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
FAT3	120114	broad.mit.edu	37	11	92568131	92568131	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr11:92568131G>A	ENST00000298047.6	+	14	9984	c.9967G>A	c.(9967-9969)Gct>Act	p.A3323T	FAT3_ENST00000409404.2_Missense_Mutation_p.A3323T|FAT3_ENST00000525166.1_Missense_Mutation_p.A3173T			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3323	Cadherin 30.				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding	p.A3323T(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGCTCTCAGCGCTGTGGCCAC	0.498000										TCGA Ovarian(4;0.039)			17	17					0	0	0.500413	0	0
SUCO	51430	broad.mit.edu	37	1	172501831	172501831	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:172501831C>T	ENST00000367723.3	+	1	343	c.219C>T	c.(217-219)aaC>aaT	p.N73N		NM_016227.2	NP_057311.2			SUN domain containing ossification factor									p.N73N(1)									ACTTCTCTAACAAAACCATGG	0.498000													6	78					0	0	0.248553	0	0
ATP6V1A	523	broad.mit.edu	37	3	113508598	113508598	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:113508598G>T	ENST00000273398.3	+	8	1007	c.899G>T	c.(898-900)gGt>gTt	p.G300V	ATP6V1A_ENST00000538620.1_Missense_Mutation_p.G267V	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	300					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	cytosol|integral to plasma membrane|proton-transporting V-type ATPase, V1 domain	ATP binding|hydrogen ion transporting ATP synthase activity, rotational mechanism|proton-transporting ATPase activity, rotational mechanism	p.G300V(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GAGGTTGATGGTAAGGTAGAG	0.353000													51	103					8.04919e-23	1.03334e-22	0.870114	1	0
ST18	9705	broad.mit.edu	37	8	53045685	53045685	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr8:53045685G>A	ENST00000276480.7	-	21	3059	c.2376C>T	c.(2374-2376)tgC>tgT	p.C792C		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)	792						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.C792C(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				TTGCACGAGGGCATCCGGACA	0.468000													4	233					0	0	0.150653	0	0
COL6A5	256076	broad.mit.edu	37	3	130159274	130159274	+	Missense_Mutation	SNP	A	A	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:130159274A>T	ENST00000265379.6	+	35	6586	c.6092A>T	c.(6091-6093)gAt>gTt	p.D2031V	COL6A5_ENST00000432398.2_Missense_Mutation_p.D2031V			A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2031	Nonhelical region.|VWFA 9.				axon guidance|cell adhesion	collagen		p.D70V(1)|p.D2031V(1)		endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						ACAGAGTTTGATTTCATCACT	0.423000													45	100					0	0	0.859065	0	0
MATN4	8785	broad.mit.edu	37	20	43926838	43926838	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr20:43926838C>T	ENST00000537548.1	-	8	1642	c.1398G>A	c.(1396-1398)tcG>tcA	p.S466S	MATN4_ENST00000372754.1_Silent_p.S507S|MATN4_ENST00000360607.5_Silent_p.S425S|MATN4_ENST00000372751.4_Silent_p.S317S|MATN4_ENST00000372756.1_Silent_p.S466S|MATN4_ENST00000342716.4_Silent_p.S466S|MATN4_ENST00000372753.1_Silent_p.S317S|MATN4_ENST00000353917.5_Silent_p.S384S			O95460	MATN4_HUMAN	matrilin 4	507	VWFA 2.					extracellular region	protein binding	p.S466S(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CTGCCCACACCGAGATGTCAT	0.672000													5	73					0	0	0.217242	0	0
TXNIP	10628	broad.mit.edu	37	1	145440347	145440347	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:145440347G>T	ENST00000369317.4	+	5	987	c.653G>T	c.(652-654)cGc>cTc	p.R218L	TXNIP_ENST00000475171.1_Intron	NM_006472.3	NP_006463.3	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	218					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding	p.R218L(1)		breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(1)|lung(5)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	21	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ATTGTGGCCCGCCACACTTAC	0.478000													21	118					9.95505e-16	1.22822e-15	0.624587	1	0
VIPAS39	63894	broad.mit.edu	37	14	77896064	77896064	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:77896064C>T	ENST00000553888.1	-	17	1736	c.1226G>A	c.(1225-1227)cGg>cAg	p.R409Q	VIPAS39_ENST00000448935.2_Missense_Mutation_p.R360Q|VIPAS39_ENST00000343765.2_Missense_Mutation_p.R409Q|VIPAS39_ENST00000327028.4_Missense_Mutation_p.R396Q|VIPAS39_ENST00000557658.1_Missense_Mutation_p.R409Q|VIPAS39_ENST00000556412.1_Missense_Mutation_p.R435Q	NM_001193314.1|NM_001193317.1|NM_022067.3	NP_001180243.1|NP_001180246.1|NP_071350.2			VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog									p.R409Q(1)									TTCGACAACCCGATGGAAGCC	0.502000													25	414					0	0	0.667858	0	0
LHX5	64211	broad.mit.edu	37	12	113909233	113909233	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:113909233G>A	ENST00000261731.3	-	1	644	c.71C>T	c.(70-72)gCg>gTg	p.A24V		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	24	LIM zinc-binding 1.					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	p.A24V(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	10						GATGTGCCACGCGCGGTCCAG	0.612000													3	16					0	0	0.115264	0	0
CROT	54677	broad.mit.edu	37	7	86990868	86990868	+	Missense_Mutation	SNP	T	T	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:86990868T>A	ENST00000331536.3	+	5	588	c.403T>A	c.(403-405)Tac>Aac	p.Y135N	CROT_ENST00000442291.1_Missense_Mutation_p.Y135N|CROT_ENST00000419147.2_Missense_Mutation_p.Y163N	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase	135					fatty acid beta-oxidation using acyl-CoA oxidase|generation of precursor metabolites and energy|transport	peroxisomal matrix	carnitine O-octanoyltransferase activity	p.Y135N(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	TAACTTGAACTACTGGCAGCT	0.398000													6	178					0	0	0.217242	0	0
SPATA31A6	389730	broad.mit.edu	37	9	43627187	43627187	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr9:43627187C>T	ENST00000332857.6	-	4	1528	c.1500G>A	c.(1498-1500)caG>caA	p.Q500Q		NM_001145196.1	NP_001138668.1			SPATA31 subfamily A, member 6									p.Q500Q(1)									GGAAAGAAGACTGAAGATGGG	0.547000													6	526					0	0	0.217242	0	0
SRMS	6725	broad.mit.edu	37	20	62178595	62178595	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr20:62178595G>A	ENST00000217188.1	-	1	262	c.222C>T	c.(220-222)cgC>cgT	p.R74R		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	74	SH3.						ATP binding|non-membrane spanning protein tyrosine kinase activity	p.R74R(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|prostate(2)|stomach(1)	19	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)			GCCTGTCCCCGCGGCGGACAC	0.701000													28	359					0	0	0.740014	0	0
