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
NRAP	4892	broad.mit.edu	37	10	115364589	115364589	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:115364589G>A	uc001lal.3	-	c.4006C>T	c.(4006-4008)CGC>TGC	p.R1336C	NRAP_uc009xyb.2_Missense_Mutation_p.R125C|NRAP_uc001laj.2_Missense_Mutation_p.R1336C|NRAP_uc001lak.2_Missense_Mutation_p.R1301C	NM_198060	NP_932326	Q86VF7	NRAP_HUMAN	nebulin-related anchoring protein isoform S	1336	Nebulin 35.					fascia adherens|muscle tendon junction	actin binding|muscle alpha-actinin binding|zinc ion binding			ovary(6)|central_nervous_system(3)	9		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)										0.053097	-12.393285	11.397326	6	107	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	115364589	115364589	11043	10	G	A	A	A	494	38	NRAP	1	1
RAB18	22931	broad.mit.edu	37	10	27826846	27826846	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:27826846G>A	uc001itw.2	+	c.574G>A	c.(574-576)GAA>AAA	p.E192K	RAB18_uc001itv.2_Missense_Mutation_p.E163K|RAB18_uc010qdq.1_Silent_p.L140L|RAB18_uc010qdr.1_Missense_Mutation_p.E99K	NM_021252	NP_067075	Q9NP72	RAB18_HUMAN	RAB18, member RAS oncogene family	163					endocytosis|protein transport|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction	intracellular|plasma membrane	ATP binding|GTP binding|GTPase activity|transcription factor binding				0														0.043478	-42.591278	24.219081	13	286	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27826846	27826846	13362	10	G	A	A	A	585	45	RAB18	2	2
RAB18	22931	broad.mit.edu	37	10	27826858	27826858	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:27826858G>A	uc001itw.2	+	c.586G>A	c.(586-588)GAA>AAA	p.E196K	RAB18_uc001itv.2_Missense_Mutation_p.E167K|RAB18_uc010qdq.1_Silent_p.L144L|RAB18_uc010qdr.1_Missense_Mutation_p.E103K	NM_021252	NP_067075	Q9NP72	RAB18_HUMAN	RAB18, member RAS oncogene family	167					endocytosis|protein transport|regulation of transcription, DNA-dependent|small GTPase mediated signal transduction	intracellular|plasma membrane	ATP binding|GTP binding|GTPase activity|transcription factor binding				0														0.043103	-51.384651	26.634043	15	333	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	27826858	27826858	13362	10	G	A	A	A	585	45	RAB18	2	2
ZNF518A	9849	broad.mit.edu	37	10	97916895	97916895	+	Silent	SNP	C	G	G			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:97916895C>G	uc001klp.2	+	c.816C>G	c.(814-816)ACC>ACG	p.T272T	ZNF518A_uc001klo.1_Intron|ZNF518A_uc001klq.2_Silent_p.T272T|ZNF518A_uc001klr.2_Silent_p.T272T	NM_014803	NP_055618	Q6AHZ1	Z518A_HUMAN	zinc finger protein 518	272	C2H2-type 4.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)										0.106667	11.541875	23.060861	8	67	KEEP	---	---	---	---	capture		Silent	SNP	97916895	97916895	18556	10	C	G	G	G	262	21	ZNF518A	3	3
SIX1	6495	broad.mit.edu	37	14	61113191	61113191	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:61113191G>C	uc001xfb.3	-	c.665C>G	c.(664-666)CCT>CGT	p.P222R		NM_005982	NP_005973	Q15475	SIX1_HUMAN	SIX homeobox 1	222					branching involved in ureteric bud morphogenesis|embryonic cranial skeleton morphogenesis|epithelial cell differentiation|inner ear morphogenesis|mesonephric tubule formation|metanephric mesenchyme development|myoblast migration|negative regulation of neuron apoptosis|organ induction|pattern specification process|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of gene-specific transcription|positive regulation of transcription from RNA polymerase II promoter|positive regulation of ureteric bud formation|protein localization to nucleus|regulation of branch elongation involved in ureteric bud branching|regulation of neuron differentiation|skeletal muscle tissue development|thymus development|thyroid gland development	nucleolus|transcription factor complex	promoter binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription activator activity				0				OV - Ovarian serous cystadenocarcinoma(108;0.0201)										0.101266	13.13054	38.156268	16	142	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	61113191	61113191	14841	14	G	C	C	C	455	35	SIX1	3	3
