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
DCDC2B	149069	broad.mit.edu	37	1	32674910	32674910	+	Silent	SNP	G	G	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr1:32674910G>A	ENST00000409358.1	+	1	216	c.216G>A	c.(214-216)aaG>aaA	p.K72K		NM_001099434.1	NP_001092904.1	A2VCK2	DCD2B_HUMAN	doublecortin domain containing 2B	72	Doublecortin 1.				intracellular signal transduction					breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				CAGACTTGAAGAACAGAGGGC	0.582													22	53	---	---	---	---
RNF220	55182	broad.mit.edu	37	1	44877961	44877961	+	Silent	SNP	C	C	T			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr1:44877961C>T	ENST00000355387.2	+	2	642	c.192C>T	c.(190-192)aaC>aaT	p.N64N	RNF220_ENST00000361799.2_Silent_p.N64N|RNF220_ENST00000372247.2_Silent_p.N64N			Q5VTB9	RN220_HUMAN	ring finger protein 220	64					protein autoubiquitination	cytoplasm	ubiquitin-protein ligase activity|zinc ion binding			endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						CTTTCACCAACGGTTCCTATA	0.547													78	244	---	---	---	---
ATP6V1C2	245973	broad.mit.edu	37	2	10915197	10915197	+	Splice_Site	SNP	T	T	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr2:10915197T>A	ENST00000381661.3	+	10	934	c.825T>A	c.(823-825)taT>taA	p.Y275*	ATP6V1C2_ENST00000272238.4_Splice_Site_p.Y275*	NM_144583.3	NP_653184.2	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	275					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|proton-transporting V-type ATPase, V1 domain				endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		AGCAACAGTATGTGAGTATGT	0.498													11	32	---	---	---	---
KRCC1	51315	broad.mit.edu	37	2	88327466	88327466	+	Missense_Mutation	SNP	G	G	C			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr2:88327466G>C	ENST00000347055.3	-	4	1010	c.617C>G	c.(616-618)aCc>aGc	p.T206S		NM_016618.1	NP_057702.1	Q9NPI7	KRCC1_HUMAN	lysine-rich coiled-coil 1	206	Lys-rich.									cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	7						GACATGTACGGTTTCTATTTC	0.383													64	145	---	---	---	---
LRP1B	53353	broad.mit.edu	37	2	140995791	140995791	+	Missense_Mutation	SNP	A	A	G			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr2:140995791A>G	ENST00000389484.3	-	89	14461	c.13490T>C	c.(13489-13491)aTg>aCg	p.M4497T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4497					protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TACCTCATACATGTTATAAGA	0.338										TSP Lung(27;0.18)			13	41	---	---	---	---
FARP2	9855	broad.mit.edu	37	2	242373670	242373670	+	Missense_Mutation	SNP	T	T	G			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr2:242373670T>G	ENST00000264042.3	+	10	1135	c.965T>G	c.(964-966)cTt>cGt	p.L322R	FARP2_ENST00000545004.1_Missense_Mutation_p.L322R|FARP2_ENST00000373287.4_Missense_Mutation_p.L322R	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	322	FERM.				axon guidance|neuron remodeling|Rac protein signal transduction|regulation of Rho protein signal transduction	cytoskeleton|cytosol|extrinsic to membrane	cytoskeletal protein binding|Rho guanyl-nucleotide exchange factor activity			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		TTTTTTAGACTTTTGGACCAA	0.478													6	77	---	---	---	---
LRRC15	131578	broad.mit.edu	37	3	194080233	194080233	+	Missense_Mutation	SNP	C	C	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr3:194080233C>A	ENST00000347624.3	-	2	1625	c.1540G>T	c.(1540-1542)Gac>Tac	p.D514Y	LRRC15_ENST00000428839.1_Missense_Mutation_p.D520Y|LRRC15_ENST00000439944.2_Missense_Mutation_p.D520Y	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	514						integral to membrane				biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TCAGTGTAGTCTTCCACAGGG	0.557													12	32	---	---	---	---
NLN	57486	broad.mit.edu	37	5	65077143	65077143	+	Silent	SNP	T	T	C			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr5:65077143T>C	ENST00000380985.5	+	6	895	c.717T>C	c.(715-717)taT>taC	p.Y239Y	NLN_ENST00000502464.1_Silent_p.Y135Y	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	239					proteolysis	mitochondrial intermembrane space	metal ion binding|metalloendopeptidase activity			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		ATGACAAGTATAAAATTACCT	0.338													12	52	---	---	---	---
