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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	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	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
SCARB1	949	broad.mit.edu	37	12	125292412	125292412	+	Missense_Mutation	SNP	C	C	G			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr12:125292412C>G	ENST00000339570.5	-	7	1100	c.904G>C	c.(904-906)Gtg>Ctg	p.V302L	SCARB1_ENST00000544327.1_Missense_Mutation_p.V248L|SCARB1_ENST00000541205.1_Missense_Mutation_p.V261L|SCARB1_ENST00000540495.1_Missense_Mutation_p.V265L|SCARB1_ENST00000415380.2_Missense_Mutation_p.V302L|SCARB1_ENST00000535005.1_5'UTR|SCARB1_ENST00000546215.1_Missense_Mutation_p.V302L|SCARB1_ENST00000376788.1_Missense_Mutation_p.V202L|SCARB1_ENST00000261693.6_Missense_Mutation_p.V302L	NM_001082959.1	NP_001076428.1	Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	302					adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|reverse cholesterol transport|triglyceride homeostasis|wound healing	caveola	1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	TTGGGAGCCACGAAGCGATAG	0.567000													16	40					0	0	1	0	0
NBPF9	400818	broad.mit.edu	37	1	144828545	144828545	+	Missense_Mutation	SNP	A	A	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr1:144828545A>T	ENST00000338347.4	+	14	1591	c.1591A>T	c.(1591-1593)Aac>Tac	p.N531Y	NBPF9_ENST00000281815.8_Missense_Mutation_p.N129Y|NBPF9_ENST00000440491.2_Silent_p.S604S|NBPF9_ENST00000468645.1_3'UTR					neuroblastoma breakpoint family, member 9									p.N531Y(1)		NS(2)|prostate(1)	3						TTCCAGGCTCAACGGCGTGCT	0.453000													5	185					0	0	1	0	0
AGAP10	728127	broad.mit.edu	37	10	47207813	47207813	+	Splice_Site	SNP	T	T	C			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr10:47207813T>C	ENST00000355232.3	-	5	3482	c.471_splice	c.e5+1	p.H157_splice	RP11-144G6.12_ENST00000605970.1_RNA|AGAP10_ENST00000413193.2_Splice_Site_p.H228_splice|AGAP10_ENST00000452145.2_Splice_Site_p.H132_splice					ArfGAP with GTPase domain, ankyrin repeat and PH domain 10									p.H228R(20)		endometrium(5)|kidney(3)|lung(1)|prostate(2)|urinary_tract(1)	12						TTTACTTACATGGTTTGTACA	0.294000													3	26					0	0	1	0	0
CYFIP2	26999	broad.mit.edu	37	5	156787349	156787349	+	Silent	SNP	C	C	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr5:156787349C>T	ENST00000347377.6	+	25	3308	c.2877C>T	c.(2875-2877)tgC>tgT	p.C959C	CYFIP2_ENST00000318218.6_Silent_p.C984C|CYFIP2_ENST00000435847.2_Silent_p.C658C|CYFIP2_ENST00000522463.1_Silent_p.C763C|CYFIP2_ENST00000442283.2_3'UTR|CYFIP2_ENST00000521420.1_Silent_p.C933C|CYFIP2_ENST00000377576.3_Silent_p.C959C|CYFIP2_ENST00000541131.1_Silent_p.C884C	NM_001037332.2	NP_001032409.2	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2	984					apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding			breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCAAGATATGCCGCTTGCCCC	0.517000													4	121					0	0	1	0	0
MAML3	55534	broad.mit.edu	37	4	140811108	140811108	+	Silent	SNP	C	C	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr4:140811108C>T	ENST00000509479.2	-	2	2338	c.1482G>A	c.(1480-1482)caG>caA	p.Q494Q	MAML3_ENST00000327122.5_Silent_p.Q338Q|MAML3_ENST00000398940.1_Silent_p.Q33Q	NM_018717.4	NP_061187.2	Q96JK9	MAML3_HUMAN	mastermind-like 3 (Drosophila)	494	Gln-rich.				Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	transcription coactivator activity			breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.537000													3	30					0	0	1	0	0