RYR1	6261	broad.mit.edu	37	19	38976722	38976722	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr19:38976722C>A	ENST00000355481.4	+	34	5558	c.5427C>A	c.(5425-5427)gaC>gaA	p.D1809E	RYR1_ENST00000359596.3_Missense_Mutation_p.D1809E|RYR1_ENST00000360985.3_Missense_Mutation_p.D1809E	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1809	6 X approximate repeats.				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	p.D1809E(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)	CCCTGCGGGACAAGGCACTGA	0.711000													43	57					8.72198e-27	1.13505e-26	0.870114	1	0
NBN	4683	broad.mit.edu	37	8	90955524	90955524	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr8:90955524C>A	ENST00000265433.3	-	14	2295	c.2141G>T	c.(2140-2142)cGa>cTa	p.R714L	NBN_ENST00000409330.1_Missense_Mutation_p.R632L	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	714					cell cycle arrest|DNA damage response, signal transduction by p53 class mediator|DNA duplex unwinding|double-strand break repair via homologous recombination|meiosis|mitotic cell cycle G1/S transition checkpoint|mitotic cell cycle G2/M transition DNA damage checkpoint|positive regulation of kinase activity|positive regulation of protein autophosphorylation|regulation of DNA-dependent DNA replication initiation|telomere maintenance	Mre11 complex|nuclear chromosome, telomeric region|nuclear inclusion body|nucleolus|nucleoplasm	protein N-terminus binding|transcription factor binding	p.R714L(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TGTATTCTTTCGAGCATGATG	0.398000								Homologous recombination					4	255					0.014758	0.0166906	0.184627	1	0
CCDC115	84317	broad.mit.edu	37	2	131096732	131096732	+	Silent	SNP	G	G	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:131096732G>C	ENST00000259229.2	-	5	727	c.504C>G	c.(502-504)ctC>ctG	p.L168L	CCDC115_ENST00000437688.2_3'UTR|CCDC115_ENST00000409127.1_Silent_p.L163L	NM_032357.2	NP_115733.2	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	168						endosome|lysosome		p.L168L(1)		central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	7	Colorectal(110;0.1)					GTTTCTCTTGGAGTCCCCGGA	0.612000													7	62					0	0	0.248553	0	0
SRSF7	6432	broad.mit.edu	37	2	38976716	38976716	+	Missense_Mutation	SNP	T	T	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:38976716T>A	ENST00000313117.6	-	3	578	c.341A>T	c.(340-342)cAt>cTt	p.H114L	SRSF7_ENST00000409276.1_Missense_Mutation_p.H114L|SRSF7_ENST00000446327.2_Missense_Mutation_p.H114L	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	114					mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	nucleoplasm	nucleotide binding|protein binding|RNA binding|zinc ion binding	p.H114L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						ATAAGCATAATGTCCCTTTTC	0.413000													27	279					0	0	0.729181	0	0
TMED9	54732	broad.mit.edu	37	5	177022271	177022271	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr5:177022271C>T	ENST00000332598.6	+	5	619	c.562C>T	c.(562-564)Cga>Tga	p.R188*		NM_017510.4	NP_059980.2	Q9BVK6	TMED9_HUMAN	transmembrane emp24 protein transport domain containing 9	188					transport	endoplasmic reticulum membrane|ER-Golgi intermediate compartment|integral to membrane		p.R188*(1)		endometrium(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(2)	10	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTGCAGTGGCGAGAGGAGCG	0.602000													29	62					0	0	0.740014	0	0
OSER1	51526	broad.mit.edu	37	20	42826279	42826279	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr20:42826279T>C	ENST00000372970.2	-	6	472	c.292A>G	c.(292-294)Ata>Gta	p.I98V	OSER1_ENST00000255174.2_Missense_Mutation_p.I98V					oxidative stress responsive serine-rich 1									p.I98V(1)									GAAGACGCTATTGTACTGCAA	0.488000													21	159					0	0	0.575678	0	0
PARP2	10038	broad.mit.edu	37	14	20822982	20822982	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:20822982G>A	ENST00000527915.1	+	9	822	c.817G>A	c.(817-819)Gca>Aca	p.A273T	PARP2_ENST00000250416.5_Missense_Mutation_p.A273T|PARP2_ENST00000429687.3_Missense_Mutation_p.A260T			Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	273	PARP alpha-helical.				protein ADP-ribosylation	nucleolus|nucleoplasm	DNA binding|NAD+ ADP-ribosyltransferase activity	p.A273T(1)|p.A224T(1)		central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		GCTGACAGTGGCACAAATCAA	0.468000								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					4	264					0	0	0.217242	0	0
APOBEC3D	140564	broad.mit.edu	37	22	39421246	39421246	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr22:39421246C>T	ENST00000216099.7	+	3	789	c.382C>T	c.(382-384)Ctg>Ttg	p.L128L	APOBEC3D_ENST00000427494.2_Intron|APOBEC3D_ENST00000381568.4_Silent_p.L128L	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D	128					negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|zinc ion binding	p.L128L(2)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11	Melanoma(58;0.04)					CAATGTCACCCTGACCATCTC	0.572000													7	103					0	0	0.278610	0	0
WASF2	10163	broad.mit.edu	37	1	27755320	27755320	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:27755320G>A	ENST00000430629.2	-	2	296	c.81C>T	c.(79-81)tgC>tgT	p.C27C	WASF2_ENST00000536657.1_Silent_p.C27C	NM_001201404.1|NM_006990.3	NP_001188333.1|NP_008921.1	Q9Y6W5	WASF2_HUMAN	WAS protein family, member 2	27					actin cytoskeleton organization|G-protein signaling, coupled to cAMP nucleotide second messenger	actin cytoskeleton|lamellipodium	actin binding	p.C27C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	18		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0446)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.7e-08)|COAD - Colon adenocarcinoma(152;2e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00139)|KIRC - Kidney renal clear cell carcinoma(1967;0.00204)|STAD - Stomach adenocarcinoma(196;0.00325)|READ - Rectum adenocarcinoma(331;0.0481)		TGTTGGTCACGCATTCCAGCT	0.577000													4	140					0	0	0.150653	0	0
ZNF518A	9849	broad.mit.edu	37	10	97916435	97916435	+	RNA	SNP	T	T	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr10:97916435T>G	ENST00000534948.1	+	0	1213							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	p.F119C(2)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		ATACTCAATTTCAGCTGTTTA	0.388000													13	277					0	0	0.435327	0	0
TAS2R1	50834	broad.mit.edu	37	5	9629679	9629679	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr5:9629679G>A	ENST00000382492.2	-	1	784	c.466C>T	c.(466-468)Cta>Tta	p.L156L	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	156					chemosensory behavior|sensory perception of taste	integral to membrane	taste receptor activity	p.L156L(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						AATTTCCTTAGGAAGTATGGG	0.393000													8	151					0	0	0.307466	0	0
KMT2D	8085	broad.mit.edu	37	12	49420423	49420423	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:49420423C>A	ENST00000301067.7	-	48	15325	c.15326G>T	c.(15325-15327)tGc>tTc	p.C5109F		NM_003482.3	NP_003473.3			lysine (K)-specific methyltransferase 2D									p.C5109F(1)|p.C4839F(1)									GACATTGGGGCAACGCATGCG	0.547000													33	71					2.08457e-15	2.5389e-15	0.750413	1	0
