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	validation_method	t_ref_count	validation_status	validation_tumor_sample	t_alt_count	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
CSK	1445	broad.mit.edu	37	15	75093415	75093415	+	Missense_Mutation	SNP	T	C	C			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr15:75093415T>C	uc010bkb.1	+	9	968	c.785T>C	c.(784-786)cTc>cCc	p.L262P	CSK_uc002ays.2_Missense_Mutation_p.L262P|CSK_uc010bkc.1_Missense_Mutation_p.L71P	NM_001127190	NP_004374	P41240	CSK_HUMAN	Homo sapiens c-src tyrosine kinase (CSK), transcript variant 2, mRNA.	262	Protein kinase.				T cell costimulation|T cell receptor signaling pathway|blood coagulation|epidermal growth factor receptor signaling pathway	Golgi apparatus|centrosome|cytosol	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein C-terminus binding	p.L262R(1)		central_nervous_system(1)|lung(2)	3						AAGGGCGGGCTCTACATCGTC	0.642000														76			4		0	0	1	0	0
PKDREJ	10343	broad.mit.edu	37	22	46653502	46653502	+	Nonsense_Mutation	SNP	C	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr22:46653502C>T	uc003bhh.3	-	0	5718	c.5718G>A	c.(5716-5718)tgG>tgA	p.W1906*		NM_006071	NP_006062	Q9NTG1	PKDRE_HUMAN	Homo sapiens polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin) (PKDREJ), mRNA.	1906					acrosome reaction|neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TCTCATCCAGCCAATTGCTTT	0.393000														186			4		0	0	1	0	0
CTNNA2	1496	broad.mit.edu	37	2	80816475	80816475	+	Missense_Mutation	SNP	A	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr2:80816475A>T	uc010ysh.2	+	13	2059	c.2054A>T	c.(2053-2055)gAg>gTg	p.E685V	CTNNA2_uc010yse.2_Missense_Mutation_p.E685V|CTNNA2_uc010ysf.2_Missense_Mutation_p.E685V|CTNNA2_uc010ysg.2_Missense_Mutation_p.E685V|CTNNA2_uc010ysi.2_Missense_Mutation_p.E317V|CTNNA2_uc010ysj.2_Missense_Mutation_p.E14V	NM_004389	NP_004380	P26232	CTNA2_HUMAN	Homo sapiens catenin (cadherin-associated protein), alpha 2 (CTNNA2), transcript variant 1, mRNA.	685					axonogenesis|brain morphogenesis|cell-cell adhesion|dendrite morphogenesis|muscle cell differentiation|positive regulation of muscle cell differentiation|prepulse inhibition|radial glia guided migration of Purkinje cell|regulation of synapse structural plasticity	actin cytoskeleton|axon|cytosol	cadherin binding|structural constituent of cytoskeleton			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						AAAATAGCTGAGCAGGTGGAG	0.507000														111			5		0	0	1	0	0
DSCAM	1826	broad.mit.edu	37	21	42080523	42080523	+	Missense_Mutation	SNP	C	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr21:42080523C>T	uc002yyq.1	-	1	670	c.218G>A	c.(217-219)cGc>cAc	p.R73H	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Homo sapiens Down syndrome cell adhesion molecule (DSCAM), transcript variant 1, mRNA.	73	Ig-like C2-type 1.				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding	p.R73L(2)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GTGGACGTGGCGGATCCCGGG	0.547000														38			19		0	0	1	0	0
UGT2B10	7365	broad.mit.edu	37	4	69870669	69870669	+	Missense_Mutation	SNP	C	A	A			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr4:69870669C>A	uc011cao.1	-	7	1486	c.1360G>T	c.(1360-1362)Gcc>Tcc	p.A454S	UGT2B10_uc011can.1_Missense_Mutation_p.A370S			P36537	UDB10_HUMAN	Homo sapiens UDP glucuronosyltransferase 2 family, polypeptide B10 (UGT2B10), transcript variant 1, mRNA.	498					lipid metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity			endometrium(3)|kidney(4)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	29						GCCACACAGGCCAGCAGGAAC	0.448000														200			7		8.12818e-05	8.49765e-05	1	1	0
