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
SH3PXD2A	9644	broad.mit.edu	37	10	105365619	105365619	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:105365619G>A	ENST00000369774.4	-	14	1640	c.1364C>T	c.(1363-1365)aCc>aTc	p.T455I	SH3PXD2A_ENST00000355946.2_Missense_Mutation_p.T427I|SH3PXD2A_ENST00000538130.1_Missense_Mutation_p.T290I|SH3PXD2A_ENST00000540321.1_Missense_Mutation_p.T322I|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000315994.6_5'UTR			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	455	SH3 3.				cell communication|superoxide metabolic process	cell junction|cell projection|cytoplasm|podosome	phosphatidylinositol binding|protein binding			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		TTCGGCAATGGTGTAGTACTC	0.537000											OREG0020500	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	32	38					0	0	0.144211	0	0
CTSW	1521	broad.mit.edu	37	11	65651008	65651008	+	Silent	SNP	T	T	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr11:65651008T>C	ENST00000307886.3	+	10	1096	c.1050T>C	c.(1048-1050)aaT>aaC	p.N350N	CTSW_ENST00000528419.1_3'UTR	NM_001335.3	NP_001326.2	P56202	CATW_HUMAN	cathepsin W	350					immune response|proteolysis		cysteine-type endopeptidase activity			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)	9				READ - Rectum adenocarcinoma(159;0.168)		GAGGGAGCAATACCTGTGGCA	0.622000													47	77					0	0	0.139131	0	0
COL5A1	1289	broad.mit.edu	37	9	137690287	137690287	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr9:137690287C>T	ENST00000371817.3	+	37	3346	c.2932C>T	c.(2932-2934)Cct>Tct	p.P978S		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	978	Triple-helical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CCCAGGACACCCTGGACAGAG	0.577000													6	65					0	0	0.029380	0	0
MTO1	25821	broad.mit.edu	37	6	74171794	74171794	+	Splice_Site	SNP	G	G	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr6:74171794G>A	ENST00000498286.1	+	1	494	c.217_splice	c.e1+1	p.G73_splice	MTO1_ENST00000370305.1_Intron|MTO1_ENST00000370300.4_Splice_Site_p.G73_splice|MTO1_ENST00000415954.2_Splice_Site_p.G73_splice			Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	73					tRNA processing	mitochondrion	flavin adenine dinucleotide binding			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						GGACACGATCGGTGAGGAGCG	0.657000													3	48					0	0	0.115264	0	0
TACC2	10579	broad.mit.edu	37	10	123970987	123970987	+	Silent	SNP	T	T	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:123970987T>C	ENST00000369005.1	+	9	7387	c.7047T>C	c.(7045-7047)ccT>ccC	p.P2349P	TACC2_ENST00000369000.1_Silent_p.P53P|TACC2_ENST00000515603.1_Silent_p.P2304P|TACC2_ENST00000369004.3_Silent_p.P427P|TACC2_ENST00000453444.2_Silent_p.P2353P|TACC2_ENST00000360561.3_Silent_p.P427P|TACC2_ENST00000358010.1_Silent_p.P495P|TACC2_ENST00000260733.3_Silent_p.P427P|TACC2_ENST00000369001.1_Silent_p.P53P|TACC2_ENST00000513429.1_Silent_p.P495P|TACC2_ENST00000515273.1_Silent_p.P2353P|TACC2_ENST00000334433.3_Silent_p.P2349P|TACC2_ENST00000368999.1_Silent_p.P427P	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2349	SPAZ.					microtubule organizing center|nucleus	nuclear hormone receptor binding			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				ATTTTAACCCTTTTTCTTCCA	0.468000													4	219					0	0	0.009096	0	0
F8	2157	broad.mit.edu	37	X	154157148	154157148	+	Silent	SNP	G	G	A	rs147629393		TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:154157148G>A	ENST00000360256.4	-	14	5117	c.4917C>T	c.(4915-4917)ccC>ccT	p.P1639P		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1639	B.				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding	p.P1639P(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CTTCTATTTCGGGCTTATTTT	0.423000													25	77					0	0	0.091800	0	0