SCARB1	949	broad.mit.edu	37	12	125348169	125348169	+	Missense_Mutation	SNP	G	G	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:125348169G>C	ENST00000339570.5	-	1	294	c.98C>G	c.(97-99)cCg>cGg	p.P33R	SCARB1_ENST00000376788.1_Missense_Mutation_p.P33R|SCARB1_ENST00000261693.6_Missense_Mutation_p.P33R|SCARB1_ENST00000546215.1_Missense_Mutation_p.P33R|SCARB1_ENST00000415380.2_Missense_Mutation_p.P33R|SCARB1_ENST00000535005.1_Intron	NM_001082959.1	NP_001076428.1	Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	33					adhesion to symbiont|cell adhesion|cholesterol efflux|cholesterol homeostasis|cholesterol import|detection of lipopolysaccharide|high-density lipoprotein particle clearance|high-density lipoprotein particle remodeling|lipopolysaccharide transport|lipoprotein metabolic process|positive regulation of cholesterol storage|positive regulation of endothelial cell migration|positive regulation of nitric-oxide synthase activity|recognition of apoptotic cell|reverse cholesterol transport|triglyceride homeostasis|wound healing	caveola	1-phosphatidylinositol binding|apolipoprotein A-I binding|high-density lipoprotein particle receptor activity|lipopolysaccharide receptor activity|low-density lipoprotein particle binding|phosphatidylserine binding|transporter activity	p.P33R(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	GATGAGCGACGGCACCATCAC	0.716000													3	15					0	0	0.115264	0	0
TBL1XR1	79718	broad.mit.edu	37	3	176755961	176755961	+	Splice_Site	SNP	C	C	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:176755961C>G	ENST00000430069.1	-	12	1307		c.e12-1		TBL1XR1_ENST00000457928.2_Splice_Site			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1						canonical Wnt receptor signaling pathway|cellular lipid metabolic process|chromatin modification|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|proteasomal ubiquitin-dependent protein catabolic process|transcription, DNA-dependent	spindle microtubule|transcriptional repressor complex	beta-catenin binding|histone binding|protein N-terminus binding|transcription corepressor activity|transcription regulatory region DNA binding	p.?(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31	all_cancers(143;1.44e-17)|Ovarian(172;0.00163)|Breast(254;0.214)	Acute lymphoblastic leukemia(1;0.00599)|all_hematologic(1;0.0632)|Prostate(884;0.215)	OV - Ovarian serous cystadenocarcinoma(80;9.83e-31)			TTACTTCATTCTAAAAATAAT	0.323000													4	57					0	0	0.184627	0	0
SPTA1	6708	broad.mit.edu	37	1	158612201	158612201	+	Splice_Site	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:158612201C>T	ENST00000368148.3	-	33	4917	c.4737_splice	c.e33+1	p.K1579_splice	SPTA1_ENST00000368147.3_Splice_Site_p.K1579_splice	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1 (elliptocytosis 2)	1579					actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton	p.K1579K(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGAGCTTTACCTTCATGGCCT	0.393000													9	269					0	0	0.361761	0	0
EHHADH	1962	broad.mit.edu	37	3	184910384	184910384	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:184910384G>A	ENST00000231887.3	-	7	1877	c.1802C>T	c.(1801-1803)tCa>tTa	p.S601L	EHHADH_ENST00000456310.1_Missense_Mutation_p.S505L	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	601						peroxisome	3-hydroxyacyl-CoA dehydrogenase activity|coenzyme binding|dodecenoyl-CoA delta-isomerase activity|enoyl-CoA hydratase activity	p.S601L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)		NADH(DB00157)	TCTATACCGTGATAGGAATTT	0.428000													34	227					0	0	0.760397	0	0
LAMA2	3908	broad.mit.edu	37	6	129601260	129601260	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr6:129601260C>T	ENST00000421865.2	+	18	2554	c.2505C>T	c.(2503-2505)tgC>tgT	p.C835C		NM_000426.3|NM_001079823.1	NP_000417.2|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	835	Laminin EGF-like 7.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity	p.C835C(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GTGATGGATGCCCTGTCGGGT	0.453000													4	77					0	0	0.150653	0	0
NRG3	10718	broad.mit.edu	37	10	84745233	84745233	+	Missense_Mutation	SNP	G	G	A	rs143042604	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr10:84745233G>A	ENST00000372142.2	+	11	1646	c.1372G>A	c.(1372-1374)Gta>Ata	p.V458I	NRG3_ENST00000404576.2_Missense_Mutation_p.V459I|NRG3_ENST00000372141.2_Missense_Mutation_p.V655I|NRG3_ENST00000556918.1_Missense_Mutation_p.V485I|NRG3_ENST00000404547.1_Missense_Mutation_p.V679I|NRG3_ENST00000545131.1_Missense_Mutation_p.V305I|NRG3_ENST00000537893.1_Missense_Mutation_p.V305I	NM_001165973.1	NP_001159445.1	P56975	NRG3_HUMAN	neuregulin 3	679					regulation of cell growth	extracellular region|integral to plasma membrane	growth factor activity|receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity	p.V655I(1)|p.V458I(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ACTGGCCAGCGTAGAAACCGA	0.473000													45	52					0	0	0.840704	0	0
CRISPLD2	83716	broad.mit.edu	37	16	84906612	84906612	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr16:84906612C>T	ENST00000262424.5	+	10	1220	c.996C>T	c.(994-996)tgC>tgT	p.C332C	CRISPLD2_ENST00000564567.1_Silent_p.C332C|CRISPLD2_ENST00000567845.1_Silent_p.C331C	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	332	LCCL 1.					extracellular region|transport vesicle		p.C332C(1)		endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						CTAGCATATGCCGCGCCGCCA	0.542000													5	184					0	0	0.184627	0	0
USP38	84640	broad.mit.edu	37	4	144133502	144133502	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr4:144133502A>G	ENST00000307017.4	+	8	2035	c.1529A>G	c.(1528-1530)gAg>gGg	p.E510G	USP38_ENST00000510377.1_Missense_Mutation_p.E510G	NM_032557.5	NP_115946.2	Q8NB14	UBP38_HUMAN	ubiquitin specific peptidase 38	510					ubiquitin-dependent protein catabolic process		cysteine-type peptidase activity|ubiquitin thiolesterase activity	p.E510G(2)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	33	all_hematologic(180;0.158)					ATATTCTTTGAGGCTTCCAGA	0.383000													3	232					0	0	0.115264	0	0
TPTE2	93492	broad.mit.edu	37	13	20024290	20024290	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr13:20024290A>G	ENST00000400230.2	-	13	943	c.899T>C	c.(898-900)tTc>tCc	p.F300S	TPTE2_ENST00000457266.2_Missense_Mutation_p.F189S|TPTE2_ENST00000255310.6_Missense_Mutation_p.F223S|TPTE2_ENST00000382975.4_Missense_Mutation_p.F260S|TPTE2_ENST00000390680.2_Missense_Mutation_p.F223S|TPTE2_ENST00000382978.1_Missense_Mutation_p.F260S|TPTE2_ENST00000382977.4_Missense_Mutation_p.F300S|TPTE2_ENST00000400103.2_Missense_Mutation_p.F189S			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	300	Phosphatase tensin-type.					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	p.F300S(1)|p.F223S(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TTCCTTGGTGAAAACCACCAT	0.323000													11	185					0	0	0.500413	0	0