DICER1	23405	broad.mit.edu	37	14	95592941	95592941	+	Silent	SNP	T	C	C			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:95592941T>C	uc001ydw.2	-	c.879A>G	c.(877-879)AGA>AGG	p.R293R	DICER1_uc001ydv.2_Silent_p.R283R|DICER1_uc001ydx.2_Silent_p.R293R	NM_030621	NP_085124	Q9UPY3	DICER_HUMAN	dicer1	293	Required for interaction with PRKRA and TARBP2.				negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-microRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			ovary(1)|pancreas(1)|lung(1)|skin(1)	4		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)						741				0.041958	-18.0746	14.1537	6	137	KEEP	---	---	---	---	capture		Silent	SNP	95592941	95592941	4700	14	T	C	C	C	699	54	DICER1	4	4
CCDC144A	9720	broad.mit.edu	37	17	16612509	16612509	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:16612509T>A	uc002gqk.1	+	c.1138T>A	c.(1138-1140)TAC>AAC	p.Y380N	CCDC144A_uc002gql.1_Intron|LOC162632_uc010cpj.1_5'Flank	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	380											0														0.2	58.803952	69.277891	25	100	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	16612509	16612509	2897	17	T	A	A	A	637	49	CCDC144A	3	3
TP53	7157	broad.mit.edu	37	17	7578175	7578175	+	Splice_Site_SNP	SNP	A	T	T			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7578175A>T	uc002gim.2	-	c.672_splice	c.e6+1	p.E224_splice	TP53_uc002gig.1_Splice_Site_SNP_p.E224_splice|TP53_uc002gih.2_Splice_Site_SNP_p.E224_splice|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Splice_Site_SNP_p.E92_splice|TP53_uc010cng.1_Splice_Site_SNP_p.E92_splice|TP53_uc002gii.1_Splice_Site_SNP_p.E92_splice|TP53_uc010cnh.1_Splice_Site_SNP_p.E224_splice|TP53_uc010cni.1_Splice_Site_SNP_p.E224_splice|TP53_uc002gij.2_Splice_Site_SNP_p.E224_splice|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Splice_Site_SNP_p.E131_splice|TP53_uc002gio.2_Splice_Site_SNP_p.E92_splice|TP53_uc010vug.1_Missense_Mutation_p.V186D	NM_001126112	NP_001119584			tumor protein p53 isoform a						activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.?(9)|p.0?(6)|p.V225fs*24(1)|p.E224_V225insXX(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		Pancreas(47;798 1329 9957 10801)		111	(CAL120-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.413043	105.829449	106.437454	38	54	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	7578175	7578175	16923	17	A	T	T	T	130	10	TP53	5	3
DAND5	199699	broad.mit.edu	37	19	13080792	13080792	+	Silent	SNP	C	T	T			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:13080792C>T	uc002mwc.1	+	c.318C>T	c.(316-318)TTC>TTT	p.F106F	DAND5_uc010dyz.1_Silent_p.F136F	NM_152654	NP_689867	Q8N907	DAND5_HUMAN	dante precursor	106	CTCK.					extracellular region				ovary(1)	1			OV - Ovarian serous cystadenocarcinoma(19;1.87e-18)											0.125	11.157231	19.950381	8	56	KEEP	---	---	---	---	capture		Silent	SNP	13080792	13080792	4397	19	C	T	T	T	402	31	DAND5	1	1
C20orf26	26074	broad.mit.edu	37	20	20232314	20232314	+	Silent	SNP	C	T	T			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:20232314C>T	uc002wru.2	+	c.2235C>T	c.(2233-2235)ACC>ACT	p.T745T	C20orf26_uc010zse.1_Silent_p.T725T|C20orf26_uc002wrw.2_Non-coding_Transcript|C20orf26_uc002wrv.2_Silent_p.T101T	NM_015585	NP_056400	Q8NHU2	CT026_HUMAN	hypothetical protein LOC26074	745								p.T745T(1)		ovary(3)|pancreas(1)	4				READ - Rectum adenocarcinoma(2;0.171)										0.053498	-25.511436	25.564282	13	230	KEEP	---	---	---	---	capture		Silent	SNP	20232314	20232314	2186	20	C	T	T	T	288	23	C20orf26	1	1