COL19A1	1310	broad.mit.edu	37	6	70866046	70866046	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr6:70866046G>A	ENST00000322773.4	+	32	2209	c.2107G>A	c.(2107-2109)Gtc>Atc	p.V703I	COL19A1_ENST00000393344.1_Missense_Mutation_p.V325I	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	703	Triple-helical region 4 (COL4).				cell differentiation|cell-cell adhesion|extracellular matrix organization|skeletal system development	collagen	extracellular matrix structural constituent|protein binding, bridging			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						CCAAGCCAGTGTCCCAGGGCT	0.463000													9	7					0	0	0.047766	0	0
PPEF1	5475	broad.mit.edu	37	X	18842187	18842187	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:18842187G>A	ENST00000361511.4	+	17	2142	c.1648G>A	c.(1648-1650)Gaa>Aaa	p.E550K	PPEF1_ENST00000544635.1_Missense_Mutation_p.E485K|PPEF1_ENST00000543630.1_3'UTR|PPEF1_ENST00000359763.6_Missense_Mutation_p.E497K|PPEF1_ENST00000349874.5_Missense_Mutation_p.E488K	NM_006240.2|NM_152224.1	NP_006231.2|NP_689410.1	O14829	PPE1_HUMAN	protein phosphatase, EF-hand calcium binding domain 1	550					detection of stimulus involved in sensory perception|protein dephosphorylation		calcium ion binding|iron ion binding|manganese ion binding|protein binding|protein serine/threonine phosphatase activity			breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	43	Hepatocellular(33;0.183)					TATCCGCATTGAAAAACCTGT	0.463000													13	27					0	0	0.093190	0	0
PROSER1	80209	broad.mit.edu	37	13	39587564	39587564	+	Missense_Mutation	SNP	T	T	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr13:39587564T>C	ENST00000352251.3	-	11	2658	c.1825A>G	c.(1825-1827)Act>Gct	p.T609A	PROSER1_ENST00000350125.3_Missense_Mutation_p.T587A|PROSER1_ENST00000484434.2_Intron	NM_025138.3	NP_079414.3	Q86XN7	CM023_HUMAN	proline and serine rich 1	609	Ser-rich.																GTGGGCTCAGTTTTGATCATA	0.532000													18	106					0	0	0.043863	0	0
MALAT1	0	broad.mit.edu	37	11	65268525	65268525	+	RNA	SNP	A	A	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr11:65268525A>C	ENST00000534336.1	+	0	3293					NR_002819.2																						TGAATTTGATAGCCAAATTGA	0.348000													25	51					0	0	0.091800	0	0
HDAC5	10014	broad.mit.edu	37	17	42170141	42170141	+	Silent	SNP	G	G	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr17:42170141G>A	ENST00000225983.6	-	7	1001	c.678C>T	c.(676-678)tcC>tcT	p.S226S	HDAC5_ENST00000586802.1_Silent_p.S225S|HDAC5_ENST00000336057.5_Silent_p.S225S|HDAC5_ENST00000393622.2_Silent_p.S225S			Q9UQL6	HDAC5_HUMAN	histone deacetylase 5	225					B cell differentiation|cellular response to insulin stimulus|chromatin remodeling|chromatin silencing|inflammatory response|negative regulation of cell migration involved in sprouting angiogenesis|negative regulation of myotube differentiation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|regulation of protein binding|transcription, DNA-dependent	cytoplasm|histone deacetylase complex	histone deacetylase activity (H3-K16 specific)|NAD-dependent histone deacetylase activity (H3-K14 specific)|NAD-dependent histone deacetylase activity (H3-K9 specific)|NAD-dependent histone deacetylase activity (H4-K16 specific)|protein kinase C binding|repressing transcription factor binding			central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	21		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.118)		TCTGGGGAGGGGAACTCTGGT	0.642000													11	20					0	0	0.080935	0	0
RAI1	10743	broad.mit.edu	37	17	17696275	17696275	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr17:17696275C>T	ENST00000353383.1	+	3	482	c.13C>T	c.(13-15)Cga>Tga	p.R5*	RAI1_ENST00000261641.6_Nonsense_Mutation_p.R5*	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	5						cytoplasm|nucleus	zinc ion binding			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GCAGTCTTTTCGAGAAAGGTG	0.562000													17	10					0	0	0.043863	0	0
