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
SLK	9748	broad.mit.edu	36	10	105742818	105742818	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:105742818A>G	uc001kxo.1	+	c.451A>G	c.(451-453)ATC>GTC	p.I151V	SLK_uc001kxp.1_Missense_Mutation_p.I151V	NM_014720	NP_055535	Q9H2G2	SLK_HUMAN	serine/threonine kinase 2	151	Protein kinase.				apoptosis|nucleotide-excision repair|protein phosphorylation	cytoplasm|plasma membrane	ATP binding|DNA binding|nuclease activity|protein serine/threonine kinase activity			ovary(2)|lung(1)|kidney(1)	4		Colorectal(252;0.178)				NSCLC(111;540 1651 1927 4474 17706)				837				0.760563	195.39111	199.801552	54	17	AA		KEEP	---	---	---	---	capture		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)	Missense_Mutation	SNP	105742818	105742818	15246	10	A	G	G	12	12	SLK	G	4	4
CALML5	51806	broad.mit.edu	36	10	5530984	5530984	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:5530984C>T	uc001iic.1	-	c.418G>A	c.(418-420)GCG>ACG	p.A140T		NM_017422	NP_059118	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	140	EF-hand 4.				epidermis development|signal transduction		calcium ion binding|protein binding				0						GBM(149;1055 3356 43077)								0.833333	16.18683	16.810293	5	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5530984	5530984	2706	10	C	T	T	27	27	CALML5	T	1	1
OR10G7	390265	broad.mit.edu	36	11	123414674	123414674	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:123414674G>A	uc001pzq.1	-	c.245C>T	c.(244-246)ACC>ATC	p.T82I		NM_001004463	NP_001004463	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G,	82	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)												0.248447	188.745676	207.281451	80	242	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)	Missense_Mutation	SNP	123414674	123414674	11308	11	G	A	A	44	44	OR10G7	A	2	2
IFITM1	8519	broad.mit.edu	36	11	304342	304342	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:304342G>A	uc001loy.2	+	c.172G>A	c.(172-174)GCC>ACC	p.A58T		NM_003641	NP_003632	P13164	IFM1_HUMAN	interferon induced transmembrane protein 1	58	Cytoplasmic (Potential).				negative regulation of cell proliferation|regulation of immune response|response to virus|type I interferon-mediated signaling pathway	integral to membrane|plasma membrane	protein binding|receptor signaling protein activity				0		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)												0.436681	279.565529	280.364621	100	129	GG		KEEP	---	---	---	---	capture		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)	Missense_Mutation	SNP	304342	304342	7827	11	G	A	A	38	38	IFITM1	A	1	1
OR5J2	282775	broad.mit.edu	36	11	55700812	55700812	+	Nonsense_Mutation	SNP	T	A	A			TCGA-27-1835-01	TCGA-27-1835-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:55700812T>A	uc001nil.1	+	c.143T>A	c.(142-144)TTA>TAA	p.L48*		NM_001005492	NP_001005492	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J,	48	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|large_intestine(1)|breast(1)|pancreas(1)	4	Esophageal squamous(21;0.00693)													0.401596	425.62377	428.813213	151	225	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	55700812	55700812	11575	11	T	A	A	61	61	OR5J2	A	5	4
POLA2	23649	broad.mit.edu	36	11	64805186	64805186	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:64805186C>A	uc001odj.1	+	c.892C>A	c.(892-894)CCT>ACT	p.P298T	POLA2_uc001odk.1_5'UTR	NM_002689	NP_002680	Q14181	DPOA2_HUMAN	polymerase (DNA directed), alpha 2 (70kD	298					DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication	nucleoplasm	DNA binding				0					Dacarbazine(DB00851)									0.395683	151.798332	153.120586	55	84	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	64805186	64805186	12616	11	C	A	A	30	30	POLA2	A	3	3
SYT9	143425	broad.mit.edu	36	11	7291347	7291347	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:7291347C>T	uc001mfe.1	+	c.643C>T	c.(643-645)CGG>TGG	p.R215W	SYT9_uc001mfd.2_Non-coding_Transcript|SYT9_uc009yfi.1_Intron	NM_175733	NP_783860	Q86SS6	SYT9_HUMAN	synaptotagmin IX	215	Cytoplasmic (Potential).					cell junction|integral to membrane|synaptic vesicle membrane	metal ion binding|transporter activity			ovary(2)|large_intestine(1)	3														0.394737	169.66811	171.141622	60	92	CC		KEEP	---	---	---	---	capture		Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)	Missense_Mutation	SNP	7291347	7291347	16002	11	C	T	T	19	19	SYT9	T	1	1
ISCU	23479	broad.mit.edu	36	12	107480642	107480642	+	Splice_Site_SNP	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107480642G>A	uc001tnd.2	+	c.114_splice	c.e2+1	p.K38_splice	SART3_uc001tmz.1_5'Flank|SART3_uc009zux.1_5'Flank|SART3_uc001tna.1_5'Flank|SART3_uc001tnb.2_5'Flank|ISCU_uc001tnc.2_Splice_Site_SNP|ISCU_uc009zuy.1_Splice_Site_SNP|ISCU_uc001tne.2_Splice_Site_SNP	NM_213595	NP_998760			iron-sulfur cluster assembly enzyme isoform						iron-sulfur cluster assembly|nitrogen fixation	cytosol|mitochondrion|nucleus	iron ion binding|iron-sulfur cluster binding|protein complex scaffold				0														0.3	6.717416	7.077238	3	7	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	107480642	107480642	8156	12	G	A	A	44	44	ISCU	A	5	2
C12orf51	283450	broad.mit.edu	36	12	111107127	111107127	+	Silent	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:111107127G>A	uc009zwc.1	-	c.8760C>T	c.(8758-8760)AGC>AGT	p.S2920S		NM_001109662	NP_001103132			chromosome 12 open reading frame 51											ovary(1)	1														0.264706	21.057458	22.760596	9	25	GG		KEEP	---	---	---	---	capture			Silent	SNP	111107127	111107127	1740	12	G	A	A	46	46	C12orf51	A	2	2
C3AR1	719	broad.mit.edu	36	12	8103131	8103131	+	Silent	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:8103131G>A	uc001qtv.1	-	c.918C>T	c.(916-918)TAC>TAT	p.Y306Y	C3AR1_uc009zfz.1_Silent_p.Y306Y	NM_004054	NP_004045	Q16581	C3AR_HUMAN	complement component 3a receptor 1	306	Extracellular (Potential).				blood circulation|chemotaxis|elevation of cytosolic calcium ion concentration|inflammatory response	integral to plasma membrane	C3a anaphylatoxin receptor activity|complement component C3a receptor activity|phosphatidylinositol phospholipase C activity			ovary(1)	1														0.460993	188.156502	188.343499	65	76	GG		KEEP	---	---	---	---	capture		Kidney(36;0.0893)	Silent	SNP	8103131	8103131	2297	12	G	A	A	40	40	C3AR1	A	1	1
C14orf109	26175	broad.mit.edu	36	14	92721540	92721540	+	Missense_Mutation	SNP	T	A	A			TCGA-27-1835-01	TCGA-27-1835-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:92721540T>A	uc010auo.1	+	c.55T>A	c.(55-57)TCT>ACT	p.S19T	MOAP1_uc001ybj.1_5'Flank|MOAP1_uc010aun.1_5'Flank|C14orf109_uc001ybk.2_Intron|C14orf109_uc010aup.1_5'Flank	NM_001098621	NP_001092091	Q8N6I4	CN109_HUMAN	hypothetical protein LOC26175 isoform 1	13						integral to membrane					0		all_cancers(154;0.11)|Acute lymphoblastic leukemia(33;0.0488)												0.384615	254.992724	257.724104	90	144	TT		KEEP	---	---	---	---	capture		Epithelial(152;0.176)|all cancers(159;0.197)|COAD - Colon adenocarcinoma(157;0.202)	Missense_Mutation	SNP	92721540	92721540	1787	14	T	A	A	54	54	C14orf109	A	4	4
