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
KIT	3815	broad.mit.edu	37	4	55561801	55561801	+	Missense_Mutation	SNP	T	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr4:55561801T>G	uc010igr.3	+	1	278	c.191T>G	c.(190-192)gTc>gGc	p.V64G	KIT_uc010igs.3_Missense_Mutation_p.V64G	NM_000222	NP_000213	P10721	KIT_HUMAN	Homo sapiens v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT), transcript variant 1, mRNA.	64	Ig-like C2-type 1.				male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCGGGCTTTGTCAAATGGACT	0.493000		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors					78			4		0	0	0.000248	0	0
HERC2P9	440248	broad.mit.edu	37	15	28929385	28929385	+	RNA	SNP	T	C	C	rs692172	by1000genomes	TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr15:28929385T>C	uc010azc.3	+	13		c.2090T>C								Homo sapiens hect domain and RLD 2 pseudogene 9 (HERC2P9), non-coding RNA.																		CACGCTGCGGTGGTCTTGCAT	0.453000														54			4		0	0	0.000248	0	0
PATZ1	23598	broad.mit.edu	37	22	31740738	31740738	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr22:31740738C>T	uc003akq.3	-	0	1512	c.851G>A	c.(850-852)gGg>gAg	p.G284E	PATZ1_uc003akp.3_Missense_Mutation_p.G284E|PATZ1_uc003akr.3_Missense_Mutation_p.G284E|PATZ1_uc003aks.3_Missense_Mutation_p.G284E|Em:AC005003.4_uc003akt.3_5'Flank	NM_014323	NP_055138	Q9HBE1	PATZ1_HUMAN	Homo sapiens POZ (BTB) and AT hook containing zinc finger 1 (PATZ1), transcript variant 1, mRNA.	284					negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding		EWSR1/PATZ1(2)	NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	12						CCTCAGGCCCCCTGGGGACCC	0.652000														18			6		0	0	0.003080	0	0
SCN10A	6336	broad.mit.edu	37	3	38793869	38793869	+	Missense_Mutation	SNP	G	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr3:38793869G>T	uc003ciq.3	-	10	1596	c.1596C>A	c.(1594-1596)agC>agA	p.S532R		NM_006514	NP_006505	Q9Y5Y9	SCNAA_HUMAN	Homo sapiens sodium channel, voltage-gated, type X, alpha subunit (SCN10A), mRNA.	532					sensory perception	voltage-gated sodium channel complex				NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cocaine(DB00907)|Dibucaine(DB00527)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)	AGCCCCGATGGCTTTCGTGGT	0.602000														82			7		0.00198382	0.00249131	0.001984	1	0
PGM1	5236	broad.mit.edu	37	1	64100510	64100510	+	Silent	SNP	G	A	A			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr1:64100510G>A	uc010ooz.2	+	4	992	c.747G>A	c.(745-747)ccG>ccA	p.P249P	PGM1_uc001dbh.3_Silent_p.P231P|PGM1_uc010ooy.2_Silent_p.P34P	NM_001172818	NP_001166290	P36871	PGM1_HUMAN	Homo sapiens phosphoglucomutase 1 (PGM1), transcript variant 2, mRNA.	231					cellular calcium ion homeostasis|galactose catabolic process|glucose 1-phosphate metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol	magnesium ion binding|phosphoglucomutase activity			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						TTGTGGGACCGTATGTAAAGA	0.473000														144			4		0	0	0.000248	0	0
PSG7	5676	broad.mit.edu	37	19	43439742	43439742	+	Missense_Mutation	SNP	A	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr19:43439742A>G	uc002ovl.4	-	1	346	c.244T>C	c.(244-246)Tat>Cat	p.Y82H	PSG3_uc002ouf.3_Intron|PSG4_uc010xwk.1_Intron|PSG7_uc010xwl.2_Intron	NM_002783	NP_002774	Q13046	PSG7_HUMAN	Homo sapiens pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene) (PSG7), transcript variant 1, mRNA.	82	Ig-like V-type.				female pregnancy	extracellular region							Prostate(69;0.00682)				TCTACTATATATGATGTAACA	0.418000														446			23		0	0	0.001882	0	0
