	NP_055236	Q9UBU2	DKK2_HUMAN	dickkopf homolog 2 precursor	6					multicellular organismal development|negative regulation of canonical Wnt receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|Wnt receptor signaling pathway	extracellular space				ovary(3)|lung(1)|skin(1)	5		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)										0.162791	26.497192	35.791255	14	72	KEEP	---	---	---	---	capture		Silent	SNP	107956733	107956733	4725	4	G	T	T	T	493	38	DKK2	1	1
ALPK1	80216	broad.mit.edu	37	4	113303646	113303646	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:113303646G>T	uc003iap.3	+	c.214G>T	c.(214-216)GTG>TTG	p.V72L	ALPK1_uc003iam.2_Missense_Mutation_p.V72L|ALPK1_uc011cfw.1_Non-coding_Transcript|ALPK1_uc003ian.3_Missense_Mutation_p.V72L|ALPK1_uc011cfx.1_Intron|ALPK1_uc003iao.3_Non-coding_Transcript|ALPK1_uc003iaq.2_Missense_Mutation_p.V16L|ALPK1_uc010imo.2_5'UTR	NM_025144	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	72					protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)						252				0.389831	70.841603	71.458318	23	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	113303646	113303646	547	4	G	T	T	T	520	40	ALPK1	1	1
SYNPO2	171024	broad.mit.edu	37	4	119951385	119951385	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:119951385A>G	uc010inb.2	+	c.1455A>G	c.(1453-1455)CCA>CCG	p.P485P	SYNPO2_uc010ina.2_Silent_p.P485P|SYNPO2_uc003icm.3_Silent_p.P485P|SYNPO2_uc011cgh.1_Intron|SYNPO2_uc010inc.2_Silent_p.P413P	NM_133477	NP_597734	Q9UMS6	SYNP2_HUMAN	synaptopodin 2 isoform a	485						nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			ovary(2)	2														0.196078	19.845941	24.350805	10	41	KEEP	---	---	---	---	capture		Silent	SNP	119951385	119951385	15978	4	A	G	G	G	80	7	SYNPO2	4	4
USP53	54532	broad.mit.edu	37	4	120213653	120213653	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:120213653G>A	uc003ics.3	+	c.2509G>A	c.(2509-2511)GAG>AAG	p.E837K	USP53_uc003icr.3_Missense_Mutation_p.E837K|USP53_uc003icu.3_Missense_Mutation_p.E460K	NM_019050	NP_061923	Q70EK8	UBP53_HUMAN	ubiquitin specific protease 53	837					ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			ovary(1)|breast(1)|kidney(1)	3														0.168675	26.895194	35.526247	14	69	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	120213653	120213653	17648	4	G	A	A	A	585	45	USP53	2	2
TRPC3	7222	broad.mit.edu	37	4	122853688	122853688	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:122853688T>A	uc003ieg.2	-	c.725A>T	c.(724-726)CAC>CTC	p.H242L	TRPC3_uc010inr.2_Missense_Mutation_p.H169L|TRPC3_uc003ief.2_Missense_Mutation_p.H169L|TRPC3_uc011cgl.1_5'UTR	NM_001130698	NP_001124170	Q13507	TRPC3_HUMAN	transient receptor potential cation channel,	157	Cytoplasmic (Potential).|ANK 4.				axon guidance|phototransduction|platelet activation	integral to plasma membrane	protein binding|store-operated calcium channel activity			ovary(2)	2														0.147059	18.018411	26.144619	10	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	122853688	122853688	17130	4	T	A	A	A	767	59	TRPC3	3	3
KIAA1530	57654	broad.mit.edu	37	4	1345538	1345538	+	Silent	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:1345538A>T	uc003gde.3	+	c.465A>T	c.(463-465)GCA>GCT	p.A155A		NM_020894	NP_065945	Q2YD98	K1530_HUMAN	hypothetical protein LOC57654	155											0			OV - Ovarian serous cystadenocarcinoma(23;0.0138)									OREG0016033	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.428571	19.7484	19.810587	6	8	KEEP	---	---	---	---	capture		Silent	SNP	1345538	1345538	8550	4	A	T	T	T	80	7	KIAA1530	3	3
PCDH18	54510	broad.mit.edu	37	4	138451915	138451915	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:138451915G>T	uc003ihe.3	-	c.1328C>A	c.(1327-1329)CCC>CAC	p.P443H	PCDH18_uc003ihf.3_Missense_Mutation_p.P436H|PCDH18_uc011cgz.1_Intron|PCDH18_uc003ihg.3_Missense_Mutation_p.P223H|PCDH18_uc011cha.1_Intron	NM_019035	NP_061908	Q9HCL0	PCD18_HUMAN	protocadherin 18 precursor	443	Cadherin 4.|Extracellular (Potential).				brain development|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			pancreas(3)	3	all_hematologic(180;0.24)													0.212121	64.938687	75.04307	28	104	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	138451915	138451915	11933	4	G	T	T	T	559	43	PCDH18	2	2
RNF150	57484	broad.mit.edu	37	4	141789440	141789440	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:141789440T>G	uc003iio.1	-	c.1292A>C	c.(1291-1293)CAG>CCG	p.Q431P	RNF150_uc010iok.1_Missense_Mutation_p.Q389P	NM_020724	NP_065775	Q9ULK6	RN150_HUMAN	ring finger protein 150 precursor	431	Cytoplasmic (Potential).					integral to membrane	zinc ion binding			ovary(1)	1	all_hematologic(180;0.162)													0.2	19.649508	23.41654	9	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141789440	141789440	13928	4	T	G	G	G	715	55	RNF150	4	4
FNIP2	57600	broad.mit.edu	37	4	159791535	159791535	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:159791535T>C	uc003iqe.3	+	c.2863T>C	c.(2863-2865)TAC>CAC	p.Y955H		NM_020840	NP_065891	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	955					DNA damage response, signal transduction resulting in induction of apoptosis|protein phosphorylation|regulation of protein phosphorylation	cytoplasm	protein binding				0	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)										0.276923	53.536122	56.438619	18	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159791535	159791535	6218	4	T	C	C	C	637	49	FNIP2	4	4
TRIM60	166655	broad.mit.edu	37	4	165961707	165961707	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:165961707G>A	uc003iqy.1	+	c.483G>A	c.(481-483)GTG>GTA	p.V161V	TRIM60_uc010iqx.1_Silent_p.V161V	NM_152620	NP_689833	Q495X7	TRI60_HUMAN	ring finger protein 129	161						intracellular	zinc ion binding			skin(1)	1	all_hematologic(180;0.221)	Prostate(90;0.0959)|Melanoma(52;0.18)		GBM - Glioblastoma multiforme(119;0.0844)										0.4	29.244082	29.462988	10	15	KEEP	---	---	---	---	capture		Silent	SNP	165961707	165961707	17081	4	G	A	A	A	574	45	TRIM60	2	2
LDB2	9079	broad.mit.edu	37	4	16760835	16760835	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:16760835C>A	uc003goz.2	-	c.181G>T	c.(181-183)GAT>TAT	p.D61Y	LDB2_uc003gpa.2_Missense_Mutation_p.D61Y|LDB2_uc003gpb.2_Missense_Mutation_p.D61Y|LDB2_uc011bxh.1_Missense_Mutation_p.D61Y|LDB2_uc010iee.2_Missense_Mutation_p.D61Y	NM_001290	NP_001281	O43679	LDB2_HUMAN	LIM domain binding 2 isoform a	61							LIM domain binding|transcription cofactor activity				0														0.226415	52.738278	60.02959	24	82	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16760835	16760835	9020	4	C	A	A	A	416	32	LDB2	2	2
PALLD	23022	broad.mit.edu	37	4	169589483	169589483	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:169589483G>C	uc011cjx.1	+	c.1051G>C	c.(1051-1053)GGC>CGC	p.G351R	PALLD_uc003iru.2_Missense_Mutation_p.G351R|PALLD_uc003irv.2_5'UTR	NM_016081	NP_057165	Q8WX93	PALLD_HUMAN	palladin isoform 2	351	Ig-like C2-type 1.				cytoskeleton organization	actin filament|focal adhesion|lamellipodium|nucleus|ruffle|sarcomere	actin binding|muscle alpha-actinin binding			ovary(1)	1		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		Esophageal Squamous(109;1482 1532 18347 40239 51172)								0.333333	91.043871	93.478399	33	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169589483	169589483	11823	4	G	C	C	C	507	39	PALLD	3	3
WDR17	116966	broad.mit.edu	37	4	177041039	177041039	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:177041039G>A	uc003iuj.2	+	c.401G>A	c.(400-402)TGG>TAG	p.W134*	WDR17_uc003iuk.2_Nonsense_Mutation_p.W110*|WDR17_uc003ium.3_Nonsense_Mutation_p.W110*|WDR17_uc003iul.1_Intron	NM_170710	NP_733828	Q8IZU2	WDR17_HUMAN	WD repeat domain 17 isoform 1	134	WD 2.									ovary(2)|pancreas(1)	3		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)										0.186275	39.159482	48.571327	19	83	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	177041039	177041039	17850	4	G	A	A	A	611	47	WDR17	5	2
SEL1L3	23231	broad.mit.edu	37	4	25834645	25834645	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:25834645C>A	uc003gru.3	-	c.1070G>T	c.(1069-1071)CGA>CTA	p.R357L		NM_015187	NP_056002	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3	357						integral to membrane	binding				0														0.168224	35.487683	46.641418	18	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25834645	25834645	14498	4	C	A	A	A	403	31	SEL1L3	1	1
FAM193A	8603	broad.mit.edu	37	4	2701538	2701538	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:2701538G>T	uc010ick.2	+	c.3366G>T	c.(3364-3366)CAG>CAT	p.Q1122H	FAM193A_uc003gfd.2_Missense_Mutation_p.Q922H|FAM193A_uc011bvm.1_Missense_Mutation_p.Q944H|FAM193A_uc011bvn.1_Missense_Mutation_p.Q922H|FAM193A_uc010icl.2_Missense_Mutation_p.Q922H|FAM193A_uc011bvo.1_Non-coding_Transcript|FAM193A_uc010icm.2_Non-coding_Transcript|FAM193A_uc003gfe.2_Missense_Mutation_p.Q776H	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	922	Potential.									ovary(3)	3														0.469697	93.918745	93.971549	31	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	2701538	2701538	5735	4	G	T	T	T	438	34	FAM193A	2	2
TLR1	7096	broad.mit.edu	37	4	38799909	38799909	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:38799909C>A	uc003gtl.2	-	c.544G>T	c.(544-546)GAG>TAG	p.E182*		NM_003263	NP_003254	Q15399	TLR1_HUMAN	toll-like receptor 1 precursor	182	Extracellular (Potential).			E -> G (in Ref. 3; CAB43364).	cellular response to triacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|inflammatory response|innate immune response|macrophage activation|positive regulation of interleukin-6 biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	integral to plasma membrane|phagocytic vesicle membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	protein heterodimerization activity|transmembrane receptor activity				0						GBM(5;216 373 40795 46382)								0.40678	69.187397	69.635651	24	35	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	38799909	38799909	16479	4	C	A	A	A	377	29	TLR1	5	2
OTOP1	133060	broad.mit.edu	37	4	4199344	4199344	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:4199344C>A	uc003ghp.1	-	c.1217G>T	c.(1216-1218)TGG>TTG	p.W406L		NM_177998	NP_819056	Q7RTM1	OTOP1_HUMAN	otopetrin 1	406	Helical; (Potential).				biomineral tissue development	extracellular space|integral to membrane				ovary(2)	2				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)										0.25641	23.019571	25.12924	10	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4199344	4199344	11717	4	C	A	A	A	273	21	OTOP1	2	2
GABRG1	2565	broad.mit.edu	37	4	46053559	46053559	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46053559G>C	uc003gxb.2	-	c.1013C>G	c.(1012-1014)TCT>TGT	p.S338C		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	338	Helical; (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)										0.21831	80.200317	90.644798	31	111	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46053559	46053559	6422	4	G	C	C	C	429	33	GABRG1	3	3
COX7B2	170712	broad.mit.edu	37	4	46737033	46737033	+	Silent	SNP	A	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46737033A>C	uc003gxf.2	-	c.177T>G	c.(175-177)ACT>ACG	p.T59T	COX7B2_uc010ige.2_Non-coding_Transcript	NM_130902	NP_570972	Q8TF08	CX7B2_HUMAN	cytochrome c oxidase subunit VIIb2 precursor	59	Helical; (By similarity).					integral to membrane|mitochondrial respiratory chain	cytochrome-c oxidase activity				0														0.080247	0.136684	29.286502	13	149	KEEP	---	---	---	---	capture		Silent	SNP	46737033	46737033	3921	4	A	C	C	C	132	11	COX7B2	4	4
GABRB1	2560	broad.mit.edu	37	4	47322175	47322175	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:47322175C>G	uc003gxh.2	+	c.493C>G	c.(493-495)CTT>GTT	p.L165V	GABRB1_uc011bze.1_Missense_Mutation_p.L95V	NM_000812	NP_000803	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	165	Extracellular (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(2)	2					Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.364486	127.080444	128.814919	39	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47322175	47322175	6417	4	C	G	G	G	416	32	GABRB1	3	3
ATP10D	57205	broad.mit.edu	37	4	47560036	47560036	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:47560036G>T	uc003gxk.1	+	c.2180G>T	c.(2179-2181)AGC>ATC	p.S727I	ATP10D_uc003gxl.1_Intron	NM_020453	NP_065186	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	727	Cytoplasmic (Potential).				ATP biosynthetic process|cation transport	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(2)|pancreas(1)	3														0.396552	63.642593	64.17527	23	35	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47560036	47560036	1137	4	G	T	T	T	442	34	ATP10D	2	2
FIP1L1	81608	broad.mit.edu	37	4	54319108	54319108	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:54319108G>A	uc003gzy.2	+	c.1307G>A	c.(1306-1308)GGT>GAT	p.G436D	PDGFRA_uc003haa.2_Intron|FIP1L1_uc011bzu.1_Missense_Mutation_p.G430D|FIP1L1_uc003gzz.2_Missense_Mutation_p.G362D|FIP1L1_uc003hab.2_Missense_Mutation_p.G401D|FIP1L1_uc003hac.2_Missense_Mutation_p.G190D|FIP1L1_uc010ign.2_Non-coding_Transcript|FIP1L1_uc003had.2_Missense_Mutation_p.V21I|FIP1L1_uc003hae.2_Missense_Mutation_p.V21I	NM_030917	NP_112179	Q6UN15	FIP1_HUMAN	FIP1 like 1 isoform 1	436					mRNA processing	nucleus	RNA binding			ovary(1)|skin(1)	2			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)							17				0.232394	82.015506	91.318159	33	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54319108	54319108	6134	4	G	A	A	A	572	44	FIP1L1	2	2
