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
FLG	2312	broad.mit.edu	37	1	152280684	152280684	+	Silent	SNP	G	G	C			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr1:152280684G>C	ENST00000368799.1	-	3	6713	c.6678C>G	c.(6676-6678)ggC>ggG	p.G2226G	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2226	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATTGTCCCTGGCCCACCAGTG	0.562									Ichthyosis				24	121	---	---	---	---
CCRL2	9034	broad.mit.edu	37	3	46450522	46450522	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr3:46450522C>T	ENST00000399036.3	+	2	1304	c.952C>T	c.(952-954)Cgt>Tgt	p.R318C	CCRL2_ENST00000357392.4_Missense_Mutation_p.R330C|CCRL2_ENST00000400882.2_Missense_Mutation_p.R318C|CCRL2_ENST00000400880.3_Missense_Mutation_p.R318C	NM_003965.4	NP_003956.2	O00421	CCRL2_HUMAN	chemokine (C-C motif) receptor-like 2						chemotaxis|inflammatory response	integral to plasma membrane	CCR chemokine receptor binding|chemokine receptor activity			lung(3)|ovary(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)		TTTCCATCTGCGTAGTAACAC	0.512													25	77	---	---	---	---
DPPA2	151871	broad.mit.edu	37	3	109031399	109031399	+	Silent	SNP	G	G	A			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr3:109031399G>A	ENST00000478945.1	-	3	420	c.174C>T	c.(172-174)taC>taT	p.Y58Y		NM_138815.3	NP_620170.3	Q7Z7J5	DPPA2_HUMAN	developmental pluripotency associated 2	58						nucleus	nucleic acid binding			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TACCTGGATTGTATTTCTTAG	0.413													12	78	---	---	---	---
FER	2241	broad.mit.edu	37	5	108382846	108382846	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr5:108382846T>C	ENST00000281092.4	+	16	2255	c.1871T>C	c.(1870-1872)aTa>aCa	p.I624T	FER_ENST00000438717.2_Missense_Mutation_p.I449T	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	624	Protein kinase.				intracellular signal transduction|peptidyl-tyrosine phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		GTCAAACTTATAGGAGTTTGC	0.313													5	43	---	---	---	---
PPP1R16A	84988	broad.mit.edu	37	8	145726591	145726591	+	Nonsense_Mutation	SNP	C	C	T			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr8:145726591C>T	ENST00000292539.4	+	10	2034	c.1117C>T	c.(1117-1119)Caa>Taa	p.Q373*	PPP1R16A_ENST00000435887.1_Nonsense_Mutation_p.Q373*			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	373						plasma membrane	protein binding			NS(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CATCGTGTGGCAACAGCCGCC	0.716													3	10	---	---	---	---
FANCF	2188	broad.mit.edu	37	11	22647295	22647295	+	Missense_Mutation	SNP	G	G	C			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr11:22647295G>C	ENST00000327470.3	-	1	92	c.62C>G	c.(61-63)aCc>aGc	p.T21S	AC103801.2_ENST00000428556.2_3'UTR	NM_022725.3	NP_073562.1	Q9NPI8	FANCF_HUMAN	Fanconi anemia, complementation group F	21					DNA repair	nucleoplasm	protein binding			kidney(3)|large_intestine(3)|lung(6)|skin(1)	13						GCTGACGTAGGTAGTGCTTGA	0.637			"""N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				8	15	---	---	---	---
PAMR1	25891	broad.mit.edu	37	11	35456159	35456159	+	Silent	SNP	C	C	G			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr11:35456159C>G	ENST00000378880.2	-	10	1972	c.1527G>C	c.(1525-1527)ctG>ctC	p.L509L	PAMR1_ENST00000378878.3_Silent_p.L398L|PAMR1_ENST00000278360.3_Silent_p.L526L|PAMR1_ENST00000532848.1_Silent_p.L469L	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	509	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						TGACCTTCCCCAGGTCAGTAA	0.557													15	48	---	---	---	---