KRTAP3-3	85293	broad.mit.edu	37	17	39150166	39150166	+	Missense_Mutation	SNP	C	C	T	rs146610892	byFrequency	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:39150166C>T	ENST00000391586.1	-	1	219	c.184G>A	c.(184-186)Gtg>Atg	p.V62M		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	62						keratin filament	structural molecule activity	p.V62M(1)		lung(2)|prostate(2)	4		Breast(137;0.00043)				CAGGTGGGCACGCAGGGCTGA	0.632000													5	149					0	0	0.184627	0	0
LINC00518	0	broad.mit.edu	37	6	10430364	10430364	+	RNA	SNP	T	T	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr6:10430364T>C	ENST00000496285.1	-	0	671					NR_027793.1													p.S42G(1)									atttggtcactctCATTGAGG	0.443000													3	178					0	0	0.115264	0	0
ARID4B	51742	broad.mit.edu	37	1	235345029	235345029	+	Missense_Mutation	SNP	T	T	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:235345029T>C	ENST00000264183.3	-	20	3702	c.3205A>G	c.(3205-3207)Att>Gtt	p.I1069V	ARID4B_ENST00000349213.3_Missense_Mutation_p.I983V|ARID4B_ENST00000494543.1_5'UTR|ARID4B_ENST00000366603.2_Missense_Mutation_p.I1069V	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	1069					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|protein binding	p.I1069V(1)		NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TCCACCTCAATTGTGCTATCA	0.493000													32	54					0	0	0.729181	0	0
CCT6P1	0	broad.mit.edu	37	7	65222986	65222986	+	RNA	SNP	G	G	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:65222986G>T	ENST00000442266.1	+	0	578																											GAATTCTGGCGTTTTTTACAA	0.289000													4	28					5.9392e-07	7.14208e-07	0.217242	1	0
MSH3	4437	broad.mit.edu	37	5	79961132	79961132	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr5:79961132G>A	ENST00000265081.6	+	3	609	c.529G>A	c.(529-531)Gca>Aca	p.A177T		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	177	Interaction with EXO1.				maintenance of DNA repeat elements|meiotic mismatch repair|negative regulation of DNA recombination|positive regulation of helicase activity|reciprocal meiotic recombination|somatic recombination of immunoglobulin gene segments	MutSbeta complex|nuclear chromosome	ATP binding|DNA-dependent ATPase activity|double-strand/single-strand DNA junction binding|enzyme binding|loop DNA binding|Y-form DNA binding	p.A168T(1)|p.A177T(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TCTTCTACACGCAAAGAATGC	0.388000								Mismatch excision repair (MMR)					45	67					0	0	0.870114	0	0
GSTM5	2949	broad.mit.edu	37	1	110256100	110256100	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:110256100A>G	ENST00000369813.1	+	2	954	c.49A>G	c.(49-51)Atc>Gtc	p.I17V	GSTM5_ENST00000369812.5_Missense_Mutation_p.I77V|GSTM5_ENST00000256593.3_Intron			P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	59	GST N-terminal.				xenobiotic metabolic process	endoplasmic reticulum membrane	glutathione transferase activity	p.?(1)		NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	TTTCCCATCTATCCAGCTGCC	0.592000													84	186					0	0	0.870114	0	0
KMT2C	58508	broad.mit.edu	37	7	151845758	151845758	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151845758C>A	ENST00000355193.2	-	53	13643	c.13425G>T	c.(13423-13425)agG>agT	p.R4475S	KMT2C_ENST00000262189.6_Missense_Mutation_p.R4418S					lysine (K)-specific methyltransferase 2C									p.R4418S(1)|p.R4475S(1)									GGTTGAGTAGCCTTGCTGGTC	0.488000													5	172					0.000602214	0.000706301	0.184627	1	0
DET1	55070	broad.mit.edu	37	15	89074916	89074916	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr15:89074916G>A	ENST00000564406.1	-	3	214	c.54C>T	c.(52-54)acC>acT	p.T18T	DET1_ENST00000444300.1_Silent_p.T18T|DET1_ENST00000268148.8_Silent_p.T7T|DET1_ENST00000558413.1_Silent_p.T7T	NM_017996.3	NP_060466.2	Q7L5Y6	DET1_HUMAN	de-etiolated homolog 1 (Arabidopsis)	7						nucleus		p.T18T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Lung NSC(78;0.105)|all_lung(78;0.182)		BRCA - Breast invasive adenocarcinoma(143;0.188)			GAGGCTTGATGGTAGAAACAT	0.413000													3	106					0	0	0.115264	0	0
MED16	10025	broad.mit.edu	37	19	881676	881676	+	Missense_Mutation	SNP	G	G	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr19:881676G>T	ENST00000312090.6	-	7	1174	c.1024C>A	c.(1024-1026)Cta>Ata	p.L342I	MED16_ENST00000606828.1_Intron|MED16_ENST00000269814.4_Missense_Mutation_p.L342I|MED16_ENST00000325464.1_Missense_Mutation_p.L342I|MED16_ENST00000395808.3_Missense_Mutation_p.L342I|MED16_ENST00000589119.1_Missense_Mutation_p.L342I			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	342					androgen receptor signaling pathway|positive regulation of transcription, DNA-dependent|regulation of transcription from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter	mediator complex	receptor activity|thyroid hormone receptor binding|thyroid hormone receptor coactivator activity|vitamin D receptor binding	p.L342I(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGGCCGATAGGATCCGCCAT	0.577000													4	136					0.184627	0.194884	0.184627	1	0
PCNXL4	64430	broad.mit.edu	37	14	60591549	60591549	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:60591549A>G	ENST00000406854.1	+	9	3214	c.2660A>G	c.(2659-2661)gAc>gGc	p.D887G	PCNXL4_ENST00000535349.1_Missense_Mutation_p.D94G|PCNXL4_ENST00000406949.1_Missense_Mutation_p.D653G|PCNXL4_ENST00000317623.4_Missense_Mutation_p.D653G|PCNXL4_ENST00000404681.2_Missense_Mutation_p.D887G					pecanex-like 4 (Drosophila)									p.D653G(1)|p.D887G(1)									CCTGCTGTTGACAAAGGAAAA	0.438000													13	384					0	0	0.435327	0	0
TRAM2	9697	broad.mit.edu	37	6	52400646	52400646	+	Splice_Site	SNP	T	T	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr6:52400646T>A	ENST00000182527.3	-	2	120		c.e2-2			NM_012288.3	NP_036420.1	Q15035	TRAM2_HUMAN	translocation associated membrane protein 2						collagen biosynthetic process|protein transport|transmembrane transport	integral to membrane	protein binding	p.?(1)		endometrium(3)|large_intestine(1)|lung(7)|prostate(1)|skin(1)	13	Lung NSC(77;0.109)					GGCTGTGACCTGTAAAACAAA	0.438000													3	88					0	0	0.115264	0	0
ZKSCAN7	55888	broad.mit.edu	37	3	44612332	44612332	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:44612332A>G	ENST00000273320.3	+	6	2159	c.1730A>G	c.(1729-1731)aAg>aGg	p.K577R	ZKSCAN7_ENST00000426540.1_Missense_Mutation_p.K577R|RP11-944L7.4_ENST00000457331.1_RNA|ZKSCAN7_ENST00000431636.1_Intron|ZKSCAN7_ENST00000341840.3_Intron	NM_018651.2	NP_061121.2			zinc finger with KRAB and SCAN domains 7									p.K577R(1)									ACTGGGGAAAAGCCATACAAA	0.433000													3	254					0	0	0.115264	0	0
GALNT11	63917	broad.mit.edu	37	7	151814291	151814291	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151814291A>G	ENST00000434507.1	+	11	1720	c.1283A>G	c.(1282-1284)aAt>aGt	p.N428S	GALNT11_ENST00000452146.2_Missense_Mutation_p.N347S|GALNT11_ENST00000320311.2_Missense_Mutation_p.N428S|GALNT11_ENST00000430044.2_Missense_Mutation_p.N428S			Q8NCW6	GLT11_HUMAN	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)	428						Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	p.N428S(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		AGCTATGGCAATATCAGTGAG	0.348000													104	238					0	0	0.870114	0	0
