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
MUC2	4583	broad.mit.edu	36	11	1070315	1070315	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0881-01	TCGA-06-0881-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:1070315C>G	uc001lsx.1	+	c.1035C>G	c.(1033-1035)TGC>TGG	p.C345W		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	345	TIL.					inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)			Pranlukast(DB01411)									0.210526	6.510143	7.971504	4	15	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Missense_Mutation	SNP	1070315	1070315	10369	11	C	G	G	27	27	MUC2	G	3	3
USH1C	10083	broad.mit.edu	36	11	17500979	17500979	+	Missense_Mutation	SNP	T	C	C			TCGA-06-0881-01	TCGA-06-0881-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:17500979T>C	uc001mne.1	-	c.947A>G	c.(946-948)GAG>GGG	p.E316G	USH1C_uc001mnd.1_Missense_Mutation_p.E280G|USH1C_uc001mnf.1_Missense_Mutation_p.E316G|USH1C_uc009yhb.1_Missense_Mutation_p.E297G|USH1C_uc001mng.1_Non-coding_Transcript	NM_153676	NP_710142	Q9Y6N9	USH1C_HUMAN	harmonin isoform b3	316	Potential.				equilibrioception|G2/M transition of mitotic cell cycle|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	apical part of cell|cytoplasm|stereocilium	protein binding			ovary(1)	1														0.238095	7.332366	8.684687	5	16	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17500979	17500979	17596	11	T	C	C	54	54	USH1C	C	4	4
DGKZ	8525	broad.mit.edu	36	11	46345004	46345004	+	Missense_Mutation	SNP	A	C	C			TCGA-06-0881-01	TCGA-06-0881-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:46345004A>C	uc001ncn.1	+	c.622A>C	c.(622-624)ACC>CCC	p.T208P	DGKZ_uc001nch.1_Intron|DGKZ_uc001nci.1_Intron|DGKZ_uc001ncj.1_Intron|DGKZ_uc001nck.1_Intron|DGKZ_uc001ncl.2_Intron|DGKZ_uc001ncm.2_Intron|DGKZ_uc009yky.1_Intron	NM_001105540	NP_001099010	Q13574	DGKZ_HUMAN	diacylglycerol kinase zeta isoform 4	208					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|cell migration|intracellular signal transduction|mitotic cell cycle G1/S transition DNA damage checkpoint|negative regulation of mitotic cell cycle|platelet activation	cytoplasm|lamellipodium|nucleus|plasma membrane	ATP binding|diacylglycerol kinase activity|diacylglycerol kinase activity|lipid kinase activity|metal ion binding|protein binding|protein C-terminus binding			pancreas(1)|central_nervous_system(1)|skin(1)	3														0.4	6.885987	6.976417	4	6	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)	Missense_Mutation	SNP	46345004	46345004	4653	11	A	C	C	6	6	DGKZ	C	4	4
KDM2B	84678	broad.mit.edu	36	12	120375450	120375450	+	Silent	SNP	T	C	C			TCGA-06-0881-01	TCGA-06-0881-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:120375450T>C	uc001uat.1	-	c.1815A>G	c.(1813-1815)GGA>GGG	p.G605G	KDM2B_uc001uas.1_Silent_p.G574G|KDM2B_uc009zxe.1_Silent_p.G574G|KDM2B_uc001uau.1_Silent_p.G488G|KDM2B_uc009zxf.1_Silent_p.G605G|KDM2B_uc001uaq.1_Silent_p.G45G|KDM2B_uc001uar.1_Silent_p.G196G	NM_032590	NP_115979	Q8NHM5	KDM2B_HUMAN	F-box and leucine-rich repeat protein 10 isoform	605					oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	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|rRNA binding|zinc ion binding			ovary(1)	1														0.285714	7.09807	7.674294	4	10	TT		KEEP	---	---	---	---	capture			Silent	SNP	120375450	120375450	8431	12	T	C	C	54	54	KDM2B	C	4	4