FOXO1	2308	broad.mit.edu	37	13	41134356	41134356	+	Nonsense_Mutation	SNP	A	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr13:41134356A>T	uc001uxl.4	-	1	1657	c.1272T>A	c.(1270-1272)taT>taA	p.Y424*	FOXO1_uc010acc.1_Nonsense_Mutation_p.Y239*	NM_002015	NP_002006	Q12778	FOXO1_HUMAN	Homo sapiens forkhead box O1 (FOXO1), mRNA.	424					anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription factor binding		PAX7/FOXO1(197)|PAX3/FOXO1(749)	central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	20		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)		GGCCATATGTATATTTTTGGT	0.488000														22			55		0	0	1	0	0
NUDT9	53343	broad.mit.edu	37	4	88379168	88379168	+	Silent	SNP	T	C	C			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr4:88379168T>C	uc003hqq.3	+	7	1378	c.1048T>C	c.(1048-1050)Ttg>Ctg	p.L350L	NUDT9_uc010ikl.3_Silent_p.L318L|NUDT9_uc003hqr.3_Silent_p.L300L	NM_024047	NP_076952	Q9BW91	NUDT9_HUMAN	Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 9 (NUDT9), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.	350						mitochondrion	ADP-ribose diphosphatase activity			endometrium(1)|large_intestine(4)|lung(6)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		CTGCCATGCGTTGTAGCTGAT	0.458000														60			16		0	0	1	0	0
CLTCL1	8218	broad.mit.edu	37	22	19203748	19203748	+	Missense_Mutation	SNP	A	G	G			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr22:19203748A>G	uc021wle.1	-	18	3013	c.2938T>C	c.(2938-2940)Tca>Cca	p.S980P	CLTCL1_uc021wld.1_Missense_Mutation_p.S980P|CLTCL1_uc021wlc.1_Missense_Mutation_p.S980P|CLTCL1_uc021wlf.1_Missense_Mutation_p.S980P|CLTCL1_uc011agw.1_Missense_Mutation_p.S980P|CLTCL1_uc002zpd.1_5'Flank|CLTCL1_uc002zpe.2_5'Flank	NM_007098	NP_009029	P53675	CLH2_HUMAN	Homo sapiens clathrin, heavy chain-like 1 (CLTCL1), transcript variant 1, mRNA.	980	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis|intracellular protein transport|mitosis|positive regulation of glucose import|receptor-mediated endocytosis	clathrin coat of coated pit|clathrin coat of trans-Golgi network vesicle|spindle|trans-Golgi network	protein binding|signal transducer activity|structural molecule activity			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CGTGTTTCTGACAATGCTGTC	0.408000			T	?	ALCL									81			4		0	0	1	0	0
RBMS3	27303	broad.mit.edu	37	3	29628650	29628650	+	Missense_Mutation	SNP	C	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr3:29628650C>T	uc003cel.3	+	3	723	c.353C>T	c.(352-354)gCg>gTg	p.A118V	RBMS3_uc010hfq.3_Missense_Mutation_p.A118V|RBMS3_uc003cek.3_Missense_Mutation_p.A118V|RBMS3_uc010hfr.3_Missense_Mutation_p.A118V|RBMS3_uc003cem.3_Missense_Mutation_p.A117V	NM_001003793	NP_001003793	Q6XE24	RBMS3_HUMAN	Homo sapiens RNA binding motif, single stranded interacting protein 3 (RBMS3), transcript variant 1, mRNA.	118	RRM 1.					cytoplasm	RNA binding|nucleotide binding			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				GCACAGAAAGCGGTAGCATCT	0.388000														113			4		0	0	1	0	0
H2AFZ	3015	broad.mit.edu	37	4	100870503	100870503	+	Missense_Mutation	SNP	G	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr4:100870503G>T	uc003hvo.1	-	2	307	c.122C>A	c.(121-123)aCg>aAg	p.T41K	DNAJB14_uc003hvl.3_5'Flank|DNAJB14_uc010ili.3_5'Flank|DNAJB14_uc003hvm.3_5'Flank|H2AFZ_uc003hvn.1_3'UTR|LOC256880_uc003hvp.1_5'Flank	NM_002106	NP_002097	P0C0S5	H2AZ_HUMAN	Homo sapiens H2A histone family, member Z (H2AFZ), mRNA.	41					nucleosome assembly	nucleosome|nucleus	DNA binding			breast(1)|endometrium(3)|lung(1)	5				OV - Ovarian serous cystadenocarcinoma(123;2.32e-08)		ATGACTGGTCGTCCTAGATTT	0.488000											OREG0016271	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		54			4		0.00024832	0.00024832	1	1	0
