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
SV2A	9900	broad.mit.edu	37	1	149884966	149884966	+	Missense_Mutation	SNP	T	T	C			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr1:149884966T>C	ENST00000369146.3	-	2	917	c.427A>G	c.(427-429)Aaa>Gaa	p.K143E	SV2A_ENST00000369145.1_Missense_Mutation_p.K143E	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	143					neurotransmitter transport	cell junction|endoplasmic reticulum|integral to membrane|synaptic vesicle membrane	transmembrane transporter activity			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	TCTCGTTCTTTCCGTCGTTGT	0.637													23	45	---	---	---	---
ZNF648	127665	broad.mit.edu	37	1	182025561	182025561	+	Nonsense_Mutation	SNP	C	C	A			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr1:182025561C>A	ENST00000339948.3	-	2	1792	c.1585G>T	c.(1585-1587)Gag>Tag	p.E529*		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	529					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)|endometrium(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						TAGGGCCTCTCTCCGTTGTGC	0.612													3	29	---	---	---	---
LCT	3938	broad.mit.edu	37	2	136570301	136570301	+	Silent	SNP	G	G	A			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr2:136570301G>A	ENST00000264162.2	-	7	1943	c.1933C>T	c.(1933-1935)Ctg>Ttg	p.L645L		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	645	4 X approximate repeats.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)		TGGGTCCTCAGGGTGGCTGGG	0.577													5	80	---	---	---	---
ILDR1	286676	broad.mit.edu	37	3	121724129	121724129	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr3:121724129C>T	ENST00000273691.3	-	3	446	c.341G>A	c.(340-342)gGg>gAg	p.G114E	ILDR1_ENST00000462014.1_Missense_Mutation_p.G126E|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000344209.5_Missense_Mutation_p.G114E|ILDR1_ENST00000393631.1_Missense_Mutation_p.G114E	NM_175924.3	NP_787120.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	114	Ig-like V-type.					cytosol|integral to membrane|plasma membrane	receptor activity			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		GTAATCTACCCCCAGCACGGG	0.642													3	32	---	---	---	---
LAMP3	27074	broad.mit.edu	37	3	182853620	182853620	+	Silent	SNP	C	C	T			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr3:182853620C>T	ENST00000265598.3	-	5	1257	c.1002G>A	c.(1000-1002)ggG>ggA	p.G334G	LAMP3_ENST00000466939.1_Silent_p.G310G	NM_014398.3	NP_055213.2	Q9UQV4	LAMP3_HUMAN	lysosomal-associated membrane protein 3	334					cell proliferation	integral to membrane|lysosomal membrane				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(9)|ovary(2)|prostate(2)	28	all_cancers(143;9.14e-14)|Ovarian(172;0.0355)		all cancers(12;2.91e-44)|Epithelial(37;5.52e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;4.16e-21)			TGAAGGAATGCCCGACTGCTG	0.468													5	383	---	---	---	---
FAT4	79633	broad.mit.edu	37	4	126372407	126372407	+	Missense_Mutation	SNP	G	G	C			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr4:126372407G>C	ENST00000394329.3	+	9	10249	c.10236G>C	c.(10234-10236)caG>caC	p.Q3412H	FAT4_ENST00000335110.5_Missense_Mutation_p.Q1710H	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3412	Cadherin 33.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						ACAGTGTGCAGATCAGTGAAG	0.463													83	90	---	---	---	---
PCDHGB1	56104	broad.mit.edu	37	5	140731932	140731932	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr5:140731932C>T	ENST00000523390.1	+	1	2105	c.2105C>T	c.(2104-2106)gCg>gTg	p.A702V	PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1														central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCTCCTCGCGGTGATTCTA	0.617													8	184	---	---	---	---
MUC17	140453	broad.mit.edu	37	7	100683689	100683689	+	Missense_Mutation	SNP	C	C	T			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr7:100683689C>T	ENST00000306151.4	+	3	9056	c.8992C>T	c.(8992-8994)Ccg>Tcg	p.P2998S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2998	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)					CAGCACCATGCCGGTGGCCAG	0.507													5	572	---	---	---	---
PDP1	54704	broad.mit.edu	37	8	94934399	94934399	+	Missense_Mutation	SNP	T	T	C			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr8:94934399T>C	ENST00000396200.3	+	3	463	c.187T>C	c.(187-189)Tac>Cac	p.Y63H	PDP1_ENST00000297598.4_Missense_Mutation_p.Y38H|PDP1_ENST00000520728.1_Missense_Mutation_p.Y38H|PDP1_ENST00000517764.1_Missense_Mutation_p.Y38H	NM_001161779.1	NP_001155251.1	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	38					pyruvate metabolic process|regulation of acetyl-CoA biosynthetic process from pyruvate	mitochondrial matrix|protein serine/threonine phosphatase complex	[pyruvate dehydrogenase (lipoamide)] phosphatase activity			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						TTCCTCATCGTACATTCCTCA	0.468													32	85	---	---	---	---