PDGFRA	5156	broad.mit.edu	37	4	55141092	55141092	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:55141092C>A	uc003han.3	+	c.1738C>A	c.(1738-1740)CTG>ATG	p.L580M	PDGFRA_uc003haa.2_Missense_Mutation_p.L340M|PDGFRA_uc010igq.1_Missense_Mutation_p.L474M|PDGFRA_uc003ham.2_Non-coding_Transcript|PDGFRA_uc003hao.1_5'Flank	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	580	Cytoplasmic (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity	p.L580M(1)		soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.448276	77.640362	77.775865	26	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55141092	55141092	12082	4	C	A	A	A	363	28	PDGFRA	2	2
KIAA1211	57482	broad.mit.edu	37	4	57181645	57181645	+	Silent	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:57181645C>G	uc003hbk.2	+	c.1977C>G	c.(1975-1977)CCC>CCG	p.P659P	KIAA1211_uc010iha.2_Silent_p.P652P|KIAA1211_uc011bzz.1_Silent_p.P569P|KIAA1211_uc003hbm.1_Silent_p.P545P	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	659										ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)													0.278689	33.814144	36.529022	17	44	KEEP	---	---	---	---	capture		Silent	SNP	57181645	57181645	8523	4	C	G	G	G	262	21	KIAA1211	3	3
REST	5978	broad.mit.edu	37	4	57797251	57797251	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:57797251G>A	uc003hch.2	+	c.2227G>A	c.(2227-2229)GAG>AAG	p.E743K	REST_uc003hci.2_Missense_Mutation_p.E743K|REST_uc010ihf.2_Missense_Mutation_p.E417K	NM_005612	NP_005603	Q13127	REST_HUMAN	RE1-silencing transcription factor	743	Pro-rich.				transcription, DNA-dependent	cytoplasm|nucleus	transcription repressor activity|zinc ion binding			skin(2)|ovary(1)|lung(1)	4	Glioma(25;0.08)|all_neural(26;0.181)													0.091216	7.486274	57.344042	27	269	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	57797251	57797251	13704	4	G	A	A	A	533	41	REST	2	2
TECRL	253017	broad.mit.edu	37	4	65180447	65180447	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:65180447A>T	uc003hcv.2	-	c.470T>A	c.(469-471)ATA>AAA	p.I157K	TECRL_uc003hcw.2_Missense_Mutation_p.I157K	NM_001010874	NP_001010874	Q5HYJ1	TECRL_HUMAN	steroid 5 alpha-reductase 2-like 2	157	Helical; (Potential).				lipid metabolic process|oxidation-reduction process	cytoplasm|integral to membrane	oxidoreductase activity, acting on the CH-CH group of donors				0														0.209302	23.253577	26.614943	9	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	65180447	65180447	16273	4	A	T	T	T	208	16	TECRL	3	3
BMP2K	55589	broad.mit.edu	37	4	79766106	79766107	+	Missense_Mutation	DNP	GG	AT	AT			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:79766106_79766107GG>AT	uc003hlk.2	+	c.571_572GG>AT	c.(571-573)GGT>ATT	p.G191I	BMP2K_uc010ijl.1_Non-coding_Transcript|BMP2K_uc003hlj.2_Missense_Mutation_p.G191I	NM_198892	NP_942595	Q9NSY1	BMP2K_HUMAN	BMP-2 inducible kinase isoform a	191	Protein kinase.				protein phosphorylation	nucleus	ATP binding|protein serine/threonine kinase activity			lung(1)	1										318				0.162162	11.024733	15.04182	6	31	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	79766106	79766107	1485	4	GG	AT	AT	AT	611	47	BMP2K	2	2
FBN2	2201	broad.mit.edu	37	5	127670448	127670448	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:127670448C>A	uc003kuu.2	-	c.4062G>T	c.(4060-4062)CTG>CTT	p.L1354L	FBN2_uc003kuv.2_Silent_p.L1321L	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	1354	EGF-like 21; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)						1552				0.040404	-14.185935	8.337709	4	95	KEEP	---	---	---	---	capture		Silent	SNP	127670448	127670448	5939	5	C	A	A	A	262	21	FBN2	2	2
FBN2	2201	broad.mit.edu	37	5	127697428	127697428	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:127697428C>A	uc003kuu.2	-	c.2542G>T	c.(2542-2544)GAG>TAG	p.E848*	FBN2_uc003kuv.2_Nonsense_Mutation_p.E815*	NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	848	EGF-like 12; calcium-binding.				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)						1552				0.281553	73.226687	77.646822	29	74	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	127697428	127697428	5939	5	C	A	A	A	416	32	FBN2	5	2
SLC27A6	28965	broad.mit.edu	37	5	128320947	128320947	+	Silent	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:128320947T>A	uc003kuy.2	+	c.603T>A	c.(601-603)CCT>CCA	p.P201P	SLC27A6_uc003kuz.2_Silent_p.P201P	NM_014031	NP_054750	Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid	201					long-chain fatty acid transport|transmembrane transport|very long-chain fatty acid metabolic process	integral to membrane|sarcolemma	fatty acid transporter activity|long-chain fatty acid-CoA ligase activity|nucleotide binding				0		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)										0.111111	4.772543	10.156028	4	32	KEEP	---	---	---	---	capture		Silent	SNP	128320947	128320947	15027	5	T	A	A	A	704	55	SLC27A6	3	3
PCDHA3	56145	broad.mit.edu	37	5	140182233	140182233	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140182233C>A	uc003lhf.2	+	c.1451C>A	c.(1450-1452)GCG>GAG	p.A484E	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Missense_Mutation_p.A484E	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	484	Cadherin 5.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(5)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.55	68.14205	68.22819	22	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140182233	140182233	11945	5	C	A	A	A	351	27	PCDHA3	1	1
PCDHB8	56128	broad.mit.edu	37	5	140559700	140559701	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140559700_140559701GG>TT	uc011dai.1	+	c.2085_2086GG>TT	c.(2083-2088)TTGGCC>TTTTCC	p.695_696LA>FS	PCDHB16_uc003liv.2_5'Flank|PCDHB16_uc010jfw.1_5'Flank	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	protocadherin beta 8 precursor	695_696	Helical; (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.453488	119.201549	119.363497	39	47	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	140559700	140559701	11968	5	GG	TT	TT	TT	607	47	PCDHB8	2	2
PCDHB12	56124	broad.mit.edu	37	5	140590654	140590654	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:140590654C>T	uc003liz.2	+	c.2175C>T	c.(2173-2175)TGC>TGT	p.C725C	PCDHB12_uc011dak.1_Silent_p.C388C|PCDHB13_uc003lja.1_5'Flank	NM_018932	NP_061755	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12 precursor	725	Cytoplasmic (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.712329	167.61756	170.566633	52	21	KEEP	---	---	---	---	capture		Silent	SNP	140590654	140590654	11957	5	C	T	T	T	363	28	PCDHB12	2	2
LPCAT1	79888	broad.mit.edu	37	5	1474215	1474215	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:1474215C>A	uc003jcm.2	-	c.1036G>T	c.(1036-1038)GAA>TAA	p.E346*		NM_024830	NP_079106	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	346	Lumenal (Potential).				phospholipid biosynthetic process	endoplasmic reticulum membrane|Golgi membrane|integral to membrane	1-acylglycerophosphocholine O-acyltransferase activity|1-alkylglycerophosphocholine O-acetyltransferase activity|calcium ion binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)										0.130435	4.207863	7.264662	3	20	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	1474215	1474215	9283	5	C	A	A	A	416	32	LPCAT1	5	2
GLRA1	2741	broad.mit.edu	37	5	151271916	151271916	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:151271916C>A	uc003lut.2	-	c.140G>T	c.(139-141)GGG>GTG	p.G47V	GLRA1_uc003lur.2_Missense_Mutation_p.G47V|GLRA1_uc003lus.2_Intron	NM_001146040	NP_001139512	P23415	GLRA1_HUMAN	glycine receptor, alpha 1 isoform 1 precursor	47	Extracellular (Probable).				muscle contraction|negative regulation of transmission of nerve impulse|neuropeptide signaling pathway|positive regulation of acrosome reaction|regulation of membrane potential|startle response	cell junction|chloride channel complex|integral to plasma membrane|intracellular membrane-bounded organelle|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|glycine binding|protein binding|receptor activity|taurine binding|transmitter-gated ion channel activity			ovary(1)|central_nervous_system(1)	2		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)									0.252033	75.608926	82.451281	31	92	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151271916	151271916	6722	5	C	A	A	A	286	22	GLRA1	2	2
LARP1	23367	broad.mit.edu	37	5	154173195	154173195	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:154173195G>T	uc003lvp.2	+	c.780G>T	c.(778-780)AAG>AAT	p.K260N	LARP1_uc003lvo.2_Missense_Mutation_p.K183N|LARP1_uc010jie.1_Missense_Mutation_p.K55N	NM_033551	NP_291029	Q6PKG0	LARP1_HUMAN	la related protein isoform 2	260							protein binding|RNA binding			ovary(2)|pancreas(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)											0.065116	-12.306865	29.911754	14	201	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	154173195	154173195	8951	5	G	T	T	T	438	34	LARP1	2	2
DOCK2	1794	broad.mit.edu	37	5	169469081	169469081	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:169469081G>A	uc003maf.2	+	c.3821G>A	c.(3820-3822)CGG>CAG	p.R1274Q	DOCK2_uc011der.1_Non-coding_Transcript|DOCK2_uc010jjm.2_Missense_Mutation_p.R766Q	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1274	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)											0.090909	0.868459	8.29461	4	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	169469081	169469081	4871	5	G	A	A	A	507	39	DOCK2	1	1
FAM153A	285596	broad.mit.edu	37	5	177156557	177156557	+	Splice_Site_SNP	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:177156557C>A	uc010jkp.1	-	c.632_splice	c.e18-1	p.S211_splice	FAM153A_uc011dgd.1_Intron|FAM153A_uc003mib.1_Splice_Site_SNP|FAM153A_uc003mic.2_Splice_Site_SNP_p.S211_splice	NM_173663	NP_775934			hypothetical protein LOC285596												0	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.234043	52.500452	58.585989	22	72	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	177156557	177156557	5658	5	C	A	A	A	312	24	FAM153A	5	2
ZNF354B	117608	broad.mit.edu	37	5	178309722	178309722	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:178309722C>T	uc003mjl.2	+	c.269C>T	c.(268-270)ACA>ATA	p.T90I	ZNF354B_uc003mjm.2_Missense_Mutation_p.T90I	NM_058230	NP_478137	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	90					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.159574	26.363057	36.74168	15	79	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	178309722	178309722	18457	5	C	T	T	T	221	17	ZNF354B	2	2
RASGEF1C	255426	broad.mit.edu	37	5	179529113	179529113	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:179529113C>T	uc003mlq.2	-	c.1334G>A	c.(1333-1335)AGC>AAC	p.S445N	RASGEF1C_uc003mlr.2_Missense_Mutation_p.S445N|RASGEF1C_uc003mlp.3_Missense_Mutation_p.S294N	NM_175062	NP_778232	Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	445	Ras-GEF.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity			ovary(1)	1	all_cancers(89;3.44e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0242)|Medulloblastoma(196;0.00498)|all_neural(177;0.0137)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)											0.28125	24.961112	26.337416	9	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	179529113	179529113	13532	5	C	T	T	T	364	28	RASGEF1C	2	2
RXFP3	51289	broad.mit.edu	37	5	33937928	33937928	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:33937928G>T	uc003jic.1	+	c.1083G>T	c.(1081-1083)CAG>CAT	p.Q361H		NM_016568	NP_057652	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	361	Helical; Name=7; (Potential).					integral to plasma membrane	N-formyl peptide receptor activity				0														0.1	6.907926	21.292945	9	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	33937928	33937928	14241	5	G	T	T	T	451	35	RXFP3	2	2
CCL28	56477	broad.mit.edu	37	5	43381991	43381991	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:43381991C>A	uc003jnu.2	-	c.355G>T	c.(355-357)GAA>TAA	p.E119*	CCL28_uc003jns.2_Non-coding_Transcript|CCL28_uc003jnt.2_Non-coding_Transcript|CCL28_uc010ivn.2_Nonsense_Mutation_p.E72*	NM_148672	NP_683513	Q9NRJ3	CCL28_HUMAN	chemokine (C-C motif) ligand 28 precursor	119					chemotaxis|immune response	extracellular space	chemokine activity			ovary(1)|kidney(1)	2						Esophageal Squamous(178;1549 1997 2043 22794 27051)								0.130952	63.916134	108.378301	44	292	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	43381991	43381991	3025	5	C	A	A	A	403	31	CCL28	5	1
KIAA0947	23379	broad.mit.edu	37	5	5464978	5464978	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:5464978G>T	uc003jdm.3	+	c.5531G>T	c.(5530-5532)AGT>ATT	p.S1844I		NM_015325	NP_056140	Q9Y2F5	K0947_HUMAN	hypothetical protein LOC23379	1844										ovary(1)|central_nervous_system(1)	2														0.147541	12.510382	19.843174	9	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5464978	5464978	8509	5	G	T	T	T	468	36	KIAA0947	2	2
ADAMTS6	11174	broad.mit.edu	37	5	64587275	64587275	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:64587275C>A	uc003jtp.2	-	c.1393G>T	c.(1393-1395)GAT>TAT	p.D465Y	ADAMTS6_uc003jto.2_Non-coding_Transcript|ADAMTS6_uc003jtq.2_Non-coding_Transcript|ADAMTS6_uc003jtr.1_Missense_Mutation_p.D86Y	NM_197941	NP_922932	Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1	465	Peptidase M12B.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding				0		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)										0.085366	0.42742	14.854321	7	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64587275	64587275	271	5	C	A	A	A	377	29	ADAMTS6	2	2
GPR98	84059	broad.mit.edu	37	5	90079719	90079719	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:90079719C>A	uc003kju.2	+	c.13498C>A	c.(13498-13500)CAC>AAC	p.H4500N	GPR98_uc003kjt.2_Missense_Mutation_p.H2206N|GPR98_uc003kjw.2_Missense_Mutation_p.H161N	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	4500	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)										0.085714	0.896541	6.986974	3	32	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90079719	90079719	6997	5	C	A	A	A	273	21	GPR98	2	2