HOXC13	3229	broad.mit.edu	36	12	52619666	52619666	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0881-01	TCGA-06-0881-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:52619666G>C	uc001sei.1	+	c.709G>C	c.(709-711)GCC>CCC	p.A237P		NM_017410	NP_059106	P31276	HXC13_HUMAN	homeobox C13	237					regulation of transcription, DNA-dependent	nucleus	protein binding|RNA polymerase II transcription factor activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity				0										22				0.428571	9.185827	9.258542	6	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52619666	52619666	7604	12	G	C	C	38	38	HOXC13	C	3	3
IPO5	3843	broad.mit.edu	36	13	97450836	97450836	+	Silent	SNP	C	T	T			TCGA-06-0881-01	TCGA-06-0881-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:97450836C>T	uc001vne.1	+	c.1098C>T	c.(1096-1098)TGC>TGT	p.C366C	IPO5_uc001vnf.1_Silent_p.C348C|IPO5_uc001vng.1_5'Flank	NM_002271	NP_002262	O00410	IPO5_HUMAN	importin 5	348	Ran-GTP binding (By similarity).				interspecies interaction between organisms|NLS-bearing substrate import into nucleus|ribosomal protein import into nucleus	cytoplasm|nuclear pore|nucleolus	GTPase inhibitor activity|protein transporter activity|Ran GTPase binding			ovary(1)|lung(1)	2														0.2	23.366632	28.390043	12	48	CC		KEEP	---	---	---	---	capture			Silent	SNP	97450836	97450836	8097	13	C	T	T	27	27	IPO5	T	1	1
MED24	9862	broad.mit.edu	36	17	35445061	35445061	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0881-01	TCGA-06-0881-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:35445061G>C	uc002hts.1	-	c.469C>G	c.(469-471)CTG>GTG	p.L157V	MED24_uc002htt.1_Missense_Mutation_p.L132V|MED24_uc002htu.1_Missense_Mutation_p.L119V|MED24_uc010cwn.1_Missense_Mutation_p.L119V	NM_014815	NP_055630	O75448	MED24_HUMAN	mediator complex subunit 24 isoform 1	132	LXXLL motif 1.				androgen receptor signaling pathway|regulation of transcription, DNA-dependent|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			ovary(1)	1	Colorectal(19;0.000442)											OREG0024387	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.181818	8.251668	12.48821	8	36	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35445061	35445061	9831	17	G	C	C	34	34	MED24	C	3	3
GAMT	2593	broad.mit.edu	36	19	1348413	1348413	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0881-01	TCGA-06-0881-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1348413T>G	uc002lsj.1	-	c.656A>C	c.(655-657)GAC>GCC	p.D219A		NM_000156	NP_000147	Q14353	GAMT_HUMAN	guanidinoacetate N-methyltransferase isoform a	219					creatine biosynthetic process|muscle contraction	cytosol	guanidinoacetate N-methyltransferase activity				0		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Lung NSC(49;0.000195)|Breast(49;0.000231)|all_lung(49;0.000247)|Hepatocellular(1079;0.137)			Creatine(DB00148)	Colon(167;1531 1939 13427 28842 31956)								0.291667	8.755284	9.805338	7	17	TT		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	1348413	1348413	6495	19	T	G	G	58	58	GAMT	G	4	4