DDX24	57062	broad.mit.edu	37	14	94524209	94524209	+	Missense_Mutation	SNP	C	A	A			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr14:94524209C>A	uc001ycj.3	-	5	2047	c.1948G>T	c.(1948-1950)Ggt>Tgt	p.G650C	DDX24_uc010twq.2_Missense_Mutation_p.G607C|DDX24_uc010twr.2_Missense_Mutation_p.G400C	NM_020414	NP_065147	Q9GZR7	DDX24_HUMAN	Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 24 (DDX24), mRNA.	650	Helicase C-terminal.				RNA metabolic process	cytoplasm|nucleolus	ATP binding|ATP-dependent RNA helicase activity|RNA binding|protein binding			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		ATATCCAGACCCCGAGCTGCC	0.423000														38			27		6.84511e-11	7.49703e-11	1	1	0
TPTE2P3	220115	broad.mit.edu	37	13	53151293	53151293	+	RNA	SNP	G	A	A			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr13:53151293G>A	uc001vgw.3	+	19		c.2058G>A								Homo sapiens transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 3 (TPTE2P3), non-coding RNA.									p.V286I(2)									AAAAAGATTAGTTATTTATTC	0.358000														5			3		0	0	1	0	0
VWCE	220001	broad.mit.edu	37	11	61026257	61026257	+	Missense_Mutation	SNP	C	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr11:61026257C>T	uc001nra.3	-	19	3037	c.2758G>A	c.(2758-2760)Gtg>Atg	p.V920M	VWCE_uc001nrb.3_Non-coding_Transcript	NM_152718	NP_689931	Q96DN2	VWCE_HUMAN	Homo sapiens von Willebrand factor C and EGF domains (VWCE), mRNA.	920						extracellular region	calcium ion binding	p.R919C(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GGAGAAAGCACGCGAGGCCCG	0.667000														63			10		0	0	1	0	0
DGKQ	1609	broad.mit.edu	37	4	961063	961063	+	Silent	SNP	G	A	A			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr4:961063G>A	uc003gbw.3	-	8	1148	c.1074C>T	c.(1072-1074)gaC>gaT	p.D358D	DGKQ_uc010ibn.3_Silent_p.D358D	NM_001347	NP_001338	P52824	DGKQ_HUMAN	Homo sapiens diacylglycerol kinase, theta 110kDa (DGKQ), mRNA.	358					activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|platelet activation|protein kinase C signaling cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to ATP|thrombin receptor signaling pathway	cytoskeleton|cytosol|nuclear speck|plasma membrane	ATP binding|activating transcription factor binding|diacylglycerol kinase activity|kinase binding|metal ion binding|phospholipase binding			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CAGCCCAGGCGTCACAGGCCT	0.726000														17			3		0	0	1	0	0
SLC24A1	9187	broad.mit.edu	37	15	65916547	65916547	+	Silent	SNP	A	G	G			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr15:65916547A>G	uc010ujf.2	+	1	416	c.129A>G	c.(127-129)agA>agG	p.R43R	SLC24A1_uc010ujd.1_Silent_p.R43R|SLC24A1_uc010uje.1_Silent_p.R43R|SLC24A1_uc010ujg.2_Silent_p.R43R|SLC24A1_uc010ujh.2_Silent_p.R43R	NM_004727	NP_004718	O60721	NCKX1_HUMAN	Homo sapiens solute carrier family 24 (sodium/potassium/calcium exchanger), member 1 (SLC24A1), transcript variant 1, mRNA.	43					response to light intensity|visual perception	integral to plasma membrane|membrane fraction|outer membrane	calcium, potassium:sodium antiporter activity|protein binding|symporter activity			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						ACCTTAGGAGACCCCGGGGCC	0.512000														145			5		0	0	1	0	0
WHAMMP2	440253	broad.mit.edu	37	15	28991148	28991148	+	RNA	SNP	G	C	C			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr15:28991148G>C	uc010azf.3	+	4		c.1093G>C			WHAMMP2_uc010uap.2_Non-coding_Transcript|WHAMMP2_uc010azg.1_Non-coding_Transcript|WHAMMP2_uc010azh.1_Non-coding_Transcript|WHAMMP2_uc001zci.1_Non-coding_Transcript|WHAMMP2_uc010azi.1_5'Flank					Homo sapiens WAS protein homolog associated with actin, golgi membranes and microtubules pseudogene 2 (WHAMMP2), non-coding RNA.																		AAATGGAACAGGATGTGAAGA	0.378000														22			4		0	0	1	0	0