FAM181B	220382	broad.mit.edu	37	11	82443541	82443541	+	Missense_Mutation	SNP	C	C	T			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr11:82443541C>T	ENST00000329203.3	-	1	1365	c.1231G>A	c.(1231-1233)Gac>Aac	p.D411N		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	411										large_intestine(1)|lung(2)|prostate(1)	4						CAAACCCCGTCGGATCTCCAA	0.692													3	14	---	---	---	---
SLC2A13	114134	broad.mit.edu	37	12	40158559	40158559	+	Missense_Mutation	SNP	T	T	C			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr12:40158559T>C	ENST00000280871.4	-	8	1597	c.1547A>G	c.(1546-1548)tAt>tGt	p.Y516C		NM_052885.3	NP_443117.3	Q96QE2	MYCT_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 13	516						integral to membrane|plasma membrane	myo-inositol:hydrogen symporter activity			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	29		Lung NSC(34;0.105)|all_lung(34;0.123)				GAAGACAAGATATAAAATAAG	0.333										HNSCC(50;0.14)			7	38	---	---	---	---
LRP1	4035	broad.mit.edu	37	12	57593708	57593708	+	Missense_Mutation	SNP	G	G	A			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr12:57593708G>A	ENST00000243077.3	+	62	10380	c.9914G>A	c.(9913-9915)tGc>tAc	p.C3305Y		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3305	EGF-like 13.				aorta morphogenesis|apoptotic cell clearance|negative regulation of platelet-derived growth factor receptor-beta signaling pathway|negative regulation of smooth muscle cell migration|negative regulation of Wnt receptor signaling pathway|positive regulation of cholesterol efflux|regulation of actin cytoskeleton organization|regulation of phospholipase A2 activity	coated pit|integral to plasma membrane|nucleus	apolipoprotein E binding|calcium ion binding|lipoprotein transporter activity|protein complex binding|receptor activity			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Becaplermin(DB00102)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AGCAACCTGTGCCTGCTGTCC	0.587													9	48	---	---	---	---
GAS2L3	283431	broad.mit.edu	37	12	101018420	101018420	+	Silent	SNP	C	C	T			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr12:101018420C>T	ENST00000537247.1	+	10	2479	c.1525C>T	c.(1525-1527)Ctg>Ttg	p.L509L	GAS2L3_ENST00000539410.1_Silent_p.L613L|GAS2L3_ENST00000547754.1_Silent_p.L613L|GAS2L3_ENST00000266754.5_Silent_p.L613L			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	613					cell cycle arrest					endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						CCGTACCCCACTGTCCATCGT	0.488													10	35	---	---	---	---
ALPK3	57538	broad.mit.edu	37	15	85402608	85402608	+	Nonsense_Mutation	SNP	G	G	T	rs142686791		TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr15:85402608G>T	ENST00000258888.5	+	7	4725	c.4558G>T	c.(4558-4560)Gag>Tag	p.E1520*		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1520	Ig-like 2.				heart development	nucleus	ATP binding|protein serine/threonine kinase activity			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CCCAGTGGGCGAGGTGGGCAG	0.552													8	34	---	---	---	---
SEMA3F	6405	broad.mit.edu	37	3	50225399	50225399	+	Frame_Shift_Del	DEL	C	C	-			TCGA-YL-A8HK-01A-11D-A364-08	TCGA-YL-A8HK-10A-01D-A362-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	61396ff0-5975-4cf6-9142-ce0349096ebc	002a3041-247d-4cf6-b81a-a4e04857e872	g.chr3:50225399delC	ENST00000002829.3	+	19	2693	c.2209delC	c.(2209-2211)ccafs	p.P737fs	SEMA3F_ENST00000413852.1_Frame_Shift_Del_p.P638fs|SEMA3F_ENST00000434342.1_Frame_Shift_Del_p.P706fs	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	737					axon guidance	extracellular space|membrane	chemorepellent activity|receptor activity			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		GCTGGCCCAGCCAGAAGTGGG	0.697													2	4	---	---	---	---