SEMA5A	9037	broad.mit.edu	37	5	9119214	9119214	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:9119214G>A	uc003jek.2	-	c.1821C>T	c.(1819-1821)TGC>TGT	p.C607C		NM_003966	NP_003957	Q13591	SEM5A_HUMAN	semaphorin 5A precursor	607	TSP type-1 2.|Extracellular (Potential).				cell adhesion|cell-cell signaling	integral to membrane|plasma membrane				ovary(1)|central_nervous_system(1)	2														0.25	9.091334	10.001164	4	12	KEEP	---	---	---	---	capture		Silent	SNP	9119214	9119214	14523	5	G	A	A	A	594	46	SEMA5A	2	2
HACE1	57531	broad.mit.edu	37	6	105192075	105192075	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:105192075G>A	uc003pqu.1	-	c.2473C>T	c.(2473-2475)CAA>TAA	p.Q825*	HACE1_uc010kcy.1_Nonsense_Mutation_p.Q307*|HACE1_uc010kcz.1_Nonsense_Mutation_p.Q610*|HACE1_uc010kcx.1_Nonsense_Mutation_p.Q234*|HACE1_uc003pqt.1_Nonsense_Mutation_p.Q478*	NM_020771	NP_065822	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing, E3	825	HECT.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process	endoplasmic reticulum	ubiquitin-protein ligase activity			ovary(5)|lung(1)	6		all_cancers(87;6.89e-05)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0216)|Colorectal(196;0.202)		BRCA - Breast invasive adenocarcinoma(108;0.122)|Epithelial(106;0.204)										0.21978	48.448574	55.031393	20	71	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	105192075	105192075	7222	6	G	A	A	A	585	45	HACE1	5	2
TRDN	10345	broad.mit.edu	37	6	123539833	123539833	+	Silent	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:123539833T>C	uc003pzj.1	-	c.2103A>G	c.(2101-2103)GGA>GGG	p.G701G	TRDN_uc010kem.1_Silent_p.G202G	NM_006073	NP_006064	Q13061	TRDN_HUMAN	triadin	701	Lumenal.				muscle contraction	integral to membrane|plasma membrane|sarcoplasmic reticulum membrane	receptor binding			ovary(1)	1				GBM - Glioblastoma multiforme(226;0.184)										0.142857	7.588301	11.023488	4	24	KEEP	---	---	---	---	capture		Silent	SNP	123539833	123539833	17012	6	T	C	C	C	639	50	TRDN	4	4
IL20RA	53832	broad.mit.edu	37	6	137330566	137330566	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:137330566G>T	uc003qhj.2	-	c.467C>A	c.(466-468)ACA>AAA	p.T156K	IL20RA_uc011edl.1_Missense_Mutation_p.T107K|IL20RA_uc003qhk.2_Missense_Mutation_p.T45K|IL20RA_uc010kgy.1_Intron|IL20RA_uc003qhi.2_5'Flank	NM_014432	NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha precursor	156	Extracellular (Potential).|Fibronectin type-III 2.					integral to membrane	receptor activity			ovary(2)	2	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)										0.222222	47.206334	52.955651	18	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	137330566	137330566	7969	6	G	T	T	T	624	48	IL20RA	2	2
RBM16	22828	broad.mit.edu	37	6	155129873	155129873	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:155129873A>G	uc011efj.1	+	c.1365A>G	c.(1363-1365)CAA>CAG	p.Q455Q	RBM16_uc011efk.1_Silent_p.Q434Q|RBM16_uc003qqa.2_Silent_p.Q389Q|RBM16_uc003qpz.2_Silent_p.Q389Q|RBM16_uc010kji.2_Silent_p.Q410Q	NM_014892	NP_055707	Q9UPN6	SCAF8_HUMAN	RNA-binding motif protein 16	389					mRNA processing|RNA splicing	nuclear matrix|spliceosomal complex	nucleotide binding|RNA binding|RNA polymerase core enzyme binding				0		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;2.33e-15)|BRCA - Breast invasive adenocarcinoma(81;0.00524)										0.416667	101.43686	101.873521	30	42	KEEP	---	---	---	---	capture		Silent	SNP	155129873	155129873	13579	6	A	G	G	G	37	3	RBM16	4	4
TULP4	56995	broad.mit.edu	37	6	158923886	158923886	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:158923886C>T	uc003qrf.2	+	c.3191C>T	c.(3190-3192)TCC>TTC	p.S1064F	TULP4_uc003qrg.2_Intron	NM_020245	NP_064630	Q9NRJ4	TULP4_HUMAN	tubby like protein 4 isoform 1	1064					intracellular signal transduction|regulation of transcription, DNA-dependent|response to nutrient	cytoplasm	protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)										0.173913	7.784918	10.094152	4	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158923886	158923886	17331	6	C	T	T	T	390	30	TULP4	2	2
FNDC1	84624	broad.mit.edu	37	6	159688877	159688877	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:159688877G>A	uc010kjv.2	+	c.5488G>A	c.(5488-5490)GAC>AAC	p.D1830N		NM_032532	NP_115921	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1830						extracellular region				large_intestine(4)|ovary(3)|central_nervous_system(1)	8		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)										0.057143	-6.061926	8.355245	4	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	159688877	159688877	6210	6	G	A	A	A	429	33	FNDC1	2	2
DCDC2	51473	broad.mit.edu	37	6	24178641	24178641	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:24178641C>T	uc003ndx.2	-	c.1243G>A	c.(1243-1245)GAG>AAG	p.E415K	DCDC2_uc003ndy.2_Missense_Mutation_p.E415K|DCDC2_uc003ndw.2_Missense_Mutation_p.E166K	NM_016356	NP_057440	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	415					cellular defense response|intracellular signal transduction|neuron migration					ovary(1)	1		Ovarian(999;0.101)												0.379085	167.530618	169.486203	58	95	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24178641	24178641	4456	6	C	T	T	T	390	30	DCDC2	2	2
LRRC16A	55604	broad.mit.edu	37	6	25450201	25450201	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:25450201C>T	uc011djw.1	+	c.447C>T	c.(445-447)ACC>ACT	p.T149T	LRRC16A_uc010jpx.2_Silent_p.T149T|LRRC16A_uc010jpy.2_Silent_p.T149T|LRRC16A_uc003nez.1_5'Flank	NM_017640	NP_060110	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	149					actin filament organization|blood coagulation|cell migration|lamellipodium assembly|ruffle organization|urate metabolic process	cytosol|lamellipodium|nucleus				ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4														0.111111	3.708414	7.742395	3	24	KEEP	---	---	---	---	capture		Silent	SNP	25450201	25450201	9345	6	C	T	T	T	288	23	LRRC16A	1	1
GPX6	257202	broad.mit.edu	37	6	28478622	28478622	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:28478622G>T	uc011dlj.1	-	c.147C>A	c.(145-147)AAC>AAA	p.N49K	GPX6_uc010jrg.1_Non-coding_Transcript	NM_182701	NP_874360	P59796	GPX6_HUMAN	glutathione peroxidase 6 precursor	49					oxidation-reduction process|response to oxidative stress	extracellular region	glutathione peroxidase activity			ovary(3)|pancreas(1)	4					Glutathione(DB00143)									0.15	7.619731	12.32666	6	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	28478622	28478622	7020	6	G	T	T	T	516	40	GPX6	1	1
MAS1L	116511	broad.mit.edu	37	6	29455361	29455361	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:29455361G>A	uc011dlq.1	-	c.319C>T	c.(319-321)CCC>TCC	p.P107S		NM_052967	NP_443199	P35410	MAS1L_HUMAN	MAS1 oncogene-like	107	Cytoplasmic (Potential).					cytoplasm|integral to membrane|nucleus|plasma membrane	G-protein coupled receptor activity			ovary(5)	5						NSCLC(153;755 1987 3859 11251 32945)								0.326531	42.991647	44.295294	16	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	29455361	29455361	9705	6	G	A	A	A	533	41	MAS1L	2	2
LTA	4049	broad.mit.edu	37	6	31540548	31540548	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:31540548C>A	uc011dnu.1	+	c.29C>A	c.(28-30)CCA>CAA	p.P10Q	LTA_uc003nue.1_Missense_Mutation_p.P10Q|LTA_uc003nuf.2_5'Flank|LTA_uc003nuh.2_5'Flank|LTA_uc003nug.2_5'Flank|LTA_uc010jsr.2_5'Flank|TNF_uc003nui.2_5'Flank	NM_001159740	NP_001153212	P01374	TNFB_HUMAN	lymphotoxin alpha precursor	10					cell-cell signaling|induction of apoptosis|signal transduction	extracellular space|membrane	cytokine activity|tumor necrosis factor receptor binding				0					Etanercept(DB00005)									0.055556	-6.742184	8.20571	4	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31540548	31540548	9444	6	C	A	A	A	273	21	LTA	2	2
DNAH8	1769	broad.mit.edu	37	6	38828271	38828271	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:38828271G>T	uc003ooe.1	+	c.5346G>T	c.(5344-5346)TGG>TGT	p.W1782C		NM_001371	NP_001362	Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy polypeptide 8	1782					ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(6)|skin(5)|lung(2)|large_intestine(1)|central_nervous_system(1)|kidney(1)|pancreas(1)	17										2979				0.375	17.945717	18.16534	6	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38828271	38828271	4790	6	G	T	T	T	546	42	DNAH8	2	2
TREML2	79865	broad.mit.edu	37	6	41166027	41166027	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:41166027C>G	uc010jxm.1	-	c.196G>C	c.(196-198)GGC>CGC	p.G66R		NM_024807	NP_079083	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid	66	Ig-like V-type.|Extracellular (Potential).				T cell activation	cell surface|integral to membrane|plasma membrane	protein binding|receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(28;0.0418)|Colorectal(47;0.196)													0.376	125.679702	127.371026	47	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41166027	41166027	17017	6	C	G	G	G	273	21	TREML2	3	3
UBR2	23304	broad.mit.edu	37	6	42626495	42626495	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:42626495G>A	uc011dur.1	+	c.3175G>A	c.(3175-3177)GAA>AAA	p.E1059K	UBR2_uc011dus.1_Missense_Mutation_p.E704K|UBR2_uc003osh.2_Non-coding_Transcript	NM_015255	NP_056070	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin	1059						nucleus|plasma membrane	zinc ion binding			ovary(3)|pancreas(1)	4	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)											0.078431	-0.638797	8.623168	4	47	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	42626495	42626495	17460	6	G	A	A	A	585	45	UBR2	2	2
ZNF318	24149	broad.mit.edu	37	6	43305759	43305759	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43305759T>A	uc003oux.2	-	c.5977A>T	c.(5977-5979)ATA>TTA	p.I1993L	ZNF318_uc003ouw.2_Intron	NM_014345	NP_055160	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1993					meiosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	nucleic acid binding|zinc ion binding			ovary(2)|breast(2)|central_nervous_system(1)	5			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)											0.208333	48.848016	56.410648	20	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	43305759	43305759	18428	6	T	A	A	A	676	52	ZNF318	3	3
MUT	4594	broad.mit.edu	37	6	49426988	49426988	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:49426988C>A	uc003ozg.3	-	c.192G>T	c.(190-192)CCG>CCT	p.P64P		NM_000255	NP_000246	P22033	MUTA_HUMAN	methylmalonyl Coenzyme A mutase precursor	64					fatty acid beta-oxidation	mitochondrial matrix	cobalamin binding|metal ion binding|methylmalonyl-CoA mutase activity				0	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)									0.446429	75.865649	76.005783	25	31	KEEP	---	---	---	---	capture		Silent	SNP	49426988	49426988	10385	6	C	A	A	A	288	23	MUT	1	1
TRAM2	9697	broad.mit.edu	37	6	52369391	52369391	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:52369391G>C	uc003paq.2	-	c.1037C>G	c.(1036-1038)TCT>TGT	p.S346C	EFHC1_uc011dwv.1_Intron	NM_012288	NP_036420	Q15035	TRAM2_HUMAN	translocation-associated membrane protein 2	346					collagen biosynthetic process|protein transport|transmembrane transport	integral to membrane	protein binding				0	Lung NSC(77;0.109)													0.444444	56.197069	56.293666	16	20	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	52369391	52369391	16997	6	G	C	C	C	429	33	TRAM2	3	3
DST	667	broad.mit.edu	37	6	56457000	56457000	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:56457000T>C	uc003pdf.2	-	c.6526A>G	c.(6526-6528)AGG>GGG	p.R2176G	DST_uc003pcz.3_Missense_Mutation_p.R1998G|DST_uc011dxj.1_Missense_Mutation_p.R2027G|DST_uc011dxk.1_Missense_Mutation_p.R2038G|DST_uc003pcy.3_Missense_Mutation_p.R1672G|DST_uc010kaa.1_Non-coding_Transcript	NM_001144769	NP_001138241	Q03001	DYST_HUMAN	dystonin isoform 2	4084	Spectrin 3.				cell adhesion|cell cycle arrest|integrin-mediated signaling pathway|intermediate filament cytoskeleton organization	basement membrane|cytoplasmic membrane-bounded vesicle|hemidesmosome|microtubule plus end|nucleus	actin binding|calcium ion binding|integrin binding|microtubule plus-end binding|protein C-terminus binding			ovary(7)|central_nervous_system(6)	13	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)							2498				0.09589	6.767427	18.725411	7	66	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	56457000	56457000	4967	6	T	C	C	C	726	56	DST	4	4
LRCH4	4034	broad.mit.edu	37	7	100176036	100176036	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100176036C>T	uc003uvj.2	-	c.834G>A	c.(832-834)CCG>CCA	p.P278P	LRCH4_uc010lgz.2_Non-coding_Transcript|LRCH4_uc003uvi.2_Non-coding_Transcript|LRCH4_uc011kjw.1_5'UTR|LRCH4_uc011kjx.1_Non-coding_Transcript	NM_002319	NP_002310	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH)	278					nervous system development	PML body	protein binding			large_intestine(1)|ovary(1)	2	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)													0.348485	64.810073	66.144787	23	43	KEEP	---	---	---	---	capture		Silent	SNP	100176036	100176036	9308	7	C	T	T	T	392	31	LRCH4	1	1
ZAN	7455	broad.mit.edu	37	7	100344279	100344279	+	Silent	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100344279G>C	uc003uwj.2	+	c.885G>C	c.(883-885)CGG>CGC	p.R295R	ZAN_uc003uwk.2_Silent_p.R295R|ZAN_uc003uwl.2_Non-coding_Transcript|ZAN_uc010lhh.2_Non-coding_Transcript|ZAN_uc010lhi.2_Non-coding_Transcript	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	295	MAM 2.|Extracellular (Potential).				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)											0.363636	60.096937	60.991648	20	35	KEEP	---	---	---	---	capture		Silent	SNP	100344279	100344279	18096	7	G	C	C	C	548	43	ZAN	3	3
