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
FAM178A	55719	broad.mit.edu	36	10	102687199	102687199	+	Silent	SNP	A	G	G			TCGA-06-2565-01	TCGA-06-2565-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:102687199A>G	uc001krs.2	+	c.2487A>G	c.(2485-2487)ACA>ACG	p.T829T	FAM178A_uc001krt.2_Silent_p.T829T	NM_018121	NP_060591	Q8IX21	F178A_HUMAN	hypothetical protein LOC55719 isoform 1	829											0														0.803279	351.892688	362.338168	98	24	AA		KEEP	---	---	---	---	capture			Silent	SNP	102687199	102687199	5709	10	A	G	G	8	8	FAM178A	G	4	4
BMI1	648	broad.mit.edu	36	10	22657615	22657615	+	Silent	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:22657615C>T	uc009xkg.1	+	c.981C>T	c.(979-981)GAC>GAT	p.D327D	BMI1_uc001irh.1_Silent_p.D184D	NM_005180	NP_005171	P35226	BMI1_HUMAN	BMI1 polycomb ring finger oncogene	184	Interaction with E4F1.				hemopoiesis|positive regulation of fibroblast proliferation|positive regulation of ubiquitin-protein ligase activity|segment specification|transcription, DNA-dependent	cytoplasm|nucleolus|ubiquitin ligase complex	RING-like zinc finger domain binding|zinc ion binding			ovary(1)	1										116				0.78481	198.479245	204.387215	62	17	CC		KEEP	---	---	---	---	capture			Silent	SNP	22657615	22657615	1480	10	C	T	T	17	17	BMI1	T	2	2
DNA2	1763	broad.mit.edu	36	10	69867003	69867003	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:69867003C>T	uc001jof.1	-	c.1675G>A	c.(1675-1677)GAG>AAG	p.E559K	DNA2_uc001jog.1_Missense_Mutation_p.E473K|DNA2_uc001joh.1_Non-coding_Transcript	NM_001080449	NP_001073918	P51530	DNA2L_HUMAN	DNA replication helicase 2 homolog	473					base-excision repair|DNA replication, removal of RNA primer|mitochondrial DNA repair|mitochondrial DNA replication|positive regulation of DNA replication|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	mitochondrial nucleoid|nucleoplasm	5'-flap endonuclease activity|ATP binding|ATP-dependent DNA helicase activity|DNA binding|site-specific endodeoxyribonuclease activity, specific for altered base				0														0.779412	179.007598	183.89301	53	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69867003	69867003	4778	10	C	T	T	30	30	DNA2	T	2	2
PTEN	5728	broad.mit.edu	36	10	89682798	89682798	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2565-01	TCGA-06-2565-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:89682798T>C	uc001kfb.1	+	c.302T>C	c.(301-303)ATC>ACC	p.I101T		NM_000314	NP_000305	P60484	PTEN_HUMAN	phosphatase and tensin homolog	101	Phosphatase tensin-type.				apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of focal adhesion assembly|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of cyclin-dependent protein kinase activity|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.I101T(7)|p.Y27_N212>Y(2)|p.H93fs*5(1)|p.I101del(1)|p.I101N(1)|p.F56fs*2(1)		endometrium(831)|central_nervous_system(654)|skin(119)|haematopoietic_and_lymphoid_tissue(101)|prostate(97)|large_intestine(90)|breast(67)|lung(63)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(21)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(12)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2308		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)						31	p.I101T(GMS10-Tumor)|p.I101T(8MGBA-Tumor)	264	TCGA GBM(2;<1E-8)|TSP Lung(26;0.18)			0.170732	33.806283	42.208005	14	68	TT		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	Missense_Mutation	SNP	89682798	89682798	13192	10	T	C	C	50	50	PTEN	C	4	4
KDM2A	22992	broad.mit.edu	36	11	66776889	66776889	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:66776889G>C	uc001ojw.1	+	c.2917G>C	c.(2917-2919)GTC>CTC	p.V973L	KDM2A_uc001ojx.1_Non-coding_Transcript|KDM2A_uc001ojy.1_Missense_Mutation_p.V667L|KDM2A_uc001ojz.1_Missense_Mutation_p.V431L|KDM2A_uc001oka.1_Missense_Mutation_p.V97L	NM_012308	NP_036440	Q9Y2K7	KDM2A_HUMAN	F-box and leucine-rich repeat protein 11	973	LRR 1.				oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|zinc ion binding			ovary(3)|skin(1)	4												OREG0021121	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.4	9.488951	9.578651	4	6	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66776889	66776889	8430	11	G	C	C	40	40	KDM2A	C	3	3
NOS1	4842	broad.mit.edu	36	12	116140317	116140317	+	Silent	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:116140317G>A	uc001twm.1	-	c.4206C>T	c.(4204-4206)GTC>GTT	p.V1402V		NM_000620	NP_000611	P29475	NOS1_HUMAN	nitric oxide synthase 1 (neuronal)	1402					arginine catabolic process|multicellular organismal response to stress|myoblast fusion|negative regulation of calcium ion transport into cytosol|neurotransmitter biosynthetic process|nitric oxide biosynthetic process|oxidation-reduction process|platelet activation|positive regulation of vasodilation|regulation of cardiac muscle contraction|response to heat|response to hypoxia	cytoskeleton|cytosol|dendritic spine|perinuclear region of cytoplasm|photoreceptor inner segment|sarcolemma|sarcoplasmic reticulum	arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|FMN binding|heme binding|NADP binding|nitric-oxide synthase activity|tetrahydrobiopterin binding			ovary(2)|pancreas(1)	3	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)				L-Citrulline(DB00155)	Esophageal Squamous(162;1748 2599 51982 52956)								0.410584	665.925155	669.762243	225	323	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(302;0.0561)	Silent	SNP	116140317	116140317	10944	12	G	A	A	45	45	NOS1	A	2	2