MEGF11	84465	broad.mit.edu	36	15	63996265	63996265	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:63996265C>G	uc002apm.2	-	c.2170G>C	c.(2170-2172)GCC>CCC	p.A724P	MEGF11_uc010bhn.1_Missense_Mutation_p.A649P|MEGF11_uc002apl.2_Missense_Mutation_p.A649P|MEGF11_uc002apn.1_Missense_Mutation_p.A724P	NM_032445	NP_115821	A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	724	EGF-like 12.					basolateral plasma membrane|integral to membrane				pancreas(1)	1												OREG0023198	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.266667	8.612621	9.338447	4	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63996265	63996265	9850	15	C	G	G	26	26	MEGF11	G	3	3
RABEP2	79874	broad.mit.edu	36	16	28829999	28829999	+	Silent	SNP	G	C	C			TCGA-27-1835-01	TCGA-27-1835-01	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)								0.363636	6.534574	6.738576	4	7	GG		KEEP	---	---	---	---	capture			Silent	SNP	28829999	28829999	13421	16	G	C	C	42	42	RABEP2	C	3	3
RLTPR	146206	broad.mit.edu	36	16	66241329	66241329	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:66241329C>T	uc002etn.1	+	c.2039C>T	c.(2038-2040)GCG>GTG	p.A680V	RLTPR_uc010cel.1_Missense_Mutation_p.A673V	NM_001013838	NP_001013860	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin	680	LRR 16.									breast(1)	1		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)												0.510638	68.993079	68.997573	24	23	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)	Missense_Mutation	SNP	66241329	66241329	13871	16	C	T	T	27	27	RLTPR	T	1	1
C17orf102	400591	broad.mit.edu	36	17	29930343	29930343	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1835-01	TCGA-27-1835-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:29930343T>C	uc002hie.1	-	c.70A>G	c.(70-72)AGG>GGG	p.R24G	TMEM132E_uc002hif.1_5'Flank	NM_207454	NP_997337	A2RUQ5	CQ102_HUMAN	hypothetical protein LOC400591	24										ovary(1)	1														0.266667	6.451107	7.227854	4	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29930343	29930343	1902	17	T	C	C	54	54	C17orf102	C	4	4
PLXDC1	57125	broad.mit.edu	36	17	34519027	34519027	+	Silent	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:34519027C>T	uc002hrg.1	-	c.399G>A	c.(397-399)TCG>TCA	p.S133S	PLXDC1_uc002hrh.1_Non-coding_Transcript|PLXDC1_uc002hri.1_Non-coding_Transcript|PLXDC1_uc002hrj.1_Non-coding_Transcript|PLXDC1_uc002hrk.1_Non-coding_Transcript	NM_020405	NP_065138	Q8IUK5	PXDC1_HUMAN	plexin domain containing 1 precursor	133	Extracellular (Potential).				angiogenesis	cytoplasm|extracellular region|integral to membrane|tight junction				ovary(1)|kidney(1)	2														0.428571	26.670791	26.764299	9	12	CC		KEEP	---	---	---	---	capture			Silent	SNP	34519027	34519027	12543	17	C	T	T	23	23	PLXDC1	T	1	1
NLRP1	22861	broad.mit.edu	36	17	5383624	5383624	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:5383624A>C	uc002gci.1	-	c.2705T>G	c.(2704-2706)GTC>GGC	p.V902G	NLRP1_uc002gcg.1_Missense_Mutation_p.V902G|NLRP1_uc002gch.2_Missense_Mutation_p.V902G|NLRP1_uc002gck.1_Missense_Mutation_p.V902G|NLRP1_uc002gcj.1_Missense_Mutation_p.V902G|NLRP1_uc002gcl.1_Missense_Mutation_p.V902G|NLRP1_uc010clh.1_Missense_Mutation_p.V902G	NM_033004	NP_127497	Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1 isoform 1	902	LRR 4.				activation of caspase activity|defense response to bacterium|induction of apoptosis|neuron apoptosis|positive regulation of interleukin-1 beta secretion|regulation of inflammatory response|response to muramyl dipeptide	cytoplasm|NALP1 inflammasome complex|nucleus	ATP binding|caspase activator activity|enzyme binding|protein domain specific binding			lung(4)|breast(2)|ovary(1)|central_nervous_system(1)|skin(1)	9		Colorectal(1115;3.48e-05)								431				0.375	6.820954	6.931281	3	5	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5383624	5383624	10874	17	A	C	C	10	10	NLRP1	C	4	4
SCN4A	6329	broad.mit.edu	36	17	59390392	59390392	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:59390392C>T	uc002jds.1	-	c.1984G>A	c.(1984-1986)GTA>ATA	p.V662I		NM_000334	NP_000325	P35499	SCN4A_HUMAN	voltage-gated sodium channel type 4 alpha	662	II.				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity			ovary(1)|pancreas(1)|skin(1)	3					Lamotrigine(DB00555)									0.414414	131.220067	131.931382	46	65	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	59390392	59390392	14402	17	C	T	T	19	19	SCN4A	T	1	1
TP53	7157	broad.mit.edu	36	17	7518928	7518928	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7518928C>T	uc002gim.2	-	c.646G>A	c.(646-648)GTG>ATG	p.V216M	TP53_uc002gig.1_Missense_Mutation_p.V216M|TP53_uc002gih.1_Missense_Mutation_p.V216M|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.V84M|TP53_uc010cng.1_Missense_Mutation_p.V84M|TP53_uc002gii.1_Missense_Mutation_p.V84M|TP53_uc010cnh.1_Missense_Mutation_p.V216M|TP53_uc010cni.1_Missense_Mutation_p.V216M|TP53_uc002gij.2_Missense_Mutation_p.V216M|TP53_uc010cnj.1_Intron|TP53_uc002gin.2_Missense_Mutation_p.V123M|TP53_uc002gio.2_Missense_Mutation_p.V84M	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	216	Required for interaction with FBXO42.||Interaction with HIPK1 (By similarity).|Interaction with AXIN1 (By similarity).		V -> A (in sporadic cancers; somatic mutation).|V -> E (in sporadic cancers; somatic mutation).|V -> W (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|V -> M (in sporadic cancers; somatic mutation).|V -> L (in sporadic cancers; somatic mutation).|V -> G (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	chromatin|cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|promoter binding|promoter binding|protease binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin protein ligase binding|zinc ion binding	p.V216M(46)|p.V216del(8)|p.V216L(7)|p.0?(6)|p.H214fs*5(2)|p.V216fs*6(2)|p.D208fs*1(1)|p.S215_V216insX(1)|p.S215fs*31(1)|p.S215_V218>R(1)|p.T211fs*28(1)|p.V216fs*5(1)|p.V216fs*32(1)|p.D207_V216del10(1)|p.S215fs*27(1)|p.V216fs*33(1)|p.V216_Y220delVVVPY(1)|p.S215fs*29(1)|p.D208_V216delDRNTFRHSV(1)		large_intestine(4614)|breast(2344)|upper_aerodigestive_tract(2150)|lung(1958)|ovary(1559)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1212)|stomach(1127)|urinary_tract(1113)|central_nervous_system(1072)|liver(805)|skin(693)|pancreas(370)|biliary_tract(247)|soft_tissue(209)|prostate(192)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(41)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	21904		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)				Pancreas(47;798 1329 9957 10801)		111	p.V216M(ECC12-Tumor)|p.V216L(LCLC103H-Tumor)|p.V216M(HT-Tumor)|p.V216M(SNU216-Tumor)	690	TCGA GBM(1;<1E-8)|TSP Lung(2;<1E-8)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			0.710526	83.535806	85.04358	27	11	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Missense_Mutation	SNP	7518928	7518928	16923	17	C	T	T	17	17	TP53	T	2	2