ZAN	7455	broad.mit.edu	37	7	100373017	100373017	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:100373017C>T	uc003uwj.2	+	c.5847C>T	c.(5845-5847)ATC>ATT	p.I1949I	ZAN_uc003uwk.2_Silent_p.I1949I|ZAN_uc003uwl.2_Non-coding_Transcript|ZAN_uc010lhh.2_Non-coding_Transcript|ZAN_uc010lhi.2_Non-coding_Transcript|ZAN_uc011kke.1_Silent_p.I36I	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	1949	Extracellular (Potential).|VWFD 3.				binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)											0.078125	-0.576619	11.069835	5	59	KEEP	---	---	---	---	capture		Silent	SNP	100373017	100373017	18096	7	C	T	T	T	382	30	ZAN	2	2
CTTNBP2	83992	broad.mit.edu	37	7	117365197	117365197	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:117365197G>A	uc003vjf.2	-	c.4170C>T	c.(4168-4170)CAC>CAT	p.H1390H		NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1390										ovary(4)	4	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)										0.042553	-34.367549	18.341697	10	225	KEEP	---	---	---	---	capture		Silent	SNP	117365197	117365197	4204	7	G	A	A	A	568	44	CTTNBP2	2	2
SPAM1	6677	broad.mit.edu	37	7	123593676	123593676	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:123593676A>C	uc003vle.2	+	c.52A>C	c.(52-54)AGT>CGT	p.S18R	SPAM1_uc011koa.1_5'Flank|SPAM1_uc003vld.2_Missense_Mutation_p.S18R|SPAM1_uc003vlf.3_Missense_Mutation_p.S18R|SPAM1_uc010lku.2_Missense_Mutation_p.S18R	NM_003117	NP_003108	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 1	18					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)									0.068966	-1.048129	10.088885	4	54	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123593676	123593676	15489	7	A	C	C	C	39	3	SPAM1	4	4
AKR1B10	57016	broad.mit.edu	37	7	134221408	134221408	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:134221408G>A	uc003vrr.2	+	c.436G>A	c.(436-438)GAG>AAG	p.E146K		NM_020299	NP_064695	O60218	AK1BA_HUMAN	aldo-keto reductase family 1, member B10	146					cellular aldehyde metabolic process|digestion|oxidation-reduction process|steroid metabolic process	cytoplasm	aldo-keto reductase (NADP) activity|protein binding				0														0.068493	-3.386236	10.674036	5	68	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	134221408	134221408	470	7	G	A	A	A	533	41	AKR1B10	2	2
NUP205	23165	broad.mit.edu	37	7	135323374	135323374	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:135323374G>T	uc003vsw.2	+	c.5335G>T	c.(5335-5337)GTG>TTG	p.V1779L	NUP205_uc003vsx.2_Non-coding_Transcript	NM_015135	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1779					carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6														0.167832	49.406643	64.358026	24	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135323374	135323374	11164	7	G	T	T	T	624	48	NUP205	2	2
DENND2A	27147	broad.mit.edu	37	7	140301849	140301849	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:140301849C>T	uc010lnj.2	-	c.349G>A	c.(349-351)GTC>ATC	p.V117I	DENND2A_uc011kre.1_Non-coding_Transcript|DENND2A_uc010lnk.2_Missense_Mutation_p.V117I|DENND2A_uc003vvw.2_Missense_Mutation_p.V117I|DENND2A_uc003vvx.2_Missense_Mutation_p.V117I	NM_015689	NP_056504	Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	117										ovary(3)|breast(1)	4	Melanoma(164;0.00956)													0.114754	23.175668	49.920138	21	162	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	140301849	140301849	4608	7	C	T	T	T	247	19	DENND2A	1	1
CASP2	835	broad.mit.edu	37	7	142997119	142997119	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:142997119A>T	uc003wco.2	+	c.851A>T	c.(850-852)TAT>TTT	p.Y284F	CASP2_uc003wcp.2_3'UTR|CASP2_uc011kta.1_Missense_Mutation_p.Y168F|CASP2_uc003wcq.2_Non-coding_Transcript|CASP2_uc011ktb.1_Missense_Mutation_p.Y34F	NM_032982	NP_116764	P42575	CASP2_HUMAN	caspase 2 isoform 1 preproprotein	284					apoptosis|cellular response to mechanical stimulus|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|protein maturation by peptide bond cleavage	cytosol	cysteine-type endopeptidase activity|enzyme binding|protein binding|protein domain specific binding				0	Melanoma(164;0.059)									155		OREG0018400	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.144231	25.664836	38.328916	15	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142997119	142997119	2790	7	A	T	T	T	208	16	CASP2	3	3
CLCN1	1180	broad.mit.edu	37	7	143047738	143047738	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143047738C>T	uc003wcr.1	+	c.2586C>T	c.(2584-2586)GCC>GCT	p.A862A	CLCN1_uc011ktc.1_Silent_p.A474A	NM_000083	NP_000074	P35523	CLCN1_HUMAN	chloride channel 1, skeletal muscle	862	CBS 2.|Cytoplasmic (By similarity).				muscle contraction	chloride channel complex|integral to plasma membrane	voltage-gated chloride channel activity			ovary(1)|breast(1)|central_nervous_system(1)	3	Melanoma(164;0.205)													0.336634	198.327617	203.053933	68	134	KEEP	---	---	---	---	capture		Silent	SNP	143047738	143047738	3598	7	C	T	T	T	275	22	CLCN1	2	2
OR2F1	26211	broad.mit.edu	37	7	143657464	143657464	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:143657464C>A	uc003wds.1	+	c.401C>A	c.(400-402)GCC>GAC	p.A134D		NM_012369	NP_036501	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F,	134	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1	Melanoma(164;0.0903)													0.183908	61.324939	77.634767	32	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143657464	143657464	11402	7	C	A	A	A	338	26	OR2F1	2	2
MLL3	58508	broad.mit.edu	37	7	151945112	151945112	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:151945112C>A	uc003wla.2	-	c.2407G>T	c.(2407-2409)GCT>TCT	p.A803S		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	803					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			pancreas(12)|ovary(7)|large_intestine(6)|central_nervous_system(4)|urinary_tract(1)|skin(1)	31	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		Colon(68;14 1149 1884 27689 34759)				1780				0.028419	-111.221749	26.698208	16	547	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	151945112	151945112	10012	7	C	A	A	A	364	28	MLL3	2	2
HDAC9	9734	broad.mit.edu	37	7	19015566	19015566	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:19015566G>T	uc003sui.2	+	c.3160G>T	c.(3160-3162)GAA>TAA	p.E1054*	HDAC9_uc003sue.2_Nonsense_Mutation_p.E1051*|HDAC9_uc003suj.2_Nonsense_Mutation_p.E1010*|HDAC9_uc003suk.2_Nonsense_Mutation_p.E299*	NM_178425	NP_848512	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9 isoform 5	Error:Variant_position_missing_in_Q9UKV0_after_alignment					B cell differentiation|cellular response to insulin stimulus|heart development|histone H3 deacetylation|histone H4 deacetylation|inflammatory response|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of transcription, DNA-dependent|peptidyl-lysine deacetylation|positive regulation of cell migration involved in sprouting angiogenesis|regulation of skeletal muscle fiber development|transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|transcription factor complex	histone deacetylase activity (H3-K16 specific)|histone deacetylase binding|histone deacetylase binding|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein binding|protein kinase C binding|repressing transcription factor binding|specific transcriptional repressor activity|transcription corepressor activity|transcription repressor activity			lung(2)|central_nervous_system(2)|kidney(1)	5	all_lung(11;0.187)				Valproic Acid(DB00313)									0.140187	18.942468	32.338267	15	92	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	19015566	19015566	7297	7	G	T	T	T	533	41	HDAC9	5	2
ABCB5	340273	broad.mit.edu	37	7	20689653	20689653	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:20689653A>T	uc010kuh.2	+	c.1215A>T	c.(1213-1215)AAA>AAT	p.K405N	ABCB5_uc003suw.3_De_novo_Start_OutOfFrame|ABCB5_uc003suv.3_De_novo_Start_OutOfFrame|ABCB5_uc011jyi.1_De_novo_Start_OutOfFrame	NM_001163941	NP_001157413	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B, member 5	589	Cytoplasmic (Potential).|ABC transporter 2.				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														0.086957	1.262464	9.208725	4	42	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	20689653	20689653	45	7	A	T	T	T	37	3	ABCB5	3	3
FAM188B	84182	broad.mit.edu	37	7	30915112	30915112	+	Silent	SNP	A	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:30915112A>G	uc003tbt.2	+	c.1812A>G	c.(1810-1812)GAA>GAG	p.E604E	FAM188B_uc010kwe.2_Silent_p.E575E|AQP1_uc011kac.1_5'UTR|FAM188B_uc003tbu.2_Silent_p.E124E	NM_032222	NP_115598	Q4G0A6	F188B_HUMAN	hypothetical protein LOC84182	604											0														0.038596	-40.693143	24.827595	11	274	KEEP	---	---	---	---	capture		Silent	SNP	30915112	30915112	5725	7	A	G	G	G	24	2	FAM188B	4	4
ADCYAP1R1	117	broad.mit.edu	37	7	31117661	31117661	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:31117661G>C	uc003tcc.1	+	c.213G>C	c.(211-213)GAG>GAC	p.E71D	ADCYAP1R1_uc003tca.1_Missense_Mutation_p.E71D|ADCYAP1R1_uc003tcb.1_Missense_Mutation_p.E71D|ADCYAP1R1_uc003tcd.1_Missense_Mutation_p.E71D|ADCYAP1R1_uc003tce.1_Missense_Mutation_p.E71D	NM_001118	NP_001109	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1	71	Extracellular (Potential).				activation of adenylate cyclase activity|cell differentiation|nerve growth factor receptor signaling pathway|spermatogenesis	integral to plasma membrane	vasoactive intestinal polypeptide receptor activity			ovary(1)	1						Ovarian(44;225 1186 2158 11092)								0.150442	35.20086	48.43326	17	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	31117661	31117661	304	7	G	C	C	C	425	33	ADCYAP1R1	3	3
DBNL	28988	broad.mit.edu	37	7	44098510	44098510	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:44098510G>T	uc003tjq.3	+	c.790G>T	c.(790-792)GTG>TTG	p.V264L	DBNL_uc003tjn.2_Missense_Mutation_p.V127L|DBNL_uc003tjo.3_Missense_Mutation_p.V256L|DBNL_uc003tjr.3_Missense_Mutation_p.V128L|DBNL_uc003tjp.3_Missense_Mutation_p.V255L|DBNL_uc011kbm.1_Missense_Mutation_p.V231L|DBNL_uc011kbn.1_Missense_Mutation_p.V152L|DBNL_uc011kbo.1_Missense_Mutation_p.V156L|DBNL_uc011kbp.1_Missense_Mutation_p.V207L|DBNL_uc011kbq.1_Missense_Mutation_p.V180L|DBNL_uc011kbr.1_Missense_Mutation_p.V204L|DBNL_uc011kbs.1_Missense_Mutation_p.V160L	NM_001122956	NP_001116428	Q9UJU6	DBNL_HUMAN	drebrin-like isoform c	255					activation of JUN kinase activity|cellular component disassembly involved in apoptosis|endocytosis|Rac protein signal transduction	cell cortex|cytoskeleton|cytosol|lamellipodium	actin binding|enzyme activator activity|identical protein binding				0						NSCLC(68;573 1327 18604 34760 37992)								0.294118	29.138738	30.427252	10	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44098510	44098510	4426	7	G	T	T	T	520	40	DBNL	1	1
MYL7	58498	broad.mit.edu	37	7	44178555	44178555	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:44178555A>T	uc003tkg.2	-	c.493T>A	c.(493-495)TAC>AAC	p.Y165N		NM_021223	NP_067046	Q01449	MLRA_HUMAN	myosin light chain 2a	165	EF-hand 3.				actin filament-based movement|smooth muscle contraction	A band|myosin complex	ATPase activity, coupled|calcium ion binding|microfilament motor activity				0														0.257143	24.359146	26.229908	9	26	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	44178555	44178555	10448	7	A	T	T	T	195	15	MYL7	3	3
COBL	23242	broad.mit.edu	37	7	51095701	51095701	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:51095701G>C	uc003tps.2	-	c.3263C>G	c.(3262-3264)GCC>GGC	p.A1088G	COBL_uc003tpr.3_Missense_Mutation_p.A1031G|COBL_uc011kcl.1_Missense_Mutation_p.A1031G|COBL_uc003tpp.3_Missense_Mutation_p.A817G|COBL_uc003tpq.3_Missense_Mutation_p.A972G|COBL_uc003tpo.3_Missense_Mutation_p.A573G	NM_015198	NP_056013	O75128	COBL_HUMAN	cordon-bleu homolog	1031										ovary(2)|skin(1)	3	Glioma(55;0.08)					NSCLC(189;2119 2138 12223 30818 34679)								0.439024	57.343159	57.476197	18	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	51095701	51095701	3791	7	G	C	C	C	546	42	COBL	3	3
WIPI2	26100	broad.mit.edu	37	7	5266848	5266848	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:5266848G>T	uc003snv.2	+	c.886G>T	c.(886-888)GGG>TGG	p.G296W	WIPI2_uc003snw.2_Missense_Mutation_p.G296W|WIPI2_uc003snx.2_Missense_Mutation_p.G278W|WIPI2_uc003sny.2_Missense_Mutation_p.G278W|WIPI2_uc010ksv.2_Missense_Mutation_p.G152W|WIPI2_uc003soa.2_Missense_Mutation_p.G237W|WIPI2_uc003sob.2_Missense_Mutation_p.G39W	NM_015610	NP_056425	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	296					autophagic vacuole assembly	cytosol|PAS complex|pre-autophagosomal structure membrane	phosphatidylinositol-3,5-bisphosphate binding|phosphatidylinositol-3-phosphate binding			ovary(2)	2		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)										0.380952	25.097391	25.357551	8	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5266848	5266848	17945	7	G	T	T	T	507	39	WIPI2	1	1
FGL2	10875	broad.mit.edu	37	7	76828787	76828787	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:76828787G>A	uc003ugb.2	-	c.324C>T	c.(322-324)GAC>GAT	p.D108D	CCDC146_uc003ufz.1_Intron|CCDC146_uc003uga.2_Intron	NM_006682	NP_006673	Q14314	FGL2_HUMAN	fibrinogen-like 2 precursor	108	Potential.				signal transduction	fibrinogen complex	receptor binding			skin(1)	1														0.318681	74.736047	77.398838	29	62	KEEP	---	---	---	---	capture		Silent	SNP	76828787	76828787	6110	7	G	A	A	A	568	44	FGL2	2	2