CD163L1	283316	broad.mit.edu	36	12	7423081	7423081	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:7423081C>T	uc001qsy.1	-	c.2131G>A	c.(2131-2133)GTG>ATG	p.V711M		NM_174941	NP_777601	Q9NR16	C163B_HUMAN	scavenger receptor cysteine-rich type 1	711	SRCR 7.|Extracellular (Potential).					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity			ovary(8)|central_nervous_system(1)	9														0.459854	192.720337	192.911053	63	74	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7423081	7423081	3095	12	C	T	T	19	19	CD163L1	T	1	1
UHRF1BP1L	23074	broad.mit.edu	36	12	99002513	99002513	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:99002513C>G	uc001tgq.1	-	c.1160G>C	c.(1159-1161)GGA>GCA	p.G387A	UHRF1BP1L_uc001tgp.1_Missense_Mutation_p.G37A|UHRF1BP1L_uc001tgr.1_Missense_Mutation_p.G387A	NM_015054	NP_055869	A0JNW5	UH1BL_HUMAN	UHRF1 (ICBP90) binding protein 1-like isoform a	387										ovary(1)	1														0.369792	237.575707	240.436437	71	121	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99002513	99002513	17527	12	C	G	G	30	30	UHRF1BP1L	G	3	3
CKB	1152	broad.mit.edu	36	14	103056081	103056081	+	Missense_Mutation	SNP	T	G	G			TCGA-06-2565-01	TCGA-06-2565-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:103056081T>G	uc001ynf.1	-	c.1019A>C	c.(1018-1020)GAC>GCC	p.D340A	CKB_uc001yne.1_Missense_Mutation_p.D162A|CKB_uc010awr.1_Missense_Mutation_p.D271A	NM_001823	NP_001814	P12277	KCRB_HUMAN	brain creatine kinase	340	Phosphagen kinase C-terminal.			D->E: No change in activity.	creatine metabolic process	cytosol	ATP binding|creatine kinase activity				0		Melanoma(154;0.155)			Creatine(DB00148)	Esophageal Squamous(186;2492 2823 49929 50127)								0.372093	48.088436	48.706532	16	27	TT		KEEP	---	---	---	---	capture	Epithelial(46;0.14)		Missense_Mutation	SNP	103056081	103056081	3582	14	T	G	G	58	58	CKB	G	4	4
THSD4	79875	broad.mit.edu	36	15	69322242	69322242	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:69322242G>A	uc002atb.1	+	c.665G>A	c.(664-666)GGG>GAG	p.G222E	THSD4_uc002atd.1_5'UTR	NM_024817	NP_079093	Q6ZMP0	THSD4_HUMAN	thrombospondin, type I, domain containing 4	222	TSP type-1 1.					proteinaceous extracellular matrix	metalloendopeptidase activity			ovary(2)	2														0.458333	206.441228	206.65762	66	78	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	69322242	69322242	16406	15	G	A	A	43	43	THSD4	A	2	2
TCF3	6929	broad.mit.edu	36	19	1574996	1574996	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1574996G>A	uc002ltq.1	-	c.350C>T	c.(349-351)ACG>ATG	p.T117M	TCF3_uc002lto.1_5'Flank|TCF3_uc002ltp.1_Missense_Mutation_p.T168M|TCF3_uc002ltr.1_Missense_Mutation_p.T168M|TCF3_uc002lts.1_Missense_Mutation_p.T84M|TCF3_uc002ltt.2_Missense_Mutation_p.T168M	NM_003200	NP_003191	P15923	TFE2_HUMAN	transcription factor 3 isoform E12	168					B cell lineage commitment|B cell lineage commitment|G1 phase of mitotic cell cycle|immunoglobulin V(D)J recombination|muscle cell differentiation|positive regulation of B cell proliferation|positive regulation of cell cycle|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of muscle cell differentiation	cytoplasm|nucleus|protein complex|transcription factor complex	bHLH transcription factor binding|DNA binding|E-box binding|identical protein binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|sequence-specific DNA binding transcription factor activity|transcription activator activity|transcription factor binding|vitamin D response element binding			large_intestine(1)|skin(1)	2		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)								128				0.177215	24.496881	32.266106	14	65	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	1574996	1574996	16220	19	G	A	A	40	40	TCF3	A	1	1
CEACAM20	125931	broad.mit.edu	36	19	49706989	49706989	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:49706989G>T	uc010ejn.1	-	c.1676C>A	c.(1675-1677)CCT>CAT	p.P559H	CEACAM20_uc010ejo.1_Missense_Mutation_p.P547H|CEACAM20_uc010ejp.1_Missense_Mutation_p.P466H|CEACAM20_uc010ejq.1_Missense_Mutation_p.P454H	NM_001102597	NP_001096067	Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion	559	Cytoplasmic (Potential).					integral to membrane				large_intestine(2)	2		Prostate(69;0.0352)												0.305556	119.841952	124.700637	44	100	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49706989	49706989	3324	19	G	T	T	35	35	CEACAM20	T	3	3