NPAS1	4861	broad.mit.edu	36	19	52236171	52236171	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:52236171A>G	uc002pfw.1	+	c.1165A>G	c.(1165-1167)AGC>GGC	p.S389G	NPAS1_uc002pfx.1_Missense_Mutation_p.S214G|NPAS1_uc002pfy.1_Missense_Mutation_p.S389G	NM_002517	NP_002508	Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	389	PAC.				central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription regulator activity				0		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)												0.714286	7.170391	7.387833	5	2	AA		KEEP	---	---	---	---	capture		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)	Missense_Mutation	SNP	52236171	52236171	10966	19	A	G	G	11	11	NPAS1	G	4	4
PLEKHO1	51177	broad.mit.edu	36	1	148398176	148398176	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:148398176C>T	uc001ett.1	+	c.1064C>T	c.(1063-1065)ACG>ATG	p.T355M	PLEKHO1_uc001etr.1_Missense_Mutation_p.T183M|PLEKHO1_uc001ets.1_Missense_Mutation_p.T172M|PLEKHO1_uc001etu.1_Missense_Mutation_p.T183M	NM_016274	NP_057358	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O	355	Negative regulator of AP-1 activity.					cytoplasm|nucleus|plasma membrane				lung(1)	1	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)													0.394366	78.286465	78.979133	28	43	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)		Missense_Mutation	SNP	148398176	148398176	12510	1	C	T	T	19	19	PLEKHO1	T	1	1
NUP210L	91181	broad.mit.edu	36	1	152377225	152377225	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152377225C>A	uc001fdw.1	-	c.831G>T	c.(829-831)ATG>ATT	p.M277I	NUP210L_uc009woq.1_5'Flank	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	277						integral to membrane				ovary(4)|large_intestine(1)|central_nervous_system(1)|skin(1)	7	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)													0.421769	184.721786	185.507613	62	85	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)		Missense_Mutation	SNP	152377225	152377225	11166	1	C	A	A	21	21	NUP210L	A	3	3
SPTA1	6708	broad.mit.edu	36	1	156893017	156893017	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156893017G>C	uc001fst.1	-	c.2859C>G	c.(2857-2859)GAC>GAG	p.D953E		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	953	Spectrin 10.				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			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.353357	330.026536	335.387943	100	183	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156893017	156893017	15630	1	G	C	C	48	48	SPTA1	C	3	3
SPTA1	6708	broad.mit.edu	36	1	156899226	156899226	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156899226C>T	uc001fst.1	-	c.2354G>A	c.(2353-2355)CGA>CAA	p.R785Q		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	785	Spectrin 8.				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			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.419048	128.39008	128.988186	44	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	156899226	156899226	15630	1	C	T	T	31	31	SPTA1	T	1	1
LAMB3	3914	broad.mit.edu	36	1	207870652	207870652	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:207870652G>A	uc001hhg.1	-	c.874C>T	c.(874-876)CGC>TGC	p.R292C	LAMB3_uc009xco.1_Missense_Mutation_p.R292C|LAMB3_uc001hhh.1_Missense_Mutation_p.R292C|LAMB3_uc009xcp.1_Missense_Mutation_p.R228C	NM_001017402	NP_001121113	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor	292	Laminin EGF-like 1.				cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|large_intestine(1)|ovary(1)	4														0.383562	75.888987	76.754057	28	45	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(81;0.0519)	Missense_Mutation	SNP	207870652	207870652	8935	1	G	A	A	38	38	LAMB3	A	1	1
SIPA1L2	57568	broad.mit.edu	36	1	230682070	230682070	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1835-01	TCGA-27-1835-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:230682070T>C	uc001hvg.1	-	c.2011A>G	c.(2011-2013)ACC>GCC	p.T671A		NM_020808	NP_065859	Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like	671	Rap-GAP.				regulation of small GTPase mediated signal transduction	intracellular	GTPase activator activity			ovary(2)|central_nervous_system(2)|pancreas(1)	5		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)												0.391667	160.206529	161.437221	47	73	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	230682070	230682070	14825	1	T	C	C	57	57	SIPA1L2	C	4	4
KIAA1804	84451	broad.mit.edu	36	1	231581653	231581653	+	Nonsense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:231581653C>T	uc001hvt.2	+	c.2278C>T	c.(2278-2280)CGA>TGA	p.R760*	KIAA1804_uc001hvu.2_Nonsense_Mutation_p.R206*	NM_032435	NP_115811	Q5TCX8	M3KL4_HUMAN	mixed lineage kinase 4	760					activation of JUN kinase activity|protein autophosphorylation		ATP binding|MAP kinase kinase kinase activity|protein homodimerization activity			lung(5)|central_nervous_system(2)	7		all_cancers(173;0.000405)|all_epithelial(177;0.0345)|Prostate(94;0.122)								196				0.398058	108.214663	109.128431	41	62	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	231581653	231581653	8570	1	C	T	T	19	19	KIAA1804	T	5	1
OR2M4	26245	broad.mit.edu	36	1	246469261	246469261	+	Missense_Mutation	SNP	G	T	T			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:246469261G>T	uc001iec.1	+	c.408G>T	c.(406-408)ATG>ATT	p.M136I		NM_017504	NP_059974	Q96R27	OR2M4_HUMAN	olfactory receptor, family 2, subfamily M,	136	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			breast(2)	2	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)													0.402597	176.212421	177.491697	62	92	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.0245)		Missense_Mutation	SNP	246469261	246469261	11418	1	G	T	T	45	45	OR2M4	T	3	3
MYH7B	57644	broad.mit.edu	36	20	33046900	33046900	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:33046900A>G	uc002xbi.1	+	c.2927A>G	c.(2926-2928)GAG>GGG	p.E976G		NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	934	Potential.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2														0.294118	8.142917	8.806433	5	12	AA		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(18;0.00691)		Missense_Mutation	SNP	33046900	33046900	10435	20	A	G	G	11	11	MYH7B	G	4	4
PTPRT	11122	broad.mit.edu	36	20	40739983	40739983	+	Nonsense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:40739983G>A	uc010ggj.1	-	c.1090C>T	c.(1090-1092)CGA>TGA	p.R364*	PTPRT_uc002xkg.1_Nonsense_Mutation_p.R364*	NM_133170	NP_573400	O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	364	Extracellular (Potential).|Fibronectin type-III 1.				homophilic cell adhesion|transmembrane receptor protein tyrosine kinase signaling pathway	cell surface|integral to membrane|plasma membrane	alpha-catenin binding|beta-catenin binding|cadherin binding|delta-catenin binding|gamma-catenin binding|protein tyrosine phosphatase activity|receptor activity			ovary(7)|lung(5)|skin(2)	14		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)								646				0.322449	211.943275	218.799348	79	166	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	40739983	40739983	13270	20	G	A	A	40	40	PTPRT	A	5	1
MATN4	8785	broad.mit.edu	36	20	43360456	43360456	+	Silent	SNP	A	T	T			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43360456A>T	uc002xnn.1	-	c.1194T>A	c.(1192-1194)CCT>CCA	p.P398P	MATN4_uc002xno.1_Silent_p.P357P|MATN4_uc002xnp.1_Silent_p.P316P|MATN4_uc002xnq.1_Silent_p.P357P|MATN4_uc002xnr.1_Silent_p.P398P	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	439	VWFA 2.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)												0.338235	59.022317	60.586922	23	45	AA		KEEP	---	---	---	---	capture			Silent	SNP	43360456	43360456	9720	20	A	T	T	11	11	MATN4	T	4	4