H2AFV	94239	broad.mit.edu	37	7	44874154	44874154	+	Missense_Mutation	SNP	G	G	C			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr7:44874154G>C	ENST00000308153.4	-	5	424	c.333C>G	c.(331-333)atC>atG	p.I111M	H2AFV_ENST00000437072.1_Intron|H2AFV_ENST00000521529.1_3'UTR|H2AFV_ENST00000350771.3_Missense_Mutation_p.I85M|H2AFV_ENST00000349299.3_Missense_Mutation_p.I73M|H2AFV_ENST00000222690.6_Intron|H2AFV_ENST00000381124.5_3'UTR	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	111					nucleosome assembly	nucleosome|nucleus	DNA binding			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						GGATGTGAGGGATCACACCTA	0.333													6	43	---	---	---	---
KIAA1324L	222223	broad.mit.edu	37	7	86537841	86537841	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr7:86537841G>A	ENST00000450689.2	-	17	2563	c.2378C>T	c.(2377-2379)aCa>aTa	p.T793I	KIAA1324L_ENST00000297222.6_Missense_Mutation_p.T553I|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.T626I|KIAA1324L_ENST00000444627.1_Missense_Mutation_p.T722I	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	793						integral to membrane				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					ATTTTTCAATGTGGTTTCAAC	0.303													22	34	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100685726	100685726	+	Missense_Mutation	SNP	G	G	T			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr7:100685726G>T	ENST00000306151.4	+	3	11093	c.11029G>T	c.(11029-11031)Gtg>Ttg	p.V3677L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3677	59 X approximate tandem repeats.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TTCATCTCCTGTGACTCCTGA	0.517													43	94	---	---	---	---
SMU1	55234	broad.mit.edu	37	9	33057683	33057683	+	Silent	SNP	A	A	G			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr9:33057683A>G	ENST00000397149.3	-	7	830	c.780T>C	c.(778-780)ttT>ttC	p.F260F	SMU1_ENST00000536631.1_Silent_p.F99F	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	260						cytoplasm|nucleus				endometrium(2)|lung(4)|ovary(2)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)		CCATCATCATAAAGTTATCTT	0.403													5	147	---	---	---	---
HSPA12A	259217	broad.mit.edu	37	10	118460629	118460629	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr10:118460629C>T	ENST00000369209.3	-	4	370	c.266G>A	c.(265-267)gGa>gAa	p.G89E		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	89							ATP binding			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		AGGGTCACCTCCCTCCCATCG	0.527													17	48	---	---	---	---
SCYL1	57410	broad.mit.edu	37	11	65302785	65302785	+	Nonsense_Mutation	SNP	G	G	T			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr11:65302785G>T	ENST00000524944.1	+	10	1351	c.1318G>T	c.(1318-1320)Gaa>Taa	p.E440*	SCYL1_ENST00000527009.1_Nonsense_Mutation_p.E297*|SCYL1_ENST00000533862.1_Nonsense_Mutation_p.E440*|SCYL1_ENST00000279270.6_Nonsense_Mutation_p.E440*|SCYL1_ENST00000270176.5_Nonsense_Mutation_p.E440*|SCYL1_ENST00000525364.1_Nonsense_Mutation_p.E440*|SCYL1_ENST00000420247.2_Nonsense_Mutation_p.E440*			Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	440					regulation of transcription, DNA-dependent|retrograde vesicle-mediated transport, Golgi to ER|transcription, DNA-dependent	cis-Golgi network|COPI vesicle coat|ER-Golgi intermediate compartment|microtubule organizing center|nucleus	ATP binding|DNA binding|protein tyrosine kinase activity			ovary(1)|skin(1)	2						GGCCAAGGATGAACAGGGCCC	0.592													17	63	---	---	---	---