ZHX3	23051	broad.mit.edu	37	20	39832386	39832386	+	Silent	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:39832386G>A	uc010ggg.1	-	c.1171C>T	c.(1171-1173)CTA>TTA	p.L391L	ZHX3_uc002xjq.1_Intron|ZHX3_uc002xjr.1_Silent_p.L391L|ZHX3_uc002xjs.1_Silent_p.L391L|ZHX3_uc002xjt.1_Silent_p.L391L|ZHX3_uc002xju.1_Silent_p.L391L|ZHX3_uc002xjv.1_Silent_p.L391L|ZHX3_uc002xjw.1_Silent_p.L391L	NM_015035	NP_055850	Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	391	Required for homodimerization and interaction with NFYA.|Required for repressor activity.				negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1		Myeloproliferative disorder(115;0.00425)												0.097015	11.873476	33.673709	13	121	KEEP	---	---	---	---	capture		Silent	SNP	39832386	39832386	18268	20	G	A	A	A	425	33	ZHX3	2	2
ZHX3	23051	broad.mit.edu	37	20	39832734	39832734	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:39832734G>A	uc010ggg.1	-	c.823C>T	c.(823-825)CAG>TAG	p.Q275*	ZHX3_uc002xjq.1_Intron|ZHX3_uc002xjr.1_Nonsense_Mutation_p.Q275*|ZHX3_uc002xjs.1_Nonsense_Mutation_p.Q275*|ZHX3_uc002xjt.1_Nonsense_Mutation_p.Q275*|ZHX3_uc002xju.1_Nonsense_Mutation_p.Q275*|ZHX3_uc002xjv.1_Nonsense_Mutation_p.Q275*|ZHX3_uc002xjw.1_Nonsense_Mutation_p.Q275*	NM_015035	NP_055850	Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	275	Required for homodimerization and interaction with NFYA.				negative regulation of transcription, DNA-dependent	cytoplasm|nucleolus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			pancreas(1)	1		Myeloproliferative disorder(115;0.00425)												0.097015	8.180624	29.983362	13	121	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	39832734	39832734	18268	20	G	A	A	A	611	47	ZHX3	5	2
KCNF1	3754	broad.mit.edu	37	2	11053385	11053385	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:11053385G>A	uc002rax.2	+	c.833G>A	c.(832-834)CGC>CAC	p.R278H		NM_002236	NP_002227	Q9H3M0	KCNF1_HUMAN	potassium voltage-gated channel, subfamily F,	278						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.128)										0.071429	-1.304591	6.640588	3	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	11053385	11053385	8331	2	G	A	A	A	494	38	KCNF1	1	1
CIB4	130106	broad.mit.edu	37	2	26806764	26806764	+	Missense_Mutation	SNP	A	C	C			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:26806764A>C	uc002rhm.2	-	c.331T>G	c.(331-333)TTT>GTT	p.F111V		NM_001029881	NP_001025052	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	111	EF-hand 2.|1 (Potential).						calcium ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.142857	26.313839	37.499001	13	78	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	26806764	26806764	3557	2	A	C	C	C	13	1	CIB4	4	4
ZNF514	84874	broad.mit.edu	37	2	95815929	95815929	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:95815929C>T	uc002sud.1	-	c.520G>A	c.(520-522)GAA>AAA	p.E174K	ZNF514_uc002sue.1_Missense_Mutation_p.E101K	NM_032788	NP_116177	Q96K75	ZN514_HUMAN	zinc finger protein 514	101					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.059432	-28.781479	49.757015	23	364	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	95815929	95815929	18553	2	C	T	T	T	390	30	ZNF514	2	2
ZDHHC23	254887	broad.mit.edu	37	3	113667649	113667649	+	De_novo_Start_InFrame	SNP	C	G	G			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:113667649C>G	uc003eau.2	+	c.0C>G	c.(-2-2)ATCAT>ATGAT		ZDHHC23_uc003eav.2_Intron	NM_173570	NP_775841			zinc finger, DHHC domain containing 23							integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2														0.056818	-5.495115	12.652163	5	83	KEEP	---	---	---	---	capture		De_novo_Start_InFrame	SNP	113667649	113667649	18202	3	C	G	G	G	365	29	ZDHHC23	5	3