KIAA1429	25962	broad.mit.edu	37	8	95538772	95538772	+	Missense_Mutation	SNP	T	T	G			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr8:95538772T>G	ENST00000297591.5	-	8	1775	c.1700A>C	c.(1699-1701)aAa>aCa	p.K567T	KIAA1429_ENST00000437199.1_Missense_Mutation_p.K567T|KIAA1429_ENST00000421249.2_Missense_Mutation_p.K567T	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	567					mRNA processing|RNA splicing	nucleus				NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ACCAAGTCTTTTAATCTCTGA	0.418													202	123	---	---	---	---
DBH	1621	broad.mit.edu	37	9	136513016	136513016	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr9:136513016G>A	ENST00000393056.2	+	6	1085	c.1073G>A	c.(1072-1074)cGg>cAg	p.R358Q		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	358					hormone biosynthetic process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Dopamine(DB00988)|Vitamin C(DB00126)	GCCAAGCTGCGGCGCTTCAAC	0.607													21	33	---	---	---	---
RECQL	5965	broad.mit.edu	37	12	21626537	21626537	+	Silent	SNP	T	T	C			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr12:21626537T>C	ENST00000444129.2	-	12	1863	c.1395A>G	c.(1393-1395)gtA>gtG	p.V465V	RECQL_ENST00000421138.2_Silent_p.V465V	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ protein-like (DNA helicase Q1-like)	465					DNA recombination|DNA repair|DNA replication	nucleus	ATP binding|ATP-dependent 3'-5' DNA helicase activity|DNA strand annealing activity|protein binding			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						CTGAGTTCCATACTTCATCAA	0.323								Other identified genes with known or suspected DNA repair function					4	49	---	---	---	---
C15orf57	90416	broad.mit.edu	37	15	40855084	40855084	+	Missense_Mutation	SNP	A	A	C			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr15:40855084A>C	ENST00000358005.3	-	2	404	c.131T>G	c.(130-132)gTg>gGg	p.V44G	C15orf57_ENST00000558113.1_Missense_Mutation_p.V44G|C15orf57_ENST00000416810.2_Missense_Mutation_p.V44G|C15orf57_ENST00000559911.1_Missense_Mutation_p.V44G|C15orf57_ENST00000560109.1_5'UTR|C15orf57_ENST00000560305.1_Missense_Mutation_p.V44G|C15orf57_ENST00000558750.1_Missense_Mutation_p.V53G|C15orf57_ENST00000561011.1_Missense_Mutation_p.V44G|C15orf57_ENST00000558871.1_Missense_Mutation_p.V44G	NM_001080791.1|NM_052849.2	NP_001074260.1|NP_443081.1	Q9BV29	CO057_HUMAN	chromosome 15 open reading frame 57	44										endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	9						GCAAGAATCCACAAAGGAGTC	0.512													24	233	---	---	---	---
CAPN3	825	broad.mit.edu	37	15	42681285	42681285	+	Silent	SNP	C	C	T			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr15:42681285C>T	ENST00000397163.3	+	5	1011	c.792C>T	c.(790-792)tgC>tgT	p.C264C	CAPN3_ENST00000357568.3_Silent_p.C264C|CAPN3_ENST00000318023.7_Silent_p.C264C|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000356316.3_Silent_p.C177C|CAPN3_ENST00000349748.3_Silent_p.C264C	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	264	Calpain catalytic.				muscle organ development|proteolysis	cytoplasm	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity|signal transducer activity			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		TCATGGGCTGCTCCATTGATG	0.527													24	65	---	---	---	---
KMT2B	9757	broad.mit.edu	37	19	36211883	36211883	+	Missense_Mutation	SNP	G	G	A			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr19:36211883G>A	ENST00000222270.7	+	3	1634	c.1634G>A	c.(1633-1635)cGa>cAa	p.R545Q	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.R545Q|KMT2B_ENST00000341701.1_Intron	NM_014727.1	NP_055542.1			lysine (K)-specific methyltransferase 2B																		ACACCCCGGCGATTTATGGAT	0.587													7	8	---	---	---	---
HLA-DQA2	3118	broad.mit.edu	37	6	32712958	32712958	+	Frame_Shift_Del	DEL	T	T	-			TCGA-KK-A7AU-01A-11D-A32B-08	TCGA-KK-A7AU-11A-11D-A329-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ce4c568d-84ca-4819-a08b-7dca4ad7fc1a	f59ccc77-35be-4949-8994-517c407d30fd	g.chr6:32712958delT	ENST00000374940.3	+	2	207	c.105delT	c.(103-105)ggtfs	p.G35fs		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	35	Alpha-1.				antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|interferon-gamma-mediated signaling pathway|T cell costimulation|T cell receptor signaling pathway	endoplasmic reticulum membrane|endosome membrane|Golgi apparatus|integral to plasma membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	CCTCCTATGGTGTGAACTTCT	0.488													7	210	---	---	---	---
