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	Genome_Change	Annotation_Transcript	Transcript_Strand	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	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	DrugBank	i_ACHILLES_Top_Genes	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CCLE_SEQ_overlapping_mutations	i_CCLE_SEQ_total_mutations_in_gene	MUTSIG_Significant_Genes	OREGANNO_ID	OREGANNO_Values	i_tumor_f	i_init_t_lod	i_t_lod_fstar	i_t_alt_count	i_t_ref_count	i_normal_best_gt	i_failure_reasons	i_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	context_orig	context65	gene_name	newbase	categ	categ_ignoring_null_categ
TRPC6	7225	broad.mit.edu	36	11	100829014	100829014	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:100829014C>A	uc001pgk.2	-	c.2678G>T	c.(2677-2679)AGT>ATT	p.S893I	TRPC6_uc009ywy.1_Missense_Mutation_p.S777I	NM_004621	NP_004612	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel,	893	Cytoplasmic (Potential).				axon guidance|platelet activation|positive regulation of calcium ion transport via store-operated calcium channel activity	integral to membrane|plasma membrane	protein binding			ovary(1)|central_nervous_system(1)	2		Acute lymphoblastic leukemia(157;0.000918)|all_hematologic(158;0.0162)				Colon(166;1315 1927 11094 12848 34731)								0.577114	375.226181	376.269501	116	85	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;0.0442)	Missense_Mutation	SNP	100829014	100829014	17134	11	C	A	A	20	20	TRPC6	A	3	3
PHRF1	57661	broad.mit.edu	36	11	597393	597393	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:597393C>T	uc001lqe.1	+	c.1937C>T	c.(1936-1938)GCG>GTG	p.A646V	PHRF1_uc009ybz.1_Missense_Mutation_p.A436V|PHRF1_uc009yca.1_Non-coding_Transcript	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	646							RNA polymerase binding|zinc ion binding				0														0.254902	91.761148	100.096247	39	114	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	597393	597393	12285	11	C	T	T	27	27	PHRF1	T	1	1
FAT3	120114	broad.mit.edu	36	11	92171434	92171434	+	Silent	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:92171434C>T	uc001pdj.2	+	c.5607C>T	c.(5605-5607)GTC>GTT	p.V1869V		NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	1869	Cadherin 16.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)									TCGA Ovarian(4;0.039)			0.313725	39.980094	41.555844	16	35	CC		KEEP	---	---	---	---	capture			Silent	SNP	92171434	92171434	5927	11	C	T	T	29	29	FAT3	T	2	2
ANO2	57101	broad.mit.edu	36	12	5778978	5778978	+	Silent	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:5778978C>T	uc001qnm.1	-	c.1002G>A	c.(1000-1002)GCG>GCA	p.A334A		NM_020373	NP_065106	Q9NQ90	ANO2_HUMAN	anoctamin 2	338	Cytoplasmic (Potential).					chloride channel complex|plasma membrane	intracellular calcium activated chloride channel activity			ovary(4)|large_intestine(2)|central_nervous_system(1)	7														0.283019	40.303882	42.544387	15	38	CC		KEEP	---	---	---	---	capture			Silent	SNP	5778978	5778978	705	12	C	T	T	27	27	ANO2	T	1	1
LECT1	11061	broad.mit.edu	36	13	52205444	52205444	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2499-01	TCGA-28-2499-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:52205444A>G	uc001vhf.1	-	c.265T>C	c.(265-267)TCA>CCA	p.S89P	LECT1_uc001vhg.1_Missense_Mutation_p.S89P|LECT1_uc001vhh.1_Missense_Mutation_p.S116P	NM_007015	NP_008946	O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1 isoform 1	89					cartilage development|proteoglycan metabolic process	endomembrane system|extracellular region|integral to membrane				ovary(1)	1		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)												0.797468	467.733933	480.721689	126	32	AA		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(99;3.38e-08)	Missense_Mutation	SNP	52205444	52205444	9036	13	A	G	G	10	10	LECT1	G	4	4