CRMP1	1400	broad.mit.edu	37	4	5837779	5837779	+	Missense_Mutation	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr4:5837779C>T	ENST00000324989.7	-	11	1574	c.1486G>A	c.(1486-1488)Gct>Act	p.A496T	CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Missense_Mutation_p.A380T|CRMP1_ENST00000397890.2_Missense_Mutation_p.A382T	NM_001014809.1	NP_001014809.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	382					axon guidance|pyrimidine base catabolic process	cytosol|microtubule organizing center|spindle	dihydropyrimidinase activity|protein binding	p.A496T(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CTGGTGACAGCGACAAACTGG	0.567000													77	143					0	0	0.870114	0	0
CCDC85A	114800	broad.mit.edu	37	2	56603059	56603059	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:56603059C>A	ENST00000407595.2	+	5	2063	c.1561C>A	c.(1561-1563)Cat>Aat	p.H521N	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	521								p.H521N(1)		breast(6)|cervix(2)|endometrium(5)|kidney(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)	38			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			ACCTGTGGTACATTCTCTTAA	0.498000													32	60					1.836e-18	2.3256e-18	0.788014	1	0
PHF20	51230	broad.mit.edu	37	20	34389529	34389529	+	Splice_Site	SNP	T	T	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr20:34389529T>G	ENST00000374012.3	+	2	212		c.e2+2		PHF20_ENST00000481202.1_Splice_Site|PHF20_ENST00000439301.1_Splice_Site			Q9BVI0	PHF20_HUMAN	PHD finger protein 20						regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding	p.?(1)		breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					AAAAAACTGGTACTTTTACAT	0.413000													4	74					0	0	0.150653	0	0
CUBN	8029	broad.mit.edu	37	10	17032435	17032435	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr10:17032435C>T	ENST00000377833.4	-	29	4313	c.4248G>A	c.(4246-4248)gaG>gaA	p.E1416E		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1416	CUB 9.				cholesterol metabolic process|cobalamin transport|hormone biosynthetic process|lipoprotein metabolic process|receptor-mediated endocytosis|tissue homeostasis|vitamin D metabolic process	brush border membrane|cytosol|endosome membrane|extrinsic to external side of plasma membrane|lysosomal lumen|lysosomal membrane	calcium ion binding|cobalamin binding|protein homodimerization activity|receptor activity|transporter activity	p.E1416E(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ACCAGATACACTCCTTGTTTG	0.517000													13	147					0	0	0.435327	0	0
TLK1	9874	broad.mit.edu	37	2	171862701	171862701	+	Silent	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:171862701A>G	ENST00000442919.2	-	18	2331	c.1716T>C	c.(1714-1716)ggT>ggC	p.G572G	TLK1_ENST00000521943.1_Silent_p.G572G|TLK1_ENST00000360843.3_Silent_p.G641G|TLK1_ENST00000431350.2_Silent_p.G620G|TLK1_ENST00000434911.2_Silent_p.G524G	NM_012290.4	NP_036422.3	Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	620	Protein kinase.				cell cycle|chromatin modification|intracellular protein transport|intracellular signal transduction|regulation of chromatin assembly or disassembly|response to DNA damage stimulus	nucleus	ATP binding|protein binding|protein serine/threonine kinase activity	p.G572G(2)|p.G620G(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TTCCATCTACACCATAGCTAT	0.398000													15	213					0	0	0.520397	0	0
AC024560.3	0	broad.mit.edu	37	3	197348668	197348668	+	RNA	SNP	C	C	G	rs79940815	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:197348668C>G	ENST00000418868.1	-	0	591					NR_003266.2																						ACTTGAGGCTCTGTCCACCAA	0.488000													4	194					0	0	0.150653	0	0
USP19	10869	broad.mit.edu	37	3	49147711	49147711	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:49147711C>A	ENST00000453664.1	-	26	4226	c.3908G>T	c.(3907-3909)cGc>cTc	p.R1303L	USP19_ENST00000434032.2_Missense_Mutation_p.R1313L|USP19_ENST00000417901.1_Missense_Mutation_p.R1315L|USP19_ENST00000398888.2_Missense_Mutation_p.R1212L|USP19_ENST00000398892.3_Missense_Mutation_p.R1252L|USP19_ENST00000398896.1_Missense_Mutation_p.R1020L|USP19_ENST00000398898.2_Missense_Mutation_p.R1252L	NM_001199161.1|NM_001199162.1	NP_001186090.1|NP_001186091.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1212					ER-associated protein catabolic process|positive regulation of cell cycle process|protein deubiquitination|regulation of protein stability|response to endoplasmic reticulum stress|skeletal muscle atrophy	endoplasmic reticulum membrane|integral to membrane	ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding	p.R1300L(1)		NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		GTTCCGCCGGCGGTAGAAGAG	0.617000													3	103					0.115264	0.123035	0.115264	1	0
USP12	219333	broad.mit.edu	37	13	27649444	27649444	+	Silent	SNP	T	T	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr13:27649444T>A	ENST00000282344.6	-	7	1072	c.816A>T	c.(814-816)acA>acT	p.T272T		NM_182488.3	NP_872294.2	O75317	UBP12_HUMAN	ubiquitin specific peptidase 12	272					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity	p.T272T(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Lung SC(185;0.0161)		all cancers(112;0.0508)|GBM - Glioblastoma multiforme(144;0.168)|Epithelial(112;0.244)|OV - Ovarian serous cystadenocarcinoma(117;0.246)		AAGAGAGTTTTGTATATCGAT	0.358000													42	61					0	0	0.819951	0	0
DHX40	79665	broad.mit.edu	37	17	57679935	57679935	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:57679935G>A	ENST00000451169.2	+	18	2074	c.1715G>A	c.(1714-1716)cGa>cAa	p.R572Q	DHX40_ENST00000425628.3_Missense_Mutation_p.R543Q|DHX40_ENST00000251241.4_Missense_Mutation_p.R620Q			Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	620							ATP binding|ATP-dependent helicase activity|nucleic acid binding	p.R620Q(3)		endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					GAAGTACTACGAAGATGTCTT	0.338000													50	109					0	0	0.870114	0	0
TRPM6	140803	broad.mit.edu	37	9	77448983	77448983	+	Missense_Mutation	SNP	T	T	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr9:77448983T>G	ENST00000451710.3	-	6	837	c.600A>C	c.(598-600)agA>agC	p.R200S	TRPM6_ENST00000359047.2_Missense_Mutation_p.R200S|TRPM6_ENST00000376872.3_Missense_Mutation_p.R200S|TRPM6_ENST00000449912.2_Missense_Mutation_p.R195S|TRPM6_ENST00000376864.4_Missense_Mutation_p.R200S|TRPM6_ENST00000376871.3_Missense_Mutation_p.R200S|TRPM6_ENST00000361255.3_Missense_Mutation_p.R195S|TRPM6_ENST00000360774.1_Missense_Mutation_p.R200S			Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	200					response to toxin	integral to membrane	ATP binding|calcium channel activity|metal ion binding|protein binding|protein serine/threonine kinase activity	p.R200S(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TCCAGATTTTTCTCAAGGAAT	0.403000													12	186					0	0	0.387290	0	0