C5orf42	65250	broad.mit.edu	37	5	37157920	37157920	+	Silent	SNP	T	T	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr5:37157920T>C	ENST00000274258.7	-	40	8090	c.4503A>G	c.(4501-4503)ctA>ctG	p.L1501L	C5orf42_ENST00000425232.2_Intron|C5orf42_ENST00000508244.1_Intron			E9PH94	E9PH94_HUMAN	chromosome 5 open reading frame 42	2604										breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GTAATTCCTGTAGAAGATCAT	0.358000													7	13					0	0	0.029380	0	0
USP9X	8239	broad.mit.edu	37	X	40988337	40988337	+	Nonsense_Mutation	SNP	G	G	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:40988337G>T	ENST00000324545.7	+	3	814	c.181G>T	c.(181-183)Gaa>Taa	p.E61*	USP9X_ENST00000378308.2_Nonsense_Mutation_p.E61*	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	61					BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						ACCACAGCTTGAAGATGAGGA	0.458000													14	15					1.52009e-12	1.90011e-12	0.132662	1	0
RHOQ	23433	broad.mit.edu	37	2	46803383	46803383	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr2:46803383G>A	ENST00000238738.4	+	3	678	c.359G>A	c.(358-360)gGa>gAa	p.G120E	RP11-417F21.1_ENST00000506009.2_RNA|RHOQ_ENST00000465198.1_3'UTR	NM_012249.3	NP_036381.2	P17081	RHOQ_HUMAN	ras homolog family member Q	120					cortical actin cytoskeleton organization|insulin receptor signaling pathway|negative regulation of establishment of protein localization in plasma membrane|positive regulation of filopodium assembly|positive regulation of glucose import|positive regulation of transcription from RNA polymerase II promoter|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	actin filament|cytosol|plasma membrane	GBD domain binding|GTP binding|GTPase activity|profilin binding			skin(2)	2		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			TTATTAATAGGAACTCAGGTA	0.418000													12	18					0	0	0.080935	0	0
AC024560.3	0	broad.mit.edu	37	3	197348674	197348674	+	RNA	SNP	A	A	G	rs144273946	by1000genomes	TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr3:197348674A>G	ENST00000418868.1	-	0	585					NR_003266.2																						GGCTCTGTCCACCAAATGCAC	0.478000													3	61					0	0	0.115264	0	0
SORCS3	22986	broad.mit.edu	37	10	106974207	106974207	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:106974207C>T	ENST00000369701.3	+	18	2610	c.2383C>T	c.(2383-2385)Cgg>Tgg	p.R795W	SORCS3_ENST00000369699.4_Missense_Mutation_p.R81W	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	795						integral to membrane	neuropeptide receptor activity			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TAGGTATCGGCGGATTGTGTC	0.483000													8	15					0	0	0.058154	0	0
DCPS	28960	broad.mit.edu	37	11	126201357	126201357	+	Missense_Mutation	SNP	G	G	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr11:126201357G>A	ENST00000263579.4	+	3	763	c.434G>A	c.(433-435)cGc>cAc	p.R145H	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	145					deadenylation-dependent decapping of nuclear-transcribed mRNA|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytosol|nucleus	exoribonuclease activity|protein binding	p.R145H(1)		endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		AAGTACCTGCGCCAGGACCTC	0.557000													4	96					0	0	0.009096	0	0
RGPD4	285190	broad.mit.edu	37	2	108477236	108477236	+	Missense_Mutation	SNP	T	T	G			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr2:108477236T>G	ENST00000408999.3	+	13	1850	c.1773T>G	c.(1771-1773)aaT>aaG	p.N591K	RGPD4_ENST00000354986.4_Missense_Mutation_p.N591K	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	591					intracellular transport		binding			breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						GTGGTCTTAATTCTTTTTATG	0.323000													38	65					0	0	0.104719	0	0