PNKP	11284	broad.mit.edu	36	19	55062236	55062236	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0881-01	TCGA-06-0881-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55062236T>G	uc002pqh.1	-	c.38A>C	c.(37-39)GAG>GCG	p.E13A	PNKP_uc002pqg.1_5'Flank|PNKP_uc002pqi.1_5'UTR|PNKP_uc002pqj.1_Missense_Mutation_p.E13A|PNKP_uc010enm.1_Missense_Mutation_p.E13A|PNKP_uc002pqk.1_Missense_Mutation_p.E13A	NM_007254	NP_009185	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	13					DNA damage response, detection of DNA damage|DNA-dependent DNA replication|nucleotide-excision repair, DNA damage removal|response to oxidative stress|response to radiation	nucleolus	ATP binding|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity|damaged DNA binding|double-stranded DNA binding|endonuclease activity|nucleotide kinase activity|polynucleotide 3'-phosphatase activity|protein binding			ovary(1)|kidney(1)	2		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)												0.217391	11.76546	13.457127	5	18	TT		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)	Missense_Mutation	SNP	55062236	55062236	12573	19	T	G	G	54	54	PNKP	G	4	4
UPK3A	7380	broad.mit.edu	36	22	44061970	44061970	+	Silent	SNP	A	C	C			TCGA-06-0881-01	TCGA-06-0881-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:44061970A>C	uc003bfy.1	+	c.462A>C	c.(460-462)GCA>GCC	p.A154A	UPK3A_uc010gzy.1_Intron	NM_006953	NP_008884	O75631	UPK3A_HUMAN	uroplakin 3A precursor	154	Lumenal (Potential).				epithelial cell differentiation	endoplasmic reticulum membrane|integral to membrane					0		Ovarian(80;0.00965)|all_neural(38;0.0416)												0.4	8.314054	8.536139	8	12	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)	Silent	SNP	44061970	44061970	17570	22	A	C	C	6	6	UPK3A	C	4	4
PECR	55825	broad.mit.edu	36	2	216654630	216654630	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0881-01	TCGA-06-0881-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:216654630G>C	uc002vft.1	-	c.80C>G	c.(79-81)GCC>GGC	p.A27G	TMEM169_uc002vfv.2_5'Flank|TMEM169_uc002vfw.1_5'Flank|TMEM169_uc002vfx.1_5'Flank|PECR_uc010fve.1_Non-coding_Transcript|PECR_uc002vfu.1_Missense_Mutation_p.A46G	NM_018441	NP_060911	Q9BY49	PECR_HUMAN	peroxisomal trans-2-enoyl-CoA reductase	27	NADP (By similarity).				fatty acid biosynthetic process|oxidation-reduction process|regulation of apoptosis	peroxisome	binding|trans-2-enoyl-CoA reductase (NADPH) activity				0		Renal(323;0.0327)			Adenine(DB00173)									0.193548	7.764421	10.395871	6	25	GG		KEEP	---	---	---	---	capture		Epithelial(149;3.8e-06)|all cancers(144;0.000272)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Missense_Mutation	SNP	216654630	216654630	12138	2	G	C	C	42	42	PECR	C	3	3
CRYBA2	1412	broad.mit.edu	36	2	219565117	219565117	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0881-01	TCGA-06-0881-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219565117C>G	uc002vjj.1	-	c.254G>C	c.(253-255)AGC>ACC	p.S85T	CRYBA2_uc002vjk.1_Missense_Mutation_p.S85T	NM_057094	NP_476435	P53672	CRBA2_HUMAN	crystallin, beta A2	85	Beta/gamma crystallin 'Greek key' 2.						structural constituent of eye lens				0		Renal(207;0.0474)												0.578947	29.118699	29.220879	11	8	CC		KEEP	---	---	---	---	capture		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Missense_Mutation	SNP	219565117	219565117	4047	2	C	G	G	28	28	CRYBA2	G	3	3