TEP1	7011	broad.mit.edu	36	14	19921612	19921612	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:19921612G>C	uc001vxe.1	-	c.3742C>G	c.(3742-3744)CTG>GTG	p.L1248V	TEP1_uc010ahk.1_Missense_Mutation_p.L598V	NM_007110	NP_009041	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1248	NACHT.				telomere maintenance via recombination|telomere maintenance via telomerase	chromosome, telomeric region|cytoplasm|nuclear matrix|soluble fraction|telomerase holoenzyme complex	ATP binding|RNA binding			ovary(5)	5	all_cancers(95;0.00123)	all_lung(585;0.235)												0.4	9.195304	9.283451	4	6	GG		KEEP	---	---	---	---	capture	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)	Missense_Mutation	SNP	19921612	19921612	16286	14	G	C	C	34	34	TEP1	C	3	3
WDR72	256764	broad.mit.edu	36	15	51695666	51695666	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:51695666C>T	uc002acj.2	-	c.2029G>A	c.(2029-2031)GTT>ATT	p.V677I	WDR72_uc010bfi.1_Missense_Mutation_p.V677I	NM_182758	NP_877435	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	677										lung(1)	1														0.454545	91.344529	91.462968	30	36	CC		KEEP	---	---	---	---	capture		all cancers(107;0.0511)	Missense_Mutation	SNP	51695666	51695666	17895	15	C	T	T	19	19	WDR72	T	1	1
TLN2	83660	broad.mit.edu	36	15	60850613	60850613	+	Silent	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:60850613C>T	uc002alb.2	+	c.5355C>T	c.(5353-5355)GGC>GGT	p.G1785G	TLN2_uc002alc.2_Silent_p.G178G|TLN2_uc002ald.2_Silent_p.G178G	NM_015059	NP_055874	Q9Y4G6	TLN2_HUMAN	talin 2	1785					cell adhesion|cell-cell junction assembly|cytoskeletal anchoring at plasma membrane	actin cytoskeleton|cell-cell junction|cytoplasm|focal adhesion|ruffle|synapse	actin binding|insulin receptor binding|structural constituent of cytoskeleton			ovary(4)|breast(2)	6														0.4375	142.156241	142.537536	49	63	CC		KEEP	---	---	---	---	capture			Silent	SNP	60850613	60850613	16478	15	C	T	T	27	27	TLN2	T	1	1
TEKT5	146279	broad.mit.edu	36	16	10695784	10695784	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2499-01	TCGA-28-2499-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:10695784A>G	uc002czz.1	-	c.448T>C	c.(448-450)TTC>CTC	p.F150L		NM_144674	NP_653275	Q96M29	TEKT5_HUMAN	tektin 5	150	Potential.				microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2														0.413223	330.261806	331.851906	100	142	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10695784	10695784	16283	16	A	G	G	3	3	TEKT5	G	4	4
AXIN1	8312	broad.mit.edu	36	16	279567	279567	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:279567G>A	uc002cgp.1	-	c.2336C>T	c.(2335-2337)CCG>CTG	p.P779L	AXIN1_uc002cgq.1_Missense_Mutation_p.P743L	NM_003502	NP_003493	O15169	AXIN1_HUMAN	axin 1 isoform a	779	Interaction with PPP2CA.				activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|negative regulation of gene-specific transcription elongation from RNA polymerase II promoter|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	armadillo repeat domain binding|beta-catenin binding|GTPase activator activity|I-SMAD binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding			liver(1)	1		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)								659				0.43956	121.903153	122.189413	40	51	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	279567	279567	1257	16	G	A	A	39	39	AXIN1	A	1	1
RABEP2	79874	broad.mit.edu	36	16	28829999	28829999	+	Silent	SNP	G	C	C			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:28829999G>C	uc002drq.1	-	c.897C>G	c.(895-897)GGC>GGG	p.G299G	RABEP2_uc010byn.1_Intron|RABEP2_uc002drr.2_Silent_p.G299G	NM_024816	NP_079092	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	299	Potential.				endocytosis|protein transport	early endosome	growth factor activity|GTPase activator activity			ovary(1)|breast(1)	2						Pancreas(66;639 1284 10093 31061 49099)								0.3125	6.383757	6.939352	5	11	GG		KEEP	---	---	---	---	capture			Silent	SNP	28829999	28829999	13421	16	G	C	C	42	42	RABEP2	C	3	3