DUS3L	56931	broad.mit.edu	36	19	5740592	5740592	+	Missense_Mutation	SNP	T	G	G			TCGA-06-2565-01	TCGA-06-2565-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:5740592T>G	uc002mdc.1	-	c.526A>C	c.(526-528)ACC>CCC	p.T176P	DUS3L_uc002mdd.1_Intron|DUS3L_uc010duk.1_5'UTR	NM_020175	NP_064560	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like	176	C3H1-type 2.				oxidation-reduction process|tRNA processing		flavin adenine dinucleotide binding|nucleic acid binding|tRNA dihydrouridine synthase activity|zinc ion binding				0														0.363636	6.916378	7.128271	4	7	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5740592	5740592	4992	19	T	G	G	58	58	DUS3L	G	4	4
TFPT	29844	broad.mit.edu	36	19	59309698	59309698	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:59309698C>T	uc002qdg.1	-	c.218G>A	c.(217-219)CGC>CAC	p.R73H	TFPT_uc010erd.1_Missense_Mutation_p.R73H|PRPF31_uc002qdh.1_5'Flank	NM_013342	NP_037474	P0C1Z6	TFPT_HUMAN	TCF3 (E2A) fusion partner	73					induction of apoptosis	cytoplasm|nucleus	DNA binding|protein binding				0	all_cancers(19;0.004)|all_epithelial(19;0.00195)|all_lung(19;0.0193)|Lung NSC(19;0.0358)|Breast(117;0.137)|Ovarian(34;0.19)									208				0.3	162.875197	170.733042	66	154	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59309698	59309698	16338	19	C	T	T	27	27	TFPT	T	1	1
CACNA1S	779	broad.mit.edu	36	1	199294992	199294992	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199294992G>A	uc001gvv.1	-	c.3473C>T	c.(3472-3474)ACT>ATT	p.T1158I		NM_000069	NP_000060	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type,	1158	IV.|Helical; Name=S2 of repeat IV; (Potential).				axon guidance	I band|T-tubule|voltage-gated calcium channel complex	high voltage-gated calcium channel activity			ovary(3)|central_nervous_system(1)	4					Magnesium Sulfate(DB00653)|Verapamil(DB00661)									0.390244	99.579663	100.445597	32	50	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199294992	199294992	2663	1	G	A	A	36	36	CACNA1S	A	2	2
OBSCN	84033	broad.mit.edu	36	1	226540431	226540431	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:226540431G>A	uc009xez.1	+	c.9034G>A	c.(9034-9036)GAG>AAG	p.E3012K	OBSCN_uc001hsn.1_Missense_Mutation_p.E3012K|OBSCN_uc001hsq.1_Missense_Mutation_p.E268K	NM_001098623	NP_001092093	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and	3012	Ig-like 30.				apoptosis|cell differentiation|induction of apoptosis by extracellular signals|multicellular organismal development|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|M band|Z disc	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity|Rho guanyl-nucleotide exchange factor activity|structural constituent of muscle|titin binding			large_intestine(7)|breast(5)|ovary(4)|skin(2)|stomach(1)|central_nervous_system(1)|pancreas(1)	21		Prostate(94;0.0405)								4006				0.2	7.016616	8.271991	3	12	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	226540431	226540431	11217	1	G	A	A	41	41	OBSCN	A	2	2
TRIM58	25893	broad.mit.edu	36	1	246094654	246094654	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246094654C>T	uc001ido.1	+	c.541C>T	c.(541-543)CGC>TGC	p.R181C		NM_015431	NP_056246	Q8NG06	TRI58_HUMAN	tripartite motif-containing 58	181						intracellular	zinc ion binding			ovary(1)|lung(1)|central_nervous_system(1)|pancreas(1)	4	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0286)												0.345455	51.716387	52.872513	19	36	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0319)		Missense_Mutation	SNP	246094654	246094654	17077	1	C	T	T	27	27	TRIM58	T	1	1
LRRC40	55631	broad.mit.edu	36	1	70384170	70384170	+	Silent	SNP	T	C	C			TCGA-06-2565-01	TCGA-06-2565-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:70384170T>C	uc001der.1	-	c.1710A>G	c.(1708-1710)TTA>TTG	p.L570L		NM_017768	NP_060238	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	570	LRR 20.									ovary(1)	1														0.545455	161.261916	161.400901	42	35	TT		KEEP	---	---	---	---	capture			Silent	SNP	70384170	70384170	9373	1	T	C	C	57	57	LRRC40	C	4	4
DNTTIP1	116092	broad.mit.edu	36	20	43865394	43865394	+	Silent	SNP	C	A	A			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43865394C>A	uc002xpk.1	+	c.573C>A	c.(571-573)TCC>TCA	p.S191S		NM_052951	NP_443183	Q9H147	TDIF1_HUMAN	terminal deoxynucleotidyltransferase interacting	191						nucleus				ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(115;0.0122)												0.269231	76.551154	81.550625	28	76	CC		KEEP	---	---	---	---	capture			Silent	SNP	43865394	43865394	4864	20	C	A	A	24	24	DNTTIP1	A	3	3
UMODL1	89766	broad.mit.edu	36	21	42412448	42412448	+	Silent	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42412448C>T	uc002zag.1	+	c.3018C>T	c.(3016-3018)ACC>ACT	p.T1006T	UMODL1_uc002zad.1_Silent_p.T806T|UMODL1_uc002zae.1_Silent_p.T934T|UMODL1_uc002zaf.1_Silent_p.T878T|UMODL1_uc002zal.1_5'Flank	NM_173568	NP_775839	Q5DID0	UROL1_HUMAN	uromodulin-like 1 isoform 2 precursor	878	Extracellular (Potential).|SEA 2.					cytoplasm|extracellular region|integral to membrane|plasma membrane	calcium ion binding|peptidase inhibitor activity			ovary(2)	2						Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)								0.255	401.724426	434.377216	153	447	CC		KEEP	---	---	---	---	capture			Silent	SNP	42412448	42412448	17538	21	C	T	T	23	23	UMODL1	T	1	1