NRL	4901	broad.mit.edu	37	14	24551759	24551759	+	Missense_Mutation	SNP	T	T	C			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr14:24551759T>C	ENST00000561028.1	-	2	618	c.299A>G	c.(298-300)cAg>cGg	p.Q100R	NRL_ENST00000397002.2_Missense_Mutation_p.Q100R|NRL_ENST00000396997.1_Missense_Mutation_p.Q100R			P54845	NRL_HUMAN	neural retina leucine zipper	100					response to stimulus|transcription from RNA polymerase II promoter|visual perception	nucleus	leucine zipper domain binding|sequence-specific DNA binding			lung(2)	2				GBM - Glioblastoma multiforme(265;0.0181)		GCCCTGACCCTGCAGCAGCTC	0.657000													3	40					0	0	1	0	0
MEGF10	84466	broad.mit.edu	37	5	126754828	126754828	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr5:126754828C>T	ENST00000274473.6	+	12	1589	c.1322C>T	c.(1321-1323)aCc>aTc	p.T441I	MEGF10_ENST00000503335.2_Missense_Mutation_p.T441I|MEGF10_ENST00000508365.1_Missense_Mutation_p.T441I|MEGF10_ENST00000418761.2_Missense_Mutation_p.T441I	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	441	Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				cell adhesion|phagocytosis	basolateral plasma membrane|cell projection|integral to membrane|phagocytic cup				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		GACTGCTCTACCCCATGCCCT	0.443000													58	57					0	0	1	0	0
PDE4A	5141	broad.mit.edu	37	19	10577609	10577609	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr19:10577609C>T	ENST00000380702.2	+	16	1907	c.1907C>T	c.(1906-1908)gCg>gTg	p.A636V	PDE4A_ENST00000344979.3_Missense_Mutation_p.A419V|PDE4A_ENST00000352831.6_Missense_Mutation_p.A658V|PDE4A_ENST00000293683.5_Missense_Mutation_p.A632V|PDE4A_ENST00000440014.2_Missense_Mutation_p.A597V|PDE4A_ENST00000592685.1_Missense_Mutation_p.A636V			P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	658	Catalytic.				signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)	GAGACCTGGGCGGACCTTGTC	0.572000													39	74					0	0	1	0	0
GPR50	9248	broad.mit.edu	37	X	150349267	150349267	+	Missense_Mutation	SNP	C	C	G			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chrX:150349267C>G	ENST00000218316.3	+	2	1281	c.1212C>G	c.(1210-1212)caC>caG	p.H404Q		NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	404	Pro-rich.				cell-cell signaling	integral to plasma membrane	melatonin receptor activity	p.H404Q(2)		breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					CTACCCACCACAAGTCTGTCT	0.602000													5	63					0	0	1	0	0
DLC1	10395	broad.mit.edu	37	8	12958214	12958214	+	Missense_Mutation	SNP	G	G	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr8:12958214G>T	ENST00000276297.4	-	9	2041	c.1632C>A	c.(1630-1632)agC>agA	p.S544R	DLC1_ENST00000520226.1_Missense_Mutation_p.S33R|DLC1_ENST00000512044.2_Missense_Mutation_p.S141R|DLC1_ENST00000358919.2_Missense_Mutation_p.S107R	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	deleted in liver cancer 1	544					actin cytoskeleton organization|activation of caspase activity|focal adhesion assembly|forebrain development|heart morphogenesis|hindbrain morphogenesis|induction of apoptosis|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of Rho protein signal transduction|negative regulation of stress fiber assembly|neural tube closure|positive regulation of protein dephosphorylation|regulation of cell shape|small GTPase mediated signal transduction	caveola|cytosol|focal adhesion|nucleus	Rho GTPase activator activity|SH2 domain binding			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						ACCACCTCTTGCTGTCCCTTT	0.552000													3	37					1	1	1	1	0
