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
RP11-146E13.4	0	broad.mit.edu	37	14	19857036	19857036	+	RNA	SNP	A	A	G			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr14:19857036A>G	ENST00000548109.1	+	0	72																											CTGGATAATAAAGTTCATCTC	0.373000													5	30					0	0	1	0	0
CTU2	348180	broad.mit.edu	37	16	88779765	88779765	+	Missense_Mutation	SNP	G	G	T			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr16:88779765G>T	ENST00000567949.1	+	8	1005	c.996G>T	c.(994-996)aaG>aaT	p.K332N	CTU2_ENST00000453996.2_Missense_Mutation_p.K261N|CTU2_ENST00000312060.5_Missense_Mutation_p.K261N|CTU2_ENST00000378384.3_Missense_Mutation_p.K174N			Q2VPK5	CTU2_HUMAN	cytosolic thiouridylase subunit 2 homolog (S. pombe)	261			V -> I (in dbSNP:rs4782321).		tRNA thio-modification|tRNA wobble uridine modification	cytoplasm|protein complex|soluble fraction	protein binding			NS(1)|breast(1)|endometrium(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11						GCTACTCCAAGGTCATGACTG	0.657000													5	115					0.248553	0.256838	1	1	0
ITPR3	3710	broad.mit.edu	37	6	33632679	33632679	+	Missense_Mutation	SNP	C	C	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr6:33632679C>A	ENST00000374316.5	+	13	2241	c.1181C>A	c.(1180-1182)aCc>aAc	p.T394N	ITPR3_ENST00000605930.1_Missense_Mutation_p.T394N			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	394	MIR 5.				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding	p.T394N(4)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85						CACCTCTGCACCAACACGTGG	0.662000													4	54					0.184627	0.19736	1	1	0
RSPH3	83861	broad.mit.edu	37	6	159403544	159403544	+	Silent	SNP	C	C	T			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr6:159403544C>T	ENST00000367069.2	-	5	1305	c.669G>A	c.(667-669)gaG>gaA	p.E223E	RSPH3_ENST00000449822.1_Silent_p.E127E|RSPH3_ENST00000297262.3_Silent_p.E269E|RSPH3_ENST00000252655.1_Silent_p.E365E			Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	365										endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		GCCTCTCTTGCTCTTCAAGTC	0.398000													5	28					0	0	1	0	0
SRP68	6730	broad.mit.edu	37	17	74068495	74068495	+	Silent	SNP	A	A	C			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr17:74068495A>C	ENST00000307877.2	-	1	239	c.78T>G	c.(76-78)ggT>ggG	p.G26G	SRP68_ENST00000355113.5_5'UTR|SRP68_ENST00000539137.1_Silent_p.G26G	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	26					response to drug	cytosol|endoplasmic reticulum|nucleolus|ribosome|signal recognition particle, endoplasmic reticulum targeting	RNA binding|signal recognition particle binding			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						caccgccgctaccgccgccgc	0.657000													3	4					0	0	1	0	0
PRPS1	5631	broad.mit.edu	37	X	106890921	106890921	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chrX:106890921G>A	ENST00000372435.4	+	6	912	c.790G>A	c.(790-792)Gca>Aca	p.A264T	PRPS1_ENST00000372418.1_Missense_Mutation_p.A164T|PRPS1_ENST00000372428.4_Missense_Mutation_p.A197T|PRPS1_ENST00000543248.1_Missense_Mutation_p.A264T	NM_002764.3	NP_002755.1	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	264					5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity			breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						CATCAACAACGCATGCTTTGA	0.453000													10	109					0	0	1	0	0
PIGZ	80235	broad.mit.edu	37	3	196674805	196674805	+	Silent	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr3:196674805G>A	ENST00000412723.1	-	3	1109	c.963C>T	c.(961-963)aaC>aaT	p.N321N		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	321					GPI anchor biosynthetic process	integral to membrane|intrinsic to endoplasmic reticulum membrane	alpha-1,2-mannosyltransferase activity			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		GCAGGAAGCCGTTGACTGCCA	0.617000													4	185					0	0	1	0	0
TSSC2	0	broad.mit.edu	37	11	3427765	3427765	+	RNA	SNP	G	G	C			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr11:3427765G>C	ENST00000529482.1	+	0	882																											CACACGTCCTGCAGTGGCCTG	0.602000													4	62					0	0	1	0	0