MATN4	8785	broad.mit.edu	36	20	43366416	43366416	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43366416G>A	uc002xnn.1	-	c.509C>T	c.(508-510)GCG>GTG	p.A170V	MATN4_uc002xno.1_Missense_Mutation_p.A170V|MATN4_uc002xnp.1_Missense_Mutation_p.A170V|MATN4_uc002xnq.1_Missense_Mutation_p.A170V|MATN4_uc002xnr.1_Missense_Mutation_p.A170V|RBPJL_uc002xns.1_5'Flank|RBPJL_uc002xnt.1_5'Flank	NM_003833	NP_003824	O95460	MATN4_HUMAN	matrilin 4 isoform 1 precursor	170	VWFA 1.					extracellular region	protein binding				0		Myeloproliferative disorder(115;0.0122)												0.325	29.460268	30.547937	13	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43366416	43366416	9720	20	G	A	A	38	38	MATN4	A	1	1
MMP9	4318	broad.mit.edu	36	20	44074490	44074490	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:44074490G>A	uc002xqz.1	+	c.1192G>A	c.(1192-1194)GTG>ATG	p.V398M		NM_004994	NP_004985	P14780	MMP9_HUMAN	matrix metalloproteinase 9 preproprotein	398					collagen catabolic process|macrophage differentiation|positive regulation of keratinocyte migration|proteolysis	extracellular space|proteinaceous extracellular matrix	collagen binding|metalloendopeptidase activity|zinc ion binding			ovary(1)|pancreas(1)	2		Myeloproliferative disorder(115;0.0122)			Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)|Simvastatin(DB00641)					462				0.268657	90.976824	97.427928	36	98	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44074490	44074490	10060	20	G	A	A	40	40	MMP9	A	1	1
ANGPT4	51378	broad.mit.edu	36	20	808425	808425	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:808425C>T	uc002wei.1	-	c.1018G>A	c.(1018-1020)GTG>ATG	p.V340M		NM_015985	NP_057069	Q9Y264	ANGP4_HUMAN	angiopoietin 4	340	Fibrinogen C-terminal.				anti-apoptosis|blood coagulation|cellular response to hypoxia|leukocyte migration|negative regulation of angiogenesis|negative regulation of blood vessel endothelial cell migration|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of peptidyl-tyrosine phosphorylation|signal transduction	extracellular space	receptor tyrosine kinase binding|transmembrane receptor protein tyrosine kinase activator activity			ovary(2)	2						Pancreas(181;481 2077 3259 31286 49856)								0.228814	58.756954	66.725473	27	91	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	808425	808425	615	20	C	T	T	19	19	ANGPT4	T	1	1
MIOX	55586	broad.mit.edu	36	22	49275096	49275096	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:49275096G>A	uc003bll.1	+	c.803G>A	c.(802-804)CGG>CAG	p.R268Q	MIOX_uc003blm.1_Silent_p.A263A|MIOX_uc003bln.1_Silent_p.A224A	NM_017584	NP_060054	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	268					inositol catabolic process|oxidation-reduction process	cytoplasm|inclusion body	aldo-keto reductase (NADP) activity|inositol oxygenase activity|iron ion binding				0		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)												0.607843	98.829744	99.348581	31	20	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Missense_Mutation	SNP	49275096	49275096	9980	22	G	A	A	39	39	MIOX	A	1	1
SULT1C4	27233	broad.mit.edu	36	2	108366338	108366338	+	Silent	SNP	A	T	T			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:108366338A>T	uc002tea.1	+	c.555A>T	c.(553-555)GGA>GGT	p.G185G	SULT1C4_uc002teb.1_Silent_p.G110G	NM_006588	NP_006579	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member	185					3'-phosphoadenosine 5'-phosphosulfate metabolic process|sulfation|xenobiotic metabolic process	cytosol	sulfotransferase activity				0														0.404762	96.346821	97.008114	34	50	AA		KEEP	---	---	---	---	capture			Silent	SNP	108366338	108366338	15899	2	A	T	T	12	12	SULT1C4	T	4	4
RPRM	56475	broad.mit.edu	36	2	154043016	154043016	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:154043016C>T	uc002tyq.1	-	c.310G>A	c.(310-312)GTG>ATG	p.V104M		NM_019845	NP_062819	Q9NS64	RPRM_HUMAN	reprimo, TP53 dependant G2 arrest mediator	104					cell cycle arrest	cytoplasm|integral to membrane	protein binding				0														0.275862	19.687794	20.999409	8	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154043016	154043016	14097	2	C	T	T	18	18	RPRM	T	2	2
ALS2	57679	broad.mit.edu	36	2	202314777	202314777	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:202314777G>A	uc002uyo.1	-	c.2216C>T	c.(2215-2217)GCT>GTT	p.A739V	ALS2_uc010ftl.1_Non-coding_Transcript|ALS2_uc002uyp.2_Missense_Mutation_p.A739V|ALS2_uc002uyq.1_Missense_Mutation_p.A739V	NM_020919	NP_065970	Q96Q42	ALS2_HUMAN	alsin isoform 1	739	DH.				cell death|endosome organization|positive regulation of Rac GTPase activity|positive regulation of Rac protein signal transduction|regulation of endosome size	centrosome|cytosol|early endosome|growth cone|lamellipodium|protein complex|ruffle	protein homodimerization activity|protein serine/threonine kinase activator activity|Rab GTPase binding|Rab guanyl-nucleotide exchange factor activity|Rac guanyl-nucleotide exchange factor activity|Ran guanyl-nucleotide exchange factor activity			skin(4)|lung(1)|breast(1)	6										498				0.173913	7.184253	9.494496	4	19	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	202314777	202314777	553	2	G	A	A	34	34	ALS2	A	2	2
CD28	940	broad.mit.edu	36	2	204307806	204307806	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:204307806C>T	uc002vah.2	+	c.589C>T	c.(589-591)CGC>TGC	p.R197C	CD28_uc002vai.2_Missense_Mutation_p.R100C|CD28_uc010ftx.1_Missense_Mutation_p.R78C|CD28_uc002vaj.2_Non-coding_Transcript	NM_006139	NP_006130	P10747	CD28_HUMAN	CD28 antigen precursor	197	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|cytokine biosynthetic process|humoral immune response|positive regulation of anti-apoptosis|positive regulation of interleukin-2 biosynthetic process|positive regulation of mitosis|positive regulation of translation|positive regulation of viral genome replication|regulation of defense response to virus by virus|regulatory T cell differentiation|T cell costimulation|viral reproduction	cytosol|external side of plasma membrane|integral to plasma membrane	coreceptor activity|protease binding|SH3/SH2 adaptor activity				0														0.477612	192.28442	192.342997	64	70	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	204307806	204307806	3121	2	C	T	T	23	23	CD28	T	1	1
IFT172	26160	broad.mit.edu	36	2	27524273	27524273	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27524273C>A	uc002rku.1	-	c.4449G>T	c.(4447-4449)AGG>AGT	p.R1483S	IFT172_uc010ezb.1_Non-coding_Transcript	NM_015662	NP_056477	Q9UG01	IF172_HUMAN	selective LIM binding factor homolog	1483					cilium assembly	cilium	binding			large_intestine(1)|ovary(1)	2	Acute lymphoblastic leukemia(172;0.155)													0.375	150.92421	153.013663	57	95	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27524273	27524273	7858	2	C	A	A	30	30	IFT172	A	3	3
