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
RP11-24M17.5	0	broad.mit.edu	37	15	76074441	76074441	+	RNA	SNP	A	A	T			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr15:76074441A>T	ENST00000395215.3	+	0	620																											CGAGCTGCAGAGAAGCGGTCC	0.557000													3	42					0	0	1	0	0
HNRNPH3	3189	broad.mit.edu	37	10	70101423	70101423	+	Missense_Mutation	SNP	G	G	A			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr10:70101423G>A	ENST00000265866.7	+	8	1022	c.857G>A	c.(856-858)gGa>gAa	p.G286E	HNRNPH3_ENST00000469172.1_3'UTR|HNRNPH3_ENST00000441000.2_Missense_Mutation_p.G178E|HNRNPH3_ENST00000354695.5_Missense_Mutation_p.G271E	NM_012207.2|NM_021644.3	NP_036339.1|NP_067676.2	P31942	HNRH3_HUMAN	heterogeneous nuclear ribonucleoprotein H3 (2H9)	286	Gly-rich.				nuclear mRNA splicing, via spliceosome	heterogeneous nuclear ribonucleoprotein complex	nucleotide binding|protein binding|RNA binding			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)	11						GGAGGCTACGGAAGAGATGGA	0.368000													22	62					0	0	1	0	0
PTPRJ	5795	broad.mit.edu	37	11	48145257	48145257	+	Silent	SNP	C	C	A			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr11:48145257C>A	ENST00000418331.2	+	5	1061	c.709C>A	c.(709-711)Cgg>Agg	p.R237R	PTPRJ_ENST00000440289.2_Silent_p.R237R	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	237	Fibronectin type-III 2.				contact inhibition|negative regulation of cell growth|negative regulation of cell migration|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of platelet-derived growth factor receptor signaling pathway|negative regulation of protein kinase B signaling cascade|negative regulation of T cell receptor signaling pathway|negative regulation of vascular permeability|platelet-derived growth factor receptor signaling pathway|positive chemotaxis|positive regulation of focal adhesion assembly|positive regulation of protein kinase B signaling cascade|positive regulation of survival gene product expression	cell surface|cell-cell junction|immunological synapse|integral to plasma membrane|ruffle membrane	beta-catenin binding|delta-catenin binding|gamma-catenin binding|mitogen-activated protein kinase binding|platelet-derived growth factor receptor binding|protein tyrosine phosphatase activity	p.R237W(2)		breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TGCCTCCTGCCGGGTTCTTCT	0.517000													3	72					0.150653	0.150653	1	1	0
DDX41	51428	broad.mit.edu	37	5	176943192	176943192	+	Missense_Mutation	SNP	G	G	A			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr5:176943192G>A	ENST00000507955.1	-	4	824	c.301C>T	c.(301-303)Cgc>Tgc	p.R101C	DDX41_ENST00000506965.1_5'UTR	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	101					apoptosis|multicellular organismal development	catalytic step 2 spliceosome	ATP binding|ATP-dependent helicase activity|protein binding|RNA binding|zinc ion binding					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			GACTCTTTGCGCGCTGAGAAA	0.537000													22	161					0	0	1	0	0
SPOP	8405	broad.mit.edu	37	17	47696432	47696432	+	Missense_Mutation	SNP	A	A	C			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr17:47696432A>C	ENST00000393331.3	-	7	861	c.391T>G	c.(391-393)Tgg>Ggg	p.W131G	SPOP_ENST00000503676.1_Missense_Mutation_p.W131G|SPOP_ENST00000347630.2_Missense_Mutation_p.W131G|SPOP_ENST00000393328.2_Missense_Mutation_p.W131G|SPOP_ENST00000504102.1_Missense_Mutation_p.W131G	NM_001007226.1|NM_001007227.1	NP_001007227.1|NP_001007228.1	O43791	SPOP_HUMAN	speckle-type POZ protein	131	MATH.|Required for nuclear localization.				mRNA processing	nucleus	protein binding	p.W131G(2)|p.W131R(1)		endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						TTGAATCCCCAGTCTTTGCCT	0.458000										Prostate(2;0.17)			55	99					0	0	1	0	0
