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
MACF1	23499	broad.mit.edu	37	1	39761487	39761487	+	Missense_Mutation	SNP	T	T	G			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr1:39761487T>G	uc021olt.1	+	18	2355	c.2303T>G	c.(2302-2304)tTg>tGg	p.L768W	MACF1_uc021ols.1_Missense_Mutation_p.L768W|MACF1_uc001cdc.2_Missense_Mutation_p.L768W|MACF1_uc001cda.1_Missense_Mutation_p.L676W	NM_012090	NP_036222	Q9UPN3	MACF1_HUMAN	Homo sapiens microtubule-actin crosslinking factor 1 (MACF1), transcript variant 1, mRNA.	768					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding	p.K768K(1)		breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CAGTCCCAGTTGCAGTGGATG	0.433												
SELRC1	65260	broad.mit.edu	37	1	53158443	53158443	+	Missense_Mutation	SNP	C	C	T			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr1:53158443C>T	uc001cui.2	-	1	243	c.203G>A	c.(202-204)aGt>aAt	p.S68N		NM_023077	NP_075565	Q96BR5	SELR1_HUMAN	Homo sapiens Sel1 repeat containing 1 (SELRC1), mRNA.	68							binding			breast(1)|lung(3)|prostate(1)|urinary_tract(1)	6						GCAGCTATCACTGTGCTGGTT	0.502												
PRG4	10216	broad.mit.edu	37	1	186277611	186277614	+	Frame_Shift_Del	DEL	AGAA	AGAA	-			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr1:186277611_186277614delAGAA	uc001gru.4	+	6	2811_2814	c.2760_2763delAGAA	c.(2758-2763)acagaafs	p.T920fs	MIR548F1_uc021pgf.1_Intron|PRG4_uc001grt.4_Frame_Shift_Del_p.T879fs|PRG4_uc009wyl.3_Frame_Shift_Del_p.T827fs|PRG4_uc009wym.3_Frame_Shift_Del_p.T786fs|PRG4_uc010poo.2_Non-coding_Transcript	NM_005807	NP_005798	Q92954	PRG4_HUMAN	Homo sapiens proteoglycan 4 (PRG4), transcript variant A, mRNA.	920					cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ACAAGACAACAGAAAGAGACTTAC	0.412												
ITIH2	3698	broad.mit.edu	37	10	7771922	7771922	+	Silent	SNP	A	A	T			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr10:7771922A>T	uc001ijs.3	+	11	1449	c.1287A>T	c.(1285-1287)ctA>ctT	p.L429L		NM_002216	NP_002207	P19823	ITIH2_HUMAN	Homo sapiens inter-alpha-trypsin inhibitor heavy chain 2 (ITIH2), mRNA.	429	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TAGGCGAACTAAAACTGTCAA	0.373												
LOC440040	440040	broad.mit.edu	37	11	49598207	49598207	+	Missense_Mutation	SNP	T	T	C	rs71479502	by1000genomes	TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr11:49598207T>C	uc010rhy.2	+	1	798	c.320T>C	c.(319-321)tTc>tCc	p.F107S	LOC440040_uc009ymb.3_Missense_Mutation_p.F107S					Homo sapiens glutamate receptor, metabotropic 5 pseudogene (LOC440040), non-coding RNA.																		TCCTCTTCCTTCTGCTCCAAG	0.502												
CLPB	81570	broad.mit.edu	37	11	72012979	72012979	+	Frame_Shift_Del	DEL	G	G	-			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr11:72012979delG	uc001osj.3	-	11	1337	c.1287delC	c.(1285-1287)ggcfs	p.G429fs	CLPB_uc010rqx.2_Frame_Shift_Del_p.G384fs|CLPB_uc010rqy.2_Frame_Shift_Del_p.G370fs|CLPB_uc001osk.3_Frame_Shift_Del_p.G399fs|CLPB_uc010rqz.2_Frame_Shift_Del_p.G228fs|CLPB_uc001osi.3_Frame_Shift_Del_p.G37fs	NM_030813	NP_110440	Q9H078	CLPB_HUMAN	Homo sapiens ClpB caseinolytic peptidase B homolog (E. coli) (CLPB), mRNA.	429					cellular response to heat		ATP binding|nucleoside-triphosphatase activity|protein binding			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						GGCCAACGTAGCCTGGTGGAG	0.522												