PKD1L2	114780	broad.mit.edu	36	16	79776638	79776638	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:79776638G>A	uc002fgh.1	-	c.1957C>T	c.(1957-1959)CTC>TTC	p.L653F	PKD1L2_uc002fgj.1_Missense_Mutation_p.L653F	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	653	REJ.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.282051	29.811469	31.474534	11	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79776638	79776638	12389	16	G	A	A	35	35	PKD1L2	A	2	2
SLC13A2	9058	broad.mit.edu	36	17	23846870	23846870	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:23846870C>T	uc002hbh.1	+	c.1379C>T	c.(1378-1380)GCC>GTC	p.A460V	SLC13A2_uc002hbi.1_Missense_Mutation_p.A389V	NM_003984	NP_003975	Q13183	S13A2_HUMAN	solute carrier family 13 (sodium-dependent	460	Helical; (Potential).					integral to plasma membrane|membrane fraction	low affinity sodium:dicarboxylate symporter activity				0	all_lung(13;0.000871)|Lung NSC(42;0.0027)				Succinic acid(DB00139)									0.455882	178.329131	178.559913	62	74	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (53;0.154)	Missense_Mutation	SNP	23846870	23846870	14887	17	C	T	T	26	26	SLC13A2	T	2	2
SCN4A	6329	broad.mit.edu	36	17	59382754	59382754	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2499-01	TCGA-28-2499-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:59382754T>C	uc002jds.1	-	c.2615A>G	c.(2614-2616)GAG>GGG	p.E872G		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	872					muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)									0.4	8.088516	8.178329	4	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59382754	59382754	14402	17	T	C	C	54	54	SCN4A	C	4	4
GPS1	2873	broad.mit.edu	36	17	77604502	77604502	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:77604502G>A	uc002kdk.1	+	c.217G>A	c.(217-219)GTC>ATC	p.V73I	RFNG_uc002kdh.1_5'Flank|RFNG_uc002kdj.1_5'Flank|GPS1_uc002kdl.1_Missense_Mutation_p.V33I|GPS1_uc010dij.1_Missense_Mutation_p.V73I|GPS1_uc002kdm.1_Missense_Mutation_p.V17I|GPS1_uc002kdn.1_Missense_Mutation_p.V33I|GPS1_uc002kdo.1_Missense_Mutation_p.V33I	NM_212492	NP_997657	Q13098	CSN1_HUMAN	G protein pathway suppressor 1 isoform 1	33					cell cycle|inactivation of MAPK activity|JNK cascade	cytoplasm|signalosome	GTPase inhibitor activity|protein binding			central_nervous_system(1)	1	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)													0.371429	37.381611	37.883588	13	22	GG		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)		Missense_Mutation	SNP	77604502	77604502	7008	17	G	A	A	40	40	GPS1	A	1	1
CALR	811	broad.mit.edu	36	19	12911871	12911871	+	Silent	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:12911871C>T	uc002mvu.1	+	c.402C>T	c.(400-402)CCC>CCT	p.P134P		NM_004343	NP_004334	P27797	CALR_HUMAN	calreticulin precursor	134	N-domain.				cell cycle arrest|cellular senescence|glucocorticoid receptor signaling pathway|negative regulation of neuron differentiation|negative regulation of retinoic acid receptor signaling pathway|negative regulation of steroid hormone receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|negative regulation of translation|peptide antigen assembly with MHC class I protein complex|positive regulation of cell cycle|positive regulation of cell proliferation|positive regulation of DNA replication|positive regulation of phagocytosis|post-translational protein modification|protein export from nucleus|protein maturation by protein folding|protein N-linked glycosylation via asparagine|protein stabilization|regulation of apoptosis|sequestering of calcium ion	cytosol|endoplasmic reticulum lumen|extracellular space|MHC class I peptide loading complex|nucleus|perinuclear region of cytoplasm|polysome|proteinaceous extracellular matrix	androgen receptor binding|calcium ion binding|chaperone binding|complement component C1q binding|DNA binding|integrin binding|mRNA binding|protein binding involved in protein folding|sugar binding|transcription repressor activity|ubiquitin protein ligase binding|unfolded protein binding|zinc ion binding			ovary(1)	1					Alteplase(DB00009)|Anistreplase(DB00029)|Antihemophilic Factor(DB00025)|Reteplase(DB00015)|Tenecteplase(DB00031)									0.45082	176.403164	176.661031	55	67	CC		KEEP	---	---	---	---	capture			Silent	SNP	12911871	12911871	2709	19	C	T	T	23	23	CALR	T	1	1
