Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Genome_Change	Annotation_Transcript	Transcript_Strand	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
OR4C12	283093	broad.mit.edu	36	11	49959773	49959773	+	Missense_Mutation	SNP	T	A	A			TCGA-14-1455-01	TCGA-14-1455-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:49959773T>A	uc001nhc.1	-	c.841A>T	c.(841-843)AAT>TAT	p.N281Y		NM_001005270	NP_001005270	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C,	281	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2														0.438596	231.884767	232.447453	75	96	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49959773	49959773	11452	11	T	A	A	64	64	OR4C12	A	4	4
CATSPER1	117144	broad.mit.edu	36	11	65544400	65544400	+	Silent	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65544400C>T	uc001ogt.1	-	c.2028G>A	c.(2026-2028)ACG>ACA	p.T676T		NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1	676	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2														0.375	10.023165	10.132869	3	5	CC		KEEP	---	---	---	---	capture			Silent	SNP	65544400	65544400	2806	11	C	T	T	23	23	CATSPER1	T	1	1
NAALAD2	10003	broad.mit.edu	36	11	89531053	89531053	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:89531053C>A	uc001pdf.2	+	c.889C>A	c.(889-891)CGC>AGC	p.R297S	NAALAD2_uc001pdd.2_Silent_p.R297R|NAALAD2_uc001pde.2_Intron|NAALAD2_uc009yvx.1_Silent_p.R297R|NAALAD2_uc009yvy.1_Intron	NM_005467	NP_005458	Q9Y3Q0	NALD2_HUMAN	N-acetylated alpha-linked acidic dipeptidase 2	297	Extracellular (Potential).|NAALADase.				proteolysis	integral to membrane	carboxypeptidase activity|dipeptidase activity|dipeptidyl-peptidase activity|metal ion binding|metallopeptidase activity|serine-type peptidase activity			pancreas(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)												0.341176	92.753972	94.646513	29	56	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89531053	89531053	10523	11	C	A	A	19	19	NAALAD2	A	3	3
B3GNT4	79369	broad.mit.edu	36	12	121256921	121256921	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121256921G>C	uc001ubx.1	+	c.170G>C	c.(169-171)GGA>GCA	p.G57A	B3GNT4_uc001uby.1_Missense_Mutation_p.G32A	NM_030765	NP_110392	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal	57	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity			ovary(1)	1	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)										0.414634	50.170087	50.429905	17	24	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	121256921	121256921	1280	12	G	C	C	41	41	B3GNT4	C	3	3
SLC38A4	55089	broad.mit.edu	36	12	45459901	45459901	+	Missense_Mutation	SNP	A	T	T			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:45459901A>T	uc001rpi.1	-	c.587T>A	c.(586-588)CTC>CAC	p.L196H	SLC38A4_uc001rpj.1_Missense_Mutation_p.L196H|SLC38A4_uc009zkl.1_Missense_Mutation_p.L196H	NM_018018	NP_060488	Q969I6	S38A4_HUMAN	solute carrier family 38, member 4	196	Helical; (Potential).				cellular nitrogen compound metabolic process|sodium ion transport	integral to membrane|plasma membrane	amino acid transmembrane transporter activity|symporter activity			ovary(2)|central_nervous_system(1)	3	Lung SC(27;0.192)|Renal(347;0.236)													0.383721	96.852181	97.87223	33	53	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45459901	45459901	15103	12	A	T	T	11	11	SLC38A4	T	4	4
KRT71	112802	broad.mit.edu	36	12	51228203	51228203	+	Silent	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51228203C>T	uc001sao.1	-	c.978G>A	c.(976-978)AAG>AAA	p.K326K		NM_033448	NP_258259	Q3SY84	K2C71_HUMAN	keratin 71	326	Coil 2.|Rod.						structural molecule activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.194)										0.388889	171.46081	173.019842	56	88	CC		KEEP	---	---	---	---	capture			Silent	SNP	51228203	51228203	8799	12	C	T	T	24	24	KRT71	T	2	2
PAN3	255967	broad.mit.edu	36	13	27739001	27739001	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:27739001C>T	uc001urz.1	+	c.1123C>T	c.(1123-1125)CGG>TGG	p.R375W	PAN3_uc001urx.1_Missense_Mutation_p.R321W|PAN3_uc001ury.1_Missense_Mutation_p.R209W	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	375	Protein kinase.|Interaction with PAN2.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|protein phosphorylation	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)										0.392857	145.587716	146.709333	44	68	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27739001	27739001	11832	13	C	T	T	31	31	PAN3	T	1	1
SPERT	220082	broad.mit.edu	36	13	45185406	45185406	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:45185406G>A	uc001van.1	+	c.245G>A	c.(244-246)CGC>CAC	p.R82H	SPERT_uc001vao.2_Missense_Mutation_p.R46H	NM_152719	NP_689932	Q8NA61	SPERT_HUMAN	spermatid associated	82						cytoplasmic membrane-bounded vesicle				central_nervous_system(1)|pancreas(1)	2		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)										0.25	18.015307	19.603592	7	21	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45185406	45185406	15551	13	G	A	A	38	38	SPERT	A	1	1
CCDC135	84229	broad.mit.edu	36	16	56298948	56298948	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:56298948C>T	uc002emi.1	+	c.934C>T	c.(934-936)CGC>TGC	p.R312C	CCDC135_uc002emj.1_Missense_Mutation_p.R312C|CCDC135_uc002emk.1_Missense_Mutation_p.R247C	NM_032269	NP_115645	Q8IY82	CC135_HUMAN	coiled-coil domain containing 135	312						cytoplasm				central_nervous_system(1)	1														0.461538	20.149108	20.165822	6	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56298948	56298948	2889	16	C	T	T	27	27	CCDC135	T	1	1