MLL	4297	broad.mit.edu	37	11	118344301	118344301	+	Silent	SNP	T	A	A			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr11:118344301T>A	uc001pta.3	+	2	2450	c.2427T>A	c.(2425-2427)tcT>tcA	p.S809S	MLL_uc001ptb.3_Silent_p.S809S|MLL_uc001psz.1_Silent_p.S842S|MLL_uc001ptd.1_Intron	NM_005933	NP_005924	Q03164	MLL1_HUMAN	Homo sapiens myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) (MLL), transcript variant 2, mRNA.	809					apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			breast(5)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(29)|lung(34)|ovary(6)|pancreas(3)|prostate(8)|skin(6)|urinary_tract(19)	131	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		CTGGGGAATCTGCAGAGAAAA	0.468000			"""T, O"""	"""MLL, MLLT1, MLLT2, MLLT3, MLLT4, MLLT7, MLLT10, MLLT6, ELL, EPS15, AF1Q, CREBBP, SH3GL1, FNBP1, PNUTL1, MSF, GPHN, GMPS, SSH3BP1, ARHGEF12, GAS7, FOXO3A, LAF4, LCX, SEPT6, LPP, CBFA2T1, GRAF, EP300, PICALM, HEAB"""	"""AML, ALL"""									167			7		0	0	0.003080	0	0
FAM178A	55719	broad.mit.edu	37	10	102683830	102683830	+	Missense_Mutation	SNP	G	C	C			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr10:102683830G>C	uc001krs.3	+	4	1614	c.1072G>C	c.(1072-1074)Gag>Cag	p.E358Q	FAM178A_uc001krr.1_Missense_Mutation_p.E358Q|FAM178A_uc001krt.4_Missense_Mutation_p.E358Q|FAM178A_uc001kru.1_Missense_Mutation_p.E293Q	NM_001136123	NP_001129595	Q8IX21	F178A_HUMAN	Homo sapiens family with sequence similarity 178, member A (FAM178A), transcript variant 2, mRNA.	358																	AAAAGCAAGAGAGTCCTTCCT	0.398000														46			5		0	0	0.001168	0	0
DCST1	149095	broad.mit.edu	37	1	155013046	155013046	+	Silent	SNP	C	T	T	rs141235792		TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr1:155013046C>T	uc001fgn.2	+	5	591	c.477C>T	c.(475-477)cgC>cgT	p.R159R	DCST1_uc010per.2_Silent_p.R184R|DCST1_uc010pes.2_Silent_p.R134R	NM_152494	NP_689707	Q5T197	DCST1_HUMAN	Homo sapiens DC-STAMP domain containing 1 (DCST1), transcript variant 1, mRNA.	159						integral to membrane	zinc ion binding			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			ACAACACCCGCGCAGCTTGGC	0.617000														9			4		0	0	0.000248	0	0
MUC17	140453	broad.mit.edu	37	7	100681682	100681682	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr7:100681682C>T	uc003uxp.1	+	2	7038	c.6985C>T	c.(6985-6987)Cca>Tca	p.P2329S	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	Homo sapiens mucin 17, cell surface associated (MUC17), mRNA.	2329	59 X approximate tandem repeats.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TACCAGCATGCCAACCTCAAC	0.478000														586			6		0	0	0.001984	0	0
SIGLEC9	27180	broad.mit.edu	37	19	51628865	51628865	+	Missense_Mutation	SNP	A	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr19:51628865A>T	uc010yct.2	+	1	528	c.433A>T	c.(433-435)Agg>Tgg	p.R145W	SIGLEC9_uc002pvu.3_Missense_Mutation_p.R145W	NM_001198558	NP_001185487	Q9Y336	SIGL9_HUMAN	Homo sapiens sialic acid binding Ig-like lectin 9 (SIGLEC9), transcript variant 1, mRNA.	145					cell adhesion|cell surface receptor linked signaling pathway	integral to plasma membrane	sugar binding			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		CTTGACCCACAGGCCCAACAT	0.642000														221			5		0	0	0.001168	0	0
GIGYF2	26058	broad.mit.edu	37	2	233655736	233655736	+	Missense_Mutation	SNP	A	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr2:233655736A>G	uc002vtj.4	+	12	1282	c.1015A>G	c.(1015-1017)Att>Gtt	p.I339V	GIGYF2_uc010zmj.1_Missense_Mutation_p.I317V|GIGYF2_uc002vtg.2_Missense_Mutation_p.I311V|GIGYF2_uc002vti.4_Missense_Mutation_p.I317V|GIGYF2_uc002vtk.4_Missense_Mutation_p.I317V|GIGYF2_uc002vth.4_Missense_Mutation_p.I311V|GIGYF2_uc010zmk.2_Non-coding_Transcript|GIGYF2_uc010zml.1_Missense_Mutation_p.I148V	NM_001103147	NP_001096617	Q6Y7W6	PERQ2_HUMAN	Homo sapiens GRB10 interacting GYF protein 2 (GIGYF2), transcript variant 1, mRNA.	317					cell death		protein binding			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GAAAGAGCCTATTCCAGAAGA	0.443000														92			3		0	0	0.004672	0	0
NKX2-2	4821	broad.mit.edu	37	20	21492966	21492966	+	Missense_Mutation	SNP	C	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr20:21492966C>G	uc002wsi.3	-	1	774	c.417G>C	c.(415-417)caG>caC	p.Q139H		NM_002509	NP_002500	O95096	NKX22_HUMAN	Homo sapiens NK2 homeobox 2 (NKX2-2), mRNA.	139					brain development|positive regulation of sequence-specific DNA binding transcription factor activity	nucleus	chromatin binding|core promoter proximal region DNA binding|transcription coactivator activity			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						GCTCGTAGGTCTGCGCCTTGG	0.692000														26			16		0	0	0.006122	0	0