RNPS1	10921	broad.mit.edu	37	16	2314324	2314324	+	Missense_Mutation	SNP	G	G	A			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr16:2314324G>A	ENST00000565678.1	-	3	625	c.80C>T	c.(79-81)tCa>tTa	p.S27L	RNPS1_ENST00000397086.2_Missense_Mutation_p.S27L|RNPS1_ENST00000566458.1_Missense_Mutation_p.S4L|RNPS1_ENST00000320225.5_Missense_Mutation_p.S27L|RNPS1_ENST00000566397.1_5'UTR|RNPS1_ENST00000301730.8_Missense_Mutation_p.S27L|RNPS1_ENST00000568631.1_Missense_Mutation_p.S27L|RNPS1_ENST00000567147.1_Missense_Mutation_p.S4L|RNPS1_ENST00000569598.2_Intron|RNPS1_ENST00000561718.1_5'UTR			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	27	Lys-rich.|Necessary for interaction with SRP54, nuclear localization and exon-skipping.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|termination of RNA polymerase II transcription	cytosol|nuclear speck	mRNA 3'-UTR binding|nucleotide binding|protein binding			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						TTTGGTAGGTGAAGGAGCCCT	0.557000													8	116					0	0	1	0	0
CRIPAK	285464	broad.mit.edu	37	4	1389323	1389323	+	Missense_Mutation	SNP	G	G	A	rs71299249	byFrequency	TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr4:1389323G>A	ENST00000324803.4	+	1	3984	c.1024G>A	c.(1024-1026)Gcc>Acc	p.A342T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	342					ER-nucleus signaling pathway|negative regulation of protein kinase activity|regulation of cytoskeleton organization|response to estrogen stimulus	endoplasmic reticulum|nucleus|plasma membrane	protein binding			NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGGAGTGCCCGCCTGCTCACA	0.667000													7	409					0	0	1	0	0
TMEM132B	114795	broad.mit.edu	37	12	126138738	126138738	+	Missense_Mutation	SNP	G	G	A			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr12:126138738G>A	ENST00000299308.3	+	9	2727	c.2719G>A	c.(2719-2721)Gtc>Atc	p.V907I	TMEM132B_ENST00000535886.1_Missense_Mutation_p.V419I	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	907						integral to membrane				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CTTGCTCTGCGTCTTCTGTCT	0.522000													4	96					0	0	1	0	0
RFTN1	23180	broad.mit.edu	37	3	16419524	16419524	+	Missense_Mutation	SNP	G	G	A			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr3:16419524G>A	ENST00000334133.4	-	5	799	c.527C>T	c.(526-528)gCt>gTt	p.A176V	RFTN1_ENST00000432519.1_Missense_Mutation_p.A140V	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	176						plasma membrane				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						AGACACCGGAGCACTGCTGCC	0.552000													3	34					0	0	1	0	0
SEMA6D	80031	broad.mit.edu	37	15	48063896	48063896	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr15:48063896C>T	ENST00000316364.5	+	19	3575	c.3136C>T	c.(3136-3138)Ccg>Tcg	p.P1046S	SEMA6D_ENST00000354744.4_Missense_Mutation_p.P990S|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000389428.3_Missense_Mutation_p.P971S|SEMA6D_ENST00000536845.2_Missense_Mutation_p.P1046S|SEMA6D_ENST00000389432.2_Missense_Mutation_p.P1003S|SEMA6D_ENST00000537942.1_Missense_Mutation_p.P984S|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000358066.4_Missense_Mutation_p.P984S|SEMA6D_ENST00000558014.1_Missense_Mutation_p.P984S|SEMA6D_ENST00000389433.2_Missense_Mutation_p.P1027S	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	1046					axon guidance	cytoplasm|integral to membrane|plasma membrane	receptor activity			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AAAGAGGACGCCGTCCTTAAA	0.512000													20	171					0	0	1	0	0