DNAH9	1770	broad.mit.edu	36	17	11713182	11713182	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:11713182A>G	uc002gne.1	+	c.9940A>G	c.(9940-9942)AAT>GAT	p.N3314D	DNAH9_uc010coo.1_Missense_Mutation_p.N2608D	NM_001372	NP_001363	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9 isoform 2	3314	Stalk (By similarity).|Potential.				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)										0.101266	9.741986	22.270901	8	71	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11713182	11713182	4791	17	A	G	G	13	13	DNAH9	G	4	4
KRT33B	3884	broad.mit.edu	36	17	36774694	36774694	+	Silent	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36774694G>A	uc002hwl.1	-	c.960C>T	c.(958-960)AAC>AAT	p.N320N		NM_002279	NP_002270	Q14525	KT33B_HUMAN	type I hair keratin 3B	320	Coil 2.|Rod.					intermediate filament	protein binding|structural molecule activity				0		Breast(137;0.000496)												0.456897	164.857846	165.045005	53	63	GG		KEEP	---	---	---	---	capture			Silent	SNP	36774694	36774694	8785	17	G	A	A	40	40	KRT33B	A	1	1
G6PC	2538	broad.mit.edu	36	17	38316865	38316865	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:38316865G>A	uc002icb.1	+	c.970G>A	c.(970-972)GTC>ATC	p.V324I		NM_000151	NP_000142	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	324	Helical; (Potential).				gluconeogenesis|glucose homeostasis|transmembrane transport	integral to endoplasmic reticulum membrane	glucose-6-phosphatase activity|phosphate binding			ovary(1)|breast(1)|kidney(1)	3		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)										0.422886	800.649585	803.767609	255	348	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38316865	38316865	6394	17	G	A	A	40	40	G6PC	A	1	1
TBX4	9496	broad.mit.edu	36	17	56912380	56912380	+	Silent	SNP	C	A	A			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:56912380C>A	uc010ddo.1	+	c.939C>A	c.(937-939)CTC>CTA	p.L313L	TBX4_uc002izi.1_Silent_p.L313L	NM_018488	NP_060958	P57082	TBX4_HUMAN	T-box 4	313					leg morphogenesis|regulation of transcription, DNA-dependent|skeletal system morphogenesis	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			skin(1)	1														0.342105	32.67576	33.506838	13	25	CC		KEEP	---	---	---	---	capture			Silent	SNP	56912380	56912380	16186	17	C	A	A	31	31	TBX4	A	3	3
MED13	9969	broad.mit.edu	36	17	57398775	57398775	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1455-01	TCGA-14-1455-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:57398775T>C	uc002izo.1	-	c.4211A>G	c.(4210-4212)CAT>CGT	p.H1404R		NM_005121	NP_005112	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1404					androgen 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|receptor activity|RNA polymerase II transcription mediator activity|thyroid hormone receptor binding|transcription activator activity|vitamin D receptor binding			large_intestine(1)|ovary(1)	2														0.476744	113.927175	113.969507	41	45	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57398775	57398775	9819	17	T	C	C	51	51	MED13	C	4	4
ZBTB4	57659	broad.mit.edu	36	17	7310615	7310615	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1455-01	TCGA-14-1455-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7310615T>G	uc002ghc.2	-	c.230A>C	c.(229-231)AAC>ACC	p.N77T	ZBTB4_uc002ghd.2_Missense_Mutation_p.N77T	NM_001128833	NP_001122305	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	77	BTB.				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)										0.272727	7.502439	8.562417	6	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7310615	7310615	18127	17	T	G	G	60	60	ZBTB4	G	4	4
CCDC40	55036	broad.mit.edu	36	17	75628512	75628512	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:75628512G>A	uc010dht.1	+	c.400G>A	c.(400-402)GGG>AGG	p.G134R		NM_017950	NP_060420	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	134					axonemal dynein complex assembly|ciliary cell motility|cilium movement involved in determination of left/right asymmetry|flagellar cell motility	cilium|cytoplasm				ovary(3)	3	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)											0.333333	35.724444	36.703065	13	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75628512	75628512	2934	17	G	A	A	39	39	CCDC40	A	1	1
KIAA1632	57724	broad.mit.edu	36	18	41751643	41751643	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:41751643G>C	uc002lbm.1	-	c.3238C>G	c.(3238-3240)CAG>GAG	p.Q1080E	KIAA1632_uc002lbn.1_5'UTR|KIAA1632_uc002lbo.1_Missense_Mutation_p.Q1080E	NM_020964	NP_066015	Q9HCE0	EPG5_HUMAN	hypothetical protein LOC57724	1080					autophagy						0														0.371795	185.712574	187.963904	58	98	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	41751643	41751643	8558	18	G	C	C	46	46	KIAA1632	C	3	3
PPFIA3	8541	broad.mit.edu	36	19	54325520	54325520	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54325520G>A	uc002pmr.1	+	c.731G>A	c.(730-732)CGG>CAG	p.R244Q	PPFIA3_uc010emt.1_Missense_Mutation_p.R168Q|PPFIA3_uc002pms.2_Missense_Mutation_p.R112Q	NM_003660	NP_003651	O75145	LIPA3_HUMAN	PTPRF interacting protein alpha 3	244	Potential.					cell surface|cytoplasm	protein binding			lung(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.36e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000203)|GBM - Glioblastoma multiforme(486;0.00307)|Epithelial(262;0.00677)										0.521739	35.397752	35.40708	12	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54325520	54325520	12741	19	G	A	A	39	39	PPFIA3	A	1	1