TTLL3	26140	broad.mit.edu	37	3	9870957	9870957	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:9870957C>A	ENST00000383827.1	+	4	3077	c.796C>A	c.(796-798)Ccc>Acc	p.P266T	ARPC4-TTLL3_ENST00000397256.1_Missense_Mutation_p.P539T|TTLL3_ENST00000547186.1_Missense_Mutation_p.P478T|TTLL3_ENST00000426895.4_Missense_Mutation_p.P621T|TTLL3_ENST00000455274.1_Missense_Mutation_p.P266T|TTLL3_ENST00000466245.1_3'UTR|TTLL3_ENST00000397241.1_Missense_Mutation_p.P266T|TTLL3_ENST00000430793.1_Missense_Mutation_p.P266T|TTLL3_ENST00000427853.3_Missense_Mutation_p.P266T			Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	478	TTL.				axoneme assembly|cilium assembly|protein polyglycylation	cilium axoneme|cytoplasm|microtubule	protein-glycine ligase activity, initiating|tubulin-tyrosine ligase activity	p.P478T(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					CACGATGGCACCCTCCACAGC	0.622000													59	91					1.08141e-31	1.42685e-31	0.870114	1	0
MARK3	4140	broad.mit.edu	37	14	103918266	103918266	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:103918266G>A	ENST00000429436.2	+	5	868	c.358G>A	c.(358-360)Gaa>Aaa	p.E120K	MARK3_ENST00000553942.1_Missense_Mutation_p.E120K|MARK3_ENST00000416682.2_Missense_Mutation_p.E120K|MARK3_ENST00000561071.1_3'UTR|MARK3_ENST00000335102.5_Missense_Mutation_p.E120K|MARK3_ENST00000303622.9_Missense_Mutation_p.E120K|MARK3_ENST00000440884.3_Missense_Mutation_p.E120K|MARK3_ENST00000216288.7_Missense_Mutation_p.E120K	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	120	Protein kinase.						ATP binding|protein binding|protein serine/threonine kinase activity	p.E120K(4)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			GAAGTTATTCGAAGTCATTGA	0.353000													26	337					0	0	0.693898	0	0
A1BG	1	broad.mit.edu	37	19	58863782	58863782	+	Silent	SNP	C	C	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr19:58863782C>T	ENST00000263100.3	-	4	541	c.480G>A	c.(478-480)gaG>gaA	p.E160E	A1BG-AS1_ENST00000595302.1_RNA|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000599728.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA	NM_130786.3	NP_570602.2	P04217	A1BG_HUMAN	alpha-1-B glycoprotein	160	Ig-like V-type 2.					extracellular region		p.E160E(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|prostate(2)	15		all_cancers(17;3.04e-16)|all_epithelial(17;7.77e-12)|Lung NSC(17;3.25e-05)|Colorectal(82;5.46e-05)|all_lung(17;0.000129)|all_neural(62;0.0182)|Ovarian(87;0.0443)|Breast(46;0.0889)|Renal(17;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0269)		CCTCAGGCACCTCCAGAAACT	0.627000													12	207					0	0	0.435327	0	0
METTL25	84190	broad.mit.edu	37	12	82792603	82792603	+	Nonsense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:82792603C>A	ENST00000248306.3	+	4	630	c.561C>A	c.(559-561)taC>taA	p.Y187*	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2			methyltransferase like 25									p.Y187*(1)									GTAAAGGCTACCTAAGCTCTT	0.318000													6	103					0.0293803	0.032082	0.248553	1	0
SACM1L	22908	broad.mit.edu	37	3	45761023	45761023	+	Silent	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:45761023A>G	ENST00000389061.5	+	8	813	c.609A>G	c.(607-609)ggA>ggG	p.G203G	SACM1L_ENST00000541314.1_Silent_p.G142G|SACM1L_ENST00000418611.1_Silent_p.G100G	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	203	SAC.					Golgi apparatus		p.G203G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		CTATTAATGGAAAATACTTTG	0.338000													6	77					0	0	0.248553	0	0
TJP1	7082	broad.mit.edu	37	15	30025006	30025006	+	Missense_Mutation	SNP	C	C	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr15:30025006C>A	ENST00000346128.6	-	14	2224	c.1750G>T	c.(1750-1752)Gcc>Tcc	p.A584S	TJP1_ENST00000356107.6_Missense_Mutation_p.A584S|TJP1_ENST00000400011.2_Missense_Mutation_p.A588S|TJP1_ENST00000545208.2_Missense_Mutation_p.A584S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	584	SH3.				cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction		p.A584S(1)		breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		TGTACACTGGCTAGCTGCTCA	0.403000													40	45					7.63091e-17	9.53864e-17	0.834066	1	0
AC024560.3	0	broad.mit.edu	37	3	197348674	197348674	+	RNA	SNP	A	A	G	rs144273946	by1000genomes	TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:197348674A>G	ENST00000418868.1	-	0	585					NR_003266.2																						GGCTCTGTCCACCAAATGCAC	0.478000													5	203					0	0	0.184627	0	0
ENPP7	339221	broad.mit.edu	37	17	77711840	77711840	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:77711840G>A	ENST00000328313.5	+	5	1593	c.1372G>A	c.(1372-1374)Gca>Aca	p.A458T		NM_178543.3	NP_848638.2	Q6UWV6	ENPP7_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 7	458					negative regulation of cell proliferation|negative regulation of DNA replication|sphingomyelin metabolic process	Golgi apparatus|integral to membrane|microvillus	sphingomyelin phosphodiesterase activity	p.A458T(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(6)|skin(3)	34			OV - Ovarian serous cystadenocarcinoma(97;0.016)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GTCTGAGGTCGCATAACGCCC	0.642000													4	117					0	0	0.184627	0	0
TECPR2	9895	broad.mit.edu	37	14	102891314	102891314	+	Splice_Site	SNP	A	A	T			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:102891314A>T	ENST00000359520.7	+	6	864		c.e6-1		TECPR2_ENST00000558678.1_Splice_Site|TECPR2_ENST00000561228.1_Intron	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2								protein binding	p.?(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						TTCTAATTTTAGTACTGGGAA	0.383000													4	137					0	0	0.150653	0	0
SGOL2	151246	broad.mit.edu	37	2	201436396	201436396	+	Missense_Mutation	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr2:201436396A>G	ENST00000357799.4	+	7	1425	c.1327A>G	c.(1327-1329)Agg>Ggg	p.R443G		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	443					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding	p.R443G(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						GGATGGCAAAAGGGGTGCAGA	0.398000													3	263					0	0	0.150653	0	0
DAK	26007	broad.mit.edu	37	11	61111398	61111398	+	Silent	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr11:61111398G>A	ENST00000394900.3	+	12	1282	c.1053G>A	c.(1051-1053)cgG>cgA	p.R351R		NM_015533.3	NP_056348.2	Q3LXA3	DHAK_HUMAN	dihydroxyacetone kinase 2 homolog (S. cerevisiae)	351					glycerol metabolic process	cytosol	ATP binding|FAD-AMP lyase (cyclizing) activity|glycerone kinase activity|metal ion binding	p.R351R(1)		NS(1)|breast(3)|endometrium(3)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	23						AGCGGAGCCGGGTAGCCCCTG	0.602000													6	85					0	0	0.278610	0	0
ARHGAP11B	89839	broad.mit.edu	37	15	30925726	30925726	+	Missense_Mutation	SNP	A	A	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr15:30925726A>C	ENST00000428041.2	+	3	379	c.234A>C	c.(232-234)gaA>gaC	p.E78D		NM_001039841.1	NP_001034930.1	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	78	Rho-GAP.				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	p.E78D(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		CTTTAGAAGAACATATTCATA	0.373000													4	186					0	0	0.150653	0	0