MIB1	57534	broad.mit.edu	37	18	19378075	19378075	+	Missense_Mutation	SNP	A	A	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr18:19378075A>T	ENST00000261537.6	+	8	1387	c.1123A>T	c.(1123-1125)Att>Ttt	p.I375F	MIB1_ENST00000578646.1_3'UTR	NM_020774.2	NP_065825.1	Q86YT6	MIB1_HUMAN	mindbomb E3 ubiquitin protein ligase 1	375					Notch signaling pathway	centrosome|nuclear membrane|plasma membrane	ubiquitin-protein ligase activity|zinc ion binding			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|ovary(5)	27			STAD - Stomach adenocarcinoma(5;0.212)			AGTACAACAGATTTATTCAGA	0.378000													10	33					0	0	0.058154	0	0
PPIL6	285755	broad.mit.edu	37	6	109757309	109757309	+	Missense_Mutation	SNP	T	T	C			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr6:109757309T>C	ENST00000521072.2	-	2	809	c.229A>G	c.(229-231)Agg>Ggg	p.R77G	PPIL6_ENST00000424445.2_Intron|PPIL6_ENST00000440797.2_Missense_Mutation_p.R77G	NM_173672.4	NP_775943.1	Q8IXY8	PPIL6_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 6	77					protein folding		peptidyl-prolyl cis-trans isomerase activity			large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.00684)|BRCA - Breast invasive adenocarcinoma(108;0.00889)|all cancers(137;0.0106)|OV - Ovarian serous cystadenocarcinoma(136;0.0259)		TCCTTTACCCTTTTTTTCTCC	0.338000													3	97					0	0	0.115264	0	0
CENPI	2491	broad.mit.edu	37	X	100383791	100383791	+	Silent	SNP	G	G	A			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:100383791G>A	ENST00000372927.1	+	11	1438	c.1161G>A	c.(1159-1161)agG>agA	p.R387R	CENPI_ENST00000372926.1_Silent_p.R387R|CENPI_ENST00000423383.1_Silent_p.R387R|CENPI_ENST00000218507.5_Silent_p.R387R	NM_006733.2	NP_006724.2	Q92674	CENPI_HUMAN	centromere protein I	387					CenH3-containing nucleosome assembly at centromere|mitotic prometaphase	cytosol|kinetochore|nucleoplasm	protein binding			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						TCTTGCTGAGGTTTTATTACT	0.413000													25	43					0	0	0.091800	0	0
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377		TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	v-raf murine sarcoma viral oncogene homolog B	600	Protein kinase.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).		activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Sorafenib(DB00398)	TCGAGATTTCACTGTAGCTAG	0.368000	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				11	11					0	0	0.080935	0	0
JAKMIP3	282973	broad.mit.edu	37	10	133930583	133930583	+	Silent	SNP	C	C	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:133930583C>T	ENST00000298622.4	+	2	276	c.138C>T	c.(136-138)gtC>gtT	p.V46V		NM_001105521.2	NP_001098991.1			Janus kinase and microtubule interacting protein 3											breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	31		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)		TCTTTCAGGTCAGCAAAGTGG	0.572000													9	32					0	0	0.069234	0	0
KRTAP4-8	728224	broad.mit.edu	37	17	39254054	39254054	+	Missense_Mutation	SNP	A	A	T	rs76270529	by1000genomes	TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	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													4	40					0	0	0.009096	0	0
HLA-DMB	3109	broad.mit.edu	37	6	32906598	32906598	+	Missense_Mutation	SNP	C	C	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr6:32906598C>T	ENST00000416244.2	-	2	394	c.200G>A	c.(199-201)gGg>gAg	p.G67E	HLA-DMB_ENST00000418107.2_Missense_Mutation_p.G67E|XXbac-BPG181M17.5_ENST00000429234.1_Missense_Mutation_p.G99E			P28068	DMB_HUMAN	major histocompatibility complex, class II, DM beta	67	Beta-1.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						ATTCAGCACCCCAAATTCGCA	0.517000													23	25					0	0	0.069288	0	0