ZNF473	25888	broad.mit.edu	36	19	55234325	55234325	+	Silent	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55234325G>A	uc002prn.1	+	c.105G>A	c.(103-105)GCG>GCA	p.A35A	ZNF473_uc002prm.1_Silent_p.A35A	NM_001006656	NP_056243	Q8WTR7	ZN473_HUMAN	zinc finger protein 473	35	KRAB.				histone mRNA 3'-end processing|regulation of transcription, DNA-dependent|termination of RNA polymerase II transcription	Cajal body	DNA binding|protein binding|zinc ion binding			ovary(1)|central_nervous_system(1)	2		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)										0.324786	108.601958	111.793705	38	79	GG		KEEP	---	---	---	---	capture			Silent	SNP	55234325	55234325	18525	19	G	A	A	40	40	ZNF473	A	1	1
KLK8	11202	broad.mit.edu	36	19	56195751	56195751	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:56195751C>T	uc002puq.1	-	c.106G>A	c.(106-108)GCG>ACG	p.A36T	KLK8_uc002pur.1_Intron|KLK8_uc002pus.1_Intron|KLK8_uc002put.1_Intron|KLK8_uc002puu.1_Intron|KLK9_uc002puv.1_Intron|KLK9_uc002puw.1_Intron	NM_144505	NP_653088	O60259	KLK8_HUMAN	kallikrein 8 isoform 2	23					cell death|keratinocyte proliferation|memory|negative regulation of axon regeneration|negative regulation of myelination|neuron projection morphogenesis|proteolysis|regulation of synapse organization|response to wounding	cytoplasm|extracellular space	protein binding|serine-type endopeptidase activity			central_nervous_system(1)	1		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.0033)|GBM - Glioblastoma multiforme(134;0.00888)										0.277778	13.867272	14.66706	5	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56195751	56195751	8724	19	C	T	T	25	25	KLK8	T	2	2
SYCP1	6847	broad.mit.edu	36	1	115218661	115218661	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:115218661C>T	uc001efr.1	+	c.610C>T	c.(610-612)CGG>TGG	p.R204W	SYCP1_uc001efq.1_Missense_Mutation_p.R204W|SYCP1_uc009wgw.1_Missense_Mutation_p.R204W	NM_003176	NP_003167	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	204	Potential.				cell division|reciprocal meiotic recombination|spermatogenesis|synaptonemal complex assembly		DNA binding				0	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)										0.416058	177.129476	177.976331	57	80	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115218661	115218661	15952	1	C	T	T	19	19	SYCP1	T	1	1
FCRL6	343413	broad.mit.edu	36	1	158046594	158046594	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:158046594G>A	uc001fud.2	+	c.973G>A	c.(973-975)GCA>ACA	p.A325T	FCRL6_uc001fuc.1_Missense_Mutation_p.A332T|FCRL6_uc009wsz.1_Missense_Mutation_p.A230T|FCRL6_uc009wta.1_Missense_Mutation_p.A325T	NM_001004310	NP_001004310	Q6DN72	FCRL6_HUMAN	Fc receptor-like 6	325	Helical; (Potential).					integral to membrane				ovary(2)	2	all_hematologic(112;0.0597)													0.141988	104.495562	165.48302	70	423	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	158046594	158046594	6036	1	G	A	A	46	46	FCRL6	A	2	2
BRP44	25874	broad.mit.edu	36	1	166155850	166155850	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:166155850C>T	uc001ges.1	-	c.338G>A	c.(337-339)CGT>CAT	p.R113H	BRP44_uc001get.1_Missense_Mutation_p.R113H|BRP44_uc001geu.1_Missense_Mutation_p.R113H	NM_015415	NP_056230	O95563	BR44_HUMAN	brain protein 44	113						mitochondrion					0	all_hematologic(923;0.215)			KIRC - Kidney renal clear cell carcinoma(1967;0.247)										0.269231	20.013393	21.262908	7	19	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	166155850	166155850	1549	1	C	T	T	19	19	BRP44	T	1	1
USH2A	7399	broad.mit.edu	36	1	213915533	213915533	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:213915533G>A	uc001hku.1	-	c.12343C>T	c.(12343-12345)CGT>TGT	p.R4115C		NM_206933	NP_996816	O75445	USH2A_HUMAN	usherin isoform B	4115	Fibronectin type-III 26.|Extracellular (Potential).		R -> C (in USH2A; uncertain pathogenicity).		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)										0.476744	271.442517	271.52311	82	90	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	213915533	213915533	17598	1	G	A	A	37	37	USH2A	A	1	1
NR0B2	8431	broad.mit.edu	36	1	27112649	27112649	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:27112649C>T	uc001bnf.1	-	c.370G>A	c.(370-372)GAG>AAG	p.E124K		NM_021969	NP_068804	Q15466	NR0B2_HUMAN	short heterodimer partner	124	Ligand-binding (By similarity).				cholesterol metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	DNA binding|protein domain specific binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity				0		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)										0.431818	60.719171	60.897148	19	25	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27112649	27112649	11019	1	C	T	T	30	30	NR0B2	T	2	2
ITGB2	3689	broad.mit.edu	36	21	45133181	45133181	+	Silent	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:45133181C>T	uc002zgd.1	-	c.1935G>A	c.(1933-1935)GCG>GCA	p.A645A	ITGB2_uc002zge.1_Silent_p.A645A|ITGB2_uc002zgf.2_Silent_p.A645A|ITGB2_uc010gpw.1_Silent_p.A588A|ITGB2_uc002zgg.1_Silent_p.A645A	NM_001127491	NP_001120963	P05107	ITB2_HUMAN	integrin, beta 2 precursor	645	Extracellular (Potential).				apoptosis|blood coagulation|cell-cell signaling|cell-matrix adhesion|inflammatory response|integrin-mediated signaling pathway|leukocyte cell-cell adhesion|multicellular organismal development|neutrophil chemotaxis|regulation of cell shape|regulation of immune response|regulation of peptidyl-tyrosine phosphorylation	integrin complex	glycoprotein binding|protein kinase binding|receptor activity			ovary(3)|central_nervous_system(3)|breast(2)	8				Colorectal(79;0.0669)	Simvastatin(DB00641)									0.25	11.594061	12.501769	4	12	CC		KEEP	---	---	---	---	capture			Silent	SNP	45133181	45133181	8198	21	C	T	T	23	23	ITGB2	T	1	1
