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
PDZD7	79955	broad.mit.edu	36	10	102768823	102768823	+	Missense_Mutation	SNP	C	G	G			TCGA-06-0139-01	TCGA-06-0139-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:102768823C>G	uc001ksn.2	-	c.1070G>C	c.(1069-1071)GGC>GCC	p.G357A	PDZD7_uc001kso.1_Missense_Mutation_p.G357A	NM_024895	NP_079171	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	357					response to stimulus|visual perception	cilium|nucleus	protein binding			breast(1)|central_nervous_system(1)	2												OREG0020453	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.5	9.796692	9.796692	4	4	CC		KEEP	---	---	---	---	capture		Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)	Missense_Mutation	SNP	102768823	102768823	12125	10	C	G	G	26	26	PDZD7	G	3	3
P2RY2	5029	broad.mit.edu	36	11	72623792	72623792	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0139-01	TCGA-06-0139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:72623792G>C	uc001otk.1	+	c.940G>C	c.(940-942)GTA>CTA	p.V314L	P2RY2_uc001otj.1_Missense_Mutation_p.V314L|P2RY2_uc001otl.1_Missense_Mutation_p.V314L|P2RY2_uc009ytm.1_Missense_Mutation_p.V314L	NM_176072	NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y2	314	Cytoplasmic (Potential).				activation of phospholipase C activity by G-protein coupled receptor protein signaling pathway coupled to IP3 second messenger	integral to plasma membrane	purinergic nucleotide receptor activity, G-protein coupled			ovary(2)	2					Suramin(DB04786)									0.277778	9.663441	10.467999	5	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72623792	72623792	11765	11	G	C	C	40	40	P2RY2	C	3	3
LRP1	4035	broad.mit.edu	36	12	55876248	55876248	+	Missense_Mutation	SNP	G	C	C			TCGA-06-0139-01	TCGA-06-0139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:55876248G>C	uc001snd.1	+	c.8813G>C	c.(8812-8814)GGC>GCC	p.G2938A		NM_002332	NP_002323	Q07954	LRP1_HUMAN	low density lipoprotein-related protein 1	2938	LDL-receptor class A 20.|Extracellular (Potential).				apoptotic cell clearance|multicellular organismal development|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein particle receptor binding|lipoprotein transporter activity|protein complex binding|receptor activity			ovary(7)|large_intestine(2)|pancreas(2)|skin(1)|central_nervous_system(1)	13					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)					1456				0.461538	10.072046	10.095401	6	7	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0103)	Missense_Mutation	SNP	55876248	55876248	9324	12	G	C	C	42	42	LRP1	C	3	3
NKPD1	284353	broad.mit.edu	36	19	50347987	50347987	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-0139-01	TCGA-06-0139-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50347987G>T	uc002pau.1	-	c.882C>A	c.(880-882)TAC>TAA	p.Y294*		NM_198478	NP_940880			NTPase, KAP family P-loop domain containing 1												0		Ovarian(192;0.0728)|all_neural(266;0.112)												0.333333	7.029141	7.246993	3	6	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)	Nonsense_Mutation	SNP	50347987	50347987	10847	19	G	T	T	44	44	NKPD1	T	5	3
SOX13	9580	broad.mit.edu	36	1	202361681	202361681	+	Silent	SNP	A	C	C			TCGA-06-0139-01	TCGA-06-0139-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:202361681A>C	uc001ham.1	+	c.1665A>C	c.(1663-1665)GCA>GCC	p.A555A		NM_005686	NP_005677	Q9UN79	SOX13_HUMAN	SRY-box 13	555					anatomical structure morphogenesis|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			breast(1)|central_nervous_system(1)	2	all_cancers(21;0.0754)|Breast(84;0.116)|all_epithelial(62;0.189)													0.428571	6.437754	6.53733	6	8	AA		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)		Silent	SNP	202361681	202361681	15444	1	A	C	C	6	6	SOX13	C	4	4
MYH7B	57644	broad.mit.edu	36	20	33046900	33046900	+	Missense_Mutation	SNP	A	G	G			TCGA-06-0139-01	TCGA-06-0139-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33046900A>G	uc002xbi.1	+	c.2927A>G	c.(2926-2928)GAG>GGG	p.E976G		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	934	Potential.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2														0.318182	11.265801	11.943553	7	15	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(18;0.00691)		Missense_Mutation	SNP	33046900	33046900	10435	20	A	G	G	11	11	MYH7B	G	4	4
SP8	221833	broad.mit.edu	36	7	20791466	20791468	+	In_Frame_Del	DEL	GCC	-	-			TCGA-06-0139-01	TCGA-06-0139-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:20791466_20791468delGCC	uc003suz.1	-	c.493_495delGGC	c.(493-495)GGCdel	p.G165del	SP8_uc003suy.1_In_Frame_Del_p.G147del|SP8_uc010kuj.1_In_Frame_Del_p.G147del	NM_182700	NP_945194	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor isoform 1	147					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)	1														0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	20791466	20791468	15470	7	GCC	-	-	34	34	SP8	-	5	5