HEPHL1	341208	broad.mit.edu	37	11	93844970	93844970	+	Silent	SNP	G	G	A	rs118037969	by1000genomes	TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr11:93844970G>A	uc001pep.2	+	19	3547	c.3390G>A	c.(3388-3390)acG>acA	p.T1130T	AF086184_uc001pen.1_Intron	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN	Homo sapiens hephaestin-like 1 (HEPHL1), mRNA.	1130					copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity	p.L1130P(1)|p.T1134T(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TAATCACCACGGTGATTCTCT	0.507												
AMN1	196394	broad.mit.edu	37	12	31850308	31850308	+	Missense_Mutation	SNP	G	G	A			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr12:31850308G>A	uc001rkq.4	-	4	744	c.578C>T	c.(577-579)gCg>gTg	p.A193V	AMN1_uc001rko.4_Missense_Mutation_p.A175V|AMN1_uc010skc.2_Missense_Mutation_p.A175V|AMN1_uc009zjs.3_Non-coding_Transcript|AMN1_uc009zjt.1_Non-coding_Transcript	NM_001113402	NP_001106873	Q8IY45	AMN1_HUMAN	Homo sapiens antagonist of mitotic exit network 1 homolog (S. cerevisiae) (AMN1), transcript variant 1, mRNA.	193										breast(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(1)	7	all_cancers(9;7.41e-12)|all_epithelial(9;1.18e-11)|all_lung(12;1.14e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0336)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.162)		OV - Ovarian serous cystadenocarcinoma(6;0.0014)			TAATTTCTTCGCACAAGGTCC	0.338												
MARCH9	92979	broad.mit.edu	37	12	58152585	58152585	+	Missense_Mutation	SNP	A	A	G			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr12:58152585A>G	uc001spx.2	+	3	1377	c.946A>G	c.(946-948)Aca>Gca	p.T316A	MARCH9_uc001spy.3_Missense_Mutation_p.T203A	NM_138396	NP_612405	Q86YJ5	MARH9_HUMAN	Homo sapiens membrane-associated ring finger (C3HC4) 9 (MARCH9), mRNA.	316						Golgi membrane|Golgi stack|integral to membrane|lysosomal membrane|trans-Golgi network	ligase activity|zinc ion binding			autonomic_ganglia(1)|large_intestine(2)|lung(1)	4	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			CTGCGGTTATACAATCTTGCA	0.652												
PMFBP1	83449	broad.mit.edu	37	16	72184633	72184633	+	Silent	SNP	C	C	T			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr16:72184633C>T	uc002fcc.4	-	4	682	c.510G>A	c.(508-510)aaG>aaA	p.K170K	PMFBP1_uc002fcd.3_Silent_p.K170K|PMFBP1_uc002fce.3_Non-coding_Transcript|PMFBP1_uc002fcf.3_Silent_p.K25K	NM_031293	NP_112583	Q8TBY8	PMFBP_HUMAN	Homo sapiens polyamine modulated factor 1 binding protein 1 (PMFBP1), transcript variant 1, mRNA.	170										NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				GAGAGGCGATCTTGTCCCCGG	0.498												
TP53	7157	broad.mit.edu	37	17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	rs121912651		TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr17:7577539G>A	uc002gim.2	-	6	936	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_uc002gig.1_Missense_Mutation_p.R248W|TP53_uc002gih.3_Missense_Mutation_p.R248W|TP53_uc010cne.1_5'Flank|TP53_uc010cng.1_Missense_Mutation_p.R116W|TP53_uc010cnf.1_Missense_Mutation_p.R116W|TP53_uc002gii.1_Missense_Mutation_p.R116W|TP53_uc010cni.1_Missense_Mutation_p.R248W|TP53_uc010cnh.1_Missense_Mutation_p.R248W|TP53_uc002gij.2_Missense_Mutation_p.R248W|TP53_uc010cnj.1_Non-coding_Transcript|TP53_uc002gin.2_Missense_Mutation_p.R155W|TP53_uc002gio.2_Missense_Mutation_p.R116W|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.	248	Interaction with AXIN1 (By similarity).|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.		NR -> IP (in a sporadic cancer; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs11540652).|R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).		