ZBTB20	26137	broad.mit.edu	37	3	114070211	114070211	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:114070211G>C	uc003ebi.2	-	c.714C>G	c.(712-714)CAC>CAG	p.H238Q	ZBTB20_uc003ebj.2_Missense_Mutation_p.H165Q|ZBTB20_uc010hqp.2_Missense_Mutation_p.H165Q|ZBTB20_uc003ebk.2_Missense_Mutation_p.H165Q|ZBTB20_uc003ebl.2_Missense_Mutation_p.H165Q|ZBTB20_uc003ebm.2_Missense_Mutation_p.H165Q|ZBTB20_uc003ebn.2_Missense_Mutation_p.H165Q	NM_015642	NP_056457	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20 isoform	238					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)	4				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		NSCLC(69;748 1344 9802 11203 30933)								0.047619	-22.132109	19.331813	9	180	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	114070211	114070211	18115	3	G	C	C	C	620	48	ZBTB20	3	3
HHATL	57467	broad.mit.edu	37	3	42734573	42734573	+	Silent	SNP	G	C	C			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:42734573G>C	uc003clw.2	-	c.1386C>G	c.(1384-1386)CTC>CTG	p.L462L	HHATL_uc003clx.2_Silent_p.L462L	NM_020707	NP_065758	Q9HCP6	HHATL_HUMAN	hedgehog acyltransferase-like	462	Helical; (Potential).				negative regulation of N-terminal protein palmitoylation	endoplasmic reticulum membrane|integral to membrane|perinuclear region of cytoplasm				ovary(3)	3				KIRC - Kidney renal clear cell carcinoma(284;0.215)										0.091799	75.772164	212.799506	75	742	KEEP	---	---	---	---	capture		Silent	SNP	42734573	42734573	7374	3	G	C	C	C	574	45	HHATL	3	3
PDZRN3	23024	broad.mit.edu	37	3	73433228	73433228	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:73433228T>C	uc003dpl.1	-	c.2489A>G	c.(2488-2490)GAC>GGC	p.D830G	PDZRN3_uc011bgh.1_Missense_Mutation_p.D487G|PDZRN3_uc010hoe.1_Missense_Mutation_p.D528G|PDZRN3_uc011bgf.1_Missense_Mutation_p.D547G|PDZRN3_uc011bgg.1_Missense_Mutation_p.D550G	NM_015009	NP_055824	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	830							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)										0.140351	11.841864	19.036717	8	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73433228	73433228	12130	3	T	C	C	C	754	58	PDZRN3	4	4
GLRB	2743	broad.mit.edu	37	4	158060051	158060051	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:158060051A>G	uc003ipj.2	+	c.701A>G	c.(700-702)AAA>AGA	p.K234R		NM_000824	NP_000815	P48167	GLRB_HUMAN	glycine receptor, beta isoform A precursor	234	Extracellular (Probable).				nervous system development|neuropeptide signaling pathway|startle response	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	extracellular-glycine-gated chloride channel activity|protein binding|receptor activity				0	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.0564)|COAD - Colon adenocarcinoma(41;0.0642)|Kidney(143;0.0707)	Glycine(DB00145)									0.121951	9.647571	15.384187	5	36	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	158060051	158060051	6726	4	A	G	G	G	13	1	GLRB	4	4
GRIA2	2891	broad.mit.edu	37	4	158281079	158281079	+	Nonsense_Mutation	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:158281079G>A	uc003ipm.3	+	c.2075G>A	c.(2074-2076)TGG>TAG	p.W692*	GRIA2_uc011cit.1_Nonsense_Mutation_p.W645*|GRIA2_uc003ipl.3_Nonsense_Mutation_p.W692*|GRIA2_uc003ipk.3_Nonsense_Mutation_p.W645*|GRIA2_uc010iqh.1_Non-coding_Transcript|GRIA2_uc011ciu.1_Nonsense_Mutation_p.W2*|GRIA2_uc011civ.1_Non-coding_Transcript|GRIA2_uc011ciw.1_Non-coding_Transcript|GRIA2_uc011cix.1_Nonsense_Mutation_p.W2*|GRIA2_uc011ciy.1_Nonsense_Mutation_p.W2*|GRIA2_uc011ciz.1_Non-coding_Transcript	NM_001083619	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2 isoform 2	692	Extracellular (Potential).				synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			central_nervous_system(3)|ovary(1)	4	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	L-Glutamic Acid(DB00142)									0.196429	26.390964	31.200819	11	45	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	158281079	158281079	7046	4	G	A	A	A	611	47	GRIA2	5	2