LARGE	9215	broad.mit.edu	36	22	32003192	32003192	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:32003192G>A	uc003and.2	-	c.1927C>T	c.(1927-1929)CGG>TGG	p.R643W	LARGE_uc003ane.2_Missense_Mutation_p.R643W|LARGE_uc010gwp.1_Missense_Mutation_p.R591W	NM_004737	NP_598397	O95461	LARGE_HUMAN	like-glycosyltransferase	643	Lumenal (Potential).				glycosphingolipid biosynthetic process|muscle cell homeostasis|N-acetylglucosamine metabolic process|protein glycosylation	integral to Golgi membrane	acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)	2		Lung NSC(1;0.219)				Colon(70;397 1175 4573 19089 45288)								0.441176	42.01843	42.121126	15	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32003192	32003192	8950	22	G	A	A	38	38	LARGE	A	1	1
ST6GAL2	84620	broad.mit.edu	36	2	106826797	106826797	+	Silent	SNP	A	G	G			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:106826797A>G	uc002tdr.1	-	c.69T>C	c.(67-69)TTT>TTC	p.F23F	ST6GAL2_uc002tds.2_Silent_p.F23F	NM_032528	NP_115917	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	23	Helical; Signal-anchor for type II membrane protein; (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(3)	9														0.431373	69.341209	69.550827	22	29	AA		KEEP	---	---	---	---	capture			Silent	SNP	106826797	106826797	15740	2	A	G	G	1	1	ST6GAL2	G	4	4
MALL	7851	broad.mit.edu	36	2	110200607	110200607	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:110200607G>A	uc002tfk.1	-	c.416C>T	c.(415-417)GCC>GTC	p.A139V	MALL_uc010fju.1_Non-coding_Transcript	NM_005434	NP_005425	Q13021	MALL_HUMAN	mal, T-cell differentiation protein-like	139	MARVEL.|Helical; (Potential).				cholesterol homeostasis	clathrin-coated vesicle|Golgi membrane|integral to membrane|membrane raft|plasma membrane	protein binding			ovary(1)	1				Epithelial(1;0.0546)|STAD - Stomach adenocarcinoma(1;0.18)										0.217899	272.990919	310.657889	112	402	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	110200607	110200607	9584	2	G	A	A	42	42	MALL	A	2	2
MYO3B	140469	broad.mit.edu	36	2	171108742	171108742	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:171108742C>G	uc002ufy.1	+	c.3731C>G	c.(3730-3732)CCT>CGT	p.P1244R	MYO3B_uc010fqb.1_3'UTR|MYO3B_uc002ufz.1_Missense_Mutation_p.P1217R|MYO3B_uc002ufw.1_Non-coding_Transcript|MYO3B_uc002ufx.1_Non-coding_Transcript|MYO3B_uc002ugb.1_Non-coding_Transcript	NM_138995	NP_620482	Q8WXR4	MYO3B_HUMAN	myosin IIIB isoform 2	1244					protein phosphorylation|response to stimulus|visual perception	cytoplasm|myosin complex	actin binding|ATP binding|motor activity|protein serine/threonine kinase activity			lung(8)|ovary(5)|skin(2)|central_nervous_system(1)	16										1118				0.458824	125.611701	125.737635	39	46	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	171108742	171108742	10472	2	C	G	G	24	24	MYO3B	G	3	3
AGPS	8540	broad.mit.edu	36	2	178009817	178009817	+	Nonsense_Mutation	SNP	C	G	G			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:178009817C>G	uc002ull.2	+	c.521C>G	c.(520-522)TCA>TGA	p.S174*		NM_003659	NP_003650	O00116	ADAS_HUMAN	alkyldihydroxyacetone phosphate synthase	174					ether lipid biosynthetic process	peroxisomal matrix|peroxisomal membrane|plasma membrane	alkylglycerone-phosphate synthase activity|flavin adenine dinucleotide binding|oxidoreductase activity			ovary(2)|central_nervous_system(1)	3			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)											0.411765	114.507676	115.086082	35	50	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	178009817	178009817	397	2	C	G	G	29	29	AGPS	G	5	3
CRIM1	51232	broad.mit.edu	36	2	36627784	36627784	+	Missense_Mutation	SNP	T	G	G			TCGA-14-1455-01	TCGA-14-1455-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:36627784T>G	uc002rpd.1	+	c.2900T>G	c.(2899-2901)ATA>AGA	p.I967R		NM_016441	NP_057525	Q9NZV1	CRIM1_HUMAN	cysteine-rich motor neuron 1	967	Cytoplasmic (Potential).				nervous system development|regulation of cell growth	extracellular region|integral to membrane|plasma membrane	insulin-like growth factor binding|insulin-like growth factor receptor activity|serine-type endopeptidase inhibitor activity			ovary(2)	2		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)												0.40625	169.880688	170.862187	52	76	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36627784	36627784	4012	2	T	G	G	49	49	CRIM1	G	4	4
USP34	9736	broad.mit.edu	36	2	61414519	61414519	+	Splice_Site_SNP	SNP	A	C	C			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:61414519A>C	uc002sbe.1	-	c.e19_splice_site				NM_014709	NP_055524			ubiquitin specific protease 34						ubiquitin-dependent protein catabolic process		binding|cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(8)|breast(1)	9			Epithelial(17;0.229)											0.5	52.982297	52.982297	16	16	AA		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	61414519	61414519	17629	2	A	C	C	14	14	USP34	C	5	4