HIST1H2AL	8332	broad.mit.edu	37	6	27833429	27833429	+	Silent	SNP	C	C	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr6:27833429C>A	ENST00000357320.2	+	1	396	c.297C>A	c.(295-297)ggC>ggA	p.G99G		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	99					nucleosome assembly	nucleosome|nucleus	DNA binding|enzyme binding			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						AGCTGCTGGGCAAAGTAACCA	0.592000													5	194					8.12818e-05	9.33236e-05	1	1	0
FAM129A	116496	broad.mit.edu	37	1	184863335	184863335	+	Silent	SNP	T	T	C			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr1:184863335T>C	ENST00000367511.3	-	3	385	c.192A>G	c.(190-192)ccA>ccG	p.P64P		NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	64					negative regulation of protein phosphorylation|positive regulation of protein phosphorylation|positive regulation of translation|response to endoplasmic reticulum stress	cytoplasm|nucleus|plasma membrane				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						CAGGCGCCAATGGTGGCTTAA	0.343000													5	54					0	0	1	0	0
LRRC4C	57689	broad.mit.edu	37	11	40137057	40137057	+	Silent	SNP	G	G	C			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr11:40137057G>C	ENST00000278198.2	-	2	2749	c.786C>G	c.(784-786)gcC>gcG	p.A262A	LRRC4C_ENST00000530763.1_Silent_p.A262A|LRRC4C_ENST00000528697.1_Silent_p.A262A|LRRC4C_ENST00000527150.1_Silent_p.A262A			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	262					regulation of axonogenesis	integral to membrane	protein binding			NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				GGTTGTCAAAGGCATTCCGTT	0.453000													7	104					0	0	1	0	0
ARAP3	64411	broad.mit.edu	37	5	141051740	141051740	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr5:141051740G>A	ENST00000239440.4	-	10	1579	c.1514C>T	c.(1513-1515)gCg>gTg	p.A505V	ARAP3_ENST00000508305.1_Missense_Mutation_p.A427V|ARAP3_ENST00000513878.1_Missense_Mutation_p.A167V	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	505	Arf-GAP.				cytoskeleton organization|negative regulation of cell migration|negative regulation of Rho protein signal transduction|regulation of ARF GTPase activity|regulation of cell shape|small GTPase mediated signal transduction|vesicle-mediated transport	cytoskeleton|cytosol|lamellipodium|plasma membrane|ruffle	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|Rho GTPase activator activity|zinc ion binding			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						CCCACAGTCCGCACACTGCCG	0.612000													5	332					0	0	1	0	0
FGF4	2249	broad.mit.edu	37	11	69588192	69588192	+	Missense_Mutation	SNP	T	T	G			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr11:69588192T>G	ENST00000168712.1	-	3	824	c.506A>C	c.(505-507)tAc>tCc	p.Y169S	FGF4_ENST00000538040.1_5'UTR	NM_002007.2	NP_001998.1	P08620	FGF4_HUMAN	fibroblast growth factor 4	169					cell-cell signaling|chondroblast differentiation|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|mesenchymal cell proliferation|positive regulation of cell division|positive regulation of cell proliferation|positive regulation of ERK1 and ERK2 cascade	extracellular region	growth factor activity|heparin binding			lung(3)	3	Melanoma(5;1.89e-05)		LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		Pentosan Polysulfate(DB00686)	GTAGGACTCGTAGGCGTTGTA	0.567000													15	174					0	0	1	0	0
PCSK5	5125	broad.mit.edu	37	9	78790192	78790192	+	Missense_Mutation	SNP	C	C	G			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr9:78790192C>G	ENST00000376767.3	+	14	2559	c.2047C>G	c.(2047-2049)Cga>Gga	p.R683G	PCSK5_ENST00000545128.1_Intron|PCSK5_ENST00000376752.4_Intron			Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	0	CRM (Cys-rich motif).				anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						ggaatggaatcgaatcgaatc	0.373000													3	5					0	0	1	0	0