GPR31	2853	broad.mit.edu	37	6	167570606	167570606	+	Silent	SNP	G	A	A			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr6:167570606G>A	uc011egq.2	-	0	714	c.714C>T	c.(712-714)tgC>tgT	p.C238C		NM_005299	NP_005290	O00270	GPR31_HUMAN	Homo sapiens G protein-coupled receptor 31 (GPR31), mRNA.	238						integral to plasma membrane	G-protein coupled receptor activity			NS(1)|endometrium(4)|large_intestine(4)|lung(7)|prostate(1)	17		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;4.81e-20)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;0.00492)		TGGCCAGGAAGCAGGGCAGAA	0.592000														118			11		0	0	0.000978	0	0
UBC	7316	broad.mit.edu	37	17	21731144	21731144	+	Missense_Mutation	SNP	T	G	G	rs149119138	by1000genomes	TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr17:21731144T>G	uc002gyy.3	+	1	571	c.446T>G	c.(445-447)cTg>cGg	p.L149R				P0CG48	UBC_HUMAN	SubName: Full=Uncharacterized protein;	301	Ubiquitin-like 2.				DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA repair|G1/S transition of mitotic cell cycle|I-kappaB kinase/NF-kappaB cascade|JNK cascade|M/G1 transition of mitotic cell cycle|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|S phase of mitotic cell cycle|T cell receptor signaling pathway|Toll signaling pathway|activation of MAPK activity|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|anti-apoptosis|apoptosis|cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|induction of apoptosis by extracellular signals|innate immune response|mRNA metabolic process|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of type I interferon production|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|nerve growth factor receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|stress-activated MAPK cascade|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|viral reproduction	cytosol|endocytic vesicle membrane|endosome membrane|nucleoplasm|plasma membrane	protein binding	p.L149R(18)|p.R148S(1)		breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		GTCCTGCGTCTGAGAGGTGGT	0.542000														128			4		0	0	0.000602	0	0
SZT2	23334	broad.mit.edu	37	1	43912025	43912025	+	Missense_Mutation	SNP	T	C	C			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr1:43912025T>C	uc001cjk.2	+	63	8923	c.6313T>C	c.(6313-6315)Tgt>Cgt	p.C2105R	SZT2_uc001cjl.2_Missense_Mutation_p.C93R	NM_015284	NP_056099	Q5T011	SZT2_HUMAN	Homo sapiens seizure threshold 2 homolog (mouse) (SZT2), mRNA.	3004						peroxisome				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CTGTTACTTCTGTGTCAAACA	0.552000														102			4		0	0	0.000602	0	0
COL6A1	1291	broad.mit.edu	37	21	47409674	47409674	+	Silent	SNP	A	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr21:47409674A>G	uc002zhu.1	+	10	1014	c.912A>G	c.(910-912)aaA>aaG	p.K304K		NM_001848	NP_001839	P12109	CO6A1_HUMAN	Homo sapiens collagen, type VI, alpha 1 (COL6A1), mRNA.	304	Triple-helical region.				axon guidance|cell adhesion|protein heterotrimerization	collagen type VI|protein complex	platelet-derived growth factor binding			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)	Palifermin(DB00039)	AGGGAGAAAAAGGGAGCCGTG	0.637000														109			3		0	0	0.004672	0	0
ATRX	546	broad.mit.edu	37	X	76845411	76845411	+	Splice_Site	SNP	C	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chrX:76845411C>T	uc004ecp.4	-	27	6343	c.6111_splice	c.e27-1	p.V2037_splice	ATRX_uc004ecq.4_Splice_Site_p.V1999_splice|ATRX_uc004eco.4_Splice_Site_p.V1822_splice	NM_000489	NP_000480	P46100	ATRX_HUMAN	Homo sapiens alpha thalassemia/mental retardation syndrome X-linked (ATRX), transcript variant 1, mRNA.	2037	Helicase C-terminal.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|DNA binding|DNA helicase activity|chromo shadow domain binding|zinc ion binding	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145					Phosphatidylserine(DB00144)	GAAAACAAGGCTAAAAAAACA	0.323000			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome							6			23		0	0	0.001882	0	0