B3GNT2	10678	broad.mit.edu	36	2	62302885	62302885	+	Missense_Mutation	SNP	A	T	T			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:62302885A>T	uc002sbs.1	+	c.26A>T	c.(25-27)AAG>ATG	p.K9M	B3GNT2_uc010fco.1_Missense_Mutation_p.K9M	NM_006577	NP_006568	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal	9	Helical; Signal-anchor for type II membrane protein; (Potential).					Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity			ovary(1)	1	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)											0.109091	23.22561	48.201591	18	147	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62302885	62302885	1278	2	A	T	T	3	3	B3GNT2	T	4	4
ALDH1L1	10840	broad.mit.edu	36	3	127356098	127356098	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:127356098C>T	uc003eim.1	-	c.709G>A	c.(709-711)GCC>ACC	p.A237T	ALDH1L1_uc010hse.1_Non-coding_Transcript|ALDH1L1_uc003eio.2_5'UTR|ALDH1L1_uc010hsf.1_Missense_Mutation_p.A263T|ALDH1L1_uc003eip.1_Missense_Mutation_p.A144T	NM_012190	NP_036322	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	237					10-formyltetrahydrofolate catabolic process|biosynthetic process|oxidation-reduction process		acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)									0.540541	59.497141	59.549646	20	17	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	127356098	127356098	497	3	C	T	T	26	26	ALDH1L1	T	2	2
IGSF10	285313	broad.mit.edu	36	3	152648312	152648312	+	Missense_Mutation	SNP	C	G	G			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:152648312C>G	uc003ezb.1	-	c.2147G>C	c.(2146-2148)AGT>ACT	p.S716T		NM_178822	NP_849144	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	716					cell differentiation|multicellular organismal development|ossification	extracellular region				ovary(4)|central_nervous_system(1)	5			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)											0.416667	280.718119	282.025459	90	126	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152648312	152648312	7898	3	C	G	G	20	20	IGSF10	G	3	3
WDR49	151790	broad.mit.edu	36	3	168737367	168737367	+	Missense_Mutation	SNP	G	C	C			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:168737367G>C	uc003fev.1	-	c.883C>G	c.(883-885)CAA>GAA	p.Q295E	WDR49_uc003few.1_Intron|WDR49_uc003feu.1_Missense_Mutation_p.Q120E	NM_178824	NP_849146	Q8IV35	WDR49_HUMAN	WD repeat domain 49	295	WD 5.									large_intestine(1)|ovary(1)	2														0.433566	209.82922	210.379395	62	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	168737367	168737367	17875	3	G	C	C	48	48	WDR49	C	3	3
CLDN11	5010	broad.mit.edu	36	3	171623685	171623685	+	Silent	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:171623685G>A	uc003fgx.1	+	c.267G>A	c.(265-267)TCG>TCA	p.S89S	CLDN11_uc003fgy.1_Silent_p.S5S	NM_005602	NP_005593	O75508	CLD11_HUMAN	claudin 11	89	Helical; (Potential).				calcium-independent cell-cell adhesion	integral to membrane|tight junction	identical protein binding|structural molecule activity			central_nervous_system(1)	1	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)											0.494186	270.966224	270.971157	85	87	GG		KEEP	---	---	---	---	capture			Silent	SNP	171623685	171623685	3609	3	G	A	A	39	39	CLDN11	A	1	1
COL7A1	1294	broad.mit.edu	36	3	48595056	48595056	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1455-01	TCGA-14-1455-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:48595056T>C	uc003ctz.2	-	c.4553A>G	c.(4552-4554)AAG>AGG	p.K1518R		NM_000094	NP_000085	Q02388	CO7A1_HUMAN	alpha 1 type VII collagen precursor	1518	Triple-helical region.				cell adhesion|epidermis development	basement membrane|collagen type VII	protein binding|serine-type endopeptidase inhibitor activity			ovary(4)|breast(3)|skin(2)	9				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)										0.6	20.551332	20.63883	6	4	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48595056	48595056	3842	3	T	C	C	56	56	COL7A1	C	4	4
PDZRN3	23024	broad.mit.edu	36	3	73515478	73515478	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:73515478C>T	uc003dpl.1	-	c.2929G>A	c.(2929-2931)GAG>AAG	p.E977K	PDZRN3_uc010hoe.1_Missense_Mutation_p.E675K	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	977	Potential.						ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|pancreas(2)|large_intestine(1)	5		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)										0.396396	114.437551	115.48992	44	67	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73515478	73515478	12130	3	C	T	T	30	30	PDZRN3	T	2	2
SLIT2	9353	broad.mit.edu	36	4	20200423	20200423	+	Silent	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:20200423C>T	uc003gpr.1	+	c.3147C>T	c.(3145-3147)CAC>CAT	p.H1049H	SLIT2_uc003gps.1_Silent_p.H1041H	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2	1049	EGF-like 4.				apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|initiation of Roundabout signal transduction|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|ovary(3)	7														0.318182	61.851767	63.791054	21	45	CC		KEEP	---	---	---	---	capture			Silent	SNP	20200423	20200423	15238	4	C	T	T	19	19	SLIT2	T	1	1
HAUS3	79441	broad.mit.edu	36	4	2210564	2210564	+	Missense_Mutation	SNP	A	C	C			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:2210564A>C	uc003ges.1	-	c.914T>G	c.(913-915)GTG>GGG	p.V305G	HAUS3_uc003get.1_Missense_Mutation_p.V305G	NM_024511	NP_078787	Q68CZ6	HAUS3_HUMAN	hypothetical protein LOC79441	305	Potential.				cell division|centrosome organization|mitosis|spindle assembly	HAUS complex|microtubule|microtubule organizing center|spindle				large_intestine(2)|breast(2)	4														0.27027	9.156732	11.078494	10	27	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2210564	2210564	7249	4	A	C	C	6	6	HAUS3	C	4	4