ATM	472	broad.mit.edu	37	11	108224576	108224576	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr11:108224576G>A	ENST00000278616.4	+	60	9140	c.8755G>A	c.(8755-8757)Ggc>Agc	p.G2919S	C11orf65_ENST00000526725.1_Intron|ATM_ENST00000452508.2_Missense_Mutation_p.G2919S|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000525178.1_3'UTR	NM_000051.3	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated	2919	PI3K/PI4K.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		GGATGGCATGGGCATTACGGG	0.408			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			28	97	---	---	---	---
ATM	472	broad.mit.edu	37	11	108224578	108224578	+	Silent	SNP	C	C	G			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr11:108224578C>G	ENST00000278616.4	+	60	9142	c.8757C>G	c.(8755-8757)ggC>ggG	p.G2919G	C11orf65_ENST00000526725.1_Intron|ATM_ENST00000452508.2_Silent_p.G2919G|C11orf65_ENST00000525729.1_Intron|ATM_ENST00000525178.1_3'UTR	NM_000051.3	NP_000042	Q13315	ATM_HUMAN	ataxia telangiectasia mutated	2919	PI3K/PI4K.				cell cycle arrest|cellular response to gamma radiation|DNA damage induced protein phosphorylation|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|double-strand break repair via homologous recombination|G2/M transition DNA damage checkpoint|histone mRNA catabolic process|mitotic cell cycle spindle assembly checkpoint|negative regulation of B cell proliferation|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|pre-B cell allelic exclusion|protein autophosphorylation|reciprocal meiotic recombination|replicative senescence	cytoplasmic membrane-bounded vesicle|nucleoplasm	1-phosphatidylinositol-3-kinase activity|ATP binding|DNA binding|DNA-dependent protein kinase activity|identical protein binding|protein complex binding|protein dimerization activity|protein N-terminus binding			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)		ATGGCATGGGCATTACGGGTG	0.403			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			28	97	---	---	---	---
UNC79	57578	broad.mit.edu	37	14	94008906	94008906	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr14:94008906T>A	ENST00000553484.1	+	14	1773	c.1619T>A	c.(1618-1620)aTg>aAg	p.M540K	UNC79_ENST00000256339.4_Missense_Mutation_p.M363K|UNC79_ENST00000555664.1_Missense_Mutation_p.M540K|UNC79_ENST00000393151.2_Missense_Mutation_p.M540K			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	540						integral to membrane				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						ACTGCGTATATGATGGATGAT	0.512													14	107	---	---	---	---
SLTM	79811	broad.mit.edu	37	15	59186349	59186349	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr15:59186349T>A	ENST00000380516.2	-	11	1508	c.1421A>T	c.(1420-1422)gAt>gTt	p.D474V	SLTM_ENST00000536328.1_Missense_Mutation_p.D43V	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	474					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						ACTCTTTTCATCATTTTCTTT	0.284													8	22	---	---	---	---
SLTM	79811	broad.mit.edu	37	15	59186350	59186350	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr15:59186350C>T	ENST00000380516.2	-	11	1507	c.1420G>A	c.(1420-1422)Gat>Aat	p.D474N	SLTM_ENST00000536328.1_Missense_Mutation_p.D43N	NM_001013843.1|NM_024755.2	NP_001013865.1|NP_079031.2	Q9NWH9	SLTM_HUMAN	SAFB-like, transcription modulator	474					apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleotide binding|RNA binding			breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CTCTTTTCATCATTTTCTTTC	0.284													8	21	---	---	---	---
ZNF319	57567	broad.mit.edu	37	16	58030795	58030795	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr16:58030795G>A	ENST00000299237.2	-	2	1997	c.1375C>T	c.(1375-1377)Cgc>Tgc	p.R459C		NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	459					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						AGCGTGCAGCGCAGGGGCTTC	0.662													3	8	---	---	---	---
FBXW10	10517	broad.mit.edu	37	17	18651256	18651256	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr17:18651256C>T	ENST00000308799.4	+	2	727	c.508C>T	c.(508-510)Ctc>Ttc	p.L170F	FBXW10_ENST00000395667.1_Missense_Mutation_p.L170F|FBXW10_ENST00000395665.4_Missense_Mutation_p.L170F|FBXW10_ENST00000301938.4_Missense_Mutation_p.L170F			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	170										NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						TGTTTCAGGGCTCAATCAAGA	0.443													7	63	---	---	---	---