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 drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|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|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|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R248W(1057)|p.R248Q(565)|p.R248L(70)|p.R155W(28)|p.R248G(24)|p.R248P(16)|p.R248R(12)|p.N247N(10)|p.0?(8)|p.N247S(7)|p.N247D(5)|p.?(5)|p.M246_P250delMNRRP(4)|p.N247_R248>KW(4)|p.N247_R248delNR(4)|p.N247T(4)|p.R248fs*97(4)|p.N247I(3)|p.N247Y(3)|p.R248fs*16(3)|p.N247_P250delNRRP(2)|p.N247K(2)|p.R248_P250delRRP(2)|p.N247_R249delNRR(2)|p.R248C(2)|p.N247_R248>IP(2)|p.R248fs*>39(1)|p.unknown(1)|p.N247F(1)|p.N247fs*98(1)|p.R248Y(1)|p.G245fs*14(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)		ATGGGCCTCCGGTTCATGCCG	0.577	R248W(786O_KIDNEY)|R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO320_LARGE_INTESTINE)|R248W(COLO680N_OESOPHAGUS)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(GCT_SOFT_TISSUE)|R248W(HCC2157_BREAST)|R248W(JIMT1_BREAST)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(LUDLU1_LUNG)|R248W(LXF289_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(RD_SOFT_TISSUE)|R248W(SW837_LARGE_INTESTINE)|R248W(VCAP_PROSTATE)	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)		
BRIP1	83990	broad.mit.edu	37	17	59876469	59876469	+	Silent	SNP	G	G	A			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr17:59876469G>A	uc002izk.2	-	8	1638	c.1332C>T	c.(1330-1332)agC>agT	p.S444S		NM_032043	NP_114432	Q9BX63	FANCJ_HUMAN	Homo sapiens BRCA1 interacting protein C-terminal helicase 1 (BRIP1), mRNA.	444					DNA damage checkpoint|double-strand break repair|regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						ACTTAATGAGGCTACAGCACA	0.358			"""F, N, Mis"""			"""AML, leukemia, breast"""		Involved in tolerance or repair of DNA crosslinks				
COLEC12	81035	broad.mit.edu	37	18	334801	334801	+	Missense_Mutation	SNP	G	G	A			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr18:334801G>A	uc002kkm.3	-	5	1972	c.1757C>T	c.(1756-1758)tCa>tTa	p.S586L		NM_130386	NP_569057	Q5KU26	COL12_HUMAN	Homo sapiens collectin sub-family member 12 (COLEC12), mRNA.	586	Collagen-like 3.				carbohydrate mediated signaling|innate immune response|phagocytosis, recognition|protein homooligomerization	collagen|integral to membrane	galactose binding|low-density lipoprotein particle binding|metal ion binding|pattern recognition receptor activity|scavenger receptor activity			cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	46		all_cancers(4;0.0442)|Myeloproliferative disorder(11;0.0426)				CACCGCTCCTGATGGGCCAGG	0.701												
ALK	238	broad.mit.edu	37	2	29917797	29917797	+	Missense_Mutation	SNP	G	G	A			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr2:29917797G>A	uc002rmy.3	-	2	1823	c.871C>T	c.(871-873)Cgc>Tgc	p.R291C		NM_004304	NP_004295	Q9UM73	ALK_HUMAN	Homo sapiens anaplastic lymphoma receptor tyrosine kinase (ALK), mRNA.	291	MAM 1.				protein autophosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|protein binding|transmembrane receptor protein tyrosine kinase activity		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)	GGGATGCGGCGCCAGGACCAG	0.602			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome			
SFTPB	6439	broad.mit.edu	37	2	85892915	85892915	+	Silent	SNP	G	G	A			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr2:85892915G>A	uc002sqj.3	-	5	532	c.432C>T	c.(430-432)gaC>gaT	p.D144D	SFTPB_uc002sqi.3_Silent_p.D144D|SFTPB_uc002sqh.3_Silent_p.D144D	NM_000542	NP_942140	P07988	PSPB_HUMAN	Homo sapiens surfactant protein B (SFTPB), transcript variant 1, mRNA.	132	Saposin B-type 1.				organ morphogenesis|respiratory gaseous exchange|sphingolipid metabolic process	extracellular space|lysosome				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)	16						TGCCGTTTGAGTCCTGGGGCA	0.642												