PDGFRA	5156	broad.mit.edu	36	4	54825917	54825917	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1455-01	TCGA-14-1455-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:54825917T>C	uc003han.2	+	c.703T>C	c.(703-705)TGT>CGT	p.C235R	PDGFRA_uc003haa.1_Intron|PDGFRA_uc003hal.2_3'UTR|PDGFRA_uc010igq.1_Missense_Mutation_p.C129R|PDGFRA_uc003ham.2_Non-coding_Transcript	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	235	Ig-like C2-type 3.|Extracellular (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			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)			0.534591	1553.978856	1554.965069	510	444	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54825917	54825917	12082	4	T	C	C	55	55	PDGFRA	C	4	4
ENAM	10117	broad.mit.edu	36	4	71726774	71726774	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71726774C>T	uc003hfm.1	+	c.767C>T	c.(766-768)CCA>CTA	p.P256L		NM_031889	NP_114095	Q9NRM1	ENAM_HUMAN	enamelin	256					bone mineralization|odontogenesis	proteinaceous extracellular matrix	structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)											0.370787	100.046948	101.354393	33	56	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71726774	71726774	5305	4	C	T	T	21	21	ENAM	T	2	2
FGF5	2250	broad.mit.edu	36	4	81426595	81426595	+	Silent	SNP	A	C	C			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:81426595A>C	uc003hmd.1	+	c.552A>C	c.(550-552)ACA>ACC	p.T184T	FGF5_uc003hme.1_3'UTR	NM_004464	NP_004455	P12034	FGF5_HUMAN	fibroblast growth factor 5 isoform 1 precursor	184					cell proliferation|cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of cell division|positive regulation of cell proliferation	extracellular space	fibroblast growth factor receptor binding|growth factor activity			ovary(1)	1														0.385542	202.267779	204.171432	64	102	AA		KEEP	---	---	---	---	capture			Silent	SNP	81426595	81426595	6092	4	A	C	C	7	7	FGF5	C	4	4
GRM6	2916	broad.mit.edu	36	5	178342648	178342648	+	Missense_Mutation	SNP	C	A	A			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:178342648C>A	uc003mjr.1	-	c.2305G>T	c.(2305-2307)GCC>TCC	p.A769S	GRM6_uc003mjq.1_Missense_Mutation_p.A172S	NM_000843	NP_000834	O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6 precursor	769	Helical; Name=5; (Potential).				detection of visible light|visual perception	integral to plasma membrane				ovary(2)|breast(1)|pancreas(1)	4	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)										0.122807	8.201448	16.126175	7	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	178342648	178342648	7080	5	C	A	A	27	27	GRM6	A	3	3
RAB3C	115827	broad.mit.edu	36	5	57949384	57949384	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:57949384G>A	uc003jrp.1	+	c.182G>A	c.(181-183)AGC>AAC	p.S61N		NM_138453	NP_612462	Q96E17	RAB3C_HUMAN	RAB3C, member RAS oncogene family	61	Effector region (By similarity).				protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding			ovary(1)|central_nervous_system(1)	2		all_cancers(5;9.93e-10)|all_epithelial(5;1.49e-10)|all_lung(5;8.97e-05)|Lung NSC(5;0.000139)|Prostate(74;0.0664)		OV - Ovarian serous cystadenocarcinoma(10;1.8e-34)										0.333333	70.613181	72.537456	26	52	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	57949384	57949384	13392	5	G	A	A	34	34	RAB3C	A	2	2
CCDC125	202243	broad.mit.edu	36	5	68614397	68614397	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:68614397A>G	uc003jvv.1	-	c.1451T>C	c.(1450-1452)ATT>ACT	p.I484T	CCDC125_uc003jvw.1_Missense_Mutation_p.I359T|CCDC125_uc003jvx.1_3'UTR|CCDC125_uc003jvy.1_Non-coding_Transcript	NM_176816	NP_789786	Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	484											0		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)										0.521277	326.353581	326.427623	98	90	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68614397	68614397	2881	5	A	G	G	4	4	CCDC125	G	4	4
ANKRD34B	340120	broad.mit.edu	36	5	79891364	79891364	+	Silent	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:79891364G>A	uc010jam.1	-	c.231C>T	c.(229-231)CCC>CCT	p.P77P	ANKRD34B_uc003kgw.1_Silent_p.P77P|ANKRD34B_uc010jan.1_Silent_p.P77P|ANKRD34B_uc010jao.1_Silent_p.P77P	NM_001004441	NP_001004441	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	77	ANK 2.					cytoplasm|nucleus				pancreas(1)	1		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)										0.133758	65.50257	106.45117	42	272	GG		KEEP	---	---	---	---	capture			Silent	SNP	79891364	79891364	670	5	G	A	A	47	47	ANKRD34B	A	2	2
ANKRD34B	340120	broad.mit.edu	36	5	79891436	79891436	+	Silent	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:79891436G>A	uc010jam.1	-	c.159C>T	c.(157-159)ACC>ACT	p.T53T	ANKRD34B_uc003kgw.1_Silent_p.T53T|ANKRD34B_uc010jan.1_Silent_p.T53T|ANKRD34B_uc010jao.1_Silent_p.T53T	NM_001004441	NP_001004441	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	53	ANK 2.					cytoplasm|nucleus				pancreas(1)	1		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)										0.110345	40.885044	84.449465	32	258	GG		KEEP	---	---	---	---	capture			Silent	SNP	79891436	79891436	670	5	G	A	A	47	47	ANKRD34B	A	2	2