DAZAP1	26528	broad.mit.edu	36	19	1385835	1385835	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:1385835G>C	uc002lsn.1	+	c.1148G>C	c.(1147-1149)GGC>GCC	p.G383A	DAZAP1_uc002lsl.1_Missense_Mutation_p.G382A|DAZAP1_uc002lsm.1_3'UTR|DAZAP1_uc002lso.1_Missense_Mutation_p.G382A	NM_018959	NP_061832	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1 isoform b	383	Pro-rich.				cell differentiation|multicellular organismal development|spermatogenesis	cytoplasm|nucleus	nucleotide binding|RNA binding			breast(1)	1		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)												0.388889	9.154421	9.396294	7	11	GG		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	1385835	1385835	4415	19	G	C	C	42	42	DAZAP1	C	3	3
BRD4	23476	broad.mit.edu	36	19	15237255	15237255	+	Silent	SNP	C	G	G			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15237255C>G	uc002nar.1	-	c.759G>C	c.(757-759)GTG>GTC	p.V253V	BRD4_uc002nas.1_Silent_p.V253V|BRD4_uc002nat.2_Silent_p.V253V|BRD4_uc002nau.2_Silent_p.V253V	NM_058243	NP_490597	O60885	BRD4_HUMAN	bromodomain-containing protein 4 isoform long	253					interspecies interaction between organisms|positive regulation of G2/M transition of mitotic cell cycle|positive regulation of gene-specific transcription elongation from RNA polymerase II promoter|regulation of transcription involved in G1 phase of mitotic cell cycle	condensed nuclear chromosome|cytoplasm	protein binding			ovary(2)	2										269				0.333333	8.880488	9.46802	7	14	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)		Silent	SNP	15237255	15237255	1535	19	C	G	G	25	25	BRD4	G	3	3
COL5A3	50509	broad.mit.edu	36	19	9938029	9938029	+	Silent	SNP	T	C	C			TCGA-28-2499-01	TCGA-28-2499-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:9938029T>C	uc002mmq.1	-	c.4743A>G	c.(4741-4743)GGA>GGG	p.G1581G		NM_015719	NP_056534	P25940	CO5A3_HUMAN	collagen, type V, alpha 3 preproprotein	1581	Fibrillar collagen NC1.				collagen fibril organization|skin development	collagen type V	collagen binding|extracellular matrix structural constituent			ovary(7)|lung(1)|central_nervous_system(1)	9														0.333333	6.388531	6.687613	4	8	TT		KEEP	---	---	---	---	capture	Epithelial(33;7.11e-05)		Silent	SNP	9938029	9938029	3836	19	T	C	C	54	54	COL5A3	C	4	4
CTSS	1520	broad.mit.edu	36	1	148994192	148994192	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:148994192C>T	uc001evn.1	-	c.308G>A	c.(307-309)AGA>AAA	p.R103K	CTSS_uc001evo.1_Missense_Mutation_p.R103K	NM_004079	NP_004070	P25774	CATS_HUMAN	cathepsin S preproprotein	103					immune response|proteolysis	extracellular region|lysosome	cysteine-type endopeptidase activity				0	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)									120				0.443272	531.05257	532.114807	168	211	CC		KEEP	---	---	---	---	capture	UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)		Missense_Mutation	SNP	148994192	148994192	4200	1	C	T	T	32	32	CTSS	T	2	2
C1orf9	51430	broad.mit.edu	36	1	170787279	170787279	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:170787279C>T	uc001giq.2	+	c.67C>T	c.(67-69)CCC>TCC	p.P23S	C1orf9_uc009wwd.1_Missense_Mutation_p.P23S	NM_014283	NP_055098	Q9UBS9	OSPT_HUMAN	chromosome 1 open reading frame 9 protein	23					multicellular organismal development|ossification	integral to membrane|rough endoplasmic reticulum membrane				ovary(2)	2		Breast(1374;0.212)				Colon(43;174 953 11768 38880 47057)								0.24	9.938657	11.589734	6	19	CC		KEEP	---	---	---	---	capture		Colorectal(1306;3.98e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00544)	Missense_Mutation	SNP	170787279	170787279	2143	1	C	T	T	30	30	C1orf9	T	2	2