RPTN	126638	broad.mit.edu	37	1	152128682	152128682	+	Missense_Mutation	SNP	G	A	A			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr1:152128682G>A	uc001ezs.1	-	2	958	c.893C>T	c.(892-894)aCg>aTg	p.T298M		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	Homo sapiens repetin (RPTN), mRNA.	298	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						TTGTCTGTCCGTCTGACCGTA	0.512000														809			81		0	0	0.003610	0	0
UCP3	7352	broad.mit.edu	37	11	73714925	73714925	+	Silent	SNP	G	A	A			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr11:73714925G>A	uc001our.3	-	5	1126	c.771C>T	c.(769-771)ctC>ctT	p.L257L	UCP3_uc001ous.2_Silent_p.L257L	NM_003356	NP_003347	P55916	UCP3_HUMAN	Homo sapiens uncoupling protein 3 (mitochondrial, proton carrier) (UCP3), nuclear gene encoding mitochondrial protein, transcript variant long, mRNA.	257					mitochondrial transport|respiratory electron transport chain|respiratory gaseous exchange	integral to membrane|mitochondrial inner membrane	binding			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					TCATACAGTCGAGGGGGCTGA	0.617000														194			8		0	0	0.004482	0	0
SLC5A8	160728	broad.mit.edu	37	12	101577979	101577979	+	Missense_Mutation	SNP	C	A	A			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr12:101577979C>A	uc001thz.4	-	7	1375	c.985G>T	c.(985-987)Gac>Tac	p.D329Y		NM_145913	NP_666018	Q8N695	SC5A8_HUMAN	Homo sapiens solute carrier family 5 (iodide transporter), member 8 (SLC5A8), mRNA.	329					apoptosis|sodium ion transport	apical plasma membrane|integral to membrane	monocarboxylic acid transmembrane transporter activity|passive transmembrane transporter activity|symporter activity	p.D329N(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGCAGAATGTCCAGTACCAAA	0.348000														48			9		0.000442599	0.000569056	0.006214	1	0
SEMA4F	10505	broad.mit.edu	37	2	74901749	74901749	+	Missense_Mutation	SNP	G	A	A			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr2:74901749G>A	uc002sna.1	+	7	1058	c.947G>A	c.(946-948)cGa>cAa	p.R316Q	SEMA4F_uc021vjn.1_Missense_Mutation_p.R316Q|SEMA4F_uc010ffq.1_Missense_Mutation_p.R283Q|SEMA4F_uc010ffr.1_5'UTR|SEMA4F_uc002snb.1_5'UTR|SEMA4F_uc002snc.1_Missense_Mutation_p.R161Q	NM_004263	NP_004254	O95754	SEM4F_HUMAN	Homo sapiens sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F (SEMA4F), mRNA.	316	Sema.				cell-cell signaling	endoplasmic reticulum|integral to plasma membrane	receptor activity			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						GCTGTGCTTCGACCTGAGCTT	0.562000														224			21		0	0	0.001882	0	0
PIP4K2B	8396	broad.mit.edu	37	17	36926734	36926734	+	Missense_Mutation	SNP	A	C	C			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr17:36926734A>C	uc002hqs.3	-	8	1606	c.1125T>G	c.(1123-1125)gaT>gaG	p.D375E		NM_003559	NP_003550	P78356	PI42B_HUMAN	Homo sapiens phosphatidylinositol-5-phosphate 4-kinase, type II, beta (PIP4K2B), mRNA.	375	PIPK.				cell surface receptor linked signaling pathway	endoplasmic reticulum membrane|plasma membrane	1-phosphatidylinositol-4-phosphate 5-kinase activity|1-phosphatidylinositol-5-phosphate 4-kinase activity|ATP binding|receptor signaling protein activity			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						TCTTCTTTGTATCGTATGGCG	0.537000														191			4		0	0	0.004482	0	0
SERPINA9	327657	broad.mit.edu	37	14	94929626	94929626	+	Missense_Mutation	SNP	T	A	A			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr14:94929626T>A	uc001ydf.3	-	4	1273	c.1112A>T	c.(1111-1113)cAc>cTc	p.H371L	SERPINA9_uc001yde.3_Missense_Mutation_p.H271L|SERPINA9_uc010avc.3_Missense_Mutation_p.H222L|SERPINA9_uc001ydg.3_Missense_Mutation_p.H335L	NM_175739	NP_783866	Q86WD7	SPA9_HUMAN	Homo sapiens serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9 (SERPINA9), transcript variant A, mRNA.	353				T -> A (in Ref. 1; AAO65242).	regulation of proteolysis	cytoplasm|extracellular region|membrane	serine-type endopeptidase inhibitor activity			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		CACAGCCTTGTGGGTTGCCTG	0.502000														75			14		0	0	0.003163	0	0