PCLO	27445	broad.mit.edu	37	7	82532040	82532040	+	Silent	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82532040C>G	uc003uhx.2	-	c.13455G>C	c.(13453-13455)GGG>GGC	p.G4485G	PCLO_uc003uhv.2_Silent_p.G4485G	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	4416					cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity|zinc ion binding			ovary(7)	7														0.282051	33.408287	35.072771	11	28	KEEP	---	---	---	---	capture		Silent	SNP	82532040	82532040	12003	7	C	G	G	G	379	30	PCLO	3	3
VPS13B	157680	broad.mit.edu	37	8	100520071	100520071	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:100520071C>T	uc003yiv.2	+	c.4231C>T	c.(4231-4233)CGC>TGC	p.R1411C	VPS13B_uc003yiw.2_Intron|VPS13B_uc003yiu.1_3'UTR|VPS13B_uc003yix.1_Missense_Mutation_p.R881C	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	1411					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			Colon(161;2205 2542 7338 31318)				1116				0.054054	-12.445776	10.87245	6	105	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100520071	100520071	17757	8	C	T	T	T	247	19	VPS13B	1	1
VPS13B	157680	broad.mit.edu	37	8	100832296	100832296	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:100832296G>A	uc003yiv.2	+	c.9015G>A	c.(9013-9015)GAG>GAA	p.E3005E	VPS13B_uc003yiw.2_Silent_p.E2980E	NM_017890	NP_060360	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13B isoform 5	3005					protein transport					ovary(7)|skin(4)|lung(3)|central_nervous_system(2)|pancreas(2)|breast(1)|kidney(1)	20	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			Colon(161;2205 2542 7338 31318)				1116				0.033175	-36.420575	13.710478	7	204	KEEP	---	---	---	---	capture		Silent	SNP	100832296	100832296	17757	8	G	A	A	A	425	33	VPS13B	2	2
C8orf74	203076	broad.mit.edu	37	8	10557779	10557779	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10557779C>A	uc003wtd.1	+	c.683C>A	c.(682-684)ACC>AAC	p.T228N	C8orf74_uc003wte.1_Non-coding_Transcript	NM_001040032	NP_001035121	Q6P047	CH074_HUMAN	hypothetical protein LOC203076	228											0				COAD - Colon adenocarcinoma(149;0.0811)										0.275862	22.08675	23.398847	8	21	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10557779	10557779	2548	8	C	A	A	A	234	18	C8orf74	2	2
ZFPM2	23414	broad.mit.edu	37	8	106456506	106456506	+	Splice_Site_SNP	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:106456506A>T	uc003ymd.2	+	c.200_splice	c.e3-2	p.G67_splice		NM_012082	NP_036214			zinc finger protein, multitype 2						blood coagulation|transcription, DNA-dependent	nucleoplasm	DNA binding|RNA polymerase II transcription factor activity|transcription corepressor activity|transcription repressor activity|zinc ion binding			ovary(4)|large_intestine(1)	5			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)											0.066667	-3.04933	8.634209	4	56	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	106456506	106456506	18248	8	A	T	T	T	91	7	ZFPM2	5	3
XKR6	286046	broad.mit.edu	37	8	10756124	10756124	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:10756124C>G	uc003wtk.1	-	c.1264G>C	c.(1264-1266)GTA>CTA	p.V422L		NM_173683	NP_775954	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related	422	Helical; (Potential).					integral to membrane				ovary(1)	1				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)										0.365854	95.730541	97.027258	30	52	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10756124	10756124	18016	8	C	G	G	G	234	18	XKR6	3	3
OXR1	55074	broad.mit.edu	37	8	107754530	107754530	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:107754530C>G	uc011lht.1	+	c.2400C>G	c.(2398-2400)TTC>TTG	p.F800L	OXR1_uc003ymf.2_Missense_Mutation_p.F772L|OXR1_uc011lhu.1_Missense_Mutation_p.F765L|OXR1_uc010mcg.2_Non-coding_Transcript|OXR1_uc010mch.2_Missense_Mutation_p.F428L|OXR1_uc003ymk.2_Missense_Mutation_p.F169L|OXR1_uc003yml.2_Missense_Mutation_p.F142L	NM_018002	NP_060472	Q8N573	OXR1_HUMAN	oxidation resistance 1 isoform 1	800	TLD.				cell wall macromolecule catabolic process|response to oxidative stress	mitochondrion					0			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)											0.245283	36.448739	39.580376	13	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107754530	107754530	11747	8	C	G	G	G	415	32	OXR1	3	3
KCNV1	27012	broad.mit.edu	37	8	110984867	110984867	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:110984867C>A	uc003ynr.3	-	c.611G>T	c.(610-612)GGA>GTA	p.G204V	KCNV1_uc010mcw.2_Missense_Mutation_p.G204V	NM_014379	NP_055194	Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	204	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)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)											0.327869	54.281882	55.883216	20	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	110984867	110984867	8399	8	C	A	A	A	390	30	KCNV1	2	2
TRPS1	7227	broad.mit.edu	37	8	116616277	116616277	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:116616277T>A	uc003yny.2	-	c.1919A>T	c.(1918-1920)GAT>GTT	p.D640V	TRPS1_uc011lhy.1_Missense_Mutation_p.D631V|TRPS1_uc010mcy.2_Missense_Mutation_p.D627V|TRPS1_uc003ynz.2_Missense_Mutation_p.D627V	NM_014112	NP_054831	Q9UHF7	TRPS1_HUMAN	zinc finger transcription factor TRPS1	627	C2H2-type 3; atypical.				negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)|pancreas(1)|lung(1)|kidney(1)|skin(1)	6	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)							312				0.2125	40.634242	46.74324	17	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	116616277	116616277	17144	8	T	A	A	A	650	50	TRPS1	3	3
ATAD2	29028	broad.mit.edu	37	8	124359640	124359640	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:124359640C>A	uc003yqh.3	-	c.1904G>T	c.(1903-1905)TGT>TTT	p.C635F	ATAD2_uc011lii.1_Missense_Mutation_p.C426F|ATAD2_uc003yqi.3_Non-coding_Transcript|ATAD2_uc003yqj.2_Missense_Mutation_p.C635F	NM_014109	NP_054828	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	635					regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrion|nucleus	ATP binding|ATPase activity			ovary(2)	2	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)											0.232558	25.334044	28.1458	10	33	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	124359640	124359640	1090	8	C	A	A	A	221	17	ATAD2	2	2
TG	7038	broad.mit.edu	37	8	133913644	133913644	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:133913644A>T	uc003ytw.2	+	c.3480A>T	c.(3478-3480)AGA>AGT	p.R1160S	TG_uc010mdw.2_Intron	NM_003235	NP_003226	P01266	THYG_HUMAN	thyroglobulin precursor	1160	Thyroglobulin type-1 10.				hormone biosynthetic process|regulation of synaptic transmission|signal transduction		carboxylesterase activity|hormone activity			ovary(8)|breast(4)|pancreas(1)	13	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)						1778				0.089888	3.359144	18.44135	8	81	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	133913644	133913644	16341	8	A	T	T	T	141	11	TG	3	3
FAM135B	51059	broad.mit.edu	37	8	139164170	139164170	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139164170C>A	uc003yuy.2	-	c.2548G>T	c.(2548-2550)GGG>TGG	p.G850W	FAM135B_uc003yux.2_Missense_Mutation_p.G751W|FAM135B_uc003yuz.2_Non-coding_Transcript|FAM135B_uc003yva.2_Missense_Mutation_p.G412W|FAM135B_uc003yvb.2_Missense_Mutation_p.G412W	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	850										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)											0.127389	26.387701	47.649287	20	137	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139164170	139164170	5646	8	C	A	A	A	312	24	FAM135B	2	2
FAM135B	51059	broad.mit.edu	37	8	139277996	139277996	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:139277996T>A	uc003yuy.2	-	c.247A>T	c.(247-249)ATA>TTA	p.I83L	FAM135B_uc003yux.2_5'UTR|FAM135B_uc003yuz.2_Non-coding_Transcript	NM_015912	NP_056996	Q49AJ0	F135B_HUMAN	hypothetical protein LOC51059	83										ovary(7)	7	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)											0.40625	125.712764	126.448399	39	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139277996	139277996	5646	8	T	A	A	A	663	51	FAM135B	3	3
FLJ43860	389690	broad.mit.edu	37	8	142505516	142505516	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:142505516C>A	uc003ywi.2	-	c.330G>T	c.(328-330)AAG>AAT	p.K110N	FLJ43860_uc011ljs.1_5'Flank|FLJ43860_uc010meu.1_5'Flank	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690	110							binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)											0.127907	13.76019	25.371951	11	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	142505516	142505516	6170	8	C	A	A	A	415	32	FLJ43860	2	2
BAI1	575	broad.mit.edu	37	8	143561102	143561102	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:143561102A>T	uc003ywm.2	+	c.1775A>T	c.(1774-1776)AAG>ATG	p.K592M		NM_001702	NP_001693	O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	592	Extracellular (Potential).				axonogenesis|cell adhesion|negative regulation of cell proliferation|neuropeptide signaling pathway|peripheral nervous system development	cell-cell junction|integral to plasma membrane	G-protein coupled receptor activity|protein binding			ovary(1)|breast(1)|central_nervous_system(1)|pancreas(1)	4	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)									829				0.306122	40.607994	42.249821	15	34	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	143561102	143561102	1319	8	A	T	T	T	39	3	BAI1	3	3
EEF1D	1936	broad.mit.edu	37	8	144668960	144668960	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:144668960T>C	uc003yyq.1	-	c.1304A>G	c.(1303-1305)GAC>GGC	p.D435G	EEF1D_uc003yyp.1_Missense_Mutation_p.D385G|EEF1D_uc011lki.1_Missense_Mutation_p.D19G|EEF1D_uc011lkj.1_Missense_Mutation_p.D384G|EEF1D_uc003yyr.2_Missense_Mutation_p.D385G|EEF1D_uc003yyt.2_Missense_Mutation_p.D385G|EEF1D_uc011lkk.1_Missense_Mutation_p.D19G|EEF1D_uc003yys.2_Missense_Mutation_p.D19G|EEF1D_uc003yyv.2_Missense_Mutation_p.D19G|EEF1D_uc003yyu.2_Missense_Mutation_p.D19G|EEF1D_uc011lkl.1_Missense_Mutation_p.D19G	NM_032378	NP_115754	P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta	19					positive regulation of I-kappaB kinase/NF-kappaB cascade	cytosol|eukaryotic translation elongation factor 1 complex	protein binding|signal transducer activity|translation elongation factor activity			ovary(1)|kidney(1)|skin(1)	3	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)							610				0.073529	-1.271628	11.43777	5	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	144668960	144668960	5113	8	T	C	C	C	754	58	EEF1D	4	4
DLGAP2	9228	broad.mit.edu	37	8	1624761	1624761	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:1624761G>T	uc003wpl.2	+	c.2025G>T	c.(2023-2025)GGG>GGT	p.G675G	DLGAP2_uc003wpm.2_Silent_p.G661G	NM_004745	NP_004736	Q9P1A6	DLGP2_HUMAN	discs large-associated protein 2	754					nerve-nerve synaptic transmission	cell junction|neurofilament|postsynaptic density|postsynaptic membrane	protein binding				0		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)										0.363636	12.097216	12.277098	4	7	KEEP	---	---	---	---	capture		Silent	SNP	1624761	1624761	4740	8	G	T	T	T	548	43	DLGAP2	2	2
ARHGEF10	9639	broad.mit.edu	37	8	1808302	1808302	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:1808302G>T	uc003wpr.2	+	c.433G>T	c.(433-435)GCC>TCC	p.A145S	ARHGEF10_uc003wpq.1_Missense_Mutation_p.A169S|ARHGEF10_uc003wps.2_Missense_Mutation_p.A145S|ARHGEF10_uc003wpt.2_Missense_Mutation_p.A59S|ARHGEF10_uc010lrd.1_Missense_Mutation_p.A59S|ARHGEF10_uc003wpu.2_Missense_Mutation_p.A59S	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10	169					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)						2844				0.323529	33.141475	34.066813	11	23	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	1808302	1808302	908	8	G	T	T	T	494	38	ARHGEF10	1	1
LPL	4023	broad.mit.edu	37	8	19813437	19813437	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:19813437G>T	uc003wzk.3	+	c.861G>T	c.(859-861)AAG>AAT	p.K287N		NM_000237	NP_000228	P06858	LIPL_HUMAN	lipoprotein lipase precursor	287					chylomicron remodeling|fatty acid biosynthetic process|lipoprotein metabolic process|phospholipid metabolic process|positive regulation of cholesterol storage|positive regulation of macrophage derived foam cell differentiation|positive regulation of sequestering of triglyceride|triglyceride catabolic process|triglyceride homeostasis|very-low-density lipoprotein particle remodeling	anchored to membrane|chylomicron|plasma membrane|very-low-density lipoprotein particle	heparin binding|lipoprotein lipase activity|phospholipase activity|receptor binding|triglyceride lipase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	Clofibrate(DB00636)|Gemfibrozil(DB01241)|Orlistat(DB01083)									0.050847	-12.95221	12.270819	6	112	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19813437	19813437	9294	8	G	T	T	T	451	35	LPL	2	2
SLC39A14	23516	broad.mit.edu	37	8	22273459	22273459	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:22273459C>T	uc003xbq.3	+	c.928C>T	c.(928-930)CTC>TTC	p.L310F	SLC39A14_uc011kzg.1_Missense_Mutation_p.L310F|SLC39A14_uc003xbp.3_Missense_Mutation_p.L310F|SLC39A14_uc011kzh.1_Missense_Mutation_p.L310F	NM_001128431	NP_001121903	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter),	310	Cytoplasmic (Potential).					endoplasmic reticulum|Golgi apparatus|integral to membrane|lamellipodium|plasma membrane	zinc ion transmembrane transporter activity				0				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)										0.25	13.636234	15.002057	6	18	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	22273459	22273459	15114	8	C	T	T	T	364	28	SLC39A14	2	2