HIST1H1T	3010	broad.mit.edu	37	6	26107824	26107824	+	Silent	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:26107824G>A	uc003ngj.2	-	c.498C>T	c.(496-498)AGC>AGT	p.S166S		NM_005323	NP_005314	P22492	H1T_HUMAN	histone cluster 1, H1t	166					cell differentiation|multicellular organismal development|nucleosome assembly|spermatogenesis	nucleosome	DNA binding			ovary(2)	2														0.039886	-55.837962	24.187093	14	337	KEEP	---	---	---	---	capture		Silent	SNP	26107824	26107824	7412	6	G	A	A	A	490	38	HIST1H1T	1	1
EGFR	1956	broad.mit.edu	37	7	55259515	55259515	+	Missense_Mutation	SNP	T	G	G	rs121434568		TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:55259515T>G	uc003tqk.2	+	c.2573T>G	c.(2572-2574)CTG>CGG	p.L858R	EGFR_uc010kzg.1_Missense_Mutation_p.L813R|EGFR_uc011kco.1_Missense_Mutation_p.L805R	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	858	Cytoplasmic (Potential).|Protein kinase.		L -> R (found in a lung cancer sample; somatic mutation).|L -> M (found in a lung cancer sample).		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	p.L858R(3084)|p.L858Q(3)|p.L858A(2)|p.L858W(1)|p.L858P(1)|p.L858L(1)|p.L858K(1)|p.L858G(1)|p.H805I(1)		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)		L858R(NCIH1975_LUNG)	8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.083851	0.770294	57.803394	27	295	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55259515	55259515	5156	7	T	G	G	G	715	55	EGFR	4	4
TSC1	7248	broad.mit.edu	37	9	135798791	135798791	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:135798791A>T	uc004cca.2	-	c.452T>A	c.(451-453)CTT>CAT	p.L151H	TSC1_uc004ccb.3_Missense_Mutation_p.L151H|TSC1_uc011mcq.1_Missense_Mutation_p.L100H|TSC1_uc011mcr.1_Missense_Mutation_p.L30H|TSC1_uc011mcs.1_Missense_Mutation_p.L30H|TSC1_uc004ccc.1_Missense_Mutation_p.L151H|TSC1_uc004ccd.2_Missense_Mutation_p.L151H|TSC1_uc004cce.1_Missense_Mutation_p.L151H	NM_000368	NP_000359	Q92574	TSC1_HUMAN	tuberous sclerosis 1 protein isoform 1	151					activation of Rho GTPase activity|cell cycle arrest|cell-matrix adhesion|insulin receptor signaling pathway|negative regulation of cell proliferation|negative regulation of protein ubiquitination|negative regulation of TOR signaling cascade|negative regulation of translation|positive regulation of focal adhesion assembly|regulation of phosphoprotein phosphatase activity|regulation of stress fiber assembly|rRNA export from nucleus	cell cortex|lamellipodium|membrane|TSC1-TSC2 complex	chaperone binding|protein N-terminus binding			lung(3)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|ovary(1)|bone(1)	9				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)						536				0.056818	-7.796298	10.355714	5	83	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	135798791	135798791	17156	9	A	T	T	T	39	3	TSC1	3	3
ACER2	340485	broad.mit.edu	37	9	19424829	19424829	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:19424829C>T	uc003zny.1	+	c.355C>T	c.(355-357)CGG>TGG	p.R119W	ACER2_uc003znx.1_Non-coding_Transcript|ACER2_uc003znz.1_Missense_Mutation_p.R70W	NM_001010887	NP_001010887	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	119	Cytoplasmic (Potential).				ceramide metabolic process|negative regulation of cell adhesion mediated by integrin|negative regulation of cell-matrix adhesion|negative regulation of protein glycosylation in Golgi|positive regulation of cell proliferation|response to retinoic acid|sphingosine biosynthetic process	integral to Golgi membrane	ceramidase activity				0														0.0625	-16.778012	24.744168	13	195	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	19424829	19424829	140	9	C	T	T	T	399	31	ACER2	1	1