TP53	7157	broad.mit.edu	37	17	7577121	7577121	+	Missense_Mutation	SNP	G	A	A	rs121913343		TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr17:7577121G>A	uc002gim.2	-	7	1011	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_uc002gig.1_Intron|TP53_uc002gih.3_Missense_Mutation_p.R273C|TP53_uc010cne.1_5'Flank|TP53_uc010cng.1_Missense_Mutation_p.R141C|TP53_uc010cnf.1_Missense_Mutation_p.R141C|TP53_uc002gii.1_Missense_Mutation_p.R141C|TP53_uc010cni.1_Missense_Mutation_p.R273C|TP53_uc010cnh.1_Missense_Mutation_p.R273C|TP53_uc002gij.2_Missense_Mutation_p.R273C|DL476366_uc021tpf.1_5'Flank|DL476309_uc021tpg.1_5'Flank|DL476358_uc021tph.1_5'Flank	NM_001126112	NP_001119587	P04637	P53_HUMAN	Homo sapiens tumor protein p53 (TP53), transcript variant 2, mRNA.	273	Interaction with AXIN1 (By similarity).|Interaction with DNA.|Interaction with E4F1.|Interaction with HIPK1 (By similarity).		R -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> G (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> H (in LFS; germline mutation and in sporadic cancers; somatic mutation; abolishes sequence-specific DNA binding; dbSNP:rs28934576).|R -> L (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in sporadic cancers; somatic mutation).|R -> S (in a familial cancer not matching LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> Y (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).		DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|Ras protein signal transduction|activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to UV|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|determination of adult lifespan|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|regulation of mitochondrial membrane permeability|replicative senescence|response to X-ray|response to antibiotic|response to gamma radiation	PML body|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|protein complex|replication fork	ATP binding|DNA strand annealing activity|RNA polymerase II transcription factor binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|histone acetyltransferase binding|p53 binding|protease binding|protein N-terminus binding|protein binding|protein heterodimerization activity|protein kinase binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R273C(952)|p.R273H(519)|p.R273L(92)|p.V272M(75)|p.R273P(31)|p.R273S(30)|p.V272L(26)|p.R273G(18)|p.V272E(8)|p.0?(8)|p.V272A(7)|p.R273fs*72(5)|p.V272G(5)|p.R273fs*33(4)|p.V272fs*73(4)|p.V272V(4)|p.R273fs*32(3)|p.V272>?(3)|p.R273_C275delRVC(2)|p.R273fs*71(2)|p.E271_R273delEVR(2)|p.?(2)|p.L265_K305del41(2)|p.F270_D281del12(2)|p.V272_K292del21(2)|p.R273R(1)|p.E258fs*71(1)|p.F270fs*72(1)|p.S269fs*21(1)|p.V272fs*34(1)|p.V272fs*74(1)|p.R273*(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		GCACAAACACGCACCTCAAAG	0.542000	R273C(8MGBA_CENTRAL_NERVOUS_SYSTEM)|R273C(BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(EFO27_OVARY)|R273C(KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(MFE319_ENDOMETRIUM)|R273C(NCIH1048_LUNG)|R273C(PANC0213_PANCREAS)|R273C(PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(RDES_BONE)|R273C(RH30_SOFT_TISSUE)|R273C(RPMI8402_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SH10TC_STOMACH)|R273C(SJRH30_SOFT_TISSUE)|R273C(SUDHL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R273C(SW1710_URINARY_TRACT)|R273C(SW1783_CENTRAL_NERVOUS_SYSTEM)|R273C(TT2609C02_THYROID)	111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)				4			33		0	0	0.002096	0	0