UNC5D	137970	broad.mit.edu	37	8	35608193	35608193	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:35608193G>C	uc003xjr.1	+	c.2029G>C	c.(2029-2031)GCG>CCG	p.A677P	UNC5D_uc003xjs.1_Missense_Mutation_p.A672P|UNC5D_uc003xju.1_Missense_Mutation_p.A253P	NM_080872	NP_543148	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D precursor	677	Cytoplasmic (Potential).				apoptosis|axon guidance	integral to membrane	receptor activity			ovary(2)|pancreas(1)	3				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)										0.322917	95.291573	97.964258	31	65	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	35608193	35608193	17553	8	G	C	C	C	598	46	UNC5D	3	3
PREX2	80243	broad.mit.edu	37	8	68934373	68934373	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:68934373T>A	uc003xxv.1	+	c.439T>A	c.(439-441)TTG>ATG	p.L147M	PREX2_uc003xxu.1_Missense_Mutation_p.L147M|PREX2_uc011lez.1_Missense_Mutation_p.L82M	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	147	DH.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			large_intestine(4)|pancreas(3)|lung(2)|skin(2)|ovary(1)|kidney(1)	13									p.L147L(KIJK-Tumor)	1011				0.098765	4.536034	17.584404	8	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	68934373	68934373	12920	8	T	A	A	A	829	64	PREX2	3	3
ZFHX4	79776	broad.mit.edu	37	8	77763856	77763856	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77763856C>A	uc003yav.2	+	c.4564C>A	c.(4564-4566)CAT>AAT	p.H1522N	ZFHX4_uc003yau.1_Missense_Mutation_p.H1567N|ZFHX4_uc003yaw.1_Missense_Mutation_p.H1522N	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1522	C2H2-type 12.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.134884	43.718665	71.511849	29	186	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77763856	77763856	18223	8	C	A	A	A	325	25	ZFHX4	2	2
ZFHX4	79776	broad.mit.edu	37	8	77765146	77765146	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77765146C>A	uc003yav.2	+	c.5854C>A	c.(5854-5856)CCA>ACA	p.P1952T	ZFHX4_uc003yau.1_Missense_Mutation_p.P1997T|ZFHX4_uc003yaw.1_Missense_Mutation_p.P1952T	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	1952	Pro-rich.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.204082	37.544812	45.517564	20	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77765146	77765146	18223	8	C	A	A	A	390	30	ZFHX4	2	2
SLC7A13	157724	broad.mit.edu	37	8	87242008	87242008	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:87242008T>C	uc003ydq.1	-	c.499A>G	c.(499-501)AAA>GAA	p.K167E	SLC7A13_uc003ydr.1_Missense_Mutation_p.K167E	NM_138817	NP_620172	Q8TCU3	S7A13_HUMAN	solute carrier family 7, (cationic amino acid	167	Helical; Name=5; (Potential).					integral to membrane	amino acid transmembrane transporter activity			central_nervous_system(1)	1														0.314917	174.023859	179.532214	57	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	87242008	87242008	15192	8	T	C	C	C	806	62	SLC7A13	4	4
CNGB3	54714	broad.mit.edu	37	8	87656851	87656851	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:87656851T>A	uc003ydx.2	-	c.1054A>T	c.(1054-1056)AGA>TGA	p.R352*	CNGB3_uc010maj.2_Nonsense_Mutation_p.R214*	NM_019098	NP_061971	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	352	Extracellular (Potential).				signal transduction|visual perception	integral to membrane	cGMP binding			ovary(2)|pancreas(1)	3														0.204082	26.22211	30.203976	10	39	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	87656851	87656851	3739	8	T	A	A	A	713	55	CNGB3	5	3
MMP16	4325	broad.mit.edu	37	8	89179958	89179958	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:89179958C>T	uc003yeb.3	-	c.649G>A	c.(649-651)GGA>AGA	p.G217R	MMP16_uc003yec.2_Missense_Mutation_p.G217R	NM_005941	NP_005932	P51512	MMP16_HUMAN	matrix metalloproteinase 16 isoform 1	217	Extracellular (Potential).				collagen catabolic process|proteolysis	cell surface|integral to plasma membrane|proteinaceous extracellular matrix	calcium ion binding|enzyme activator activity|metalloendopeptidase activity|zinc ion binding			ovary(2)|urinary_tract(1)|kidney(1)|central_nervous_system(1)	5														0.078947	-1.814201	11.958877	6	70	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	89179958	89179958	10045	8	C	T	T	T	273	21	MMP16	2	2
PDP1	54704	broad.mit.edu	37	8	94935646	94935646	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:94935646G>T	uc011lgn.1	+	c.1536G>T	c.(1534-1536)GTG>GTT	p.V512V	PDP1_uc003yge.2_Silent_p.V453V|PDP1_uc003ygf.2_Silent_p.V478V|PDP1_uc010max.2_Silent_p.V478V|PDP1_uc011lgm.1_Silent_p.V453V	NM_001161778	NP_001155250	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic	453					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.318966	98.233587	101.612507	37	79	KEEP	---	---	---	---	capture		Silent	SNP	94935646	94935646	12106	8	G	T	T	T	574	45	PDP1	2	2
GEM	2669	broad.mit.edu	37	8	95262803	95262803	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:95262803C>A	uc003ygj.2	-	c.626G>T	c.(625-627)TGT>TTT	p.C209F	GEM_uc003ygi.2_Missense_Mutation_p.C209F	NM_005261	NP_005252	P55040	GEM_HUMAN	GTP-binding mitogen-induced T-cell protein	209					cell surface receptor linked signaling pathway|immune response|small GTPase mediated signal transduction	internal side of plasma membrane	calmodulin binding|GDP binding|GTP binding|GTPase activity|magnesium ion binding				0	Breast(36;4.65e-06)	Myeloproliferative disorder(644;0.204)	BRCA - Breast invasive adenocarcinoma(8;0.00691)			GBM(125;80 1653 28655 32188 47338)|Esophageal Squamous(19;97 579 13602 49091 51766)								0.177778	35.646284	44.444118	16	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95262803	95262803	6597	8	C	A	A	A	221	17	GEM	2	2
OR13C8	138802	broad.mit.edu	37	9	107331963	107331963	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107331963A>T	uc011lvo.1	+	c.515A>T	c.(514-516)AAT>ATT	p.N172I		NM_001004483	NP_001004483	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C,	172	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.129412	17.566086	28.929869	11	74	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107331963	107331963	11344	9	A	T	T	T	52	4	OR13C8	3	3
ABCA1	19	broad.mit.edu	37	9	107560864	107560864	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:107560864C>A	uc004bcl.2	-	c.4959G>T	c.(4957-4959)GTG>GTT	p.V1653V		NM_005502	NP_005493	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A member 1	1653	Extracellular.				Cdc42 protein signal transduction|cellular lipid metabolic process|cholesterol efflux|cholesterol homeostasis|cholesterol metabolic process|endosome transport|G-protein coupled receptor protein signaling pathway|high-density lipoprotein particle assembly|interleukin-1 beta secretion|intracellular cholesterol transport|lysosome organization|negative regulation of cholesterol storage|negative regulation of macrophage derived foam cell differentiation|phospholipid efflux|phospholipid homeostasis|platelet dense granule organization|positive regulation of cAMP biosynthetic process|reverse cholesterol transport	integral to plasma membrane|membrane fraction|membrane raft|phagocytic vesicle	anion transmembrane transporter activity|apolipoprotein A-I receptor activity|ATP binding|ATPase activity|cholesterol binding|cholesterol transporter activity|phospholipid binding|phospholipid transporter activity|small GTPase binding|syntaxin-13 binding			large_intestine(4)|ovary(4)|central_nervous_system(1)|pancreas(1)	10				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glibenclamide(DB01016)									0.306931	86.78604	90.143451	31	70	KEEP	---	---	---	---	capture		Silent	SNP	107560864	107560864	29	9	C	A	A	A	262	21	ABCA1	2	2
PAPPA	5069	broad.mit.edu	37	9	118950437	118950437	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:118950437T>A	uc004bjn.2	+	c.1420T>A	c.(1420-1422)TGT>AGT	p.C474S	PAPPA_uc011lxp.1_Missense_Mutation_p.C267S|PAPPA_uc011lxq.1_Missense_Mutation_p.C267S	NM_002581	NP_002572	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A	474	Metalloprotease.				cell differentiation|female pregnancy	cytoplasm|extracellular region|membrane	metalloendopeptidase activity|zinc ion binding			ovary(4)|pancreas(1)	5										611				0.367347	56.53804	57.295774	18	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	118950437	118950437	11849	9	T	A	A	A	715	55	PAPPA	3	3
OR1L6	392390	broad.mit.edu	37	9	125512600	125512600	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:125512600G>A	uc011lzc.1	+	c.582G>A	c.(580-582)CTG>CTA	p.L194L		NM_001004453	NP_001004453	Q8NGR2	OR1L6_HUMAN	olfactory receptor, family 1, subfamily L,	194	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.286765	97.058555	102.613283	39	97	KEEP	---	---	---	---	capture		Silent	SNP	125512600	125512600	11372	9	G	A	A	A	613	48	OR1L6	2	2
SLC24A2	25769	broad.mit.edu	37	9	19786048	19786048	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:19786048A>C	uc003zoa.1	-	c.817T>G	c.(817-819)TAT>GAT	p.Y273D	SLC24A2_uc003zob.1_Missense_Mutation_p.Y273D	NM_020344	NP_065077	Q9UI40	NCKX2_HUMAN	solute carrier family 24	273	Helical; (Potential).				visual perception	integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(3)	3				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)										0.291667	62.563372	65.352291	21	51	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19786048	19786048	14963	9	A	C	C	C	169	13	SLC24A2	4	4
NOL6	65083	broad.mit.edu	37	9	33467824	33467824	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:33467824C>T	uc003zsz.2	-	c.1467G>A	c.(1465-1467)CTG>CTA	p.L489L	SUGT1P1_uc010mjq.1_Intron|NOL6_uc003zsy.2_5'Flank|NOL6_uc003zta.2_Silent_p.L489L|NOL6_uc010mjv.2_Silent_p.L486L|NOL6_uc011lob.1_Silent_p.L437L|NOL6_uc003ztb.1_Silent_p.L489L	NM_022917	NP_075068	Q9H6R4	NOL6_HUMAN	nucleolar protein family 6 alpha isoform	489					rRNA processing	condensed nuclear chromosome|nucleolus	RNA binding			ovary(2)	2			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)										0.384615	11.753229	11.910645	5	8	KEEP	---	---	---	---	capture		Silent	SNP	33467824	33467824	10928	9	C	T	T	T	366	29	NOL6	2	2
RUSC2	9853	broad.mit.edu	37	9	35547523	35547523	+	Nonsense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:35547523T>A	uc003zww.2	+	c.1005T>A	c.(1003-1005)TAT>TAA	p.Y335*	RUSC2_uc010mkq.2_Non-coding_Transcript|RUSC2_uc003zwx.3_Nonsense_Mutation_p.Y335*	NM_014806	NP_055621	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	335						cytosol				ovary(1)	1			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)											0.133333	12.659254	20.487802	8	52	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	35547523	35547523	14231	9	T	A	A	A	660	51	RUSC2	5	3
PAX5	5079	broad.mit.edu	37	9	36882019	36882019	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:36882019G>T	uc003zzo.1	-	c.994C>A	c.(994-996)CTG>ATG	p.L332M	PAX5_uc011lpt.1_Missense_Mutation_p.L128M|PAX5_uc011lpu.1_Intron|PAX5_uc011lpv.1_Intron|PAX5_uc011lpw.1_Intron|PAX5_uc011lpx.1_Intron|PAX5_uc011lpy.1_Intron|PAX5_uc010mls.1_Intron|PAX5_uc011lpz.1_Missense_Mutation_p.L289M|PAX5_uc011lqa.1_Missense_Mutation_p.L224M|PAX5_uc010mlq.1_Non-coding_Transcript|PAX5_uc011lqb.1_Non-coding_Transcript|PAX5_uc010mlo.1_Intron|PAX5_uc010mlp.1_Missense_Mutation_p.L332M|PAX5_uc011lqc.1_Missense_Mutation_p.L289M|PAX5_uc010mlr.1_Intron	NM_016734	NP_057953	Q02548	PAX5_HUMAN	paired box 5	332					cell differentiation|humoral immune response|nervous system development|organ morphogenesis|spermatogenesis|transcription from RNA polymerase II promoter	nucleus	DNA binding	p.?(22)	PAX5/JAK2(18)	haematopoietic_and_lymphoid_tissue(139)|central_nervous_system(2)	141		all_cancers(2;3.46e-10)|Acute lymphoblastic leukemia(2;7.09e-56)|all_hematologic(2;6.65e-44)		GBM - Glioblastoma multiforme(29;0.0108)						323				0.238095	11.163267	12.480177	5	16	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36882019	36882019	11902	9	G	T	T	T	438	34	PAX5	2	2
FRMPD1	22844	broad.mit.edu	37	9	37745336	37745336	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:37745336G>T	uc004aag.1	+	c.3307G>T	c.(3307-3309)GAG>TAG	p.E1103*	FRMPD1_uc004aah.1_Nonsense_Mutation_p.E1103*	NM_014907	NP_055722	Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1103						cytoskeleton|cytosol|plasma membrane				ovary(4)|central_nervous_system(2)|breast(1)	7				GBM - Glioblastoma multiforme(29;0.00655)										0.079365	-0.777447	10.606219	5	58	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	37745336	37745336	6307	9	G	T	T	T	429	33	FRMPD1	5	2
ALDH1B1	219	broad.mit.edu	37	9	38396569	38396569	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:38396569G>T	uc004aay.2	+	c.824G>T	c.(823-825)GGC>GTC	p.G275V		NM_000692	NP_000683	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1B1 precursor	275					carbohydrate metabolic process|oxidation-reduction process	mitochondrial matrix|nucleus	aldehyde dehydrogenase (NAD) activity				0				GBM - Glioblastoma multiforme(29;0.043)|Lung(182;0.115)	NADH(DB00157)									0.303571	45.356243	47.283218	17	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38396569	38396569	496	9	G	T	T	T	546	42	ALDH1B1	2	2
KIAA1432	57589	broad.mit.edu	37	9	5765719	5765719	+	Nonsense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:5765719C>T	uc003zji.2	+	c.2821C>T	c.(2821-2823)CAG>TAG	p.Q941*	KIAA1432_uc003zjh.2_Nonsense_Mutation_p.Q941*|KIAA1432_uc003zjl.3_Nonsense_Mutation_p.Q904*|KIAA1432_uc003zjj.1_Nonsense_Mutation_p.Q483*|ERMP1_uc011lme.1_Non-coding_Transcript	NM_020829	NP_065880	Q4ADV7	RIC1_HUMAN	connexin 43-interacting protein 150 isoform a	1020						integral to membrane					0		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)										0.15	48.006816	71.515298	30	170	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	5765719	5765719	8542	9	C	T	T	T	273	21	KIAA1432	5	2