SMARCA2	6595	broad.mit.edu	37	9	2056743	2056743	+	Silent	SNP	C	T	T			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:2056743C>T	uc003zhc.2	+	c.1245C>T	c.(1243-1245)TAC>TAT	p.Y415Y	SMARCA2_uc003zhd.2_Silent_p.Y415Y|SMARCA2_uc010mha.2_Silent_p.Y406Y	NM_003070	NP_003061	P51531	SMCA2_HUMAN	SWI/SNF-related matrix-associated	415					chromatin remodeling|negative regulation of gene-specific transcription from RNA polymerase II promoter|nervous system development|positive regulation of gene-specific transcription from RNA polymerase II promoter|transcription, DNA-dependent	intermediate filament cytoskeleton|nBAF complex|npBAF complex|nucleoplasm|SWI/SNF complex|WINAC complex	ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|protein binding|transcription activator activity|transcription coactivator activity			ovary(2)|central_nervous_system(1)	3		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)										0.184615	23.18118	29.23157	12	53	KEEP	---	---	---	---	capture		Silent	SNP	2056743	2056743	15267	9	C	T	T	T	220	17	SMARCA2	2	2
FLJ46321	389763	broad.mit.edu	37	9	84606360	84606360	+	Silent	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:84606360G>A	uc004amn.2	+	c.975G>A	c.(973-975)CCG>CCA	p.P325P		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	325						integral to membrane					0														0.030435	-81.809641	29.382705	14	446	KEEP	---	---	---	---	capture		Silent	SNP	84606360	84606360	6174	9	G	A	A	A	496	39	FLJ46321	1	1
NR0B1	190	broad.mit.edu	37	X	30322723	30322723	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:30322723C>A	uc004dcf.3	-	c.1386G>T	c.(1384-1386)ATG>ATT	p.M462I		NM_000475	NP_000466	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	462	AF-2 motif.|Ligand-binding (By similarity).			MM->AA: Strongly reduces homodimerization and interaction with NR0B2.	adrenal gland development|hypothalamus development|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of steroid hormone receptor signaling pathway|pituitary gland development|protein localization|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|steroid biosynthetic process	cytoplasm|membrane fraction|nucleoplasm|nucleus|polysomal ribosome	AF-2 domain binding|basal transcription repressor activity|DNA hairpin binding|ligand-regulated transcription factor activity|protein domain specific binding|protein homodimerization activity|RNA binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|steroid hormone receptor binding|transcription corepressor activity|transcription factor binding			ovary(1)|lung(1)	2					Dexamethasone(DB01234)|Tretinoin(DB00755)									0.06	-10.032465	20.317074	9	141	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	30322723	30322723	11018	23	C	A	A	A	325	25	NR0B1	2	2
FAM47A	158724	broad.mit.edu	37	X	34149571	34149571	+	Silent	SNP	G	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34149571G>A	uc004ddg.2	-	c.825C>T	c.(823-825)GAC>GAT	p.D275D		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	275										ovary(4)|central_nervous_system(1)	5														0.272727	38.406333	40.963827	15	40	KEEP	---	---	---	---	capture		Silent	SNP	34149571	34149571	5790	23	G	A	A	A	516	40	FAM47A	1	1
PIM2	11040	broad.mit.edu	37	X	48772395	48772395	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z047-01	TCGA-17-Z047-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:48772395T>A	uc004dls.2	-	c.497A>T	c.(496-498)GAT>GTT	p.D166V		NM_006875	NP_006866	Q9P1W9	PIM2_HUMAN	serine/threonine protein kinase pim-2	166	Protein kinase.				anti-apoptosis|cell proliferation|male meiosis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|protein phosphorylation|response to virus		ATP binding|protein serine/threonine kinase activity			lung(2)|stomach(1)	3										33				0.4	79.738454	80.306292	26	39	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	48772395	48772395	12352	23	T	A	A	A	650	50	PIM2	3	3