COL6A3	1293	broad.mit.edu	36	2	237909757	237909757	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0881-01	TCGA-06-0881-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:237909757C>T	uc002vwl.2	-	c.8725G>A	c.(8725-8727)GCT>ACT	p.A2909T	COL6A3_uc002vwj.2_Missense_Mutation_p.A290T|COL6A3_uc002vwk.2_Missense_Mutation_p.A2742T|COL6A3_uc002vwm.2_Missense_Mutation_p.A2708T|COL6A3_uc002vwn.2_Missense_Mutation_p.A2709T|COL6A3_uc002vwo.2_Missense_Mutation_p.A2703T	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	2909	Nonhelical region.|Ala-rich.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|pancreas(1)	15		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)												0.092527	11.253468	58.199925	26	255	CC		KEEP	---	---	---	---	capture		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)	Missense_Mutation	SNP	237909757	237909757	3839	2	C	T	T	27	27	COL6A3	T	1	1
ESPNL	339768	broad.mit.edu	36	2	238704155	238704155	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0881-01	TCGA-06-0881-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:238704155C>G	uc002vxq.2	+	c.2061C>G	c.(2059-2061)TGC>TGG	p.C687W	ESPNL_uc010fyw.1_Missense_Mutation_p.C383W	NM_194312	NP_919288	Q6ZVH7	ESPNL_HUMAN	espin-like	687										pancreas(1)	1		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)												0.333333	7.401126	7.69382	4	8	CC		KEEP	---	---	---	---	capture		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)	Missense_Mutation	SNP	238704155	238704155	5448	2	C	G	G	28	28	ESPNL	G	3	3
PCDHB16	57717	broad.mit.edu	36	5	140543329	140543329	+	Silent	SNP	G	T	T			TCGA-06-0881-01	TCGA-06-0881-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140543329G>T	uc003liv.1	+	c.1011G>T	c.(1009-1011)GTG>GTT	p.V337V	PCDHB16_uc010jfw.1_Silent_p.V9V	NM_020957	NP_066008	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16 precursor	337	Extracellular (Potential).|Cadherin 3.				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)|pancreas(1)	2														0.102041	10.311626	33.529503	15	132	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Silent	SNP	140543329	140543329	11961	5	G	T	T	47	47	PCDHB16	T	3	3
PRELID1	27166	broad.mit.edu	36	5	176666174	176666174	+	Silent	SNP	G	T	T			TCGA-06-0881-01	TCGA-06-0881-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176666174G>T	uc003mfx.1	+	c.657G>T	c.(655-657)GTG>GTT	p.V219V	RAB24_uc003mfu.1_5'Flank|RAB24_uc003mfv.1_5'Flank|RAB24_uc003mfw.1_5'Flank|PRELID1_uc003mfy.1_Silent_p.V217V|MXD3_uc010jkk.1_3'UTR	NM_013237	NP_037369	Q9Y255	PRLD1_HUMAN	PRELI domain containing 1	219					immune response|multicellular organismal development	mitochondrion|nucleus					0	all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)												0.375	9.709673	9.940766	6	10	GG		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Silent	SNP	176666174	176666174	12914	5	G	T	T	48	48	PRELID1	T	3	3
CDH18	1016	broad.mit.edu	36	5	19556581	19556582	+	Missense_Mutation	DNP	GG	AC	AC			TCGA-06-0881-01	TCGA-06-0881-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:19556581_19556582GG>AC	uc003jgc.1	-	c.1453_1454CC>GT	c.(1453-1455)CCA>GTA	p.P485V	CDH18_uc003jgd.1_Missense_Mutation_p.P485V|CDH18_uc010iua.1_Missense_Mutation_p.P485V|CDH18_uc010itz.1_Missense_Mutation_p.P485V	NM_004934	NP_004925	Q13634	CAD18_HUMAN	cadherin 18, type 2 preproprotein	485	Extracellular (Potential).|Cadherin 4.				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)|large_intestine(1)	6	Lung NSC(1;0.00734)|all_lung(1;0.0197)													0.138298	36.019441	59.807832	26	162	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	19556581	19556582	3232	5	GG	AC	AC	47	47	CDH18	AC	2	2