DNMT3L	29947	broad.mit.edu	36	21	44503954	44503954	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44503954C>T	uc002zeh.1	-	c.220G>A	c.(220-222)GCC>ACC	p.A74T	DNMT3L_uc002zeg.1_Missense_Mutation_p.A74T	NM_013369	NP_037501	Q9UJW3	DNM3L_HUMAN	cytosine-5-methyltransferase 3-like protein	74	GATA-type; atypical.|ADD.				DNA methylation|regulation of gene expression by genetic imprinting|spermatogenesis	cytosol	enzyme activator activity|enzyme binding|transcription repressor activity|zinc ion binding				0														0.231579	53.415257	59.676592	22	73	CC		KEEP	---	---	---	---	capture		Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)	Missense_Mutation	SNP	44503954	44503954	4861	21	C	T	T	27	27	DNMT3L	T	1	1
INPP5J	27124	broad.mit.edu	36	22	29853358	29853358	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:29853358G>A	uc003aju.2	+	c.1627G>A	c.(1627-1629)GTG>ATG	p.V543M	INPP5J_uc003ajw.2_De_novo_Start_InFrame|INPP5J_uc003ajv.2_Missense_Mutation_p.V176M|INPP5J_uc003ajs.2_Missense_Mutation_p.V176M|INPP5J_uc010gwg.1_Missense_Mutation_p.V108M|INPP5J_uc003ajt.2_Missense_Mutation_p.V175M|INPP5J_uc003ajx.1_5'Flank|INPP5J_uc003ajy.1_5'Flank|INPP5J_uc003ajz.1_5'Flank	NM_001002837	NP_001002837	Q15735	PI5PA_HUMAN	phosphatidylinositol (4,5) bisphosphate	543	Catalytic (Potential).					cytoplasm|ruffle	inositol 1,3,4,5-tetrakisphosphate 5-phosphatase activity|inositol-1,4,5-trisphosphate 5-phosphatase activity|inositol-polyphosphate 5-phosphatase activity|SH3 domain binding			skin(1)	1														0.434783	30.251043	30.335273	10	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29853358	29853358	8060	22	G	A	A	40	40	INPP5J	A	1	1
SFI1	9814	broad.mit.edu	36	22	30287290	30287290	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:30287290C>T	uc003ale.1	+	c.677C>T	c.(676-678)ACG>ATG	p.T226M	SFI1_uc003ald.1_Missense_Mutation_p.T202M|SFI1_uc003alf.1_Missense_Mutation_p.T226M|SFI1_uc003alg.1_Missense_Mutation_p.T144M|SFI1_uc003alh.1_Non-coding_Transcript	NM_001007467	NP_001007468	A8K8P3	SFI1_HUMAN	spindle assembly associated Sfi1 homolog isoform	226					G2/M transition of mitotic cell cycle	centriole|cytosol				central_nervous_system(1)	1												OREG0026480	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.368421	58.956924	59.82502	21	36	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30287290	30287290	14645	22	C	T	T	19	19	SFI1	T	1	1
SLC5A1	6523	broad.mit.edu	36	22	30830780	30830780	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:30830780G>A	uc003amc.1	+	c.1673G>A	c.(1672-1674)CGT>CAT	p.R558H		NM_000343	NP_000334	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose	558	Cytoplasmic (Potential).				carbohydrate metabolic process	integral to plasma membrane	glucose:sodium symporter activity|protein binding				0														0.388889	107.910947	108.882188	35	55	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30830780	30830780	15158	22	G	A	A	40	40	SLC5A1	A	1	1
GTSE1	51512	broad.mit.edu	36	22	45104007	45104007	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2565-01	TCGA-06-2565-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:45104007T>C	uc003bhk.1	+	c.1958T>C	c.(1957-1959)TTC>TCC	p.F653S	GTSE1_uc003bhn.1_Non-coding_Transcript|GTSE1_uc003bho.2_5'Flank	NM_016426	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	653					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G2 phase of mitotic cell cycle|microtubule-based process	cytoplasmic microtubule				ovary(1)	1		Ovarian(80;0.00965)|all_neural(38;0.0416)				GBM(153;542 1915 12487 29016 50495)				471				0.46129	496.49865	496.902278	143	167	TT		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)	Missense_Mutation	SNP	45104007	45104007	7165	22	T	C	C	62	62	GTSE1	C	4	4
GCC2	9648	broad.mit.edu	36	2	108458465	108458465	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2565-01	TCGA-06-2565-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:108458465A>G	uc002tec.1	+	c.2903A>G	c.(2902-2904)AAT>AGT	p.N968S	GCC2_uc002ted.1_Missense_Mutation_p.N867S	NM_181453	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain-containing 2 isoform	968	Potential.				Golgi ribbon formation|late endosome to Golgi transport|microtubule anchoring|microtubule organizing center organization|protein localization in Golgi apparatus|protein targeting to lysosome|recycling endosome to Golgi transport|regulation of protein exit from endoplasmic reticulum	membrane|trans-Golgi network	identical protein binding			ovary(1)	1														0.40625	42.939653	43.192397	13	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	108458465	108458465	6552	2	A	G	G	4	4	GCC2	G	4	4
KIF5C	3800	broad.mit.edu	36	2	149575069	149575069	+	Silent	SNP	C	A	A			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:149575069C>A	uc002twr.1	+	c.2725C>A	c.(2725-2727)CGG>AGG	p.R909R	KIF5C_uc002tws.1_Non-coding_Transcript|KIF5C_uc002twu.1_Silent_p.R191R	NM_004522	NP_004513	O60282	KIF5C_HUMAN	kinesin family member 5C	909	|Globular.				microtubule-based movement|organelle organization	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity			skin(1)	1														0.666667	11.464066	11.60164	4	2	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.108)	Silent	SNP	149575069	149575069	8618	2	C	A	A	27	27	KIF5C	A	3	3