PTCRA	171558	broad.mit.edu	37	6	42890951	42890951	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr6:42890951C>T	ENST00000304672.1	+	2	326	c.245C>T	c.(244-246)aCg>aTg	p.T82M	PTCRA_ENST00000441198.1_Missense_Mutation_p.T57M|PTCRA_ENST00000446507.1_Intron	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	82						integral to membrane	receptor activity			large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			TCCCCAGCAACGGATGGCACC	0.622000													14	55					0	0	1	0	0
TFAP4	7023	broad.mit.edu	37	16	4312678	4312678	+	Silent	SNP	G	G	C			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr16:4312678G>C	ENST00000204517.6	-	2	442	c.114C>G	c.(112-114)ccC>ccG	p.P38P		NM_003223.2	NP_003214.1	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer binding protein 4)	38					DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation by host of viral transcription|negative regulation of cell cycle arrest|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of DNA binding|negative regulation of transcription, DNA-dependent|positive regulation by host of viral transcription|positive regulation of apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein complex assembly|regulation of S phase of mitotic cell cycle	transcriptional repressor complex	E-box binding|histone deacetylase binding|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity			NS(1)|endometrium(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						GCTGAGTCTCGGGGGTTAGTG	0.622000													4	69					0	0	1	0	0
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	byFrequency	TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr22:29091840T>C	ENST00000544772.1	-	12	1890	c.454A>G	c.(454-456)Aag>Gag	p.K152E	CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000405598.1_Missense_Mutation_p.K373E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E	NM_001257387.1	NP_001244316.1	O96017	CHK2_HUMAN	checkpoint kinase 2	373	FHA.				cell cycle|DNA damage checkpoint|DNA damage response, signal transduction resulting in induction of apoptosis|replicative senescence	PML body	ATP binding|metal ion binding|protein binding|protein serine/threonine kinase activity	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418000			F			breast		Direct reversal of damage;Other conserved DNA damage response genes					3	71					0	0	1	0	0
ECT2	1894	broad.mit.edu	37	3	172480266	172480266	+	Missense_Mutation	SNP	T	T	G			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr3:172480266T>G	ENST00000417960.1	+	9	1200	c.723T>G	c.(721-723)gaT>gaG	p.D241E	ECT2_ENST00000441497.2_Missense_Mutation_p.D242E|ECT2_ENST00000540509.1_Missense_Mutation_p.D273E|ECT2_ENST00000232458.5_Missense_Mutation_p.D242E|ECT2_ENST00000392692.3_Missense_Mutation_p.D273E|ECT2_ENST00000427830.1_Missense_Mutation_p.D242E	NM_001258316.1	NP_001245245.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming sequence 2 oncogene	242	BRCT 2.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity|signal transducer activity			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			CATTTCAAGATTGTATTTTAA	0.294000													5	34					0	0	1	0	0
ZP1	22917	broad.mit.edu	37	11	60637317	60637317	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr11:60637317C>T	ENST00000278853.5	+	3	626	c.626C>T	c.(625-627)gCt>gTt	p.A209V		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	209					single fertilization	integral to membrane|plasma membrane|proteinaceous extracellular matrix				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						GCCACCCTGGCTCAACCCCAC	0.587000													3	37					0	0	1	0	0
ADAMTSL3	57188	broad.mit.edu	37	15	84611672	84611672	+	Silent	SNP	C	C	T			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr15:84611672C>T	ENST00000286744.5	+	19	2552	c.2328C>T	c.(2326-2328)ggC>ggT	p.G776G	ADAMTSL3_ENST00000567476.1_Silent_p.G776G	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	776	TSP type-1 6.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGACTTGTGGCGGGGGAACTC	0.537000													3	29					0	0	1	0	0