WWC3	55841	broad.mit.edu	37	X	10085245	10085245	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:10085245C>A	uc004csx.3	+	c.1146C>A	c.(1144-1146)AGC>AGA	p.S382R	WWC3_uc010nds.2_Missense_Mutation_p.S46R|WWC3_uc010ndt.2_Non-coding_Transcript	NM_015691	NP_056506	Q9ULE0	WWC3_HUMAN	WWC family member 3	382	Ser-rich.									ovary(4)	4														0.208333	11.261943	13.15257	5	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10085245	10085245	17987	23	C	A	A	A	337	26	WWC3	2	2
WBP5	51186	broad.mit.edu	37	X	102612685	102612685	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:102612685C>A	uc004ekd.2	+	c.73C>A	c.(73-75)CCT>ACT	p.P25T	WBP5_uc004eke.2_Missense_Mutation_p.P25T|WBP5_uc004ekf.2_Missense_Mutation_p.P25T|WBP5_uc004ekg.2_Missense_Mutation_p.P25T	NM_001006612	NP_001006613	Q9UHQ7	WPB5_HUMAN	WW domain binding protein 5	25	Glu-rich.										0														0.153061	26.257623	37.545576	15	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	102612685	102612685	17834	23	C	A	A	A	338	26	WBP5	2	2
MID2	11043	broad.mit.edu	37	X	107084310	107084310	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:107084310T>G	uc004enl.2	+	c.415T>G	c.(415-417)TGC>GGC	p.C139G	MID2_uc004enk.2_Missense_Mutation_p.C139G	NM_012216	NP_036348	Q9UJV3	TRIM1_HUMAN	midline 2 isoform 1	139	B box-type 1; degenerate.					centrosome|microtubule	ligase activity|zinc ion binding			ovary(1)	1														0.191781	31.508979	37.987226	14	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	107084310	107084310	9968	23	T	G	G	G	819	63	MID2	4	4
RGAG1	57529	broad.mit.edu	37	X	109698546	109698546	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:109698546G>T	uc004eor.1	+	c.4164G>T	c.(4162-4164)AAG>AAT	p.K1388N		NM_020769	NP_065820	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1388										lung(2)|ovary(1)	3														0.127193	43.010511	73.922112	29	199	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109698546	109698546	13747	23	G	T	T	T	464	36	RGAG1	2	2
DOCK11	139818	broad.mit.edu	37	X	117749590	117749590	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:117749590C>T	uc004eqp.2	+	c.3208C>T	c.(3208-3210)CTG>TTG	p.L1070L	DOCK11_uc004eqq.2_Silent_p.L836L	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1070					blood coagulation	cytosol	GTP binding			ovary(3)	3														0.211538	27.295191	31.296521	11	41	KEEP	---	---	---	---	capture		Silent	SNP	117749590	117749590	4870	23	C	T	T	T	415	32	DOCK11	2	2
AIFM1	9131	broad.mit.edu	37	X	129274513	129274513	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:129274513G>T	uc004evg.2	-	c.776C>A	c.(775-777)GCA>GAA	p.A259E	AIFM1_uc011mur.1_5'Flank|AIFM1_uc011mus.1_Missense_Mutation_p.A259E|AIFM1_uc004evh.2_Missense_Mutation_p.A255E|AIFM1_uc004evi.2_Intron|AIFM1_uc004evk.2_Non-coding_Transcript	NM_004208	NP_004199	O95831	AIFM1_HUMAN	programmed cell death 8 isoform 1	259	FAD-dependent oxidoreductase (By similarity).				activation of caspase activity|apoptosis in response to endoplasmic reticulum stress|cell redox homeostasis|DNA damage response, signal transduction resulting in induction of apoptosis|DNA fragmentation involved in apoptotic nuclear change|oxidation-reduction process	cytosol|mitochondrial inner membrane|mitochondrial intermembrane space|nucleus|perinuclear region of cytoplasm	DNA binding|electron carrier activity|flavin adenine dinucleotide binding|oxidoreductase activity|protein binding			ovary(4)|central_nervous_system(1)	5										210				0.093525	8.062732	31.157908	13	126	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	129274513	129274513	429	23	G	T	T	T	598	46	AIFM1	2	2
TLR8	51311	broad.mit.edu	37	X	12940114	12940114	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:12940114G>A	uc004cvd.2	+	c.3009G>A	c.(3007-3009)CAG>CAA	p.Q1003Q	TLR8_uc004cve.2_Silent_p.Q985Q	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	985	Cytoplasmic (Potential).|TIR.				cellular response to mechanical stimulus|defense response to virus|I-kappaB kinase/NF-kappaB cascade|immunoglobulin mediated immune response|inflammatory response|innate immune response|positive regulation of innate immune response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process	endosome membrane|integral to membrane	DNA binding|double-stranded RNA binding|single-stranded RNA binding|transmembrane receptor activity			ovary(4)|large_intestine(1)	5														0.3	49.824441	51.969999	18	42	KEEP	---	---	---	---	capture		Silent	SNP	12940114	12940114	16487	23	G	A	A	A	438	34	TLR8	2	2
CXorf66	347487	broad.mit.edu	37	X	139038644	139038644	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:139038644T>A	uc004fbb.2	-	c.497A>T	c.(496-498)AAG>ATG	p.K166M		NM_001013403	NP_001013421	Q5JRM2	CX066_HUMAN	hypothetical protein LOC347487 precursor	166	Ser-rich.|Cytoplasmic (Potential).					integral to membrane					0														0.185771	102.071224	125.490457	47	206	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	139038644	139038644	4283	23	T	A	A	A	728	56	CXorf66	3	3
MAGEC2	51438	broad.mit.edu	37	X	141290725	141290725	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:141290725G>C	uc004fbu.1	-	c.1049C>G	c.(1048-1050)ACC>AGC	p.T350S		NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	350						cytoplasm|nucleus				breast(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.142045	96.691124	140.109099	50	302	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141290725	141290725	9562	23	G	C	C	C	572	44	MAGEC2	3	3
TKTL1	8277	broad.mit.edu	37	X	153524338	153524338	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153524338G>T	uc004fkg.2	+	c.126G>T	c.(124-126)ACG>ACT	p.T42T	TEX28_uc004fke.2_5'Flank|TEX28_uc004fkf.2_5'Flank|TEX28_uc010nut.1_5'Flank|TKTL1_uc011mzl.1_Silent_p.T42T|TKTL1_uc011mzm.1_Silent_p.T42T	NM_012253	NP_036385	P51854	TKTL1_HUMAN	transketolase-like 1 isoform a	42					glucose catabolic process|thiamine metabolic process	cytoplasm|nucleus	metal ion binding|transketolase activity			ovary(3)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.299213	98.912462	103.481536	38	89	KEEP	---	---	---	---	capture		Silent	SNP	153524338	153524338	16464	23	G	T	T	T	470	37	TKTL1	1	1
TKTL1	8277	broad.mit.edu	37	X	153551620	153551620	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153551620G>A	uc004fkg.2	+	c.1254G>A	c.(1252-1254)ACG>ACA	p.T418T	TKTL1_uc011mzl.1_Silent_p.T412T|TKTL1_uc011mzm.1_Silent_p.T214T|TKTL1_uc004fkh.2_Silent_p.T362T	NM_012253	NP_036385	P51854	TKTL1_HUMAN	transketolase-like 1 isoform a	418					glucose catabolic process|thiamine metabolic process	cytoplasm|nucleus	metal ion binding|transketolase activity			ovary(3)	3	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)													0.042424	-24.545791	12.487326	7	158	KEEP	---	---	---	---	capture		Silent	SNP	153551620	153551620	16464	23	G	A	A	A	470	37	TKTL1	1	1
VBP1	7411	broad.mit.edu	37	X	154448519	154448519	+	Silent	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:154448519G>A	uc004fnc.2	+	c.153G>A	c.(151-153)AAG>AAA	p.K51K	VBP1_uc004fnd.2_Silent_p.K14K	NM_003372	NP_003363	P61758	PFD3_HUMAN	von Hippel-Lindau binding protein 1	51					'de novo' posttranslational protein folding	nucleus|prefoldin complex	unfolded protein binding				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)													0.138889	9.249882	13.786753	5	31	KEEP	---	---	---	---	capture		Silent	SNP	154448519	154448519	17701	23	G	A	A	A	425	33	VBP1	2	2
PTCHD1	139411	broad.mit.edu	37	X	23397857	23397857	+	Silent	SNP	T	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:23397857T>C	uc004dal.3	+	c.501T>C	c.(499-501)AAT>AAC	p.N167N	PTCHD1_uc010nfu.1_Silent_p.N167N	NM_173495	NP_775766	Q96NR3	PTHD1_HUMAN	patched domain containing 1	167					cognition|smoothened signaling pathway	integral to membrane|plasma membrane	hedgehog receptor activity			ovary(4)|kidney(1)	5														0.246753	46.486838	50.983507	19	58	KEEP	---	---	---	---	capture		Silent	SNP	23397857	23397857	13186	23	T	C	C	C	647	50	PTCHD1	4	4
POLA1	5422	broad.mit.edu	37	X	24844714	24844714	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:24844714G>T	uc004dbl.2	+	c.3714G>T	c.(3712-3714)TGG>TGT	p.W1238C		NM_016937	NP_058633	P09884	DPOLA_HUMAN	DNA-directed DNA polymerase alpha 1	1238					cell proliferation|DNA replication checkpoint|DNA replication, synthesis of RNA primer|DNA-dependent DNA replication initiation|double-strand break repair via nonhomologous end joining|interspecies interaction between organisms|lagging strand elongation|leading strand elongation|M/G1 transition of mitotic cell cycle|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	alpha DNA polymerase:primase complex|cytoplasm|nuclear envelope|nuclear matrix|nucleolus|nucleoplasm	chromatin binding|DNA-directed DNA polymerase activity|metal ion binding|nucleoside binding			ovary(2)|skin(1)	3					Clofarabine(DB00631)|Fludarabine(DB01073)									0.1875	6.314584	7.778954	3	13	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	24844714	24844714	12615	23	G	T	T	T	572	44	POLA1	2	2
FAM47A	158724	broad.mit.edu	37	X	34148327	34148327	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34148327C>A	uc004ddg.2	-	c.2069G>T	c.(2068-2070)CGT>CTT	p.R690L		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	690										ovary(4)|central_nervous_system(1)	5														0.242105	63.299563	69.046643	23	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34148327	34148327	5790	23	C	A	A	A	247	19	FAM47A	1	1
FAM47A	158724	broad.mit.edu	37	X	34150064	34150064	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34150064T>A	uc004ddg.2	-	c.332A>T	c.(331-333)CAG>CTG	p.Q111L		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	111										ovary(4)|central_nervous_system(1)	5														0.051471	-13.092518	15.866016	7	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34150064	34150064	5790	23	T	A	A	A	715	55	FAM47A	3	3
FAM47A	158724	broad.mit.edu	37	X	34150393	34150393	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34150393C>T	uc004ddg.2	-	c.3G>A	c.(1-3)ATG>ATA	p.M1I		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	1										ovary(4)|central_nervous_system(1)	5														0.25	7.518925	8.200942	3	9	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34150393	34150393	5790	23	C	T	T	T	273	21	FAM47A	2	2
FAM47B	170062	broad.mit.edu	37	X	34961280	34961280	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34961280A>T	uc004ddi.1	+	c.332A>T	c.(331-333)CAG>CTG	p.Q111L		NM_152631	NP_689844	Q8NA70	FA47B_HUMAN	hypothetical protein LOC170062	111										ovary(3)|breast(1)	4														0.330709	129.111835	132.334881	42	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34961280	34961280	5791	23	A	T	T	T	91	7	FAM47B	3	3
LANCL3	347404	broad.mit.edu	37	X	37518781	37518781	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:37518781C>T	uc011mkd.1	+	c.764C>T	c.(763-765)TCA>TTA	p.S255L	LANCL3_uc004ddp.1_Missense_Mutation_p.S255L	NM_198511	NP_940913	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3	255							catalytic activity				0														0.093023	4.032285	18.3633	8	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	37518781	37518781	8945	23	C	T	T	T	377	29	LANCL3	2	2
ZNF674	641339	broad.mit.edu	37	X	46360580	46360580	+	Silent	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:46360580T>A	uc004dgr.2	-	c.444A>T	c.(442-444)TCA>TCT	p.S148S	ZNF674_uc011mlg.1_Silent_p.S142S	NM_001039891	NP_001034980	Q2M3X9	ZN674_HUMAN	zinc finger family member 674 isoform 1	148					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)	2														0.162162	13.326712	17.341362	6	31	KEEP	---	---	---	---	capture		Silent	SNP	46360580	46360580	18676	23	T	A	A	A	652	51	ZNF674	3	3
TIMP1	7076	broad.mit.edu	37	X	47444636	47444636	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47444636C>A	uc004dif.2	+	c.234C>A	c.(232-234)GCC>GCA	p.A78A	SYN1_uc004did.2_Intron|SYN1_uc004die.2_Intron|TIMP1_uc011mlr.1_Missense_Mutation_p.P2Q|TIMP1_uc010nht.1_Missense_Mutation_p.P2Q	NM_003254	NP_003245	P01033	TIMP1_HUMAN	tissue inhibitor of metalloproteinase 1	78	NTR.				erythrocyte maturation|negative regulation of membrane protein ectodomain proteolysis|platelet activation|platelet degranulation|positive regulation of cell proliferation	platelet alpha granule lumen	metal ion binding|metalloendopeptidase inhibitor activity|protein binding				0														0.2	9.432293	11.567757	5	20	KEEP	---	---	---	---	capture		Silent	SNP	47444636	47444636	16446	23	C	A	A	A	288	23	TIMP1	1	1
SYN1	6853	broad.mit.edu	37	X	47464643	47464643	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47464643G>T	uc004die.2	-	c.663C>A	c.(661-663)AAC>AAA	p.N221K	SYN1_uc004did.2_Missense_Mutation_p.N221K	NM_006950	NP_008881	P17600	SYN1_HUMAN	synapsin I isoform Ia	221	C; actin-binding and synaptic-vesicle binding.					cell junction|Golgi apparatus	actin binding|ATP binding|ligase activity|transporter activity			ovary(1)	1														0.096774	1.900461	6.952597	3	28	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	47464643	47464643	15961	23	G	T	T	T	464	36	SYN1	2	2
UXT	8409	broad.mit.edu	37	X	47516658	47516658	+	Nonsense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:47516658C>A	uc004dim.2	-	c.316G>T	c.(316-318)GGA>TGA	p.G106*	UXT_uc004din.2_Nonsense_Mutation_p.G94*|LOC100133957_uc011mls.1_5'Flank|LOC100133957_uc011mlt.1_5'Flank	NM_153477	NP_705582	Q9UBK9	UXT_HUMAN	ubiquitously-expressed transcript isoform 1	94					centrosome organization|mitochondrion transport along microtubule|protein folding	centrosome|nucleus|prefoldin complex	beta-tubulin binding|microtubule binding|unfolded protein binding				0														0.25	24.930172	27.203097	10	30	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	47516658	47516658	17675	23	C	A	A	A	286	22	UXT	5	2