IDH1	3417	broad.mit.edu	37	2	209113113	209113113	+	Missense_Mutation	SNP	G	G	C	rs121913499		TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr2:209113113G>C	uc002vcs.3	-	3	640	c.394C>G	c.(394-396)Cgt>Ggt	p.R132G	IDH1_uc002vct.3_Missense_Mutation_p.R132G|IDH1_uc002vcu.3_Missense_Mutation_p.R132G	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|cellular lipid metabolic process|glyoxylate cycle|isocitrate metabolic process|NADPH regeneration|tricarboxylic acid cycle	cytosol|peroxisomal matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding|protein homodimerization activity	p.R132H(3651)|p.R132C(1036)|p.R132G(298)|p.R132S(246)|p.R132?(189)|p.R132L(71)|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)		TAAGCATGACGACCTATGATG	0.398			Mis		gliobastoma							
DNAJC13	23317	broad.mit.edu	37	3	132198097	132198097	+	Silent	SNP	G	G	A	rs61748099	byFrequency	TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr3:132198097G>A	uc003eor.3	+	24	2801	c.2736G>A	c.(2734-2736)agG>agA	p.R912R		NM_015268	NP_056083	O75165	DJC13_HUMAN	Homo sapiens DnaJ (Hsp40) homolog, subfamily C, member 13 (DNAJC13), mRNA.	912							heat shock protein binding			breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						AACGAGATAGGTTGATTCTCT	0.294												
WDR1	9948	broad.mit.edu	37	4	10080542	10080542	+	Silent	SNP	G	G	A			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr4:10080542G>A	uc021xlv.1	-	11	1651	c.1368C>T	c.(1366-1368)ggC>ggT	p.G456G	WDR1_uc021xlw.1_Silent_p.G316G|WDR1_uc010idm.3_Non-coding_Transcript|MIR3138_uc021xlx.1_5'Flank	NM_017491	NP_059830	O75083	WDR1_HUMAN	Homo sapiens WD repeat domain 1 (WDR1), transcript variant 1, mRNA.	456					platelet activation|platelet degranulation|sensory perception of sound	cytoskeleton|cytosol|extracellular region	actin binding			endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CCGTGTCCCCGCCGGGGTGCA	0.592												
FRYL	285527	broad.mit.edu	37	4	48621289	48621289	+	Splice_Site	SNP	A	A	G			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr4:48621289A>G	uc003gyh.1	-	7	1016	c.411_splice	c.e7+1	p.Q137_splice	FRYL_uc003gyk.3_Splice_Site_p.Q137_splice|FRYL_uc003gyl.1_Missense_Mutation_p.V189A	NM_015030	NP_055845	O94915	FRYL_HUMAN	Homo sapiens FRY-like (FRYL), mRNA.	137					regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						AAAAGAGCTTACCTGCTTTAG	0.363												
NFKB1	4790	broad.mit.edu	37	4	103518775	103518775	+	Missense_Mutation	SNP	G	G	A	rs139575566		TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr4:103518775G>A	uc011ceq.2	+	14	2058	c.1591G>A	c.(1591-1593)Gtc>Atc	p.V531I	NFKB1_uc011cep.2_Missense_Mutation_p.V532I|NFKB1_uc011cer.2_Missense_Mutation_p.V351I	NM_001165412	NP_001158884	P19838	NFKB1_HUMAN	Homo sapiens nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (NFKB1), transcript variant 2, mRNA.	531	Interaction with CFLAR.				anti-apoptosis|apoptosis|cellular response to mechanical stimulus|inflammatory response|innate immune response|membrane protein intracellular domain proteolysis|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of calcidiol 1-monooxygenase activity|nerve growth factor receptor signaling pathway|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|positive regulation of transcription, DNA-dependent|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transcription from RNA polymerase II promoter	cytosol|I-kappaB/NF-kappaB complex|mitochondrion|nucleoplasm	protein binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding	p.V532I(1)		biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Dexamethasone(DB01234)|Pranlukast(DB01411)|Thalidomide(DB01041)	GCTGCTGGCCGTCCAGCGCCA	0.522												