PRAMEF19	645414	broad.mit.edu	37	1	13695960	13695960	+	Silent	SNP	G	G	T			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr1:13695960G>T	ENST00000540591.1	-	3	1051	c.1005C>A	c.(1003-1005)atC>atA	p.I335I	PRAMEF19_ENST00000376101.2_Silent_p.I266I	NM_001099790.1	NP_001093260.2			PRAME family member 19											lung(3)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCTCAAGACGGATGAAGCGCA	0.517000													7	180					0.00448238	0.0046484	1	1	0
MED13	9969	broad.mit.edu	37	17	60112846	60112846	+	Silent	SNP	T	T	C			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr17:60112846T>C	ENST00000397786.2	-	4	670	c.594A>G	c.(592-594)caA>caG	p.Q198Q		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	198					androgen receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	ligand-dependent nuclear receptor transcription coactivator activity|receptor activity|RNA polymerase II transcription cofactor activity|thyroid hormone receptor binding|vitamin D receptor binding			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TATTAGACTGTTGAGCAAGGG	0.343000													10	71					0	0	1	0	0
DGKK	139189	broad.mit.edu	37	X	50119074	50119074	+	RNA	SNP	G	G	A			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chrX:50119074G>A	ENST00000376025.2	-	0	3421							Q5KSL6	DGKK_HUMAN	diacylglycerol kinase, kappa						activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|diacylglycerol metabolic process|intracellular signal transduction|platelet activation|response to oxidative stress	cytoplasm|plasma membrane	ATP binding|diacylglycerol kinase activity|metal ion binding			central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Ovarian(276;0.236)					TGTCTTGGCCGTAAAATATAT	0.428000													3	29					0	0	1	0	0
BSN	8927	broad.mit.edu	37	3	49693080	49693080	+	Missense_Mutation	SNP	C	C	T			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr3:49693080C>T	ENST00000296452.4	+	5	6205	c.6091C>T	c.(6091-6093)Cgc>Tgc	p.R2031C		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2031					synaptic transmission	cell junction|cytoplasm|cytoskeleton|nucleus|synaptosome	metal ion binding			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		TGCGGATGGACGCTACCTAGG	0.602000													30	93					0	0	1	0	0
CLCN6	1185	broad.mit.edu	37	1	11888182	11888182	+	Missense_Mutation	SNP	C	C	T			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr1:11888182C>T	ENST00000346436.6	+	11	912	c.860C>T	c.(859-861)gCc>gTc	p.A287V	CLCN6_ENST00000376487.3_Missense_Mutation_p.A265V|CLCN6_ENST00000312413.6_Missense_Mutation_p.A287V|CLCN6_ENST00000376496.3_Missense_Mutation_p.A287V|CLCN6_ENST00000376492.3_3'UTR	NM_001286.3	NP_001277.1	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	287					cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TCCATGTCTGCCACCTTCACC	0.512000													10	270					0	0	1	0	0
ENTPD3	956	broad.mit.edu	37	3	40465423	40465423	+	Missense_Mutation	SNP	A	A	C			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr3:40465423A>C	ENST00000301825.3	+	10	1440	c.1322A>C	c.(1321-1323)gAg>gCg	p.E441A	ENTPD3_ENST00000456402.1_Missense_Mutation_p.E441A|ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3_ENST00000445129.1_Missense_Mutation_p.E441A|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3-AS1_ENST00000452768.1_RNA	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	441						integral to membrane	ATP binding|hydrolase activity			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		TTCACAGAGGAGACTTGGCCC	0.418000													31	79					0	0	1	0	0