CAPN13	92291	broad.mit.edu	36	2	30812917	30812917	+	Missense_Mutation	SNP	G	T	T			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:30812917G>T	uc002rnn.1	-	c.1678C>A	c.(1678-1680)CAA>AAA	p.Q560K	CAPN13_uc002rnm.1_Non-coding_Transcript	NM_144575	NP_653176	Q6MZZ7	CAN13_HUMAN	calpain 13	560	EF-hand 1.				proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity			large_intestine(1)|ovary(1)	2	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)													0.422535	87.327366	87.701029	30	41	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30812917	30812917	2743	2	G	T	T	47	47	CAPN13	T	3	3
FAM82A1	151393	broad.mit.edu	36	2	38055949	38055949	+	Missense_Mutation	SNP	T	C	C			TCGA-27-1835-01	TCGA-27-1835-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:38055949T>C	uc002rqn.1	+	c.1252T>C	c.(1252-1254)TAT>CAT	p.Y418H	FAM82A1_uc002rqk.1_Missense_Mutation_p.Y95H|FAM82A1_uc002rql.1_Missense_Mutation_p.Y240H|FAM82A1_uc002rqm.1_Missense_Mutation_p.Y95H	NM_144713	NP_653314	Q96LZ7	RMD2_HUMAN	family with sequence similarity 82, member A1	240						cytoplasm|integral to membrane|microtubule|spindle pole	binding			ovary(1)	1														0.441176	162.897625	163.198083	45	57	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38055949	38055949	5856	2	T	C	C	61	61	FAM82A1	C	4	4
SNRK	54861	broad.mit.edu	36	3	43356838	43356838	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:43356838A>C	uc003cms.2	+	c.787A>C	c.(787-789)ATT>CTT	p.I263L	SNRK_uc003cmt.2_Missense_Mutation_p.I263L|SNRK_uc010hik.1_Missense_Mutation_p.I263L	NM_017719	NP_060189	Q9NRH2	SNRK_HUMAN	SNF related kinase	263	Protein kinase.				myeloid cell differentiation|protein phosphorylation	nucleus	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity			ovary(3)|breast(1)	4										165				0.393393	441.154081	444.465663	131	202	AA		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.0636)|Kidney(284;0.0792)	Missense_Mutation	SNP	43356838	43356838	15351	3	A	C	C	12	12	SNRK	C	4	4
WHSC1	7468	broad.mit.edu	36	4	1948176	1948176	+	Silent	SNP	C	A	A			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:1948176C>A	uc003gdz.2	+	c.3798C>A	c.(3796-3798)TCC>TCA	p.S1266S	WHSC1_uc003geb.2_Silent_p.S1266S|WHSC1_uc003gec.2_Silent_p.S1266S|WHSC1_uc003ged.2_Silent_p.S1266S|WHSC1_uc003gee.2_Non-coding_Transcript|WHSC1_uc003gef.2_Non-coding_Transcript|WHSC1_uc003gei.2_Silent_p.S485S|WHSC1_uc010icf.1_Silent_p.S614S	NM_001042424	NP_579890	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1 protein	1266	PHD-type 4; atypical.				anatomical structure morphogenesis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|cytoplasm|nuclear membrane|nucleolus	DNA binding|histone-lysine N-methyltransferase activity|zinc ion binding			ovary(3)|skin(2)|pancreas(1)|lung(1)	7		all_epithelial(65;1.34e-05)								355				0.881356	324.852558	341.691989	104	14	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)	Silent	SNP	1948176	1948176	17936	4	C	A	A	24	24	WHSC1	A	3	3
USP46	64854	broad.mit.edu	36	4	53162824	53162824	+	Silent	SNP	C	G	G			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:53162824C>G	uc003gzn.1	-	c.876G>C	c.(874-876)CTG>CTC	p.L292L		NM_022832	NP_073743	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46 isoform 1	292					behavior|protein deubiquitination|regulation of synaptic transmission, GABAergic|ubiquitin-dependent protein catabolic process		protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(1)	1														0.4	88.880045	89.580361	32	48	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(32;0.0295)		Silent	SNP	53162824	53162824	17641	4	C	G	G	21	21	USP46	G	3	3
KIAA1211	57482	broad.mit.edu	36	4	56877433	56877433	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:56877433C>T	uc003hbk.2	+	c.3008C>T	c.(3007-3009)CCG>CTG	p.P1003L	KIAA1211_uc010iha.1_Missense_Mutation_p.P996L|KIAA1211_uc003hbm.1_Missense_Mutation_p.P889L	NM_020722	NP_065773	Q6ZU35	K1211_HUMAN	hypothetical protein LOC57482	1003	Pro-rich.									ovary(1)|skin(1)	2	Glioma(25;0.08)|all_neural(26;0.101)													0.275862	20.702598	22.004986	8	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56877433	56877433	8523	4	C	T	T	23	23	KIAA1211	T	1	1
C4orf40	401137	broad.mit.edu	36	4	71058888	71058888	+	Silent	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71058888G>A	uc003hfa.2	+	c.330G>A	c.(328-330)CCG>CCA	p.P110P	C4orf40_uc003hfb.2_Silent_p.P110P	NM_214711	NP_999876	Q6MZM9	CD040_HUMAN	hypothetical protein LOC401137	110						extracellular region					0														0.42	478.333138	480.564745	168	232	GG		KEEP	---	---	---	---	capture			Silent	SNP	71058888	71058888	2364	4	G	A	A	40	40	C4orf40	A	1	1
ADAMTS19	171019	broad.mit.edu	36	5	128985860	128985860	+	Missense_Mutation	SNP	C	G	G			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:128985860C>G	uc003kvb.1	+	c.1672C>G	c.(1672-1674)CTG>GTG	p.L558V	ADAMTS19_uc010jdh.1_Non-coding_Transcript	NM_133638	NP_598377	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1	558	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(5)|breast(2)|lung(1)	8		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)								425				0.427083	133.156358	133.602247	41	55	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)	Missense_Mutation	SNP	128985860	128985860	265	5	C	G	G	28	28	ADAMTS19	G	3	3
GABRA6	2559	broad.mit.edu	36	5	161048747	161048747	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:161048747C>A	uc003lyu.2	+	c.440C>A	c.(439-441)ACC>AAC	p.T147N	GABRA6_uc003lyv.2_5'Flank	NM_000811	NP_000802	Q16445	GBRA6_HUMAN	gamma-aminobutyric acid A receptor, alpha 6	147	Extracellular (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	benzodiazepine receptor activity|chloride channel activity			ovary(7)|large_intestine(1)|central_nervous_system(1)	9	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)			Alprazolam(DB00404)|Ethchlorvynol(DB00189)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Lorazepam(DB00186)|Meprobamate(DB00371)|Midazolam(DB00683)						TCGA Ovarian(5;0.080)			0.346939	98.53288	100.553855	34	64	CC		KEEP	---	---	---	---	capture	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Missense_Mutation	SNP	161048747	161048747	6416	5	C	A	A	18	18	GABRA6	A	3	3
HMP19	51617	broad.mit.edu	36	5	173467064	173467064	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:173467064G>C	uc003mcx.1	+	c.466G>C	c.(466-468)GCA>CCA	p.A156P		NM_015980	NP_057064	Q9Y328	NSG2_HUMAN	HMP19 protein	156	Lumenal (Potential).				dopamine receptor signaling pathway	cytoplasmic vesicle membrane|Golgi cisterna membrane|integral to membrane|multivesicular body membrane	dopamine receptor binding			central_nervous_system(1)	1	Renal(175;0.000159)|Lung NSC(126;0.00925)|all_lung(126;0.0148)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)												0.285714	7.892494	8.470839	4	10	GG		KEEP	---	---	---	---	capture	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Missense_Mutation	SNP	173467064	173467064	7537	5	G	C	C	34	34	HMP19	C	3	3