GALNT14	79623	broad.mit.edu	36	2	31032074	31032074	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:31032074C>T	uc002rns.1	-	c.583G>A	c.(583-585)GCC>ACC	p.A195T	GALNT14_uc002rnq.1_Missense_Mutation_p.A170T|GALNT14_uc002rnr.1_Missense_Mutation_p.A190T|GALNT14_uc010ezo.1_Missense_Mutation_p.A157T|GALNT14_uc010ezp.1_Missense_Mutation_p.A161T	NM_024572	NP_078848	Q96FL9	GLT14_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide	190	Lumenal (Potential).|Catalytic subdomain A.					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding				0	Acute lymphoblastic leukemia(172;0.155)													0.418605	109.38816	109.884604	36	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31032074	31032074	6476	2	C	T	T	27	27	GALNT14	T	1	1
ZAP70	7535	broad.mit.edu	36	2	97717564	97717564	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:97717564G>A	uc002syd.1	+	c.1039G>A	c.(1039-1041)GGC>AGC	p.G347S	ZAP70_uc002sye.1_Missense_Mutation_p.G237S|ZAP70_uc002syf.1_Missense_Mutation_p.G40S	NM_001079	NP_997402	P43403	ZAP70_HUMAN	zeta-chain associated protein kinase 70kDa	347	Protein kinase.|ATP (By similarity).				immune response|intracellular protein kinase cascade|positive thymic T cell selection|T cell receptor signaling pathway	cytosol|T cell receptor complex	ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(3)|upper_aerodigestive_tract(1)|ovary(1)	5										138				0.544304	279.254276	279.523975	86	72	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	97717564	97717564	18097	2	G	A	A	39	39	ZAP70	A	1	1
CD96	10225	broad.mit.edu	36	3	112839679	112839679	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:112839679C>T	uc003dxw.1	+	c.1499C>T	c.(1498-1500)ACG>ATG	p.T500M	CD96_uc003dxx.1_Missense_Mutation_p.T484M|CD96_uc010hpy.1_Missense_Mutation_p.T483M	NM_198196	NP_937839	P40200	TACT_HUMAN	CD96 antigen isoform 1 precursor	500	Extracellular (Potential).|Pro/Ser/Thr-rich.				cell adhesion|immune response|regulation of immune response	integral to plasma membrane				central_nervous_system(1)	1														0.486772	297.599308	297.627797	92	97	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	112839679	112839679	3176	3	C	T	T	19	19	CD96	T	1	1
SCN5A	6331	broad.mit.edu	36	3	38614420	38614420	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:38614420C>T	uc003cio.1	-	c.2066G>A	c.(2065-2067)CGT>CAT	p.R689H	SCN5A_uc003cim.1_Missense_Mutation_p.R555H|SCN5A_uc003cin.1_Missense_Mutation_p.R689H|SCN5A_uc003cil.2_Missense_Mutation_p.R689H|SCN5A_uc010hhi.1_Missense_Mutation_p.R689H|SCN5A_uc010hhj.1_Missense_Mutation_p.R300H|SCN5A_uc010hhk.1_Missense_Mutation_p.R555H	NM_198056	NP_932173	Q14524	SCN5A_HUMAN	voltage-gated sodium channel type V alpha	689					blood circulation|muscle contraction|regulation of heart contraction	sarcolemma|voltage-gated sodium channel complex	protein binding|voltage-gated sodium channel activity			ovary(4)|pancreas(2)|central_nervous_system(1)	7	Medulloblastoma(35;0.163)				Benzonatate(DB00868)|Bepridil(DB01244)|Carbamazepine(DB00564)|Cocaine(DB00907)|Dibucaine(DB00527)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lamotrigine(DB00555)|Lidocaine(DB00281)|Mephenytoin(DB00532)|Mexiletine(DB00379)|Mibefradil(DB01388)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine(DB00908)|Riluzole(DB00740)|Tocainide(DB01056)|Verapamil(DB00661)									0.414474	189.990035	190.961738	63	89	CC		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Missense_Mutation	SNP	38614420	38614420	14404	3	C	T	T	19	19	SCN5A	T	1	1
PKD2	5311	broad.mit.edu	36	4	89206026	89206026	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:89206026C>T	uc003hre.1	+	c.2329C>T	c.(2329-2331)CAG>TAG	p.Q777*		NM_000297	NP_000288	Q13563	PKD2_HUMAN	polycystin 2	777	EF-hand.|EF-hand domain.|Cytoplasmic (Potential).					basal cortex|basal plasma membrane|endoplasmic reticulum|integral to membrane|lamellipodium|microtubule basal body	calcium ion binding|cytoskeletal protein binding|voltage-gated chloride channel activity|voltage-gated sodium channel activity				0		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)												0.484277	231.25955	231.294105	77	82	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)	Nonsense_Mutation	SNP	89206026	89206026	12391	4	C	T	T	25	25	PKD2	T	5	2
FBN2	2201	broad.mit.edu	36	5	127756781	127756781	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:127756781C>T	uc003kuu.1	-	c.1411G>A	c.(1411-1413)GTT>ATT	p.V471I		NM_001999	NP_001990	P35556	FBN2_HUMAN	fibrillin 2 precursor	471					bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent			ovary(8)|large_intestine(4)|kidney(1)|pancreas(1)	14		all_cancers(142;0.0216)|Prostate(80;0.0551)							p.V471I(HCC1569-Tumor)	1552				0.352657	189.08988	193.06141	73	134	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)	Missense_Mutation	SNP	127756781	127756781	5939	5	C	T	T	19	19	FBN2	T	1	1