MROH2B	133558	broad.mit.edu	37	5	41065560	41065560	+	Silent	SNP	C	C	T			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr5:41065560C>T	ENST00000399564.4	-	4	684	c.234G>A	c.(232-234)gaG>gaA	p.E78E		NM_173489.4	NP_775760.3			maestro heat-like repeat family member 2B																		ACACCAAAACCTCACCAGCTA	0.413000													3	44					0	0	1	0	0
LL22NC03-80A10.6	0	broad.mit.edu	37	22	22664141	22664141	+	RNA	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr22:22664141G>A	ENST00000426066.1	+	0	664					NR_027293.1																						AAATTTGAAGGTGCTGTGATT	0.448000													5	74					0	0	1	0	0
DNAH9	1770	broad.mit.edu	37	17	11835360	11835360	+	Silent	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr17:11835360G>A	ENST00000262442.3	+	64	12203	c.12135G>A	c.(12133-12135)acG>acA	p.T4045T	DNAH9_ENST00000396001.2_Silent_p.T357T|DNAH9_ENST00000454412.2_Silent_p.T3969T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4045	AAA 6 (By similarity).				cell projection organization|cellular component movement|microtubule-based movement|spermatogenesis	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CTCGGGAGACGGAGTTTAAGA	0.493000													6	332					0	0	1	0	0
KIAA0100	9703	broad.mit.edu	37	17	26961608	26961608	+	Silent	SNP	A	A	G			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr17:26961608A>G	ENST00000528896.2	-	16	3071	c.2997T>C	c.(2995-2997)ccT>ccC	p.P999P	KIAA0100_ENST00000389003.3_Silent_p.P856P|RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000544884.1_Silent_p.P856P	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	999						extracellular region		p.P999P(1)		breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					CAGGGGGAAAAGGGCTGCCTG	0.493000													4	150					0	0	1	0	0
CCDC22	28952	broad.mit.edu	37	X	49093732	49093732	+	Splice_Site	SNP	T	T	G			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chrX:49093732T>G	ENST00000376227.3	+	2	398		c.e2+2		CCDC22_ENST00000496651.1_Splice_Site	NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22											NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						GCCTGCATGGTGAGTGGCCCT	0.562000													5	88					0	0	1	0	0
CCDC173	129881	broad.mit.edu	37	2	170518798	170518798	+	Silent	SNP	G	G	T			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr2:170518798G>T	ENST00000447353.1	-	5	916	c.811C>A	c.(811-813)Cgg>Agg	p.R271R		NM_001085447.1	NP_001078916.1			coiled-coil domain containing 173																		ACAAGAAACCGTCTCCTGCTT	0.313000													5	145					0.0293803	0.0325282	1	1	0
IDH2	3418	broad.mit.edu	37	15	90631839	90631839	+	Missense_Mutation	SNP	T	T	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr15:90631839T>A	ENST00000330062.3	-	4	627	c.514A>T	c.(514-516)Agg>Tgg	p.R172W	IDH2_ENST00000540499.2_Missense_Mutation_p.R120W|IDH2_ENST00000539790.1_Missense_Mutation_p.R42W|IDH2_ENST00000559482.1_Intron	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	172					2-oxoglutarate metabolic process|glyoxylate cycle|isocitrate metabolic process|tricarboxylic acid cycle	mitochondrial matrix	isocitrate dehydrogenase (NADP+) activity|magnesium ion binding|NAD binding	p.R172W(12)|p.R172G(2)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			TGGGCGTGCCTGCCAATGGTG	0.627000			M		GBM								8	80					0	0	1	0	0
NHEJ1	79840	broad.mit.edu	37	2	220012390	220012390	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr2:220012390G>A	ENST00000356853.5	-	4	651	c.518C>T	c.(517-519)aCg>aTg	p.T173M	NHEJ1_ENST00000409720.1_Missense_Mutation_p.T173M	NM_024782.2	NP_079058.1	Q9H9Q4	NHEJ1_HUMAN	nonhomologous end-joining factor 1	173					B cell differentiation|central nervous system development|DNA recombination|double-strand break repair via nonhomologous end joining|positive regulation of ligase activity|response to ionizing radiation|T cell differentiation	nonhomologous end joining complex|nucleus	DNA binding|identical protein binding			kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(2)	12		Renal(207;0.0915)		Epithelial(149;2.15e-06)|all cancers(144;0.000339)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0112)		TCGAATCAGCGTAGCCCCACT	0.478000								Non-homologous end-joining					4	54					0	0	1	0	0