ZGPAT	84619	broad.mit.edu	37	20	62364966	62364966	+	Missense_Mutation	SNP	A	A	G			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr20:62364966A>G	ENST00000328969.5	+	4	873	c.746A>G	c.(745-747)aAg>aGg	p.K249R	ZGPAT_ENST00000490623.1_3'UTR|ZGPAT_ENST00000369967.3_Missense_Mutation_p.K249R|ZGPAT_ENST00000448100.1_Missense_Mutation_p.K249R|ZGPAT_ENST00000357119.4_Missense_Mutation_p.K249R|ZGPAT_ENST00000355969.6_Missense_Mutation_p.K249R	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	249					negative regulation of epidermal growth factor receptor activity|negative regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	14	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					TACACAGTCAAGTTTGACTCG	0.612000													132	195					0	0	1	0	0
KIAA0922	23240	broad.mit.edu	37	4	154544236	154544236	+	Splice_Site	SNP	G	G	A			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr4:154544236G>A	ENST00000409959.3	+	29	4094		c.e29+1		KIAA0922_ENST00000440693.1_Splice_Site|KIAA0922_ENST00000409663.3_Splice_Site	NM_001131007.1	NP_001124479.1	A2VDJ0	T131L_HUMAN	KIAA0922							integral to membrane				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				CTGCCGGCCGGTGAGTCCTGA	0.672000													5	14					0	0	1	0	0
AC024560.3	0	broad.mit.edu	37	3	197348646	197348646	+	RNA	SNP	T	T	C	rs138265355	by1000genomes	TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr3:197348646T>C	ENST00000418868.1	-	0	613					NR_003266.2																						TGGGCCTGCCTGCCCTTTCCA	0.532000													5	73					0	0	1	0	0
KRT26	353288	broad.mit.edu	37	17	38925341	38925341	+	Missense_Mutation	SNP	G	G	C			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr17:38925341G>C	ENST00000335552.4	-	6	1025	c.977C>G	c.(976-978)tCc>tGc	p.S326C		NM_181539.4	NP_853517.2	Q7Z3Y9	K1C26_HUMAN	keratin 26	326	Coil 2.|Rod.					intermediate filament	structural molecule activity			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				GCATTCATAGGAATGTTTCTG	0.363000													4	45					0	0	1	0	0
SNW1	22938	broad.mit.edu	37	14	78184773	78184773	+	Missense_Mutation	SNP	G	G	C			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr14:78184773G>C	ENST00000261531.7	-	13	1411	c.1349C>G	c.(1348-1350)cCc>cGc	p.P450R	SNW1_ENST00000555761.1_Missense_Mutation_p.P450R|SLIRP_ENST00000557623.1_Intron|SNW1_ENST00000554775.1_Missense_Mutation_p.P288R|SLIRP_ENST00000557431.1_Intron	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	450					negative regulation of transcription, DNA-dependent|nuclear mRNA splicing, via spliceosome|regulation of transcription from RNA polymerase II promoter	catalytic step 2 spliceosome|nucleoplasm	Notch binding			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		ATTTTTACTGGGCCTATAAAT	0.413000													27	48					0	0	1	0	0
CROCCP2	0	broad.mit.edu	37	1	16945409	16945409	+	RNA	SNP	T	T	A	rs13566		TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr1:16945409T>A	ENST00000412962.1	-	0	2110																											GCGGGATAGCTCGGTGGAGAG	0.612000													3	34					0	0	1	0	0
C2orf73	129852	broad.mit.edu	37	2	54587362	54587362	+	Missense_Mutation	SNP	G	G	C			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr2:54587362G>C	ENST00000398634.2	+	5	569	c.527G>C	c.(526-528)aGa>aCa	p.R176T	C2orf73_ENST00000491538.1_3'UTR|C2orf73_ENST00000405749.1_Intron	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	176										breast(2)	2						TTTGTACAGAGAGAGATAAAA	0.448000													3	8					0	0	1	0	0