HK3	3101	broad.mit.edu	36	5	176241119	176241119	+	Missense_Mutation	SNP	A	C	C			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:176241119A>C	uc003mfa.1	-	c.2417T>G	c.(2416-2418)GTC>GGC	p.V806G	HK3_uc003mez.1_Missense_Mutation_p.V362G	NM_002115	NP_002106	P52790	HXK3_HUMAN	hexokinase 3	806	Catalytic.				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity			ovary(3)|large_intestine(1)|breast(1)	5	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)												0.307692	6.970357	7.415855	4	9	AA		KEEP	---	---	---	---	capture	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Missense_Mutation	SNP	176241119	176241119	7483	5	A	C	C	10	10	HK3	C	4	4
GPR98	84059	broad.mit.edu	36	5	90017368	90017368	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:90017368G>A	uc003kju.1	+	c.6290G>A	c.(6289-6291)CGT>CAT	p.R2097H	GPR98_uc003kjt.1_5'UTR	NM_032119	NP_115495	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98 precursor	2097	Extracellular (Potential).				cell communication|cell-cell adhesion|maintenance of organ identity|neuropeptide signaling pathway|photoreceptor cell maintenance	cell surface|cytoplasm|integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity			ovary(11)|central_nervous_system(3)|pancreas(2)	16		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)												0.392857	95.459218	96.30248	33	51	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)	Missense_Mutation	SNP	90017368	90017368	6997	5	G	A	A	40	40	GPR98	A	1	1
SLC16A10	117247	broad.mit.edu	36	6	111605534	111605534	+	Silent	SNP	T	C	C			TCGA-27-1835-01	TCGA-27-1835-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:111605534T>C	uc003pus.1	+	c.915T>C	c.(913-915)TTT>TTC	p.F305F	SLC16A10_uc003pur.2_Silent_p.F305F|SLC16A10_uc003put.1_5'UTR	NM_018593	NP_061063	Q8TF71	MOT10_HUMAN	solute carrier family 16, member 10	305	Helical; (Potential).				aromatic amino acid transport|cellular nitrogen compound metabolic process|ion transport	basolateral plasma membrane|integral to membrane	amino acid transmembrane transporter activity				0		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)												0.46371	361.801792	362.085963	115	133	TT		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)	Silent	SNP	111605534	111605534	14899	6	T	C	C	63	63	SLC16A10	C	4	4
RSPH4A	345895	broad.mit.edu	36	6	117044744	117044744	+	Nonsense_Mutation	SNP	G	T	T			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:117044744G>T	uc003pxe.1	+	c.265G>T	c.(265-267)GAG>TAG	p.E89*	RSPH4A_uc010kee.1_Nonsense_Mutation_p.E89*	NM_001010892	NP_001010892	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A	89					cilium axoneme assembly|cilium movement	cilium axoneme|cytoplasm|cytoskeleton|motile cilium|radial spoke					0														0.342105	60.782054	62.477192	26	50	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	117044744	117044744	14186	6	G	T	T	41	41	RSPH4A	T	5	3
RFX6	222546	broad.mit.edu	36	6	117350972	117350972	+	Missense_Mutation	SNP	C	A	A			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:117350972C>A	uc003pxm.1	+	c.1447C>A	c.(1447-1449)CAA>AAA	p.Q483K		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	483					glucose homeostasis|pancreatic A cell differentiation|pancreatic D cell differentiation|pancreatic E cell differentiation|positive regulation of transcription, DNA-dependent|regulation of insulin secretion|transcription, DNA-dependent|type B pancreatic cell differentiation	nucleus	promoter binding|protein binding|transcription activator activity			ovary(1)|pancreas(1)	2														0.337349	161.640002	165.528501	56	110	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117350972	117350972	13739	6	C	A	A	17	17	RFX6	A	3	3
DLL1	28514	broad.mit.edu	36	6	170441128	170441128	+	Silent	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:170441128G>A	uc003qxm.1	-	c.25C>T	c.(25-27)CTG>TTG	p.L9L	DLL1_uc003qxn.2_Silent_p.L9L	NM_005618	NP_005609	O00548	DLL1_HUMAN	delta-like 1	9					cell communication|cell fate determination|hemopoiesis|Notch receptor processing|Notch signaling pathway|regulation of cell adhesion	extracellular region|integral to plasma membrane	calcium ion binding|Notch binding			ovary(1)	1		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)								187				0.4375	62.66683	62.830332	21	27	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)	Silent	SNP	170441128	170441128	4746	6	G	A	A	35	35	DLL1	A	2	2
GPR116	221395	broad.mit.edu	36	6	46934073	46934073	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:46934073C>T	uc003oyo.2	-	c.3526G>A	c.(3526-3528)GCC>ACC	p.A1176T	GPR116_uc003oyp.2_Missense_Mutation_p.A1034T|GPR116_uc003oyq.2_Missense_Mutation_p.A1176T|GPR116_uc010jzi.1_Missense_Mutation_p.A848T	NM_001098518	NP_056049	Q8IZF2	GP116_HUMAN	G-protein coupled receptor 116	1176	Helical; Name=5; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(1)	1						NSCLC(59;410 1274 8751 36715 50546)								0.404494	105.284972	105.99372	36	53	CC		KEEP	---	---	---	---	capture	Lung(136;0.192)		Missense_Mutation	SNP	46934073	46934073	6907	6	C	T	T	27	27	GPR116	T	1	1
MAP3K7	6885	broad.mit.edu	36	6	91338174	91338174	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:91338174A>G	uc003pnz.1	-	c.194T>C	c.(193-195)ATA>ACA	p.I65T	MAP3K7_uc003poa.1_Missense_Mutation_p.I65T|MAP3K7_uc003pob.1_Missense_Mutation_p.I65T|MAP3K7_uc003poc.1_Missense_Mutation_p.I65T	NM_145331	NP_663304	O43318	M3K7_HUMAN	mitogen-activated protein kinase kinase kinase 7	65	Protein kinase.				activation of MAPK activity|activation of NF-kappaB-inducing kinase activity|histone H3 acetylation|I-kappaB phosphorylation|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-2 production|positive regulation of JUN kinase activity|positive regulation of NF-kappaB transcription factor activity|positive regulation of T cell activation|positive regulation of T cell cytokine production|stress-activated MAPK cascade|T cell receptor signaling pathway|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway|transforming growth factor beta receptor signaling pathway	Ada2/Gcn5/Ada3 transcription activator complex|cytosol|endosome membrane	ATP binding|magnesium ion binding|MAP kinase kinase kinase activity|protein binding|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3		all_cancers(76;6.4e-08)|Acute lymphoblastic leukemia(125;1.43e-09)|Prostate(29;9.32e-09)|all_hematologic(105;3.69e-06)|all_epithelial(107;0.000187)|Ovarian(999;0.0164)								329				0.421687	118.113629	118.557037	35	48	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(136;2.05e-11)|all cancers(137;3.25e-11)|GBM - Glioblastoma multiforme(226;0.0416)|BRCA - Breast invasive adenocarcinoma(108;0.0429)	Missense_Mutation	SNP	91338174	91338174	9638	6	A	G	G	16	16	MAP3K7	G	4	4
MUC17	140453	broad.mit.edu	36	7	100468566	100468566	+	Silent	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:100468566C>T	uc003uxp.1	+	c.7149C>T	c.(7147-7149)GAC>GAT	p.D2383D	MUC17_uc010lho.1_Non-coding_Transcript	NM_001040105	NP_001035194	Q685J3	MUC17_HUMAN	mucin 17	2383	Extracellular (Potential).|59 X approximate tandem repeats.|38.|Ser-rich.					extracellular region|integral to membrane|plasma membrane	extracellular matrix constituent, lubricant activity			ovary(14)|breast(3)|lung(2)	19	Lung NSC(181;0.136)|all_lung(186;0.182)													0.266556	397.694717	427.436402	161	443	CC		KEEP	---	---	---	---	capture			Silent	SNP	100468566	100468566	10368	7	C	T	T	19	19	MUC17	T	1	1