FREM1	158326	broad.mit.edu	37	9	14845980	14845980	+	Missense_Mutation	SNP	C	C	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr9:14845980C>A	ENST00000380881.4	-	9	2189	c.1374G>T	c.(1372-1374)caG>caT	p.Q458H	FREM1_ENST00000380880.3_Missense_Mutation_p.Q457H|FREM1_ENST00000422223.2_Missense_Mutation_p.Q457H			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	457					cell communication|multicellular organismal development	basement membrane|integral to membrane	metal ion binding|sugar binding			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		GCCATCCATGCTGCAGGCCAC	0.443000													3	27					1	1	1	1	0
GAB2	9846	broad.mit.edu	37	11	77934697	77934697	+	Missense_Mutation	SNP	G	G	A			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr11:77934697G>A	ENST00000361507.4	-	6	1413	c.1328C>T	c.(1327-1329)tCg>tTg	p.S443L	GAB2_ENST00000340149.2_Missense_Mutation_p.S405L	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	443					osteoclast differentiation|phosphatidylinositol-mediated signaling|positive regulation of cell proliferation|positive regulation of mast cell degranulation	cytosol|plasma membrane	phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|transmembrane receptor protein tyrosine kinase adaptor activity		INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			GGTGCTGTCCGATCGGCCCAC	0.478000													6	316					0	0	1	0	0
HLA-A	3105	broad.mit.edu	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr6:29910607G>C	ENST00000396634.1	+	4	488	c.147G>C	c.(145-147)gtG>gtC	p.V49V	HLA-A_ENST00000376802.2_Silent_p.V49V|HLA-A_ENST00000376809.5_Silent_p.V49V|HLA-A_ENST00000376806.5_Silent_p.V49V			P30443	1A01_HUMAN	major histocompatibility complex, class I, A	49	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|regulation of immune response|type I interferon-mediated signaling pathway	integral to plasma membrane|MHC class I protein complex	MHC class I receptor activity	p.V49V(2)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TCATCGCCGTGGGCTACGTGG	0.692000									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			4	68					0	0	1	0	0
RYR2	6262	broad.mit.edu	37	1	237954771	237954771	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr1:237954771delT	ENST00000366574.2	+	93	13836	c.13519delT	c.(13519-13521)tafs	p.L4507fs	RYR2_ENST00000542537.1_Frame_Shift_Del_p.L4491fs|RYR2_ENST00000360064.6_Frame_Shift_Del_p.L4513fs	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4507					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			AATGTTAGCCTTATTTGTCGC	0.343													2	4	---	---	---	---					
RP11-119F19.2	0	broad.mit.edu	37	10	81444708	81444708	+	RNA	DEL	G	G	-			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr10:81444708delG	ENST00000600376.1	-	0	54				RP11-119F19.2_ENST00000596088.1_RNA																							AGCAGTGCAAGGTCCACGTGC	0.577													2	4	---	---	---	---					
RP13-329D4.3	0	broad.mit.edu	37	20	26113543	26113543	+	RNA	DEL	A	A	-			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chr20:26113543delA	ENST00000416563.1	-	0	250																											TCTTTGCCTTAACAACATTAT	0.363													2	4	---	---	---	---					
CD99L2	83692	broad.mit.edu	37	X	149984524	149984526	+	In_Frame_Del	DEL	GTG	GTG	-			TCGA-FG-8189-01B-11D-A289-08	TCGA-FG-8189-10A-01D-A289-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	aec88520-3464-4c47-afcc-36130f51125e	13bc5e25-1a60-4107-b129-99b0995a6897	g.chrX:149984524_149984526delGTG	ENST00000370377.3	-	3	273_275	c.156_158delCAC	c.(154-159)aca>ac	p.TT52del	CD99L2_ENST00000466436.1_Intron|CD99L2_ENST00000355149.3_Intron|CD99L2_ENST00000437787.2_In_Frame_Del_p.TT52del|CD99L2_ENST00000346693.4_5'UTR	NM_001242614.1|NM_031462.3	NP_001229543.1|NP_113650.2	Q8TCZ2	C99L2_HUMAN	CD99 molecule-like 2	52	Poly-Thr.				cell adhesion	cell junction|integral to membrane				endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CCTATTGGTTGTGGTGGTGGTGG	0.552													7	347	---	---	---	---					