PIK3R1	5295	broad.mit.edu	37	5	67591098	67591109	+	In_Frame_Del	DEL	ACAGCATTAAAC	ACAGCATTAAAC	-			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr5:67591098_67591109delACAGCATTAAAC	uc003jva.3	+	12	2271_2282	c.1691_1702delACAGCATTAAAC	c.(1690-1704)aacagcattaaacca>aca	p.564_568NSIKP>T	PIK3R1_uc003jvc.3_In_Frame_Del_p.264_268NSIKP>T|PIK3R1_uc003jvd.3_In_Frame_Del_p.294_298NSIKP>T|PIK3R1_uc003jve.3_In_Frame_Del_p.243_247NSIKP>T|PIK3R1_uc021xzn.1_In_Frame_Del_p.201_205NSIKP>T|PIK3R1_uc011crb.2_In_Frame_Del_p.234_238NSIKP>T	NM_181523	NP_852664	P27986	P85A_HUMAN	Homo sapiens phosphoinositide-3-kinase, regulatory subunit 1 (alpha) (PIK3R1), transcript variant 1, mRNA.	564					epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	p.N564D(4)|p.N564K(4)|p.K567E(3)|p.D560_S565del(2)|p.K567_L570delKPDL(2)|p.R562_M563ins13(1)|p.K267_L270delKPDL(1)|p.0?(1)|p.?(1)|p.K297E(1)|p.N294K(1)|p.N264K(1)|p.K267E(1)|p.K297_L300delKPDL(1)|p.N564fs*?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoproterenol(DB01064)	AAACGTATGAACAGCATTAAACCAGACCTTAT	0.373			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)		
GRINA	2907	broad.mit.edu	37	8	145065758	145065758	+	Missense_Mutation	SNP	C	C	G			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr8:145065758C>G	uc003zan.1	+	1	533	c.367C>G	c.(367-369)Caa>Gaa	p.Q123E	GRINA_uc003zao.1_Missense_Mutation_p.Q123E|GRINA_uc003zap.1_Missense_Mutation_p.Q123E	NM_001009184	NP_001009184	Q7Z429	GRINA_HUMAN	Homo sapiens glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (glutamate binding) (GRINA), transcript variant 2, mRNA.	123	Pro-rich.					integral to membrane				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	9	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTTCCCAGGACAAGACCCTGA	0.672												
TYRP1	7306	broad.mit.edu	37	9	12702411	12702414	+	Frame_Shift_Del	DEL	ACAA	ACAA	-			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chr9:12702411_12702414delACAA	uc003zkv.4	+	4	1232_1235	c.1054_1057delACAA	c.(1054-1059)acaaacfs	p.T352fs		NM_000550	NP_000541	P17643	TYRP1_HUMAN	Homo sapiens tyrosinase-related protein 1 (TYRP1), mRNA.	352					melanin biosynthetic process	clathrin-coated endocytic vesicle membrane|endosome membrane|integral to membrane|melanosome membrane	copper ion binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen|protein heterodimerization activity|protein homodimerization activity	p.N353fs*31(4)		NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		TTCCAACTCTACAAACAGTTTCCG	0.387									Oculocutaneous Albinism			
ATRX	546	broad.mit.edu	37	X	76814207	76814208	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-15-1444-01A-02D-1696-08	TCGA-15-1444-10A-01D-1696-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbd4d4e7-f1c4-446c-8dbc-ce06c872ec14	41190f35-e3af-46e3-9b2d-41bc41d5891b	g.chrX:76814207_76814208delTG	uc004ecp.4	-	28	6668_6669	c.6436_6437delCA	c.(6436-6438)cagfs	p.Q2146fs	ATRX_uc004ecq.4_Frame_Shift_Del_p.Q2108fs|ATRX_uc004eco.4_Frame_Shift_Del_p.Q1931fs	NM_000489	NP_000480	P46100	ATRX_HUMAN	Homo sapiens alpha thalassemia/mental retardation syndrome X-linked (ATRX), transcript variant 1, mRNA.	2146	Helicase C-terminal.				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|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)	GAATATACTCTGGATGTCATAA	0.337			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome					