TERT	7015	broad.mit.edu	36	5	1332521	1332521	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:1332521C>T	uc003jcb.1	-	c.2015G>A	c.(2014-2016)CGC>CAC	p.R672H	TERT_uc003jbz.1_5'UTR|TERT_uc003jca.1_Missense_Mutation_p.R672H|TERT_uc003jcc.1_Missense_Mutation_p.R672H|TERT_uc003jcd.1_Non-coding_Transcript|TERT_uc003jce.1_Non-coding_Transcript	NM_198253	NP_937983	O14746	TERT_HUMAN	telomerase reverse transcriptase isoform 1	672	Reverse transcriptase.				anti-apoptosis|DNA strand elongation|replicative senescence|telomere formation via telomerase	cytoplasm|nuclear telomere cap complex|nucleolus|PML body|telomerase holoenzyme complex	protein homodimerization activity|telomeric DNA binding|telomeric RNA binding|telomeric template RNA reverse transcriptase activity	p.R672H(1)		lung(6)|central_nervous_system(2)|ovary(1)|skin(1)	10	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)									563				0.5	6.35094	6.350918	2	2	CC		KEEP	---	---	---	---	capture	Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Missense_Mutation	SNP	1332521	1332521	16291	5	C	T	T	27	27	TERT	T	1	1
PCDHGA1	56114	broad.mit.edu	36	5	140692169	140692169	+	Silent	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140692169G>A	uc003lji.1	+	c.1734G>A	c.(1732-1734)GCG>GCA	p.A578A	PCDHGA1_uc003ljh.1_Silent_p.A578A	NM_018912	NP_061735	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1 isoform 1	578	Extracellular (Potential).|Cadherin 6.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|breast(1)|pancreas(1)	3														0.430052	223.221611	224.034004	83	110	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140692169	140692169	11970	5	G	A	A	38	38	PCDHGA1	A	1	1
BASP1	10409	broad.mit.edu	36	5	17328820	17328820	+	Silent	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:17328820C>T	uc003jfx.1	+	c.495C>T	c.(493-495)GAC>GAT	p.D165D	BASP1_uc010ity.1_Silent_p.D165D	NM_006317	NP_006308	P80723	BASP1_HUMAN	brain abundant, membrane attached signal protein	165					glomerular visceral epithelial cell differentiation|negative regulation of gene-specific transcription	cytoplasm|cytoskeleton|growth cone|nuclear speck|plasma membrane	promoter binding|protein domain specific binding|specific transcriptional repressor activity|transcription corepressor activity				0														0.333333	18.217368	18.734297	7	14	CC		KEEP	---	---	---	---	capture			Silent	SNP	17328820	17328820	1338	5	C	T	T	19	19	BASP1	T	1	1
ADAMTS16	170690	broad.mit.edu	36	5	5275920	5275920	+	Missense_Mutation	SNP	T	G	G			TCGA-06-2565-01	TCGA-06-2565-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:5275920T>G	uc003jdl.1	+	c.1624T>G	c.(1624-1626)TGG>GGG	p.W542G	ADAMTS16_uc003jdj.1_Missense_Mutation_p.W542G|ADAMTS16_uc003jdk.1_Missense_Mutation_p.W542G	NM_139056	NP_620687	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1	542	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(3)|lung(2)|large_intestine(1)|breast(1)|pancreas(1)	8														0.350877	132.477482	134.708492	40	74	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5275920	5275920	262	5	T	G	G	59	59	ADAMTS16	G	4	4
GPR116	221395	broad.mit.edu	36	6	46934129	46934129	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:46934129G>A	uc003oyo.2	-	c.3470C>T	c.(3469-3471)ACG>ATG	p.T1157M	GPR116_uc003oyp.2_Missense_Mutation_p.T1015M|GPR116_uc003oyq.2_Missense_Mutation_p.T1157M|GPR116_uc010jzi.1_Missense_Mutation_p.T829M	NM_001098518	NP_056049	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116	1157	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1						NSCLC(59;410 1274 8751 36715 50546)								0.38961	87.729939	88.552453	30	47	GG		KEEP	---	---	---	---	capture	Lung(136;0.192)		Missense_Mutation	SNP	46934129	46934129	6907	6	G	A	A	40	40	GPR116	A	1	1
EGFR	1956	broad.mit.edu	36	7	55178574	55178574	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55178574G>A	uc003tqk.1	+	c.323G>A	c.(322-324)AGA>AAA	p.R108K	EGFR_uc003tqh.1_Missense_Mutation_p.R108K|EGFR_uc003tqi.1_Missense_Mutation_p.R108K|EGFR_uc003tqj.1_Missense_Mutation_p.R108K|EGFR_uc010kzg.1_Missense_Mutation_p.R108K	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	108	Approximate.|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	p.R108K(7)|p.V30_R297>G(5)		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)				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)			0.941117	3341.997907	3495.225048	927	58	GG		KEEP	---	---	---	---	capture	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)		Missense_Mutation	SNP	55178574	55178574	5156	7	G	A	A	33	33	EGFR	A	2	2
TYW1	55253	broad.mit.edu	36	7	66120297	66120297	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:66120297G>A	uc003tvn.1	+	c.593G>A	c.(592-594)TGG>TAG	p.W198*	TYW1_uc010lai.1_Non-coding_Transcript	NM_018264	NP_060734	Q9NV66	TYW1_HUMAN	radical S-adenosyl methionine and flavodoxin	198	FMN (By similarity).|Flavodoxin-like.				oxidation-reduction process|tRNA processing		4 iron, 4 sulfur cluster binding|FMN binding|iron ion binding|oxidoreductase activity				0		Lung NSC(55;0.0846)|all_lung(88;0.183)								1				0.5	183.745083	183.745083	58	58	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	66120297	66120297	17375	7	G	A	A	47	47	TYW1	A	5	2