EIF4G3	8672	broad.mit.edu	37	1	21133862	21133862	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr1:21133862C>T	uc001bec.3	-	31	4964	c.4708G>A	c.(4708-4710)Gca>Aca	p.A1570T	EIF4G3_uc010odi.2_Missense_Mutation_p.A1174T|EIF4G3_uc010odj.2_Missense_Mutation_p.A1569T|EIF4G3_uc009vpz.3_Missense_Mutation_p.A1290T|EIF4G3_uc001bef.3_Missense_Mutation_p.A1606T|EIF4G3_uc001bee.3_Missense_Mutation_p.A1576T	NM_003760	NP_003751	O43432	IF4G3_HUMAN	Homo sapiens eukaryotic translation initiation factor 4 gamma, 3 (EIF4G3), transcript variant 3, mRNA.	1570	EIF4A-binding (By similarity).|W2.				RNA metabolic process|interspecies interaction between organisms|regulation of translational initiation	eukaryotic translation initiation factor 4F complex	RNA cap binding|protein binding|translation initiation factor activity			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		GTGAAGAATGCCGTGACAGAT	0.453000														326			5		0	0	0.000602	0	0
NOS3	4846	broad.mit.edu	37	7	150693876	150693876	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr7:150693876C>T	uc003wif.3	+	4	741	c.445C>T	c.(445-447)Cgg>Tgg	p.R149W	NOS3_uc011kuy.2_Intron|NOS3_uc011kva.2_Missense_Mutation_p.R149W|NOS3_uc011kuz.2_Missense_Mutation_p.R149W|NOS3_uc011kvb.2_Missense_Mutation_p.R149W	NM_000603	NP_000594	P29474	NOS3_HUMAN	Homo sapiens nitric oxide synthase 3 (endothelial cell) (NOS3), transcript variant 1, mRNA.	149	Interaction with NOSIP.				anti-apoptosis|arginine catabolic process|blood vessel remodeling|endothelial cell migration|mitochondrion organization|negative regulation of muscle hyperplasia|negative regulation of platelet activation|nitric oxide biosynthetic process|platelet activation|positive regulation of angiogenesis|positive regulation of guanylate cyclase activity|positive regulation of vasodilation|regulation of blood vessel size|regulation of nitric-oxide synthase activity|regulation of systemic arterial blood pressure by endothelin|response to fluid shear stress|response to heat|smooth muscle hyperplasia	Golgi membrane|caveola|cytoskeleton|cytosol	FMN binding|NADP binding|actin monomer binding|arginine binding|cadmium ion binding|calmodulin binding|flavin adenine dinucleotide binding|heme binding|nitric-oxide synthase activity|tetrahydrobiopterin binding	p.R149R(2)		NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	L-Arginine(DB00125)|L-Citrulline(DB00155)|Rosuvastatin(DB01098)|Tetrahydrobiopterin(DB00360)	CCACGAACAGCGGCTTCAAGA	0.657000														23			6		0	0	0.006214	0	0
PCDHGC5	56097	broad.mit.edu	37	5	140730818	140730818	+	Missense_Mutation	SNP	A	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr5:140730818A>G	uc003ljo.2	+	0	991	c.991A>G	c.(991-993)Ata>Gta	p.I331V	PCDHGC5_uc003lji.2_Intron|PCDHGC5_uc003ljk.2_Intron|PCDHGC5_uc003ljm.2_Intron|PCDHGC5_uc011daq.2_Missense_Mutation_p.I331V	NM_018922	NP_061745	Q9Y5F6	PCDGM_HUMAN	Homo sapiens protocadherin gamma subfamily B, 1 (PCDHGB1), transcript variant 1, mRNA.	338	Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAATGTTCAAATAGAAATTGT	0.428000														76			6		0	0	0.001984	0	0
UNC93A	54346	broad.mit.edu	37	6	167717405	167717405	+	Splice_Site	SNP	A	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr6:167717405A>G	uc003qvq.3	+	5	801	c.626_splice	c.e5-2	p.G209_splice	UNC93A_uc003qvr.3_Splice_Site_p.G167_splice	NM_018974	NP_061847	Q86WB7	UN93A_HUMAN	Homo sapiens unc-93 homolog A (C. elegans) (UNC93A), transcript variant 1, mRNA.	209						integral to membrane|plasma membrane				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		ATGTCCTTTCAGGGAGTGGTG	0.537000														105			27		0	0	0.002836	0	0
IDH1	3417	broad.mit.edu	37	2	209113112	209113112	+	Missense_Mutation	SNP	C	T	T	rs121913500		TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr2:209113112C>T	uc002vcs.3	-	3	641	c.395G>A	c.(394-396)cGt>cAt	p.R132H	IDH1_uc002vct.3_Missense_Mutation_p.R132H|IDH1_uc002vcu.3_Missense_Mutation_p.R132H	NM_005896	NP_005887	O75874	IDHC_HUMAN	Homo sapiens isocitrate dehydrogenase 1 (NADP+), soluble (IDH1), mRNA.	132			R -> C (in colorectal cancer and glioma samples; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha- ketoglutarate but instead alpha- ketoglutarate is converted to R(-)-2- hydroxyglutarate).