ARID1B	57492	broad.mit.edu	36	6	157264306	157264306	+	Silent	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:157264306G>A	uc003qqn.1	+	c.1668G>A	c.(1666-1668)GCG>GCA	p.A556A	ARID1B_uc003qqo.1_Silent_p.A569A|ARID1B_uc003qqp.1_Silent_p.A556A	NM_017519	NP_059989	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	614	Gln-rich.				chromatin-mediated maintenance of transcription|nervous system development|transcription, DNA-dependent	SWI/SNF complex	DNA binding|protein binding|transcription coactivator activity			breast(1)	1		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)										0.346154	24.205344	24.730994	9	17	GG		KEEP	---	---	---	---	capture			Silent	SNP	157264306	157264306	929	6	G	A	A	38	38	ARID1B	A	1	1
LPA	4018	broad.mit.edu	36	6	160888899	160888899	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:160888899G>A	uc003qtl.1	-	c.5216C>T	c.(5215-5217)ACG>ATG	p.T1739M		NM_005577	NP_005568	P08519	APOA_HUMAN	lipoprotein Lp(a) precursor	4247	Kringle 38.				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|pancreas(1)	4		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)									0.453125	355.547942	356.03727	116	140	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	160888899	160888899	9276	6	G	A	A	40	40	LPA	A	1	1
FKBP5	2289	broad.mit.edu	36	6	35652798	35652798	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:35652798C>T	uc003okx.1	-	c.1217G>A	c.(1216-1218)CGC>CAC	p.R406H	FKBP5_uc003oky.1_Missense_Mutation_p.R406H	NM_004117	NP_004108	Q13451	FKBP5_HUMAN	FK506 binding protein 5	406					protein folding	cytoplasm|membrane|nucleus	FK506 binding|heat shock protein binding|peptidyl-prolyl cis-trans isomerase activity			ovary(1)	1														0.567251	314.38343	315.056486	97	74	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35652798	35652798	6149	6	C	T	T	27	27	FKBP5	T	1	1
WNT2	7472	broad.mit.edu	36	7	116705570	116705570	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:116705570G>A	uc003viz.1	-	c.958C>T	c.(958-960)CGG>TGG	p.R320W	WNT2_uc003vja.1_Missense_Mutation_p.R224W	NM_003391	NP_003382	P09544	WNT2_HUMAN	wingless-type MMTV integration site family	320					atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|negative regulation of gene-specific transcription from RNA polymerase II promoter|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			central_nervous_system(2)|ovary(1)|breast(1)	4	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)										0.303571	96.900238	100.762811	34	78	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	116705570	116705570	17960	7	G	A	A	39	39	WNT2	A	1	1
ATP6V0A4	50617	broad.mit.edu	36	7	138051068	138051068	+	Silent	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:138051068G>A	uc003vuf.1	-	c.2238C>T	c.(2236-2238)GCC>GCT	p.A746A	ATP6V0A4_uc003vug.1_Silent_p.A746A|ATP6V0A4_uc003vuh.1_Silent_p.A746A	NM_130841	NP_570856	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit	746	Helical; (Potential).				cellular iron ion homeostasis|excretion|insulin receptor signaling pathway|ossification|regulation of pH|sensory perception of sound|transferrin transport	apical plasma membrane|brush border membrane|endosome membrane|integral to membrane|proton-transporting two-sector ATPase complex, proton-transporting domain	ATPase binding|hydrogen ion transmembrane transporter activity			pancreas(1)	1														0.435897	52.180844	52.317887	17	22	GG		KEEP	---	---	---	---	capture			Silent	SNP	138051068	138051068	1189	7	G	A	A	43	43	ATP6V0A4	A	2	2
C7orf34	135927	broad.mit.edu	36	7	142347658	142347658	+	Silent	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142347658G>A	uc003wca.2	+	c.231G>A	c.(229-231)TCG>TCA	p.S77S		NM_178829	NP_849151	Q96L11	CG034_HUMAN	hypothetical protein LOC135927	77						extracellular region					0	Melanoma(164;0.059)													0.207469	106.850819	125.968834	50	191	GG		KEEP	---	---	---	---	capture			Silent	SNP	142347658	142347658	2496	7	G	A	A	40	40	C7orf34	A	1	1
MLL3	58508	broad.mit.edu	36	7	151466914	151466914	+	Missense_Mutation	SNP	T	C	C			TCGA-14-1455-01	TCGA-14-1455-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:151466914T>C	uc003wla.1	-	c.14543A>G	c.(14542-14544)AAC>AGC	p.N4848S	MLL3_uc003wkz.1_Missense_Mutation_p.N3962S|MLL3_uc003wkx.1_Missense_Mutation_p.N1006S|MLL3_uc003wky.2_Missense_Mutation_p.N2408S	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	4848	SET.|S-adenosyl-L-methionine binding (By similarity).				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				0.220544	187.202353	210.998644	73	258	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151466914	151466914	10012	7	T	C	C	60	60	MLL3	C	4	4
HECW1	23072	broad.mit.edu	36	7	43451459	43451459	+	Silent	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:43451459C>T	uc003tid.1	+	c.2163C>T	c.(2161-2163)TCC>TCT	p.S721S		NM_015052	NP_055867	Q76N89	HECW1_HUMAN	NEDD4-like ubiquitin-protein ligase 1	721					protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	ubiquitin-protein ligase activity			ovary(7)|breast(2)|skin(2)|pancreas(1)|lung(1)	13										944				0.283688	107.332114	113.264218	40	101	CC		KEEP	---	---	---	---	capture			Silent	SNP	43451459	43451459	7325	7	C	T	T	23	23	HECW1	T	1	1
EGFR	1956	broad.mit.edu	36	7	55191801	55191801	+	Missense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55191801C>T	uc003tqk.1	+	c.1088C>T	c.(1087-1089)ACC>ATC	p.T363I	EGFR_uc003tqh.1_Missense_Mutation_p.T363I|EGFR_uc003tqi.1_Missense_Mutation_p.T363I|EGFR_uc003tqj.1_Missense_Mutation_p.T363I|EGFR_uc010kzg.1_Missense_Mutation_p.T318I	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	363	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.212219	143.354553	167.201849	66	245	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55191801	55191801	5156	7	C	T	T	18	18	EGFR	T	2	2