PLA2G2A	5320	broad.mit.edu	36	1	20177511	20177511	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:20177511C>G	uc001bcu.1	-	c.134G>C	c.(133-135)GGC>GCC	p.G45A	PLA2G2A_uc001bcv.1_Missense_Mutation_p.G45A	NM_000300	NP_000291	P14555	PA2GA_HUMAN	phospholipase A2, group IIA	45					defense response to Gram-positive bacterium|lipid catabolic process|low-density lipoprotein particle remodeling|phosphatidic acid metabolic process|positive regulation of inflammatory response|positive regulation of macrophage derived foam cell differentiation	endoplasmic reticulum|extracellular space|membrane	calcium ion binding|calcium-dependent phospholipase A2 activity|phospholipid binding				0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)												0.384615	9.259994	9.415329	5	8	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Missense_Mutation	SNP	20177511	20177511	12421	1	C	G	G	26	26	PLA2G2A	G	3	3
SRGAP2	23380	broad.mit.edu	36	1	204632796	204632796	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:204632796G>A	uc001hdy.1	+	c.353G>A	c.(352-354)CGC>CAC	p.R118H	SRGAP2_uc009xbt.1_Missense_Mutation_p.R42H|SRGAP2_uc001hdx.1_Missense_Mutation_p.R118H	NM_015326	NP_056141	O75044	FNBP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	205					axon guidance|regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding				0	Breast(84;0.137)													0.159091	11.332417	16.177042	7	37	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	204632796	204632796	15660	1	G	A	A	38	38	SRGAP2	A	1	1
PABPC1L	80336	broad.mit.edu	36	20	42992675	42992675	+	Nonsense_Mutation	SNP	T	A	A			TCGA-28-2499-01	TCGA-28-2499-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:42992675T>A	uc010ggv.1	+	c.1133T>A	c.(1132-1134)TTG>TAG	p.L378*	PABPC1L_uc002xmv.2_Non-coding_Transcript|PABPC1L_uc002xmw.2_5'Flank|PABPC1L_uc002xmx.2_5'Flank	NM_001124756	NP_001118228	Q4VXU2	PAP1L_HUMAN	poly(A)-binding protein, cytoplasmic 1-like	378							nucleotide binding|RNA binding			ovary(1)	1														0.470738	522.391566	522.683498	185	208	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	42992675	42992675	11777	20	T	A	A	63	63	PABPC1L	A	5	4
DSCAM	1826	broad.mit.edu	36	21	40387535	40387535	+	Missense_Mutation	SNP	A	C	C			TCGA-28-2499-01	TCGA-28-2499-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:40387535A>C	uc002yyq.1	-	c.3833T>G	c.(3832-3834)GTC>GGC	p.V1278G	DSCAM_uc002yyr.1_Non-coding_Transcript	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1278	Fibronectin type-III 4.|Extracellular (Potential).				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)	6		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				Melanoma(134;970 1778 1785 21664 32388)								0.2	8.626476	11.150133	6	24	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40387535	40387535	4952	21	A	C	C	10	10	DSCAM	C	4	4
SPP2	6694	broad.mit.edu	36	2	234632286	234632286	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234632286G>A	uc002vvk.1	+	c.278G>A	c.(277-279)AGG>AAG	p.R93K	SPP2_uc010fyl.1_Missense_Mutation_p.R13K	NM_006944	NP_008875	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa precursor	93					bone remodeling|skeletal system development	extracellular region	endopeptidase inhibitor activity				0		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)												0.426966	241.553164	242.384703	76	102	GG		KEEP	---	---	---	---	capture		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)	Missense_Mutation	SNP	234632286	234632286	15600	2	G	A	A	35	35	SPP2	A	2	2