PITPNC1	26207	broad.mit.edu	37	17	65688807	65688807	+	Missense_Mutation	SNP	G	G	A			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:65688807G>A	ENST00000335257.6	+	9	1149	c.802G>A	c.(802-804)Gtc>Atc	p.V268I	PITPNC1_ENST00000581322.1_Missense_Mutation_p.V268I|PITPNC1_ENST00000299954.9_3'UTR|PITPNC1_ENST00000580974.1_3'UTR			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1	268					signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding	p.V268I(2)		breast(1)|kidney(2)|large_intestine(3)|liver(2)|lung(4)|prostate(2)|skin(3)	17	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			GCCTTCTTCCGTCCGCAGTGC	0.557000													34	153					0	0	0.769981	0	0
ABCB4	5244	broad.mit.edu	37	7	87082328	87082328	+	Silent	SNP	A	A	G			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:87082328A>G	ENST00000265723.4	-	6	579	c.468T>C	c.(466-468)gcT>gcC	p.A156A	ABCB4_ENST00000359206.3_Silent_p.A156A|ABCB4_ENST00000358400.3_Silent_p.A156A|ABCB4_ENST00000545634.1_Silent_p.A156A|ABCB4_ENST00000453593.1_Silent_p.A156A	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	156	ABC transmembrane type-1 1.				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity	p.A156A(1)		breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)					GTCGTAGAATAGCATGAAAAA	0.413000													3	189					0	0	0.115264	0	0
GBP2	2634	broad.mit.edu	37	1	89587611	89587611	+	Silent	SNP	G	G	C			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr1:89587611G>C	ENST00000370466.3	-	2	307	c.39C>G	c.(37-39)ctC>ctG	p.L13L		NM_004120.3	NP_004111.2	P32456	GBP2_HUMAN	guanylate binding protein 2, interferon-inducible	13					interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity	p.L13L(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(1)	20		Lung NSC(277;0.0908)		all cancers(265;0.0151)|Epithelial(280;0.0284)		TGTTATCAATGAGGCTCATTG	0.498000													5	252					0	0	0.184627	0	0
CTNNB1	1499	broad.mit.edu	37	3	41266136	41266136	+	Missense_Mutation	SNP	T	T	C	rs121913407		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:41266136T>C	ENST00000349496.5	+	3	413	c.133T>C	c.(133-135)Tct>Cct	p.S45P	CTNNB1_ENST00000396185.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S45P|CTNNB1_ENST00000453024.1_Missense_Mutation_p.S38P|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S45P	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	45			Missing (in colorectal cancer).|S -> F (in hepatocellular carcinoma).|S -> P (in hepatocellular carcinoma).		adherens junction assembly|androgen receptor signaling pathway|branching involved in ureteric bud morphogenesis|canonical Wnt receptor signaling pathway involved in negative regulation of apoptosis|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell-cell adhesion|cell-matrix adhesion|cellular component disassembly involved in apoptosis|cellular response to growth factor stimulus|cellular response to indole-3-methanol|central nervous system vasculogenesis|cytoskeletal anchoring at plasma membrane|determination of dorsal/ventral asymmetry|dorsal/ventral axis specification|ectoderm development|embryonic axis specification|embryonic foregut morphogenesis|embryonic leg joint morphogenesis|endodermal cell fate commitment|endothelial tube morphogenesis|epithelial to mesenchymal transition|gastrulation with mouth forming second|glial cell fate determination|hair follicle morphogenesis|hair follicle placode formation|hindbrain development|liver development|lung cell differentiation|lung induction|lung-associated mesenchyme development|male genitalia development|mesenchymal cell proliferation involved in lung development|mesenchymal to epithelial transition involved in metanephros morphogenesis|negative regulation of cell proliferation|negative regulation of chondrocyte differentiation|negative regulation of heart induction by canonical Wnt receptor signaling pathway|negative regulation of osteoclast differentiation|negative regulation of transcription from RNA polymerase II promoter|nephron tubule formation|odontogenesis of dentine-containing tooth|oocyte development|pancreas development|positive regulation of anti-apoptosis|positive regulation of apoptosis|positive regulation of branching involved in lung morphogenesis|positive regulation of epithelial cell proliferation involved in prostate gland development|positive regulation of fibroblast growth factor receptor signaling pathway|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of muscle cell differentiation|positive regulation of osteoblast differentiation|positive regulation of transcription from RNA polymerase II promoter|protein localization at cell surface|proximal/distal pattern formation|regulation of angiogenesis|regulation of calcium ion import|regulation of centriole-centriole cohesion|regulation of centromeric sister chromatid cohesion|regulation of fibroblast proliferation|regulation of nephron tubule epithelial cell differentiation|regulation of protein localization at cell surface|regulation of smooth muscle cell proliferation|regulation of T cell proliferation|renal inner medulla development|renal outer medulla development|renal vesicle formation|response to drug|response to estradiol stimulus|Schwann cell proliferation|smooth muscle cell differentiation|synapse organization|synaptic vesicle transport|T cell differentiation in thymus|thymus development|trachea formation	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin-TCF7L2 complex|catenin complex|cell cortex|cell-substrate adherens junction|centrosome|dendritic shaft|desmosome|fascia adherens|internal side of plasma membrane|lamellipodium|lateral plasma membrane|microvillus membrane|perinuclear region of cytoplasm|protein-DNA complex|synapse|transcription factor complex|Z disc|zonula adherens	alpha-catenin binding|androgen receptor binding|cadherin binding|estrogen receptor binding|I-SMAD binding|ion channel binding|protein binding|protein C-terminus binding|protein kinase binding|protein phosphatase binding|R-SMAD binding|RPTP-like protein binding|signal transducer activity|specific RNA polymerase II transcription factor activity|structural molecule activity|transcription coactivator activity|transcription regulatory region DNA binding	p.S45P(168)|p.A5_A80del(53)|p.S45del(50)|p.S45A(11)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.W25_I140del(3)|p.T3_A126del(2)|p.D32_S47del(2)|p.P44_S45del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.S45_G48del(1)|p.Q28_Q61del(1)|p.T41_N51del(1)|p.M1_A87del(1)|p.S45_L46del(1)|p.A20_N141del(1)|p.D11_Y142>H(1)|p.P44_N51del(1)|p.I35_K170del(1)|p.Y30_A97del(1)|p.T42_G48del(1)|p.S45_D58del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.T40_L46del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.H24_M131del(1)|p.S45E(1)|p.M8_A80del(1)|p.A5_E54del(1)|p.S45T(1)|p.A21_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.A20_S111del(1)|p.T42_K49>Q(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)	Lithium(DB01356)	CACAGCTCCTTCTCTGAGTGG	0.502000		15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of				5	105					0	0	0.184627	0	0