CD36	948	broad.mit.edu	36	7	80128399	80128399	+	Silent	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:80128399C>T	uc003uhc.1	+	c.366C>T	c.(364-366)TTC>TTT	p.F122F	CD36_uc003uhd.2_Silent_p.F122F|CD36_uc003uhe.2_Silent_p.F122F|CD36_uc003uhf.2_Silent_p.F122F|CD36_uc003uhg.2_Silent_p.F122F|CD36_uc003uhh.2_Silent_p.F122F	NM_001127444	NP_001120916	P16671	CD36_HUMAN	CD36 antigen	122	Extracellular (Potential).				cell adhesion|cGMP-mediated signaling|cholesterol transport|lipid metabolic process|lipid storage|lipoprotein transport|low-density lipoprotein particle clearance|nitric oxide mediated signal transduction|plasma membrane long-chain fatty acid transport|platelet activation|platelet degranulation|positive regulation of cell-matrix adhesion|positive regulation of macrophage derived foam cell differentiation	integral to plasma membrane|membrane fraction|platelet alpha granule membrane	lipid binding|low-density lipoprotein receptor activity|thrombospondin receptor activity|transforming growth factor beta binding			ovary(1)	1														0.391892	171.417846	172.93201	58	90	CC		KEEP	---	---	---	---	capture			Silent	SNP	80128399	80128399	3135	7	C	T	T	31	31	CD36	T	1	1
KLF10	7071	broad.mit.edu	36	8	103731636	103731636	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:103731636G>A	uc003ykv.1	-	c.1343C>T	c.(1342-1344)GCC>GTC	p.A448V	KLF10_uc003yku.1_Missense_Mutation_p.A437V	NM_005655	NP_005646	Q13118	KLF10_HUMAN	Kruppel-like factor 10 isoform a	448	C2H2-type 3.				cell proliferation|cell-cell signaling|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|skeletal system development|transforming growth factor beta receptor signaling pathway	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)					Esophageal Squamous(16;495 519 2144 16528 44005)								0.435028	211.328716	211.981451	77	100	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)		Missense_Mutation	SNP	103731636	103731636	8650	8	G	A	A	42	42	KLF10	A	2	2
ANK1	286	broad.mit.edu	36	8	41640384	41640384	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:41640384C>T	uc003xom.1	-	c.5551G>A	c.(5551-5553)GTG>ATG	p.V1851M	NKX6-3_uc010lxa.1_Intron|ANK1_uc003xoh.1_Missense_Mutation_p.V964M|ANK1_uc003xoi.1_Missense_Mutation_p.V1810M|ANK1_uc003xoj.1_Missense_Mutation_p.V1810M|ANK1_uc003xok.1_Missense_Mutation_p.V1810M|ANK1_uc003xol.1_Missense_Mutation_p.V1648M|ANK1_uc003xob.1_Non-coding_Transcript|ANK1_uc003xoc.1_Missense_Mutation_p.V85M|ANK1_uc003xod.1_Missense_Mutation_p.V85M|ANK1_uc003xof.1_Missense_Mutation_p.V85M	NM_020475	NP_065208	P16157	ANK1_HUMAN	ankyrin 1 isoform 4	1810	55 kDa regulatory domain.				axon guidance|cytoskeleton organization|exocytosis|maintenance of epithelial cell apical/basal polarity|signal transduction	basolateral plasma membrane|cytosol|sarcomere|sarcoplasmic reticulum|spectrin-associated cytoskeleton	cytoskeletal adaptor activity|enzyme binding|protein binding|spectrin binding|structural constituent of cytoskeleton			ovary(3)|lung(2)|central_nervous_system(2)|breast(1)	8	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)												0.428571	204.42809	205.112816	66	88	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)		Missense_Mutation	SNP	41640384	41640384	623	8	C	T	T	18	18	ANK1	T	2	2
SLCO5A1	81796	broad.mit.edu	36	8	70812981	70812981	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2565-01	TCGA-06-2565-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:70812981G>T	uc003xyl.1	-	c.1271C>A	c.(1270-1272)GCA>GAA	p.A424E	SLCO5A1_uc010lzb.1_Intron|SLCO5A1_uc003xyk.1_Missense_Mutation_p.A424E	NM_030958	NP_112220	Q9H2Y9	SO5A1_HUMAN	solute carrier organic anion transporter family,	424	Cytoplasmic (Potential).					integral to membrane|plasma membrane	transporter activity			ovary(3)	3	Breast(64;0.0654)													0.44	172.016396	172.406856	55	70	GG		KEEP	---	---	---	---	capture	Epithelial(68;0.0141)|OV - Ovarian serous cystadenocarcinoma(28;0.0315)|all cancers(69;0.0594)		Missense_Mutation	SNP	70812981	70812981	15228	8	G	T	T	46	46	SLCO5A1	T	3	3
FRMD7	90167	broad.mit.edu	36	X	131039927	131039927	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:131039927C>T	uc004ewn.1	-	c.1799G>A	c.(1798-1800)CGT>CAT	p.R600H		NM_194277	NP_919253	Q6ZUT3	FRMD7_HUMAN	nystagmus 1 protein	600					regulation of neuron projection development	cytoskeleton|growth cone|neuronal cell body	binding				0	Acute lymphoblastic leukemia(192;0.000127)													0.868613	405.816147	423.910913	119	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	131039927	131039927	6305	23	C	T	T	19	19	FRMD7	T	1	1
MAP7D3	79649	broad.mit.edu	36	X	135129497	135129497	+	Splice_Site_SNP	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:135129497C>T	uc004ezt.2	-	c.2487_splice	c.e17-1	p.R829_splice	MAP7D3_uc004ezs.2_Splice_Site_SNP_p.R793_splice|MAP7D3_uc010nsa.1_Intron	NM_024597	NP_078873			MAP7 domain containing 3							cytoplasm|spindle				ovary(2)|central_nervous_system(1)|skin(1)	4	Acute lymphoblastic leukemia(192;0.000127)													0.923077	397.801771	419.234869	108	9	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	135129497	135129497	9652	23	C	T	T	32	32	MAP7D3	T	5	2