SSX5	6758	broad.mit.edu	37	X	48053578	48053578	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48053578G>T	uc004diz.1	-	c.390C>A	c.(388-390)AAC>AAA	p.N130K	SSX5_uc004dja.1_Missense_Mutation_p.N89K	NM_021015	NP_066295	O60225	SSX5_HUMAN	synovial sarcoma, X breakpoint 5 isoform a	89					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0														0.241379	31.816555	35.359832	14	44	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48053578	48053578	15726	23	G	T	T	T	568	44	SSX5	2	2
CCDC22	28952	broad.mit.edu	37	X	49093592	49093592	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:49093592C>T	uc004dnd.1	+	c.90C>T	c.(88-90)ACC>ACT	p.T30T	CCDC22_uc011mna.1_Silent_p.T30T|CCDC22_uc004dnc.1_Non-coding_Transcript	NM_014008	NP_054727	O60826	CCD22_HUMAN	coiled-coil domain containing 22	30										central_nervous_system(1)	1														0.415094	66.940939	67.274406	22	31	KEEP	---	---	---	---	capture		Silent	SNP	49093592	49093592	2919	23	C	T	T	T	262	21	CCDC22	2	2
TSPYL2	64061	broad.mit.edu	37	X	53114877	53114877	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:53114877G>A	uc004drw.2	+	c.1303G>A	c.(1303-1305)GAC>AAC	p.D435N	TSPYL2_uc004drv.2_3'UTR|TSPYL2_uc004drx.1_Missense_Mutation_p.D40N	NM_022117	NP_071400	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	435					cell cycle|chromatin modification|negative regulation of cell cycle|negative regulation of cell growth|negative regulation of DNA replication|nucleosome assembly|regulation of protein kinase activity|regulation of signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|rDNA binding				0														0.215686	28.196887	32.00095	11	40	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	53114877	53114877	17213	23	G	A	A	A	429	33	TSPYL2	2	2
WNK3	65267	broad.mit.edu	37	X	54337551	54337551	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54337551C>T	uc004dtc.1	-	c.710_splice	c.e3+1	p.T237_splice	WNK3_uc004dtd.1_Splice_Site_SNP_p.T237_splice	NM_020922	NP_065973			WNK lysine deficient protein kinase 3 isoform 1						intracellular protein kinase cascade|protein phosphorylation		ATP binding|protein binding|protein serine/threonine kinase activity			lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11										290				0.5	19.050576	19.050576	6	6	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	54337551	54337551	17953	23	C	T	T	T	247	19	WNK3	5	1
ITIH5L	347365	broad.mit.edu	37	X	54777633	54777633	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:54777633T>A	uc004dtj.2	-	c.3533A>T	c.(3532-3534)CAA>CTA	p.Q1178L		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	inter-alpha (globulin) inhibitor H5-like	1178					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|ovary(1)|breast(1)|skin(1)	5										249				0.6	45.523256	45.740858	15	10	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	54777633	54777633	8212	23	T	A	A	A	819	63	ITIH5L	3	3
TEX11	56159	broad.mit.edu	37	X	69960564	69960564	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:69960564T>G	uc004dyl.2	-	c.875A>C	c.(874-876)AAC>ACC	p.N292T	TEX11_uc004dym.2_Missense_Mutation_p.N277T	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN	testis expressed sequence 11 isoform 1	292							protein binding			ovary(3)|breast(1)|skin(1)	5	Renal(35;0.156)													0.242424	21.683635	23.680208	8	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	69960564	69960564	16301	23	T	G	G	G	780	60	TEX11	4	4
MED12	9968	broad.mit.edu	37	X	70347238	70347238	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70347238G>C	uc004dyy.2	+	c.2902G>C	c.(2902-2904)GAG>CAG	p.E968Q	MED12_uc011mpq.1_Missense_Mutation_p.E968Q|MED12_uc004dyz.2_Missense_Mutation_p.E968Q|MED12_uc004dza.2_Missense_Mutation_p.E815Q|MED12_uc010nla.2_5'Flank	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	968					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)													0.238095	38.290579	42.240506	15	48	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70347238	70347238	9817	23	G	C	C	C	429	33	MED12	3	3
MED12	9968	broad.mit.edu	37	X	70348171	70348171	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:70348171G>T	uc004dyy.2	+	c.3235G>T	c.(3235-3237)GCA>TCA	p.A1079S	MED12_uc011mpq.1_Missense_Mutation_p.A1079S|MED12_uc004dyz.2_Missense_Mutation_p.A1079S|MED12_uc004dza.2_Missense_Mutation_p.A926S|MED12_uc010nla.2_5'Flank	NM_005120	NP_005111	Q93074	MED12_HUMAN	mediator complex subunit 12	1079					androgen receptor signaling pathway|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|protein C-terminus binding|protein domain specific binding|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	4	Renal(35;0.156)													0.166667	34.0075	44.755327	17	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	70348171	70348171	9817	23	G	T	T	T	598	46	MED12	2	2
PHKA1	5255	broad.mit.edu	37	X	71840577	71840577	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:71840577T>A	uc004eax.3	-	c.2135A>T	c.(2134-2136)CAG>CTG	p.Q712L	PHKA1_uc004eay.3_Missense_Mutation_p.Q712L|PHKA1_uc011mqi.1_Intron	NM_002637	NP_002628	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle) isoform	712					glucose metabolic process|glycogen catabolic process	cytosol|plasma membrane	calmodulin binding|glucan 1,4-alpha-glucosidase activity|phosphorylase kinase activity			ovary(3)	3	Renal(35;0.156)													0.311111	41.133235	42.563186	14	31	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	71840577	71840577	12267	23	T	A	A	A	715	55	PHKA1	3	3
BRWD3	254065	broad.mit.edu	37	X	79932142	79932142	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:79932142G>C	uc004edt.2	-	c.5375C>G	c.(5374-5376)GCC>GGC	p.A1792G	BRWD3_uc010nmi.1_Non-coding_Transcript|BRWD3_uc004edo.2_Missense_Mutation_p.A1388G|BRWD3_uc004edp.2_Missense_Mutation_p.A1621G|BRWD3_uc004edq.2_Missense_Mutation_p.A1388G|BRWD3_uc010nmj.1_Missense_Mutation_p.A1388G|BRWD3_uc004edr.2_Missense_Mutation_p.A1462G|BRWD3_uc004eds.2_Missense_Mutation_p.A1388G|BRWD3_uc004edu.2_Missense_Mutation_p.A1462G|BRWD3_uc004edv.2_Missense_Mutation_p.A1388G|BRWD3_uc004edw.2_Missense_Mutation_p.A1388G|BRWD3_uc004edx.2_Missense_Mutation_p.A1388G|BRWD3_uc004edy.2_Missense_Mutation_p.A1388G|BRWD3_uc004edz.2_Missense_Mutation_p.A1462G|BRWD3_uc004eea.2_Missense_Mutation_p.A1462G|BRWD3_uc004eeb.2_Missense_Mutation_p.A1388G	NM_153252	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	1792										ovary(4)	4														0.147727	26.715088	37.20105	13	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	79932142	79932142	1557	23	G	C	C	C	546	42	BRWD3	3	3
KLHL4	56062	broad.mit.edu	37	X	86877378	86877378	+	Silent	SNP	G	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:86877378G>T	uc004efa.2	+	c.1092G>T	c.(1090-1092)CTG>CTT	p.L364L	KLHL4_uc004efb.2_Silent_p.L364L	NM_057162	NP_476503	Q9C0H6	KLHL4_HUMAN	kelch-like 4 isoform 2	364						cytoplasm|microtubule cytoskeleton|nucleolus	actin binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5														0.12782	25.478691	43.439205	17	116	KEEP	---	---	---	---	capture		Silent	SNP	86877378	86877378	8705	23	G	T	T	T	600	47	KLHL4	2	2
CPXCR1	53336	broad.mit.edu	37	X	88008697	88008697	+	Silent	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:88008697C>A	uc004efd.3	+	c.282C>A	c.(280-282)ACC>ACA	p.T94T	CPXCR1_uc004efc.3_Silent_p.T94T	NM_033048	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	94						intracellular	zinc ion binding			ovary(3)	3														0.15625	13.202449	20.629515	10	54	KEEP	---	---	---	---	capture		Silent	SNP	88008697	88008697	3975	23	C	A	A	A	275	22	CPXCR1	2	2
PABPC5	140886	broad.mit.edu	37	X	90691483	90691483	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:90691483C>A	uc004efg.2	+	c.907C>A	c.(907-909)CCT>ACT	p.P303T	PABPC5_uc004eff.1_Missense_Mutation_p.P139T	NM_080832	NP_543022	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	303	RRM 4.					cytoplasm	nucleotide binding|RNA binding			ovary(1)|lung(1)|pancreas(1)	3														0.132353	10.232504	19.184706	9	59	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	90691483	90691483	11783	23	C	A	A	A	338	26	PABPC5	2	2
GPR143	4935	broad.mit.edu	37	X	9709396	9709396	+	Silent	SNP	C	T	T			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:9709396C>T	uc004cst.1	-	c.927G>A	c.(925-927)AAG>AAA	p.K309K		NM_000273	NP_000264	P51810	GP143_HUMAN	G protein-coupled receptor 143	289	Extracellular (Potential).				calcium-mediated signaling using intracellular calcium source|eye pigment biosynthetic process|melanosome organization|melanosome transport|phosphatidylinositol-mediated signaling|regulation of calcium-mediated signaling|visual perception	apical plasma membrane|Golgi apparatus|integral to membrane|lysosomal membrane|melanosome membrane|membrane fraction	dopamine binding|L-DOPA receptor activity|protein binding|tyrosine binding			ovary(1)	1		Hepatocellular(5;0.000888)												0.4	12.698101	12.785542	4	6	KEEP	---	---	---	---	capture		Silent	SNP	9709396	9709396	6925	23	C	T	T	T	415	32	GPR143	2	2
DNHD1	144132	broad.mit.edu	37	11	6567895	6567896	+	In_Frame_Ins	INS	-	TGCCCTACTGCA	TGCCCTACTGCA	rs35369957		TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:6567895_6567896insTGCCCTACTGCA	uc001mdw.3	+	c.5726_5727insTGCCCTACTGCA	c.(5725-5727)GCT>GCTGCCCTACTGCAT	p.1909_1910insALLH	DNHD1_uc001mds.1_3'UTR	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	1909_1910					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)										0.43			3	4		---	---	---	---	capture_indel		In_Frame_Ins	INS	6567895	6567896	4851	11	-	TGCCCTACTGCA	TGCCCTACTGCA	TGCCCTACTGCA	364	28	DNHD1	5	5
PLA2G15	23659	broad.mit.edu	37	16	68289854	68289855	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68289854_68289855insG	uc002evr.2	+	c.688_689insG	c.(688-690)TGGfs	p.W230fs	PLA2G15_uc010vld.1_Frame_Shift_Ins_p.L188fs|PLA2G15_uc010vle.1_Frame_Shift_Ins_p.W136fs|PLA2G15_uc010vlf.1_Intron|PLA2G15_uc002evs.2_Frame_Shift_Ins_p.W51fs	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)	230					fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1														0.43			3	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	68289854	68289855	12418	16	-	G	G	G	715	55	PLA2G15	5	5
DAB1	1600	broad.mit.edu	37	1	57480680	57480680	+	Frame_Shift_Del	DEL	T	-	-			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:57480680_57480680delT	uc001cys.1	-	c.1320_1320delA	c.(1318-1320)TCAfs	p.S440fs	DAB1_uc001cyt.1_Frame_Shift_Del_p.S438fs|DAB1_uc001cyq.1_Frame_Shift_Del_p.S438fs|DAB1_uc001cyr.1_Frame_Shift_Del_p.S354fs|DAB1_uc009vzw.1_Frame_Shift_Del_p.S422fs|DAB1_uc009vzx.1_Frame_Shift_Del_p.S440fs	NM_021080	NP_066566	O75553	DAB1_HUMAN	disabled homolog 1	473					cell differentiation|nervous system development					ovary(1)	1										395				0.47			20	23		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	57480680	57480680	4383	1	T	-	-	-	704	55	DAB1	5	5
ABCA4	24	broad.mit.edu	37	1	94495002	94495003	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:94495002_94495003insG	uc001dqh.2	-	c.4537_4538insC	c.(4537-4539)CAGfs	p.Q1513fs		NM_000350	NP_000341	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A member 4	1513	Extracellular.		Q -> R (in STGD1).		phototransduction, visible light|visual perception	integral to plasma membrane|membrane fraction	ATP binding|ATPase activity, coupled to transmembrane movement of substances			ovary(4)|central_nervous_system(2)|breast(1)	7		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)										0.38			3	5		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	94495002	94495003	35	1	-	G	G	G	715	55	ABCA4	5	5
GTPBP2	54676	broad.mit.edu	37	6	43596785	43596786	+	Frame_Shift_Ins	INS	-	C	C			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:43596785_43596786insC	uc003ovt.1	-	c.114_115insG	c.(112-117)GGGCCAfs	p.G38fs	GTPBP2_uc010jyv.2_5'Flank|GTPBP2_uc003ovs.2_Frame_Shift_Ins_p.G38fs|MAD2L1BP_uc003ovu.2_5'Flank	NM_019096	NP_061969	Q9BX10	GTPB2_HUMAN	GTP binding protein 2	38_39							GTP binding|GTPase activity			liver(1)	1	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GBM(116;405 1620 28302 32150 44768)								0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	43596785	43596786	7160	6	-	C	C	C	546	42	GTPBP2	5	5
COL19A1	1310	broad.mit.edu	37	6	70856740	70856740	+	Frame_Shift_Del	DEL	G	-	-			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:70856740_70856740delG	uc003pfc.1	+	c.1852_1852delG	c.(1852-1854)GGGfs	p.G618fs	COL19A1_uc010kam.1_Frame_Shift_Del_p.G514fs	NM_001858	NP_001849	Q14993	COJA1_HUMAN	alpha 1 type XIX collagen precursor	618	Triple-helical region 3 (COL3).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			ovary(2)|breast(2)	4														0.59			32	22		---	---	---	---	capture_indel		Frame_Shift_Del	DEL	70856740	70856740	3814	6	G	-	-	-	455	35	COL19A1	5	5
IL9R	3581	broad.mit.edu	37	X	155239822	155239827	+	In_Frame_Del	DEL	CAACAA	-	-			TCGA-17-Z014-01	TCGA-17-Z014-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:155239822_155239827delCAACAA	uc004fnv.1	+	c.1314_1319delCAACAA	c.(1312-1320)AGCAACAAC>AGC	p.NN441del	IL9R_uc004fnu.1_3'UTR	NM_002186	NP_002177	Q01113	IL9R_HUMAN	interleukin 9 receptor precursor	441_442	Poly-Asn.|Cytoplasmic (Potential).				cell proliferation	extracellular space|integral to plasma membrane	interleukin-9 receptor activity				0	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)													0.50			4	4		---	---	---	---	capture_indel		In_Frame_Del	DEL	155239822	155239827	8009	23	CAACAA	-	-	-	324	25	IL9R	5	5