ABCB4	5244	broad.mit.edu	36	7	86879148	86879148	+	Missense_Mutation	SNP	A	G	G			TCGA-14-1455-01	TCGA-14-1455-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86879148A>G	uc003uiv.1	-	c.2921T>C	c.(2920-2922)ATT>ACT	p.I974T	ABCB4_uc003uiw.1_Missense_Mutation_p.I974T|ABCB4_uc003uix.1_Intron	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	974	Helical; (By similarity).|ABC transmembrane type-1 2.				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|pancreas(1)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)													0.371429	79.919224	80.940157	26	44	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86879148	86879148	44	7	A	G	G	4	4	ABCB4	G	4	4
RIMS2	9699	broad.mit.edu	36	8	104993547	104993547	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-1455-01	TCGA-14-1455-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:104993547C>T	uc003yls.2	+	c.1117C>T	c.(1117-1119)CGA>TGA	p.R373*	RIMS2_uc003ylp.2_Nonsense_Mutation_p.R595*|RIMS2_uc003ylw.2_Nonsense_Mutation_p.R403*|RIMS2_uc003ylq.2_Nonsense_Mutation_p.R403*|RIMS2_uc003ylr.2_Nonsense_Mutation_p.R450*|RIMS2_uc003ylt.2_5'UTR	NM_014677	NP_055492	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	673	PDZ.				intracellular protein transport	cell junction|presynaptic membrane	Rab GTPase binding|zinc ion binding			ovary(6)|lung(2)|breast(2)|large_intestine(1)|central_nervous_system(1)|skin(1)|pancreas(1)	14			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)							728				0.377778	108.734086	109.911516	34	56	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	104993547	104993547	13845	8	C	T	T	31	31	RIMS2	T	5	1
ZHX1	11244	broad.mit.edu	36	8	124335627	124335627	+	Missense_Mutation	SNP	G	A	A			TCGA-14-1455-01	TCGA-14-1455-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:124335627G>A	uc003yqe.1	-	c.1741C>T	c.(1741-1743)CGT>TGT	p.R581C	C8orf76_uc003yqd.2_Intron|ZHX1_uc003yqf.1_Missense_Mutation_p.R581C|ZHX1_uc003yqg.1_Intron|ZHX1_uc010mdi.1_Missense_Mutation_p.R581C|ZHX1_uc010mdj.1_Missense_Mutation_p.R581C	NM_007222	NP_009153	Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	581	Homeobox 3.				negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)											0.496552	241.998944	242.000408	72	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124335627	124335627	18266	8	G	A	A	37	37	ZHX1	A	1	1
NPAS3	64067	broad.mit.edu	36	14	33338791	33338791	+	Frame_Shift_Del	DEL	C	-	-			TCGA-14-1455-01	TCGA-14-1455-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:33338791_33338791delC	uc001wru.1	+	c.1527_1527delC	c.(1525-1527)AACfs	p.N509fs	NPAS3_uc001wrt.1_Frame_Shift_Del_p.N477fs|NPAS3_uc001wrv.1_Frame_Shift_Del_p.N479fs|NPAS3_uc001wrs.1_Frame_Shift_Del_p.N496fs	NM_022123	NP_071406	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3 isoform 1	509					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity|transcription regulator activity			ovary(1)	1	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)										0.77			10	3				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	33338791	33338791	10968	14	C	-	-	19	19	NPAS3	-	5	5
LYST	1130	broad.mit.edu	36	1	233976398	233976399	+	Frame_Shift_Del	DEL	AC	-	-			TCGA-14-1455-01	TCGA-14-1455-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:233976398_233976399delAC	uc001hxj.1	-	c.7832_7833delGT	c.(7831-7833)CGTfs	p.R2611fs	LYST_uc009xga.1_Frame_Shift_Del_p.R247fs	NM_000081	NP_000072	Q99698	LYST_HUMAN	lysosomal trafficking regulator	2611					defense response to bacterium|defense response to protozoan|defense response to virus|endosome to lysosome transport via multivesicular body sorting pathway|leukocyte chemotaxis|mast cell secretory granule organization|melanosome organization|natural killer cell mediated cytotoxicity|protein transport	cytoplasm|microtubule cytoskeleton	protein binding			ovary(6)|breast(4)|central_nervous_system(2)	12	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)											0.45			43	52				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	233976398	233976399	9505	1	AC	-	-	2	2	LYST	-	5	5
FLNA	2316	broad.mit.edu	36	X	153244017	153244018	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-1455-01	TCGA-14-1455-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:153244017_153244018insC	uc004fkk.2	-	c.2527_2528insG	c.(2527-2529)GCTfs	p.A843fs	FLNA_uc010nuu.1_Frame_Shift_Ins_p.A843fs	NM_001110556	NP_001104026	P21333	FLNA_HUMAN	filamin A, alpha isoform 2	843	Filamin 6.				actin crosslink formation|actin cytoskeleton reorganization|cell junction assembly|cytoplasmic sequestering of protein|establishment of protein localization|inhibition of adenylate cyclase activity by dopamine receptor signaling pathway|negative regulation of protein catabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|platelet activation|platelet degranulation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of transcription factor import into nucleus|protein localization at cell surface|protein stabilization|receptor clustering	actin cytoskeleton|cell cortex|cytosol|extracellular region|nucleus|plasma membrane	actin filament binding|Fc-gamma receptor I complex binding|glycoprotein binding|GTP-Ral binding|protein homodimerization activity|Rac GTPase binding|signal transducer activity|transcription factor binding			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)									518				0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	153244017	153244018	6175	23	-	C	C	34	34	FLNA	C	5	5