ENTPD3-AS1	0	broad.mit.edu	37	3	40418607	40418610	+	RNA	DEL	AGGA	AGGA	-	rs112497421		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr3:40418607_40418610delAGGA	ENST00000439293.1	-	0	143																											ggagggagggaggaaggaaggaag	0.554													3	5	---	---	---	---					
RP3-433F14.3	0	broad.mit.edu	37	6	92356678	92356679	+	RNA	DEL	AA	AA	-	rs56890015		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr6:92356678_92356679delAA	ENST00000437768.1	-	0	263																											aattttagccAAAAAAAAAAAA	0.337													5	6	---	---	---	---					
KMT2C	58508	broad.mit.edu	37	7	151853293	151853293	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151853293delC	ENST00000355193.2	-	46	12198	c.11980delG	c.(11980-11982)aafs	p.E3994fs	KMT2C_ENST00000262189.6_Frame_Shift_Del_p.E3937fs					lysine (K)-specific methyltransferase 2C																		ATCATACCTTCATGGCTCACT	0.438													22	271	---	---	---	---					
KMT2C	58508	broad.mit.edu	37	7	151859486	151859487	+	Frame_Shift_Ins	INS	-	-	TT			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151859486_151859487insTT	ENST00000355193.2	-	43	11393_11394	c.11175_11176insAA	c.(11173-11178)acagtcfs	p.V3726fs	KMT2C_ENST00000262189.6_Frame_Shift_Ins_p.V3726fs					lysine (K)-specific methyltransferase 2C																		GGGCAGGACTCTGTCTCAGCCT	0.480													196	453	---	---	---	---					
KMT2C	58508	broad.mit.edu	37	7	151873437	151873437	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr7:151873437delG	ENST00000355193.2	-	38	9319	c.9101delC	c.(9100-9102)ctfs	p.P3034fs	KMT2C_ENST00000262189.6_Frame_Shift_Del_p.P3034fs					lysine (K)-specific methyltransferase 2C																		TAATGTTTGAGGAATCATTAG	0.473													61	145	---	---	---	---					
DSCC1	79075	broad.mit.edu	37	8	120850633	120850638	+	In_Frame_Del	DEL	CACCAG	CACCAG	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr8:120850633_120850638delCACCAG	ENST00000313655.4	-	8	1148_1153	c.934_939delCTGGTG	c.(934-939)del	p.LV312del		NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	DNA replication and sister chromatid cohesion 1	312					DNA replication|maintenance of mitotic sister chromatid cohesion|post-translational protein acetylation|regulation of DNA replication	chromatin|chromosome, centromeric region|nucleoplasm	DNA binding|protein binding			NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|pancreas(1)	9	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AGTGTCTATCCACCAGCGCTAAACCC	0.364													47	170	---	---	---	---					
CYC1	1537	broad.mit.edu	37	8	145151373	145151373	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr8:145151373delA	ENST00000318911.4	+	4	660	c.587delA	c.(586-588)gcfs	p.D196fs		NM_001916.3	NP_001907.2	P08574	CY1_HUMAN	cytochrome c-1	196	Cytochrome c.				respiratory electron transport chain|transport	cell junction|integral to membrane|mitochondrial inner membrane|respiratory chain	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity|heme binding			endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(2)	15	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-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;3.38e-41)|Epithelial(56;8.71e-40)|all cancers(56;3e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TTGCCCCCTGACCTCAGCTAC	0.577											OREG0019052	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	20	145	---	---	---	---					
C9orf84	158401	broad.mit.edu	37	9	114489999	114490000	+	Frame_Shift_Ins	INS	-	-	CCAAA			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr9:114489999_114490000insCCAAA	ENST00000394779.3	-	9	1682_1683	c.1438_1439insTTTGG	c.(1438-1440)cctfs	p.P480fs	C9orf84_ENST00000394777.4_Frame_Shift_Ins_p.P480fs|C9orf84_ENST00000318737.4_Frame_Shift_Ins_p.P519fs|C9orf84_ENST00000374287.3_Frame_Shift_Ins_p.P519fs	NM_001080551.1	NP_001074020.1	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	519										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GCTCAAAAGGTCCAAATCATTC	0.332													22	326	---	---	---	---					
CDKN1B	1027	broad.mit.edu	37	12	12870803	12870803	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:12870803delC	ENST00000228872.4	+	1	746	c.30delC	c.(28-30)agfs	p.S10fs	CDKN1B_ENST00000396340.1_Frame_Shift_Del_p.S10fs|CDKN1B_ENST00000477087.1_Intron	NM_004064.3	NP_004055.1	P46527	CDN1B_HUMAN	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	10					autophagic cell death|cell cycle arrest|cellular response to lithium ion|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of transcription, DNA-dependent|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|positive regulation of protein catabolic process|S phase of mitotic cell cycle	cytosol|endosome|nucleoplasm	cyclin-dependent protein kinase inhibitor activity|protein phosphatase binding|transforming growth factor beta receptor, cytoplasmic mediator activity			breast(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(5)	13		Prostate(47;0.0322)|all_epithelial(100;0.159)		BRCA - Breast invasive adenocarcinoma(232;0.0336)		CTAACGGGAGCCCTAGCCTGG	0.607													10	77	---	---	---	---					
ARID2	196528	broad.mit.edu	37	12	46246234	46246241	+	Frame_Shift_Del	DEL	GTGGTACT	GTGGTACT	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr12:46246234_46246241delGTGGTACT	ENST00000334344.6	+	15	4500_4507	c.4328_4335delGTGGTACT	c.(4327-4335)afs	p.SGT1443fs	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_Frame_Shift_Del_p.SGT51fs|ARID2_ENST00000444670.1_Frame_Shift_Del_p.SGT1053fs|ARID2_ENST00000422737.1_Frame_Shift_Del_p.SGT1294fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1443					chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CAGCAATTTAGTGGTACTGATTTGCTTA	0.418			"""N, S, F"""		hepatocellular carcinoma								67	315	---	---	---	---					
RP11-116N8.1	0	broad.mit.edu	37	14	36463290	36463291	+	RNA	INS	-	-	TCCT	rs71124732		TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr14:36463290_36463291insTCCT	ENST00000550089.1	+	0	242																											GACCATATTTAtccttccttcc	0.366													3	3	---	---	---	---					
CCDC144NL	339184	broad.mit.edu	37	17	20768756	20768756	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CH-5752-01A-11D-1576-08	TCGA-CH-5752-10A-01D-1576-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	f691ec8f-d3dd-4385-bc02-c29254d37c37	12e9a8b5-35d2-401b-aa04-653ab14c2331	g.chr17:20768756delT	ENST00000327925.5	-	4	757	c.638delA	c.(637-639)agfs	p.K213fs	CCDC144NL_ENST00000539484.1_5'UTR	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	213										large_intestine(3)|lung(3)|skin(1)	7						CACATGATTCTTCCCCTTTCT	0.368													7	162	---	---	---	---					