|R -> G (in a glioma sample; glioblastoma multiforme; somatic mutation).|R -> H (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> L (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).|R -> S (in a glioma sample; glioblastoma multiforme; somatic mutation; abolishes magnesium binding and alters enzyme activity so that isocitrate is no longer converted to alpha-ketoglutarate but instead alpha-ketoglutarate is converted to R(-)-2-hydroxyglutarate).		2-oxoglutarate metabolic process|NADPH regeneration|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle	cytosol|peroxisomal matrix	NAD binding|isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|protein homodimerization activity	p.R132H(6425)|p.R132C(590)|p.R132?(189)|p.R132G(173)|p.R132S(140)|p.R132L(130)|p.R132V(2)|p.G131_R132>VL(2)|p.R132P(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		ATAAGCATGACGACCTATGAT	0.393000			Mis		gliobastoma									45			38		0	0	0.002522	0	0
ATP5B	506	broad.mit.edu	37	12	57036472	57036472	+	Silent	SNP	G	C	C			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr12:57036472G>C	uc001slr.3	-	5	1041	c.936C>G	c.(934-936)acC>acG	p.T312T		NM_001686	NP_001677	P06576	ATPB_HUMAN	Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide (ATP5B), nuclear gene encoding mitochondrial protein, mRNA.	312					ATP hydrolysis coupled proton transport|angiogenesis|regulation of intracellular pH|respiratory electron transport chain	cell surface|mitochondrial nucleoid|mitochondrial proton-transporting ATP synthase, catalytic core|plasma membrane	ATP binding|MHC class I protein binding|eukaryotic cell surface binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|hydrogen-exporting ATPase activity, phosphorylative mechanism|proton-transporting ATPase activity, rotational mechanism			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AACCAGCCTGGGTGAAGCGAA	0.483000														67			25		0	0	0.006320	0	0
KCNB1	3745	broad.mit.edu	37	20	47989844	47989844	+	Silent	SNP	A	C	C			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr20:47989844A>C	uc002xur.1	-	1	2419	c.2253T>G	c.(2251-2253)ggT>ggG	p.G751G	KCNB1_uc002xus.1_Silent_p.G751G	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	Homo sapiens potassium voltage-gated channel, Shab-related subfamily, member 1 (KCNB1), mRNA.	751					energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity	p.G751G(4)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			ACTGGTGGACACCCGCCTCAA	0.572000														184			17		0	0	0.003610	0	0
CHAD	1101	broad.mit.edu	37	17	48543081	48543081	+	Missense_Mutation	SNP	G	A	A	rs138200891		TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr17:48543081G>A	uc010dbr.3	-	1	978	c.925C>T	c.(925-927)Cgg>Tgg	p.R309W	ACSF2_uc002iqu.2_Intron|ACSF2_uc010wml.1_Intron|ACSF2_uc010wmm.1_Intron|ACSF2_uc010wmn.1_Intron|ACSF2_uc010wmo.1_Intron|CHAD_uc010dbs.3_Missense_Mutation_p.R309W|ACSF2_uc010dbt.1_5'Flank	NM_001267	NP_001258	O15335	CHAD_HUMAN	Homo sapiens chondroadherin (CHAD), mRNA.	309	LRRCT.				regulation of cell growth	proteinaceous extracellular matrix	extracellular matrix structural constituent			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CGAAGGCCCCGGAGCTGGCAG	0.562000														196			4		0	0	0.000602	0	0
KIAA1429	25962	broad.mit.edu	37	8	95523837	95523837	+	Missense_Mutation	SNP	A	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr8:95523837A>G	uc003ygo.2	-	12	3037	c.2966T>C	c.(2965-2967)cTc>cCc	p.L989P	KIAA1429_uc003ygp.3_Missense_Mutation_p.L989P|KIAA1429_uc010maz.2_Non-coding_Transcript	NM_015496	NP_056311	Q69YN4	VIR_HUMAN	Homo sapiens KIAA1429 (KIAA1429), transcript variant 1, mRNA.	989					RNA splicing|mRNA processing	nucleus				NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			GTTGACATGGAGCCTCCAAGG	0.428000														111			3		0	0	0.004672	0	0