KCNK12	56660	broad.mit.edu	37	2	47797390	47797392	+	In_Frame_Del	DEL	GCA	GCA	-			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr2:47797390_47797392delGCA	ENST00000327876.3	-	1	686_688	c.79_81delTGC	c.(79-81)del	p.C27del	KCNK12_ENST00000493527.1_5'UTR	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	27	Poly-Cys.					integral to membrane	potassium channel activity|voltage-gated ion channel activity	p.0?(2)|p.?(1)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GCGAAcggcggcagcagcagcag	0.759													2	4	---	---	---	---					
SNX18	112574	broad.mit.edu	37	5	53814143	53814143	+	Frame_Shift_Del	DEL	C	C	-			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr5:53814143delC	ENST00000343017.6	+	1	555	c.361delC	c.(361-363)cgfs	p.P122fs	SNX18_ENST00000326277.3_Frame_Shift_Del_p.P122fs|SNX18_ENST00000381410.4_Frame_Shift_Del_p.P122fs	NM_001145427.1	NP_001138899.1	Q96RF0	SNX18_HUMAN	sorting nexin 18	122					cell communication|endocytosis|positive regulation of GTPase activity|protein transport	endomembrane system|endosome membrane|extrinsic to internal side of plasma membrane	phosphatidylinositol binding|protein binding			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				CACCTTCCAGCCGCCCGGCGC	0.746													2	4	---	---	---	---					
MMS19	64210	broad.mit.edu	37	10	99220481	99220481	+	Frame_Shift_Del	DEL	G	G	-			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr10:99220481delG	ENST00000438925.2	-	25	2775	c.2440delC	c.(2440-2442)atfs	p.H814fs	MMS19_ENST00000370782.2_Frame_Shift_Del_p.H814fs|MMS19_ENST00000355839.6_Frame_Shift_Del_p.H771fs|MMS19_ENST00000327277.7_3'UTR|MMS19_ENST00000327238.10_Frame_Shift_Del_p.H716fs	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	814					chromosome segregation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|response to hormone stimulus|transcription, DNA-dependent|two-component signal transduction system (phosphorelay)	cytoplasm|holo TFIIH complex|MMXD complex	estrogen receptor binding|protein binding, bridging|receptor signaling complex scaffold activity|transcription coactivator activity			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		CTGAGAGGATGGTATCTGAGC	0.488								Direct reversal of damage					2	4	---	---	---	---					
CTSA	5476	broad.mit.edu	37	20	44520006	44520007	+	Frame_Shift_Ins	INS	-	-	T			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chr20:44520006_44520007insT	ENST00000372484.3	+	1	324_325	c.42_43insT	c.(40-45)cgggggfs	p.RG14fs	CTSA_ENST00000354880.5_Frame_Shift_Ins_p.RG14fs|CTSA_ENST00000191018.5_5'UTR	NM_000308.2|NM_001127695.1	NP_000299.2|NP_001121167.1	P10619	PPGB_HUMAN	cathepsin A	0					intracellular protein transport|proteolysis	endoplasmic reticulum|lysosome|nucleus	enzyme activator activity|protein binding|serine-type carboxypeptidase activity			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				AGCAAGGACGCGGGGGAGCAGA	0.698													2	4	---	---	---	---					
FAM120C	54954	broad.mit.edu	37	X	54209302	54209303	+	In_Frame_Ins	INS	-	-	GGCGGC			TCGA-FE-A22Z-01A-11D-A17V-08	TCGA-FE-A22Z-10A-01D-A17V-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ec59b115-b96a-42ff-9649-a9a518456c2b	c79d1a81-e40f-439c-ace4-aaaef0237060	g.chrX:54209302_54209303insGGCGGC	ENST00000375180.2	-	1	385_386	c.329_330insGCCGCC	c.(328-330)ccc>cGCCGCCcc	p.109_110insRR	FAM120C_ENST00000328235.4_In_Frame_Ins_p.109_110insRR|FAM120C_ENST00000477084.1_In_Frame_Ins_p.109_110insRR	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	109										breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						GCAGCTGAGGGGGCGGCGGCGG	0.748													4	8	---	---	---	---					