ID4	3400	broad.mit.edu	36	6	19946200	19946200	+	Missense_Mutation	SNP	T	G	G			TCGA-06-0881-01	TCGA-06-0881-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:19946200T>G	uc003ncw.1	+	c.236T>G	c.(235-237)GTG>GGG	p.V79G		NM_001546	NP_001537	P47928	ID4_HUMAN	inhibitor of DNA binding 4, dominant negative	79	Helix-loop-helix motif.			RLV -> WL (in Ref. 3; AAA82882).		nucleus	transcription corepressor activity|transcription repressor activity				0	Ovarian(93;0.0355)|Breast(50;0.0654)|all_epithelial(95;0.12)					Esophageal Squamous(13;105 518 19978 28644 46870)								0.571429	8.088002	8.11782	4	3	TT		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(7;0.00659)|all cancers(50;0.0327)|Epithelial(50;0.0621)		Missense_Mutation	SNP	19946200	19946200	7792	6	T	G	G	59	59	ID4	G	4	4
C7orf52	375607	broad.mit.edu	36	7	100604567	100604567	+	Missense_Mutation	SNP	G	A	A			TCGA-06-0881-01	TCGA-06-0881-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100604567G>A	uc003uxy.1	-	c.242C>T	c.(241-243)CCT>CTT	p.P81L	C7orf52_uc003uxz.1_Missense_Mutation_p.P81L|C7orf52_uc003uya.1_Missense_Mutation_p.P81L|C7orf52_uc003uyb.1_Missense_Mutation_p.P81L	NM_198571	NP_940973	Q8N8M0	CG052_HUMAN	hypothetical protein LOC375607	81	N-acetyltransferase.						N-acetyltransferase activity			ovary(1)	1	Lung NSC(181;0.168)|all_lung(186;0.215)													0.259259	12.295681	13.731962	7	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100604567	100604567	2508	7	G	A	A	35	35	C7orf52	A	2	2
EGFR	1956	broad.mit.edu	36	7	55189316	55189316	+	Missense_Mutation	SNP	C	T	T			TCGA-06-0881-01	TCGA-06-0881-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189316C>T	uc003tqk.1	+	c.866C>T	c.(865-867)GCC>GTC	p.A289V	EGFR_uc003tqh.1_Missense_Mutation_p.A289V|EGFR_uc003tqi.1_Missense_Mutation_p.A289V|EGFR_uc003tqj.1_Missense_Mutation_p.A289V|EGFR_uc010kzg.1_Missense_Mutation_p.A244V	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	289	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.A289V(20)|p.V30_R297>G(10)|p.A289D(3)		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	p.A289V(HEC6-Tumor)|p.A289D(HS683-Tumor)|p.A289V(RL952-Tumor)	608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.176587	174.109213	223.682201	89	415	CC		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	55189316	55189316	5156	7	C	T	T	26	26	EGFR	T	2	2
SUSD3	203328	broad.mit.edu	36	9	94877910	94877910	+	Missense_Mutation	SNP	C	A	A			TCGA-06-0881-01	TCGA-06-0881-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:94877910C>A	uc004atb.1	+	c.112C>A	c.(112-114)CCC>ACC	p.P38T	SUSD3_uc004atc.1_Missense_Mutation_p.P25T	NM_145006	NP_659443	Q96L08	SUSD3_HUMAN	sushi domain containing 3	38	Sushi.|Extracellular (Potential).					integral to membrane				breast(2)|skin(2)|ovary(1)|lung(1)	6														0.264706	19.531626	23.045411	18	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94877910	94877910	15929	9	C	A	A	18	18	SUSD3	A	3	3
FXR2	9513	broad.mit.edu	36	17	7448081	7448082	+	Frame_Shift_Ins	INS	-	C	C			TCGA-06-0881-01	TCGA-06-0881-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7448081_7448082insC	uc002gia.1	-	c.270_271insG	c.(268-273)TGGCTGfs	p.W90fs		NM_004860	NP_004851	P51116	FXR2_HUMAN	fragile X mental retardation syndrome related	90_91						cytosolic large ribosomal subunit	protein binding|RNA binding	p.0?(1)|p.?(1)			0				READ - Rectum adenocarcinoma(115;0.17)										0.55			6	5				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	7448081	7448082	6367	17	-	C	C	34	34	FXR2	C	5	5