MLL3	58508	broad.mit.edu	37	7	151842271	151842271	+	Missense_Mutation	SNP	T	G	G			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr7:151842271T>G	uc003wla.3	-	53	14360	c.14141A>C	c.(14140-14142)aAa>aCa	p.K4714T	MLL3_uc003wkz.3_Missense_Mutation_p.K3832T|MLL3_uc003wkx.3_Missense_Mutation_p.K872T|MLL3_uc003wky.3_Missense_Mutation_p.K2278T	NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	Homo sapiens myeloid/lymphoid or mixed-lineage leukemia 3 (MLL3), mRNA.	4714					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			NS(6)|biliary_tract(9)|breast(24)|central_nervous_system(18)|cervix(6)|endometrium(31)|haematopoietic_and_lymphoid_tissue(1)|kidney(26)|large_intestine(52)|liver(1)|lung(102)|ovary(10)|pancreas(17)|prostate(15)|skin(20)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(8)|urinary_tract(15)	365	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		GGCACTCATTTTAGGTTCAGA	0.448000			N		medulloblastoma									117			16		0	0	0.004990	0	0
CD200	4345	broad.mit.edu	37	3	112064083	112064083	+	Silent	SNP	C	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr3:112064083C>T	uc003dyw.3	+	3	588	c.444C>T	c.(442-444)ttC>ttT	p.F148F	CD200_uc010hqd.1_Missense_Mutation_p.S9L|CD200_uc003dyx.3_Silent_p.F123F|CD200_uc003dyz.3_Silent_p.F49F|CD200_uc003dyy.3_Missense_Mutation_p.S9L	NM_001004196	NP_001004196	P41217	OX2G_HUMAN	Homo sapiens CD200 molecule (CD200), transcript variant 2, mRNA.	123	Ig-like C2-type.				regulation of immune response	integral to plasma membrane				endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				TGTGTCTCTTCAATACCTTTG	0.443000														125			4		0	0	0.000248	0	0
KRT8	3856	broad.mit.edu	37	12	53293635	53293635	+	Missense_Mutation	SNP	C	T	T			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr12:53293635C>T	uc009zmk.1	-	5	1009	c.989G>A	c.(988-990)cGc>cAc	p.R330H	KRT8_uc001sbd.2_Missense_Mutation_p.R302H|KRT8_uc009zml.1_Missense_Mutation_p.R302H|KRT8_uc009zmm.1_Missense_Mutation_p.R302H	NM_002273	NP_002264	P05787	K2C8_HUMAN	Homo sapiens keratin 8 (KRT8), transcript variant 2, mRNA.	302	Coil 2.|Necessary for interaction with PNN.|Rod.				cytoskeleton organization|interspecies interaction between organisms	cytoplasm|keratin filament|nuclear matrix|nucleoplasm	protein binding|structural molecule activity			endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)	AGTCTTTGTGCGCCGCAGGTC	0.602000														35			30		0	0	0.007291	0	0
ARID1A	8289	broad.mit.edu	37	1	27057936	27057937	+	Frame_Shift_Ins	INS	-	C	C			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr1:27057936_27057937insC	uc001bmv.1	+	2	2017_2018	c.1644_1645insC	c.(1642-1647)cagcccfs	p.Q548fs	ARID1A_uc001bmt.1_Frame_Shift_Ins_p.Q548fs|ARID1A_uc001bmu.1_Frame_Shift_Ins_p.Q548fs|ARID1A_uc001bmw.1_Frame_Shift_Ins_p.Q165fs	NM_006015	NP_006006	O14497	ARI1A_HUMAN	Homo sapiens AT rich interactive domain 1A (SWI-like) (ARID1A), transcript variant 1, mRNA.	548					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	SWI/SNF complex|nBAF complex|npBAF complex	DNA binding|protein binding	p.Y551fs*72(1)|p.Q548*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCCAGAGCCAGCCCCCCTACTC	0.649			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""								---	431	---	---	23	---					
DDX5	1655	broad.mit.edu	37	17	62500099	62500102	+	Splice_Site	DEL	ACAG	-	-			TCGA-DU-5853-01A-11D-1893-08	TCGA-DU-5853-10A-01D-1893-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	0750c06c-d62b-42d9-804a-a9b9d76b90ed	fb0e600b-10e0-43fb-b877-0981c762da9b	g.chr17:62500099_62500102delACAG	uc010deh.2	-	4	484	c.441_splice	c.e4+1	p.S147_splice	DDX5_uc002jek.2_Splice_Site_p.S147_splice|DDX5_uc002jej.2_Splice_Site_p.S42_splice|DDX5_uc010wqa.1_Intron|MIR5047_uc021ubs.1_5'Flank|DDX5_uc002jel.1_5'Flank	NM_004396	NP_004387	P17844	DDX5_HUMAN	Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5), mRNA.	147	Helicase ATP-binding.				cell growth|regulation of alternative nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nucleolus	ATP binding|ATP-dependent helicase activity|RNA helicase activity|mRNA binding|protein binding|transcription cofactor activity			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			TCCCAAACTTACAGACAATGTTTT	0.397			T	ETV4	prostate								---	202	---	---	7	---					