FOXM1	2305	broad.mit.edu	37	12	2983155	2983155	+	Missense_Mutation	SNP	G	G	A	rs143720765	byFrequency	TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr12:2983155G>A	ENST00000342628.2	-	2	603	c.490C>T	c.(490-492)Cgg>Tgg	p.R164W	FOXM1_ENST00000359843.3_Missense_Mutation_p.R164W|FOXM1_ENST00000361953.3_Missense_Mutation_p.R164W|FOXM1_ENST00000537018.1_5'UTR	NM_202002.2	NP_973731.1	Q08050	FOXM1_HUMAN	forkhead box M1	164					cell cycle|embryo development|liver development|negative regulation of cell aging|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|positive regulation of cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell cycle arrest|regulation of cell growth|regulation of cell proliferation|regulation of oxygen and reactive oxygen species metabolic process|regulation of Ras protein signal transduction|regulation of reactive oxygen species metabolic process|regulation of sequence-specific DNA binding transcription factor activity|tissue development|transcription from RNA polymerase II promoter|vasculogenesis	cytoplasm|transcription factor complex	DNA bending activity|DNA binding|double-stranded DNA binding|promoter binding|protein binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|transcription factor binding			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			CAGGTCTCCCGTTTCTGCTCG	0.537000													24	42					0	0	1	0	0
MUC16	94025	broad.mit.edu	37	19	9087137	9087137	+	Missense_Mutation	SNP	C	C	T			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr19:9087137C>T	ENST00000397910.4	-	1	4881	c.4678G>A	c.(4678-4680)Gca>Aca	p.A1560T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1560	Thr-rich.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCATCGTTGCAGAAAGGGTG	0.498000													4	168					0	0	1	0	0
ITFG1	81533	broad.mit.edu	37	16	47196504	47196504	+	Missense_Mutation	SNP	C	C	T			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr16:47196504C>T	ENST00000320640.6	-	15	1753	c.1525G>A	c.(1525-1527)Gca>Aca	p.A509T	RP11-329J18.2_ENST00000564705.1_RNA|ITFG1_ENST00000544001.2_Missense_Mutation_p.A396T|RP11-329J18.2_ENST00000565694.1_RNA|ITFG1_ENST00000568047.1_5'UTR	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	509						extracellular region|integral to membrane				breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	19		all_cancers(37;0.0613)|all_lung(18;0.0543)|Lung NSC(13;0.227)				AGAAAATTTGCGCTCCGACCT	0.358000													4	110					0	0	1	0	0
KRTAP4-8	728224	broad.mit.edu	37	17	39254054	39254054	+	Missense_Mutation	SNP	A	A	T	rs76270529	by1000genomes	TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr17:39254054A>T	ENST00000333822.4	-	1	339	c.283T>A	c.(283-285)Tgc>Agc	p.C95S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	95	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].					keratin filament		p.C95S(4)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ctggagatgcagcagcTAGGG	0.677000													3	24					0	0	1	0	0
NOTCH2	4853	broad.mit.edu	37	1	120612003	120612004	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr1:120612003_120612004delGG	ENST00000256646.2	-	1	236_237	c.17_18delCC	c.(16-18)cfs	p.P6fs		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	6					anti-apoptosis|bone remodeling|cell cycle arrest|cell fate determination|cell growth|hemopoiesis|induction of apoptosis|negative regulation of cell proliferation|nervous system development|Notch receptor processing|Notch signaling pathway|organ morphogenesis|positive regulation of Ras protein signal transduction|regulation of transcription, DNA-dependent|stem cell maintenance|transcription, DNA-dependent	cell surface|cytosol|endoplasmic reticulum lumen|extracellular region|Golgi lumen|integral to plasma membrane|nucleoplasm	calcium ion binding|ligand-regulated transcription factor activity|protein binding|receptor activity	p.P6fs*27(2)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACAGCAGAGCGGGGCGCAGGGC	0.762			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				6	10	---	---	---	---					