PIK3CG	5294	broad.mit.edu	36	7	106295493	106295493	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106295493C>T	uc003vdv.2	+	c.251C>T	c.(250-252)GCG>GTG	p.A84V	PIK3CG_uc003vdu.1_Missense_Mutation_p.A84V|PIK3CG_uc003vdw.1_Missense_Mutation_p.A84V	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	84					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.390625	69.460547	70.130685	25	39	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106295493	106295493	12340	7	C	T	T	27	27	PIK3CG	T	1	1
HOXA6	3203	broad.mit.edu	36	7	27153467	27153467	+	Missense_Mutation	SNP	T	G	G			TCGA-27-1835-01	TCGA-27-1835-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:27153467T>G	uc003syo.1	-	c.427A>C	c.(427-429)ATG>CTG	p.M143L		NM_024014	NP_076919	P31267	HXA6_HUMAN	homeobox A6	143					regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)|central_nervous_system(1)	2														0.253807	144.47303	155.298793	50	147	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27153467	27153467	7588	7	T	G	G	50	50	HOXA6	G	4	4
TXNDC3	51314	broad.mit.edu	36	7	37870506	37870506	+	Silent	SNP	G	C	C			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:37870506G>C	uc003tfn.1	+	c.486G>C	c.(484-486)CCG>CCC	p.P162P		NM_016616	NP_057700	Q8N427	TXND3_HUMAN	thioredoxin domain containing 3	162	NDK 1.				cell differentiation|cell redox homeostasis|CTP biosynthetic process|GTP biosynthetic process|multicellular organismal development|spermatogenesis|UTP biosynthetic process	cytoplasm|microtubule cytoskeleton	ATP binding|nucleoside diphosphate kinase activity			ovary(1)|breast(1)|central_nervous_system(1)	3						Ovarian(108;903 1537 27096 29907 47400)								0.176471	20.350222	25.375768	9	42	GG		KEEP	---	---	---	---	capture			Silent	SNP	37870506	37870506	17354	7	G	C	C	39	39	TXNDC3	C	3	3
ABCB1	5243	broad.mit.edu	36	7	87017192	87017192	+	Missense_Mutation	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:87017192G>A	uc003uiz.1	-	c.1465C>T	c.(1465-1467)CGC>TGC	p.R489C		NM_000927	NP_000918	P08183	MDR1_HUMAN	ATP-binding cassette, subfamily B, member 1	489	ABC transporter 1.|Cytoplasmic (Potential).					apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Esophageal squamous(14;0.00164)				Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)									0.246334	205.139698	225.111776	84	257	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	87017192	87017192	41	7	G	A	A	37	37	ABCB1	A	1	1
MCM7	4176	broad.mit.edu	36	7	99531632	99531632	+	Silent	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99531632C>T	uc003usw.1	-	c.1296G>A	c.(1294-1296)GGG>GGA	p.G432G	MCM7_uc003usv.1_Silent_p.G256G|MCM7_uc003usx.1_Silent_p.G256G|MIR25_hsa-mir-25|MI0000082_5'Flank|MIR93_hsa-mir-93|MI0000095_5'Flank|MIR106B_hsa-mir-106b|MI0000734_5'Flank	NM_005916	NP_005907	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	432	MCM.				cell cycle checkpoint|DNA strand elongation involved in DNA replication|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|regulation of phosphorylation|response to DNA damage stimulus|S phase of mitotic cell cycle	chromatin|MCM complex	ATP binding|protein binding				0	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)				Atorvastatin(DB01076)									0.25	62.275779	68.416396	27	81	CC		KEEP	---	---	---	---	capture			Silent	SNP	99531632	99531632	9781	7	C	T	T	22	22	MCM7	T	2	2
EBF2	64641	broad.mit.edu	36	8	25821969	25821969	+	Missense_Mutation	SNP	G	T	T			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:25821969G>T	uc003xes.1	-	c.571C>A	c.(571-573)CTC>ATC	p.L191I	PPP2R2A_uc003xek.1_Intron	NM_022659	NP_073150	Q9HAK2	COE2_HUMAN	early B-cell factor 2	191					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|metal ion binding|transcription regulator activity			ovary(3)	3		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)				Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)								0.397436	91.90825	92.626305	31	47	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)	Missense_Mutation	SNP	25821969	25821969	5067	8	G	T	T	35	35	EBF2	T	3	3
COL5A1	1289	broad.mit.edu	36	9	136760341	136760341	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:136760341C>T	uc004cfe.1	+	c.791C>T	c.(790-792)ACG>ATG	p.T264M		NM_000093	NP_000084	P20908	CO5A1_HUMAN	alpha 1 type V collagen preproprotein	264	Nonhelical region.				axon guidance|cell adhesion|collagen biosynthetic process|collagen fibril organization|eye morphogenesis|fibril organization|integrin biosynthetic process|skin development|wound healing, spreading of epidermal cells	collagen type V	heparin binding|integrin binding|platelet-derived growth factor binding|proteoglycan binding			ovary(3)|pancreas(2)|central_nervous_system(1)|kidney(1)|skin(1)	8		Myeloproliferative disorder(178;0.0341)												0.345622	204.255812	208.823729	75	142	CC		KEEP	---	---	---	---	capture		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)	Missense_Mutation	SNP	136760341	136760341	3834	9	C	T	T	19	19	COL5A1	T	1	1
COL4A6	1288	broad.mit.edu	36	X	107294485	107294485	+	Splice_Site_SNP	SNP	C	A	A			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:107294485C>A	uc004enw.2	-	c.4072_splice	c.e40+1	p.G1358_splice	COL4A6_uc004env.2_Splice_Site_SNP_p.G1357_splice|COL4A6_uc010npk.1_Intron|COL4A6_uc010npj.1_5'Flank	NM_001847	NP_001838			type IV alpha 6 collagen isoform A precursor						cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						Melanoma(87;1895 1945 2589 7165)								0.340996	250.963942	256.810509	89	172	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	107294485	107294485	3833	23	C	A	A	18	18	COL4A6	A	5	3
NKAP	79576	broad.mit.edu	36	X	118961288	118961288	+	Missense_Mutation	SNP	G	C	C			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:118961288G>C	uc004esh.1	-	c.309C>G	c.(307-309)AGC>AGG	p.S103R		NM_024528	NP_078804	Q8N5F7	NKAP_HUMAN	NFKB activating protein	103	Ser-rich.				Notch signaling pathway|positive regulation of alpha-beta T cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	chromatin binding|protein binding|transcription repressor activity			ovary(2)	2														0.1875	6.917537	9.875037	6	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118961288	118961288	10840	23	G	C	C	34	34	NKAP	C	3	3
MAGEC2	51438	broad.mit.edu	36	X	141119257	141119257	+	Silent	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:141119257C>T	uc004fbu.1	-	c.183G>A	c.(181-183)CTG>CTA	p.L61L	MAGEC2_uc010nsm.1_Silent_p.L61L	NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	61						cytoplasm|nucleus				breast(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.477707	226.902117	226.97073	75	82	CC		KEEP	---	---	---	---	capture			Silent	SNP	141119257	141119257	9562	23	C	T	T	29	29	MAGEC2	T	2	2
EIF1AX	1964	broad.mit.edu	36	X	20058555	20058555	+	Silent	SNP	G	A	A			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:20058555G>A	uc004czt.1	-	c.429C>T	c.(427-429)GAC>GAT	p.D143D		NM_001412	NP_001403	P47813	IF1AX_HUMAN	X-linked eukaryotic translation initiation	143						cytosol	translation initiation factor activity			ovary(1)	1														0.363636	125.069356	127.047596	44	77	GG		KEEP	---	---	---	---	capture			Silent	SNP	20058555	20058555	5181	23	G	A	A	40	40	EIF1AX	A	1	1