GOSR1	9527	broad.mit.edu	37	17	28808252	28808252	+	Missense_Mutation	SNP	T	T	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr17:28808252T>A	ENST00000225724.5	+	2	195	c.123T>A	c.(121-123)agT>agA	p.S41R	GOSR1_ENST00000467337.2_5'UTR|GOSR1_ENST00000579905.1_3'UTR|GOSR1_ENST00000581721.1_Missense_Mutation_p.S41R|GOSR1_ENST00000451249.2_Missense_Mutation_p.S41R	NM_001007024.1|NM_001007025.1|NM_004871.2	NP_001007025.1|NP_001007026.1|NP_004862.1	O95249	GOSR1_HUMAN	golgi SNAP receptor complex member 1	41					intra-Golgi vesicle-mediated transport|protein transport|retrograde transport, endosome to Golgi	Golgi membrane|integral to membrane|SNARE complex	SNAP receptor activity			endometrium(2)|kidney(2)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	12						GTCATAGCAGTACCCGAGATG	0.373													23	82	---	---	---	---
SP2	6668	broad.mit.edu	37	17	46002397	46002397	+	Silent	SNP	G	G	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr17:46002397G>A	ENST00000376741.4	+	5	1622	c.1485G>A	c.(1483-1485)caG>caA	p.Q495Q	AC003665.1_ENST00000433001.1_RNA|AC003665.1_ENST00000585280.1_RNA|AC003665.1_ENST00000451140.2_RNA|AC003665.1_ENST00000411573.2_RNA	NM_003110.5	NP_003101.3	Q02086	SP2_HUMAN	Sp2 transcription factor	495					immune response|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding|histone deacetylase binding|zinc ion binding			endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						GAGAGACCCAGCCCGGGGAGA	0.602													13	39	---	---	---	---
LILRA6	79168	broad.mit.edu	37	19	54745451	54745451	+	Splice_Site	SNP	C	C	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr19:54745451C>A	ENST00000440558.2	-	4	707		c.e4+1		LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Splice_Site|LILRA6_ENST00000245621.5_Splice_Site|LILRA6_ENST00000391735.3_Intron|LILRA6_ENST00000396365.2_Splice_Site|LILRA6_ENST00000270464.5_Splice_Site					leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6											central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGCTCCCTCACCTGAGGGCAG	0.572													14	41	---	---	---	---
BAGE2	85319	broad.mit.edu	37	21	11039424	11039424	+	RNA	SNP	T	T	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr21:11039424T>A	ENST00000470054.1	-	0	779									B melanoma antigen family, member 2															Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TCCAATTCGGTATTCACTGTA	0.279													4	110	---	---	---	---
ASXL2	55252	broad.mit.edu	37	2	25972970	25972979	+	Frame_Shift_Del	DEL	ATCCTTTGGG	ATCCTTTGGG	-			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr2:25972970_25972979delATCCTTTGGG	ENST00000435504.4	-	12	1739_1748	c.1446_1455delCCCAAAGGAT	c.(1444-1455)tgcccaaaggatfs	p.CPKD482fs	ASXL2_ENST00000336112.4_Frame_Shift_Del_p.CPKD454fs|ASXL2_ENST00000272341.4_Frame_Shift_Del_p.CPKD222fs|ASXL2_ENST00000404843.1_Frame_Shift_Del_p.CPKD222fs			Q76L83	ASXL2_HUMAN	additional sex combs like 2 (Drosophila)	482					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	metal ion binding|protein binding			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGAGATCCTCATCCTTTGGGCACTTGATGG	0.481													29	110	---	---	---	---
GBA3	57733	broad.mit.edu	37	4	22737844	22737845	+	RNA	INS	-	-	A			TCGA-YL-A8SC-01A-11D-A377-08	TCGA-YL-A8SC-10A-01D-A37A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	30cbe211-6ed8-49bd-b2da-428fd8c90f37	55773b06-5d25-4338-a0b2-943b79062d10	g.chr4:22737844_22737845insA	ENST00000511446.2	+	0	290				GBA3_ENST00000503442.1_RNA|GBA3_ENST00000508166.1_RNA	NM_001277225.1	NP_001264154.1	Q9H227	GBA3_HUMAN	glucosidase, beta, acid 3 (gene/pseudogene)						glycoside catabolic process|glycosylceramide catabolic process	cytosol	beta-galactosidase activity|beta-glucosidase activity|cation binding|glycosylceramidase activity			breast(1)|kidney(2)|large_intestine(4)|lung(20)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						AAGTGTTTCTTAAAAATAGAAG	0.396													7	78	---	---	---	---