MLK4	0	broad.mit.edu	37	1	233482217	233482219	+	In_Frame_Del	DEL	GAC	GAC	-			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr1:233482217_233482219delGAC	ENST00000366624.3	+	2	1096_1098	c.835_837delGAC	c.(835-837)del	p.D279del	MLK4_ENST00000366623.3_In_Frame_Del_p.D279del	NM_032435.2	NP_115811.2																					AGAACATGATGACATCTGCAATA	0.394													19	40	---	---	---	---					
FER1L5	90342	broad.mit.edu	37	2	97364482	97364483	+	RNA	DEL	AG	AG	-			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr2:97364482_97364483delAG	ENST00000457909.1	+	0	3934_3935							A0AVI2	FR1L5_HUMAN	fer-1-like 5 (C. elegans)							integral to membrane				NS(1)|autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(9)|large_intestine(9)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(2)	38						TGGTTTGGCCAGAGAGAGAGGA	0.604													2	4	---	---	---	---					
NCKIPSD	51517	broad.mit.edu	37	3	48711990	48711991	+	Frame_Shift_Ins	INS	-	-	C			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr3:48711990_48711991insC	ENST00000294129.2	-	13	2274_2275	c.2155_2156insG	c.(2155-2157)ggcfs	p.G719fs	NCKIPSD_ENST00000341520.4_Intron|NCKIPSD_ENST00000416649.2_Frame_Shift_Ins_p.G712fs	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	719					cytoskeleton organization|NLS-bearing substrate import into nucleus|signal transduction	intermediate filament|nucleus	cytoskeletal protein binding|SH3 domain binding			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GCTGGGAGCCTCCCCCAGCACC	0.579													2	4	---	---	---	---					
LINC00882	0	broad.mit.edu	37	3	106824710	106824710	+	RNA	DEL	T	T	-	rs139188639		TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr3:106824710delT	ENST00000484698.1	-	0	295																											tttttatatcttttttttttt	0.448													2	4	---	---	---	---					
PPRC1	23082	broad.mit.edu	37	10	103901076	103901077	+	Frame_Shift_Ins	INS	-	-	C			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr10:103901076_103901077insC	ENST00000278070.2	+	5	2850_2851	c.2811_2812insC	c.(2809-2814)ctccccfs	p.LP937fs	PPRC1_ENST00000413464.2_Frame_Shift_Ins_p.LP937fs	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	937	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		ATCCTTGCCTGCCCCCCCCACC	0.604													16	42	---	---	---	---					
ARL2BPP3	0	broad.mit.edu	37	13	37368677	37368677	+	RNA	DEL	T	T	-			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr13:37368677delT	ENST00000580773.1	+	0	271																											CTGATGCACATTTTGATGCTG	0.458													2	4	---	---	---	---					
IGHV4OR15-8	0	broad.mit.edu	37	15	22473095	22473096	+	RNA	INS	-	-	G			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr15:22473095_22473096insG	ENST00000557788.2	-	0	174_175																											CCCTGGGGGCTGGCGGACCCAG	0.594													7	162	---	---	---	---					
MGA	23269	broad.mit.edu	37	15	42035324	42035325	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-V1-A9OF-01A-11D-A41K-08	TCGA-V1-A9OF-10A-01D-A41N-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dfdee3c3-dfff-4ca8-9750-946c41e688ee	37744749-dd3a-43dc-b690-4270748f7885	g.chr15:42035324_42035325delTA	ENST00000219905.7	+	15	5347_5348	c.5166_5167delTA	c.(5164-5169)attafs	p.II1722fs	MGA_ENST00000570161.1_Frame_Shift_Del_p.II1722fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.II1722fs|MGA_ENST00000566586.1_Intron|MGA_ENST00000545763.1_Intron	NM_001164273.1	NP_001157745.1	Q8IWI9	MGAP_HUMAN	MGA, MAX dimerization protein	1722						MLL1 complex	DNA binding|sequence-specific DNA binding transcription factor activity			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)		CTGTTCCTATTATACTCTCAGG	0.465													8	15	---	---	---	---					