FRAS1	80144	broad.mit.edu	36	4	79622006	79622006	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:79622006G>A	uc003hkx.2	+	c.8465G>A	c.(8464-8466)CGC>CAC	p.R2822H	FRAS1_uc003hlb.1_Missense_Mutation_p.R1044H	NM_025074	NP_079350	Q86XX4	FRAS1_HUMAN	Fraser syndrome 1	2818	Calx-beta 3.|Extracellular (Potential).				cell communication	integral to membrane|plasma membrane	metal ion binding			large_intestine(5)	5														0.423459	621.040694	623.597762	213	290	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79622006	79622006	6288	4	G	A	A	38	38	FRAS1	A	1	1
CDH9	1007	broad.mit.edu	36	5	26938564	26938564	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:26938564G>T	uc003jgs.1	-	c.1031C>A	c.(1030-1032)ACT>AAT	p.T344N		NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 preproprotein	344	Cadherin 3.|Extracellular (Potential).				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(5)	5						Melanoma(8;187 585 15745 40864 52829)								0.461538	99.84503	99.928697	30	35	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26938564	26938564	3246	5	G	T	T	36	36	CDH9	T	3	3
PTCD2	79810	broad.mit.edu	36	5	71653781	71653781	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:71653781G>A	uc003kcb.1	+	c.154G>A	c.(154-156)GTG>ATG	p.V52M	MRPS27_uc003kca.2_5'Flank|MRPS27_uc003kbz.2_5'Flank|MRPS27_uc010iza.1_5'Flank|PTCD2_uc003kcc.1_De_novo_Start_InFrame|PTCD2_uc003kcd.2_Non-coding_Transcript	NM_024754	NP_079030	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	52											0		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)												0.378238	198.715394	201.230313	73	120	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)	Missense_Mutation	SNP	71653781	71653781	13182	5	G	A	A	48	48	PTCD2	A	2	2
HLA-DOB	3112	broad.mit.edu	36	6	32890870	32890870	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32890870C>T	uc003oca.1	-	c.290G>A	c.(289-291)AGC>AAC	p.S97N		NM_002120	NP_002111	P13765	DOB_HUMAN	major histocompatibility complex, class II, DO	97	Beta-1.|Extracellular (Potential).				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	endosome membrane|integral to membrane|lysosomal membrane|MHC class II protein complex	MHC class II receptor activity				0														0.5	127.616104	127.616104	43	43	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32890870	32890870	7492	6	C	T	T	28	28	HLA-DOB	T	2	2
FAM83B	222584	broad.mit.edu	36	6	54914534	54914534	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:54914534C>T	uc003pck.1	+	c.2806C>T	c.(2806-2808)CGT>TGT	p.R936C		NM_001010872	NP_001010872	Q5T0W9	FA83B_HUMAN	hypothetical protein LOC222584	936										ovary(6)	6	Lung NSC(77;0.0178)|Renal(3;0.122)													0.391753	220.585674	222.56556	76	118	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54914534	54914534	5860	6	C	T	T	31	31	FAM83B	T	1	1
LAMB4	22798	broad.mit.edu	36	7	107533551	107533551	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:107533551C>T	uc010ljo.1	-	c.817G>A	c.(817-819)GAA>AAA	p.E273K	LAMB4_uc003vey.2_Missense_Mutation_p.E273K	NM_007356	NP_031382	A4D0S4	LAMB4_HUMAN	laminin, beta 4	273	Laminin EGF-like 1.				cell adhesion	basement membrane				ovary(4)|breast(2)|large_intestine(1)	7														0.280255	235.889966	249.506746	88	226	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	107533551	107533551	8936	7	C	T	T	31	31	LAMB4	T	1	1
DDX56	54606	broad.mit.edu	36	7	44578499	44578499	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:44578499G>A	uc003tlg.1	-	c.617C>T	c.(616-618)GCA>GTA	p.A206V	DDX56_uc003tle.1_Non-coding_Transcript|DDX56_uc003tlf.1_Missense_Mutation_p.A142V|DDX56_uc003tlh.1_Non-coding_Transcript|DDX56_uc010kyg.1_Missense_Mutation_p.A206V|DDX56_uc010kyh.1_Non-coding_Transcript	NM_019082	NP_061955	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 56	206	Helicase ATP-binding.				rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding				0														0.228571	69.419326	78.887863	32	108	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44578499	44578499	4545	7	G	A	A	46	46	DDX56	A	2	2