SMC1A	8243	broad.mit.edu	36	X	53447274	53447274	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2565-01	TCGA-06-2565-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:53447274C>T	uc004dsg.1	-	c.2369G>A	c.(2368-2370)CGG>CAG	p.R790Q	SMC1A_uc004dsh.1_Missense_Mutation_p.R768Q	NM_006306	NP_006297	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	790	Potential.		R -> Q (in CDLS2).		cell cycle checkpoint|cell division|DNA repair|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|mitotic sister chromatid cohesion|mitotic spindle organization|negative regulation of DNA endoreduplication|nuclear mRNA splicing, via spliceosome|response to radiation|signal transduction in response to DNA damage	cohesin core heterodimer|condensed chromosome kinetochore|condensed nuclear chromosome|cytoplasm|meiotic cohesin complex|nucleoplasm	ATP binding|chromatin binding|microtubule motor activity|protein heterodimerization activity			ovary(5)	5														0.421053	23.789896	23.894535	8	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	53447274	53447274	15279	23	C	T	T	23	23	SMC1A	T	1	1
ATAD3B	83858	broad.mit.edu	36	1	1397162	1397163	+	Frame_Shift_Ins	INS	-	G	G			TCGA-06-2565-01	TCGA-06-2565-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:1397162_1397163insG	uc001afv.1	+	c.35_36insG	c.(34-36)AAGfs	p.K12fs		NM_031921	NP_114127	Q5T9A4	ATD3B_HUMAN	AAA-ATPase  TOB3	12							ATP binding|nucleoside-triphosphatase activity				0	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	1397162	1397163	1093	1	-	G	G	3	3	ATAD3B	G	5	5
FMN2	56776	broad.mit.edu	36	1	238322192	238322194	+	In_Frame_Del	DEL	GGC	-	-			TCGA-06-2565-01	TCGA-06-2565-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:238322192_238322194delGGC	uc009xgl.1	+	c.589_591delGGC	c.(589-591)GGCdel	p.G202del		NM_020066	NP_064450	Q9NZ56	FMN2_HUMAN	formin 2	59					actin cytoskeleton organization|establishment of meiotic spindle localization|intracellular signal transduction|meiotic chromosome movement towards spindle pole|meiotic metaphase I|multicellular organismal development|oogenesis|polar body extrusion after meiotic divisions		actin binding			ovary(4)|pancreas(3)|large_intestine(1)|central_nervous_system(1)	9	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)							1289				0.60			6	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	238322192	238322194	6192	1	GGC	-	-	43	43	FMN2	-	5	5
TNK2	10188	broad.mit.edu	36	3	197083599	197083600	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-06-2565-01	TCGA-06-2565-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:197083599_197083600delCT	uc003fvt.1	-	c.1584_1585delAG	c.(1582-1587)ACAGGGfs	p.T528fs	TNK2_uc003fvq.1_5'Flank|TNK2_uc003fvr.1_5'UTR|TNK2_uc003fvs.1_Frame_Shift_Del_p.T497fs|TNK2_uc003fvu.1_Frame_Shift_Del_p.T465fs|TNK2_uc010hzw.1_Non-coding_Transcript|TNK2_uc003fvv.1_Frame_Shift_Del_p.T295fs	NM_001010938	NP_001010938	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2 isoform 2	465_466	CRIB.			Missing (in Ref. 4; AAH08884).	positive regulation of peptidyl-tyrosine phosphorylation|protein phosphorylation|protein ubiquitination|small GTPase mediated signal transduction	adherens junction|cytoplasmic vesicle membrane|endosome|nucleus	ATP binding|GTPase inhibitor activity|metal ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|central_nervous_system(3)|lung(2)|stomach(1)|skin(1)	10	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)					288				0.69			25	11				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	197083599	197083600	16859	3	CT	-	-	24	24	TNK2	-	5	5
NUP205	23165	broad.mit.edu	36	7	134961650	134961651	+	Splice_Site_Ins	INS	-	T	T			TCGA-06-2565-01	TCGA-06-2565-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:134961650_134961651insT	uc003vsw.1	+	c.e33_splice_site			NUP205_uc003vsx.1_Splice_Site_Ins	NM_015135	NP_055950			nucleoporin 205kDa						carbohydrate metabolic process|glucose transport|mRNA transport|protein import into nucleus, docking|regulation of glucose transport|transmembrane transport|viral reproduction	nuclear pore	protein binding			ovary(3)|breast(1)|central_nervous_system(1)|skin(1)	6														0.38			56	92				---	---	---	---	capture_indel			Splice_Site_Ins	INS	134961650	134961651	11164	7	-	T	T	44	44	NUP205	T	5	5
SEMA3E	9723	broad.mit.edu	36	7	82872766	82872766	+	Frame_Shift_Del	DEL	C	-	-			TCGA-06-2565-01	TCGA-06-2565-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:82872766_82872766delC	uc003uhy.1	-	c.934_934delG	c.(934-936)GTTfs	p.V312fs		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E	312	Sema.				axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)												0.41			41	58				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	82872766	82872766	14514	7	C	-	-	19	19	SEMA3E	-	5	5