IL1RAPL1	11141	broad.mit.edu	36	X	29883565	29883565	+	Silent	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:29883565C>T	uc004dby.2	+	c.1798C>T	c.(1798-1800)CTA>TTA	p.L600L		NM_014271	NP_055086	Q9NZN1	IRPL1_HUMAN	interleukin 1 receptor accessory protein-like 1	600	Cytoplasmic (Potential).|Interaction with NCS1.				innate immune response|negative regulation of calcium ion transport via voltage-gated calcium channel activity|negative regulation of exocytosis|regulation of neuron projection development	cytoplasm|integral to membrane|plasma membrane	protein binding|transmembrane receptor activity			ovary(3)|lung(1)|pancreas(1)	5														0.24	7.620241	9.185747	6	19	CC		KEEP	---	---	---	---	capture			Silent	SNP	29883565	29883565	7962	23	C	T	T	32	32	IL1RAPL1	T	2	2
ZNF674	641339	broad.mit.edu	36	X	46244429	46244429	+	Silent	SNP	G	T	T			TCGA-27-1835-01	TCGA-27-1835-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:46244429G>T	uc004dgr.1	-	c.1539C>A	c.(1537-1539)ATC>ATA	p.I513I		NM_001039891	NP_001034980	Q2M3X9	ZN674_HUMAN	zinc finger family member 674	513	C2H2-type 9.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(2)	2														0.373134	70.755494	71.703548	25	42	GG		KEEP	---	---	---	---	capture			Silent	SNP	46244429	46244429	18676	23	G	T	T	45	45	ZNF674	T	3	3
ACRC	93953	broad.mit.edu	36	X	70747316	70747316	+	Missense_Mutation	SNP	A	G	G			TCGA-27-1835-01	TCGA-27-1835-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:70747316A>G	uc004eae.1	+	c.1672A>G	c.(1672-1674)AGC>GGC	p.S558G		NM_052957	NP_443189	Q96QF7	ACRC_HUMAN	ACRC protein	558						nucleus				ovary(3)	3	Renal(35;0.156)													0.348485	64.080844	65.428626	23	43	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70747316	70747316	172	23	A	G	G	7	7	ACRC	G	4	4
RPS4X	6191	broad.mit.edu	36	X	71409304	71409304	+	Missense_Mutation	SNP	C	T	T			TCGA-27-1835-01	TCGA-27-1835-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:71409304C>T	uc004ear.1	-	c.734G>A	c.(733-735)CGC>CAC	p.R245H		NM_001007	NP_000998	P62701	RS4X_HUMAN	ribosomal protein S4, X-linked X isoform	245					endocrine pancreas development|positive regulation of cell proliferation|positive regulation of translation|translational elongation|translational termination|viral transcription	cytosolic small ribosomal subunit|polysome	rRNA binding|structural constituent of ribosome				0	Renal(35;0.156)													0.311688	64.572328	67.003434	24	53	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71409304	71409304	14125	23	C	T	T	27	27	RPS4X	T	1	1
IQSEC3	440073	broad.mit.edu	36	12	118513	118515	+	In_Frame_Del	DEL	GAG	-	-			TCGA-27-1835-01	TCGA-27-1835-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:118513_118515delGAG	uc001qhw.1	+	c.814_816delGAG	c.(814-816)GAGdel	p.E276del	IQSEC3_uc001qhu.1_In_Frame_Del_p.E276del|IQSEC3_uc001qht.1_In_Frame_Del_p.E361del	NM_015232	NP_056047	Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	579	Poly-Glu.				regulation of ARF protein signal transduction	cytoplasm	ARF guanyl-nucleotide exchange factor activity			central_nervous_system(2)|large_intestine(1)	3	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)										0.33			2	4				---	---	---	---	capture_indel			In_Frame_Del	DEL	118513	118515	8122	12	GAG	-	-	33	33	IQSEC3	-	5	5
NACA	4666	broad.mit.edu	36	12	55398199	55398206	+	Frame_Shift_Del	DEL	TTGTGGGT	-	-			TCGA-27-1835-01	TCGA-27-1835-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:55398199_55398206delTTGTGGGT	uc009zoy.1	-	c.3375_3382delACCCACAA	c.(3373-3384)GCACCCACAACCfs	p.A1125fs	NACA_uc001slz.2_Intron|NACA_uc001sly.2_Intron|NACA_uc001smc.2_Intron|NACA_uc001sma.2_Intron|NACA_uc001smb.2_Intron	NM_001113203	NP_001106674	Q13765	NACA_HUMAN	nascent polypeptide-associated complex alpha	Error:Variant_position_missing_in_Q13765_after_alignment					interspecies interaction between organisms|protein transport|transcription, DNA-dependent|translation	nascent polypeptide-associated complex|nucleus	DNA binding			ovary(1)	1									p.A1125fs(SW837-Tumor)|p.A1125fs(KYSE180-Tumor)|p.A1125fs(NCIH684-Tumor)|p.T1127I(BICR31-Tumor)|p.A1125fs(DMS273-Tumor)	449				0.79			30	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	55398199	55398206	10528	12	TTGTGGGT	-	-	60	60	NACA	-	5	5
PRDM5	11107	broad.mit.edu	36	4	121940331	121940334	+	Frame_Shift_Del	DEL	CAAT	-	-			TCGA-27-1835-01	TCGA-27-1835-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:121940331_121940334delCAAT	uc003idn.1	-	c.962_965delATTG	c.(961-966)GATTGTfs	p.D321fs	PRDM5_uc003ido.1_Frame_Shift_Del_p.D290fs|PRDM5_uc010ine.1_Frame_Shift_Del_p.D290fs	NM_018699	NP_061169	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	321_322	C2H2-type 6.				histone deacetylation|histone H3-K9 methylation|mitotic cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	promoter binding|repressing transcription factor binding|specific transcriptional repressor activity|zinc ion binding			central_nervous_system(1)|pancreas(1)	2														0.36			21	38				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	121940331	121940334	12902	4	CAAT	-	-	17	17	PRDM5	-	5	5
FAM193A	8603	broad.mit.edu	36	4	2662464	2662465	+	Frame_Shift_Del	DEL	CA	-	-			TCGA-27-1835-01	TCGA-27-1835-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:2662464_2662465delCA	uc010icl.1	+	c.1899_1900delCA	c.(1897-1902)TTCAGAfs	p.F633fs	FAM193A_uc003gfd.1_Frame_Shift_Del_p.F633fs|FAM193A_uc010icm.1_Non-coding_Transcript|FAM193A_uc003gfe.1_Frame_Shift_Del_p.F487fs	NM_003704	NP_003695	P78312	F193A_HUMAN	hypothetical protein LOC8603	633_634										ovary(3)	3														0.33			35	72				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	2662464	2662465	5735	4	CA	-	-	29	29	FAM193A	-	5	5
MDN1	23195	broad.mit.edu	36	6	90419441	90419441	+	Frame_Shift_Del	DEL	C	-	-			TCGA-27-1835-01	TCGA-27-1835-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:90419441_90419441delC	uc003pnn.1	-	c.15816_15816delG	c.(15814-15816)ACGfs	p.T5272fs		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	5272					protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding			ovary(8)	8		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)										0.37			143	241				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	90419441	90419441	9804	6	C	-	-	31	31	MDN1	-	5	5
TMC1	117531	broad.mit.edu	36	9	74631608	74631609	+	Frame_Shift_Ins	INS	-	A	A			TCGA-27-1835-01	TCGA-27-1835-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:74631608_74631609insA	uc004aiz.1	+	c.2007_2008insA	c.(2005-2010)GGCAAAfs	p.G669fs	TMC1_uc010moz.1_Frame_Shift_Ins_p.G627fs|TMC1_uc004aja.1_Non-coding_Transcript|TMC1_uc004ajb.1_Non-coding_Transcript|TMC1_uc004ajc.1_Frame_Shift_Ins_p.G523fs|TMC1_uc010mpa.1_Frame_Shift_Ins_p.G523fs	NM_138691	NP_619636	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	669_670	Extracellular (Potential).				sensory perception of sound	integral to membrane				ovary(1)	1						Pancreas(75;173 1345 14232 34245 43413)								0.31			83	183				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	74631608	74631609	16514	9	-	A	A	25	25	TMC1	A	5	5