COL11A2	1302	broad.mit.edu	37	6	33134291	33134291	+	Splice_Site	SNP	G	G	C			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr6:33134291G>C	ENST00000341947.2	-	60	4618	c.4392_splice	c.e60+1	p.P1464_splice	COL11A2_ENST00000357486.1_Splice_Site_p.P1443_splice|COL11A2_ENST00000374714.1_Splice_Site_p.P1438_splice|COL11A2_ENST00000361917.1_Splice_Site_p.P1357_splice|COL11A2_ENST00000395197.1_Splice_Site_p.P1404_splice|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000374713.1_Splice_Site_p.P1417_splice|COL11A2_ENST00000374708.4_Splice_Site_p.P1378_splice|COL11A2_ENST00000374712.1_Splice_Site_p.P1383_splice	NM_080680.2	NP_542411.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1464	Triple-helical region.				cartilage development|cell adhesion|collagen fibril organization|sensory perception of sound|soft palate development	collagen type XI	extracellular matrix structural constituent conferring tensile strength|protein binding, bridging			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						AGTACTCACGGGGAGGCCGGG	0.612000													3	42					0	0	1	0	0
ING1	3621	broad.mit.edu	37	13	111366587	111366587	+	Missense_Mutation	SNP	C	C	G			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr13:111366587C>G	ENST00000333219.7	+	1	963	c.91C>G	c.(91-93)Cag>Gag	p.Q31E	ING1_ENST00000375775.3_Intron|ING1_ENST00000338450.7_Intron	NM_001267728.1|NM_198219.2	NP_001254657.1|NP_937862.1	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	0					cell cycle|negative regulation of cell growth|negative regulation of cell proliferation	nucleus	zinc ion binding			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			TTTCGACTTGCAGAGAAATGT	0.627000													12	34					0	0	1	0	0
GCKR	2646	broad.mit.edu	37	2	27728649	27728649	+	Missense_Mutation	SNP	C	C	G			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr2:27728649C>G	ENST00000264717.2	+	10	878	c.815C>G	c.(814-816)aCc>aGc	p.T272S	GCKR_ENST00000424318.2_Missense_Mutation_p.T82S	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	272	SIS 1.				carbohydrate metabolic process|glucose transport|negative regulation of glucokinase activity|positive regulation of gene expression|protein import into nucleus, translocation|regulation of glucose transport|response to fructose stimulus|transmembrane transport|triglyceride homeostasis|urate metabolic process	cytosol|nucleoplasm	fructose-6-phosphate binding|protein binding			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					CTGCTGGAAACCCTGTTATTA	0.542000													5	65					0	0	1	0	0
PHB	5245	broad.mit.edu	37	17	47486440	47486440	+	Silent	SNP	G	G	A			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr17:47486440G>A	ENST00000300408.3	-	5	546	c.474C>T	c.(472-474)gcC>gcT	p.A158A	PHB_ENST00000511832.1_Intron|PHB_ENST00000508009.1_5'UTR|RP11-81K2.1_ENST00000576461.1_Intron	NM_002634.2	NP_002625.1	P35232	PHB_HUMAN	prohibitin	158					cellular response to interleukin-6|DNA replication|glucocorticoid receptor signaling pathway|histone deacetylation|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|progesterone receptor signaling pathway|regulation of apoptosis	integral to plasma membrane|mitochondrial inner membrane|nucleoplasm	histone deacetylase binding|transcription regulatory region DNA binding			endometrium(4)|large_intestine(2)|lung(4)	10	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			CAAAGGTGGCGGCTCGCTCTG	0.587000													11	41					0	0	1	0	0