TPTE2P3	220115	broad.mit.edu	37	13	53151292	53151292	+	RNA	SNP	A	C	C	rs146809843	by1000genomes	TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr13:53151292A>C	uc001vgw.3	+	19		c.2057A>C								Homo sapiens transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 3 (TPTE2P3), non-coding RNA.									p.L285F(2)									TAAAAAGATTAGTTATTTATT	0.358000														5			3		0	0	1	0	0
C12orf70	341346	broad.mit.edu	37	12	27654933	27654933	+	Missense_Mutation	SNP	G	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr12:27654933G>T	uc010sjq.2	+	8	1087	c.911G>T	c.(910-912)gGt>gTt	p.G304V		NM_001145010	NP_001138482	A6NFE2	CL070_HUMAN	Homo sapiens chromosome 12 open reading frame 70 (C12orf70), mRNA.	304						integral to membrane				kidney(1)	1						CTATTTTTTGGTGCTACATTT	0.433000														102			62		5.00936e-31	5.76076e-31	1	1	0
BIRC6	57448	broad.mit.edu	37	2	32694461	32694461	+	Splice_Site	SNP	A	G	G			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr2:32694461A>G	uc010ezu.3	+	30	6262	c.6128_splice	c.e30-2	p.G2043_splice		NM_016252	NP_057336	Q9NR09	BIRC6_HUMAN	Homo sapiens baculoviral IAP repeat containing 6 (BIRC6), mRNA.	2043					anti-apoptosis|apoptosis	intracellular	acid-amino acid ligase activity|cysteine-type endopeptidase inhibitor activity|protein binding			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TTCTTGTAATAGGACACTCTG	0.368000														114			5		0	0	1	0	0
AHNAK	79026	broad.mit.edu	37	11	62294617	62294617	+	Silent	SNP	C	T	T	rs143003772		TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr11:62294617C>T	uc001ntl.3	-	4	7572	c.7272G>A	c.(7270-7272)ggG>ggA	p.G2424G	AHNAK_uc001ntk.1_Intron	NM_001620	NP_001611	Q09666	AHNK_HUMAN	Homo sapiens AHNAK nucleoprotein (AHNAK), transcript variant 1, mRNA.	2424					nervous system development	nucleus	protein binding			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CAATGTCTGGCCCACTGACAT	0.478000														176			5		0	0	1	0	0
RAD54L2	23132	broad.mit.edu	37	3	51690165	51690165	+	Nonsense_Mutation	SNP	C	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr3:51690165C>T	uc011bdt.2	+	18	3330	c.3205C>T	c.(3205-3207)Cag>Tag	p.Q1069*	RAD54L2_uc003dbh.3_Nonsense_Mutation_p.Q658*|RAD54L2_uc011bdu.2_Nonsense_Mutation_p.Q763*|RAD54L2_uc003dbj.3_Nonsense_Mutation_p.Q395*	NM_015106	NP_055921	Q9Y4B4	ARIP4_HUMAN	Homo sapiens RAD54-like 2 (S. cerevisiae) (RAD54L2), mRNA.	1069						nucleus	ATP binding|DNA binding|helicase activity			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		AGTCCTTGTGCAGAAGGTGGT	0.493000														42			3		0	0	1	0	0
KIAA0430	9665	broad.mit.edu	37	16	15695994	15695994	+	Missense_Mutation	SNP	C	A	A			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr16:15695994C>A	uc002ddr.3	-	22	4687	c.4480G>T	c.(4480-4482)Gtg>Ttg	p.V1494L	KIAA0430_uc002ddq.3_Missense_Mutation_p.V1328L|KIAA0430_uc010uzv.2_Missense_Mutation_p.V1491L|KIAA0430_uc010uzw.2_Missense_Mutation_p.V1494L	NM_014647	NP_055462	Q9Y4F3	LKAP_HUMAN	Homo sapiens KIAA0430 (KIAA0430), transcript variant 1, mRNA.	1493						peroxisome	RNA binding|nucleotide binding			breast(4)|endometrium(8)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(5)|skin(1)	40						AAAGACCGCACATTCTTTGCA	0.388000														76			57		5.10652e-33	6.18158e-33	1	1	0
TRIM4	89122	broad.mit.edu	37	7	99514382	99514382	+	Silent	SNP	G	A	A			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr7:99514382G>A	uc003usd.3	-	1	613	c.414C>T	c.(412-414)caC>caT	p.H138H	TRIM4_uc003use.3_Intron|TRIM4_uc011kjc.2_Intron|TRIM4_uc003usf.3_Intron	NM_033017	NP_148977	Q9C037	TRIM4_HUMAN	Homo sapiens tripartite motif containing 4 (TRIM4), transcript variant alpha, mRNA.	138					protein trimerization	cytoplasm|plasma membrane	zinc ion binding	p.H138N(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)	17	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				attcatccacgtggatgtcaa	0.403000														65			3		0	0	1	0	0