MAGI2	9863	broad.mit.edu	36	7	77594454	77594454	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:77594454G>T	uc003ugx.1	-	c.3419C>A	c.(3418-3420)CCC>CAC	p.P1140H	MAGI2_uc003ugy.1_Missense_Mutation_p.P1126H|MAGI2_uc010ldx.1_Missense_Mutation_p.P733H	NM_012301	NP_036433	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ	1140						cell junction|synapse|synaptosome	phosphatase binding			ovary(5)	5		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)												0.123867	40.448249	86.170414	41	290	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77594454	77594454	9574	7	G	T	T	43	43	MAGI2	T	3	3
GML	2765	broad.mit.edu	36	8	143925004	143925004	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:143925004G>A	uc003yxg.1	+	c.373G>A	c.(373-375)GAT>AAT	p.D125N		NM_002066	NP_002057	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule	125	UPAR/Ly6.				apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|negative regulation of cell proliferation	anchored to membrane|extrinsic to membrane|plasma membrane				central_nervous_system(2)	2	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)													0.453988	222.838151	223.137415	74	89	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	143925004	143925004	6761	8	G	A	A	37	37	GML	A	1	1
LGI3	203190	broad.mit.edu	36	8	22061944	22061944	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:22061944G>A	uc003xav.1	-	c.1321C>T	c.(1321-1323)CGC>TGC	p.R441C	LGI3_uc010ltu.1_Missense_Mutation_p.R417C	NM_139278	NP_644807	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	441	EAR 5.				exocytosis	cell junction|extracellular region|synaptic vesicle|synaptosome				ovary(1)	1														0.352941	52.734619	53.707269	18	33	GG		KEEP	---	---	---	---	capture		Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)	Missense_Mutation	SNP	22061944	22061944	9079	8	G	A	A	39	39	LGI3	A	1	1
OR2K2	26248	broad.mit.edu	36	9	113130375	113130375	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:113130375G>A	uc004bfd.1	-	c.160C>T	c.(160-162)CGC>TGC	p.R54C		NM_205859	NP_995581	Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K,	83	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.782051	199.611894	205.331574	61	17	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	113130375	113130375	11411	9	G	A	A	40	40	OR2K2	A	1	1
ZNF275	10838	broad.mit.edu	36	X	152266207	152266207	+	Silent	SNP	C	A	A			TCGA-28-2499-01	TCGA-28-2499-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:152266207C>A	uc004fhh.1	+	c.1038C>A	c.(1036-1038)GCC>GCA	p.A346A	ZNF275_uc004fhg.1_Silent_p.A290A	NM_001080485	NP_001073954	A6NFS0	A6NFS0_HUMAN	zinc finger protein 275	290										ovary(1)	1	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)													0.333333	7.492326	7.789522	4	8	CC		KEEP	---	---	---	---	capture			Silent	SNP	152266207	152266207	18402	23	C	A	A	21	21	ZNF275	A	3	3
CCDC120	90060	broad.mit.edu	36	X	48809558	48809558	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2499-01	TCGA-28-2499-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48809558G>C	uc010nik.1	+	c.667G>C	c.(667-669)GCC>CCC	p.A223P	CCDC120_uc004dmf.1_Missense_Mutation_p.A223P|CCDC120_uc010nil.1_Missense_Mutation_p.A223P	NM_033626	NP_296375	Q96HB5	CC120_HUMAN	coiled-coil domain containing 120	223							protein binding			pancreas(1)	1														0.214286	7.505518	9.678789	6	22	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48809558	48809558	2876	23	G	C	C	42	42	CCDC120	C	3	3
ZNF337	26152	broad.mit.edu	36	20	25603873	25603873	+	Frame_Shift_Del	DEL	G	-	-			TCGA-28-2499-01	TCGA-28-2499-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:25603873_25603873delG	uc002wva.1	-	c.2051_2051delC	c.(2050-2052)CCTfs	p.P684fs	ZNF337_uc002wvb.1_Frame_Shift_Del_p.P684fs|ZNF337_uc002wvc.1_Frame_Shift_Del_p.P684fs	NM_015655	NP_056470	Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	684					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.46			147	173				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	25603873	25603873	18445	20	G	-	-	35	35	ZNF337	-	5	5