KIAA1324	57535	broad.mit.edu	37	1	109656849	109656849	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr1:109656849delG	ENST00000369939.3	+	1	227	c.44delG	c.(43-45)agfs	p.R15fs	KIAA1324_ENST00000529753.1_Frame_Shift_Del_p.R15fs	NM_020775.4	NP_065826.2	Q6UXG2	K1324_HUMAN	KIAA1324	15					macroautophagy|positive regulation of vacuole organization|regulation of apoptosis	integral to plasma membrane				NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		GCCAGAGTCAGGGGAAGAACT	0.662													2	4	---	---	---	---					
PMS2CL	0	broad.mit.edu	37	7	6775132	6775133	+	RNA	INS	-	-	T	rs72390141		TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr7:6775132_6775133insT	ENST00000486256.1	+	0	833					NR_002217.1																						GGTCATGTAAGTTTTTTTTTTT	0.401													3	6	---	---	---	---					
PLEC	5339	broad.mit.edu	37	8	145000031	145000031	+	Frame_Shift_Del	DEL	C	C	-			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr8:145000031delC	ENST00000322810.4	-	31	4646	c.4477delG	c.(4477-4479)cafs	p.A1493fs	PLEC_ENST00000345136.3_Frame_Shift_Del_p.A1356fs|PLEC_ENST00000357649.2_Frame_Shift_Del_p.A1360fs|PLEC_ENST00000527096.1_Frame_Shift_Del_p.A1379fs|PLEC_ENST00000356346.3_Frame_Shift_Del_p.A1342fs|PLEC_ENST00000398774.2_Frame_Shift_Del_p.A1324fs|PLEC_ENST00000354589.3_Frame_Shift_Del_p.A1356fs|PLEC_ENST00000436759.2_Frame_Shift_Del_p.A1383fs|PLEC_ENST00000354958.2_Frame_Shift_Del_p.A1334fs	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1493	Central fibrous rod domain.				cellular component disassembly involved in apoptosis|hemidesmosome assembly	cytosol|focal adhesion|hemidesmosome|intermediate filament cytoskeleton|sarcolemma	actin binding|structural constituent of muscle			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CGCTCCTCTGCCCGCTGCTGC	0.701													2	4	---	---	---	---					
PHOSPHO1	0	broad.mit.edu	37	17	47302390	47302392	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr17:47302390_47302392delAGG	ENST00000413580.1	-	3	512_514	c.95_97delCCT	c.(94-99)tgc>t	p.SC32del	PHOSPHO1_ENST00000310544.4_Intron|PHOSPHO1_ENST00000514112.1_In_Frame_Del_p.SC32del	NM_001143804.1|NM_178500.3	NP_001137276.1|NP_848595.1	Q8TCT1	PHOP1_HUMAN	phosphatase, orphan 1	0					regulation of bone mineralization		metal ion binding|phosphoethanolamine/phosphocholine phosphatase activity							Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)		Choline(DB00122)	ggagagcagcaggaggaggagga	0.700													3	5	---	---	---	---					
CTD-2369P2.5	0	broad.mit.edu	37	19	10377498	10377498	+	RNA	DEL	T	T	-			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chr19:10377498delT	ENST00000592893.1	-	0	141																											TCCATAGCCCTTTTTTTTTCC	0.428													3	6	---	---	---	---					
RP11-258C19.5	0	broad.mit.edu	37	X	53142506	53142507	+	RNA	INS	-	-	A	rs146094031		TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chrX:53142506_53142507insA	ENST00000604849.1	+	0	96																											AAAACACACACACAAAAAAAAA	0.356													3	4	---	---	---	---					
NRK	203447	broad.mit.edu	37	X	105149314	105149314	+	Frame_Shift_Del	DEL	C	C	-			TCGA-WB-A80K-01A-11D-A35I-08	TCGA-WB-A80K-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	8a1af203-5d3f-48c4-88bd-be808fe0f6f8	731b0a29-9ad3-4daf-98c1-7cf7ba584796	g.chrX:105149314delC	ENST00000428173.2	+	10	1126	c.823delC	c.(823-825)ccfs	p.P275fs	NRK_ENST00000243300.9_Frame_Shift_Del_p.P275fs			Q7Z2Y5	NRK_HUMAN	Nik related kinase	275	Protein kinase.						ATP binding|protein serine/threonine kinase activity|small GTPase regulator activity			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						GGAATCTGCTCCCACAGTCAA	0.368										HNSCC(51;0.14)			2	4	---	---	---	---					