POM121C	100101267	broad.mit.edu	37	7	75055685	75055686	+	Frame_Shift_Ins	INS	-	CC	CC			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr7:75055685_75055686insCC	uc003udk.4	-	7	1415_1416	c.530_531insGG	c.(529-531)tcafs	p.S177fs		NM_001099415	NP_001092885	A8CG34	P121C_HUMAN	Homo sapiens POM121 membrane glycoprotein C (POM121C), mRNA.	419	Pore side (Potential).|Pro-rich.|Required for targeting to the nucleus and nuclear pore complex.				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						GGGAGCGGGATGAGGCTGGGCT	0.505													---	4	---	---	2	---					
LOC120824	120824	broad.mit.edu	37	11	49002503	49002504	+	Frame_Shift_Ins	INS	-	T	T			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr11:49002503_49002504insT	uc021qiw.1	-	1	461_462	c.461_462insA	c.(460-462)aatfs	p.N154fs		NM_001206625	NP_001193554			Homo sapiens tripartite motif-containing protein ENSP00000309378-like (LOC120824), mRNA.																		GGTTTCTGTGATTTTCACACAT	0.391													---	129	---	---	83	---					
CLEC17A	388512	broad.mit.edu	37	19	14710546	14710548	+	In_Frame_Del	DEL	CTA	-	-			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr19:14710546_14710548delCTA	uc010dzn.2	+	10	741_743	c.664_666delCTA	c.(664-666)ctadel	p.L222del	CLEC17A_uc010dzo.2_In_Frame_Del_p.L222del|CLEC17A_uc002mzh.2_In_Frame_Del_p.L205del|CLEC17A_uc010xnt.2_Non-coding_Transcript|CLEC17A_uc010xnu.2_In_Frame_Del_p.L222del	NM_001204118	NP_001191047	Q6ZS10	CL17A_HUMAN	Homo sapiens C-type lectin domain family 17, member A (CLEC17A), transcript variant 1, mRNA.	222						cell surface|integral to membrane	fucose binding|mannose binding|metal ion binding|receptor activity										CATGGCAGGGCTAGCTGGCCTGA	0.547													---	111	---	---	8	---					
KPTN	11133	broad.mit.edu	37	19	47987306	47987307	+	Frame_Shift_Ins	INS	-	C	C			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr19:47987306_47987307insC	uc002pgy.3	-	0	215_216	c.111_112insG	c.(109-114)gggcgcfs	p.G37fs	KPTN_uc010xys.2_Non-coding_Transcript|LOC100505681_uc021uwo.1_5'Flank	NM_007059	NP_008990	Q9Y664	KPTN_HUMAN	Homo sapiens kaptin (actin binding protein) (KPTN), mRNA.	37					actin filament organization|cellular component movement|sensory perception of sound	actin cytoskeleton|growth cone|microtubule organizing center|nucleus|perinuclear region of cytoplasm|stereocilium	actin binding			breast(1)|lung(3)|ovary(2)|pancreas(2)	8		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000428)|all cancers(93;0.000631)|Epithelial(262;0.0153)|GBM - Glioblastoma multiforme(486;0.0694)		AGCTccccgcgcccgccggcgc	0.683											OREG0025593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	4	---	---	2	---					
SCARF2	91179	broad.mit.edu	37	22	20791941	20791943	+	In_Frame_Del	DEL	AGC	-	-			TCGA-KM-8440-01A-11D-2310-10	TCGA-KM-8440-10A-01D-2311-10								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cdf313c8-59f9-41c6-9bd2-f47cb4287da5	f6d8bf61-9da3-4ce4-b6cc-e1391c0c0186	g.chr22:20791941_20791943delAGC	uc002zsj.2	-	0	204_206	c.99_101delGCT	c.(97-102)ctgctc>ctc	p.33_34LL>L	SCARF2_uc002zsk.2_In_Frame_Del_p.33_34LL>L	NM_153334	NP_699165	Q96GP6	SREC2_HUMAN	Homo sapiens scavenger receptor class F, member 2 (SCARF2), transcript variant 1, mRNA.	33					cell adhesion	integral to membrane	protein binding|receptor activity			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	10	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			CAGCATCCAGagcagcagcagca	0.778													---	4	---	---	2	---					
