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
PRRG4	79056	broad.mit.edu	36	11	32831584	32831584	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:32831584C>T	uc001mtx.1	+	c.616C>T	c.(616-618)CCA>TCA	p.P206S		NM_024081	NP_076986	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4	206	Cytoplasmic (Potential).|Poly-Pro.					extracellular region|Golgi apparatus|integral to membrane	calcium ion binding				0	Breast(20;0.206)													0.378641	111.200004	112.530856	39	64	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32831584	32831584	13057	11	C	T	T	18	18	PRRG4	T	2	2
DNHD1	144132	broad.mit.edu	36	11	6545248	6545248	+	Missense_Mutation	SNP	G	C	C			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:6545248G>C	uc001mea.2	+	c.740G>C	c.(739-741)CGA>CCA	p.R247P	DNHD1_uc001mdw.2_Missense_Mutation_p.R2032P|DNHD1_uc001meb.2_Missense_Mutation_p.R246P|DNHD1_uc001mec.1_Missense_Mutation_p.R246P|DNHD1_uc009yfg.1_5'Flank	NM_144666	NP_653267	Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1 isoform 1	3978					microtubule-based movement	dynein complex	microtubule motor activity			ovary(2)	2		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)												0.166667	6.785031	9.313972	4	20	GG		KEEP	---	---	---	---	capture		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)	Missense_Mutation	SNP	6545248	6545248	4851	11	G	C	C	37	37	DNHD1	C	3	3
TRIM49	57093	broad.mit.edu	36	11	89171342	89171342	+	Silent	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:89171342G>A	uc001pdb.1	-	c.963C>T	c.(961-963)TTC>TTT	p.F321F		NM_020358	NP_065091	P0CI25	TRI49_HUMAN	ring finger protein 18	321	B30.2/SPRY.					intracellular	zinc ion binding				0		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00556)												0.202899	30.907692	36.5665	14	55	GG		KEEP	---	---	---	---	capture			Silent	SNP	89171342	89171342	17069	11	G	A	A	45	45	TRIM49	A	2	2
GPR81	27198	broad.mit.edu	36	12	121780131	121780131	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:121780131C>T	uc001ucz.1	-	c.709G>A	c.(709-711)GTG>ATG	p.V237M	GPR81_uc001ucw.1_Non-coding_Transcript	NM_032554	NP_115943	Q9BXC0	GPR81_HUMAN	G protein-coupled receptor 81	237	Helical; Name=6; (Potential).				response to estradiol stimulus	integral to membrane|plasma membrane	G-protein coupled receptor activity			breast(2)|ovary(1)|pancreas(1)	4	all_neural(191;0.0837)|Medulloblastoma(191;0.163)													0.484848	138.279031	138.299081	48	51	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;2.14e-05)|Epithelial(86;3.25e-05)|BRCA - Breast invasive adenocarcinoma(302;0.197)	Missense_Mutation	SNP	121780131	121780131	6986	12	C	T	T	19	19	GPR81	T	1	1
ZNF10	7556	broad.mit.edu	36	12	132242352	132242352	+	Silent	SNP	A	G	G			TCGA-06-2564-01	TCGA-06-2564-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:132242352A>G	uc009zzb.1	+	c.447A>G	c.(445-447)CAA>CAG	p.Q149Q	ZNF10_uc001ulq.1_Silent_p.Q149Q|ZNF10_uc009zzc.1_Intron	NM_015394	NP_056209	P21506	ZNF10_HUMAN	zinc finger protein 10	149				Missing (in Ref. 1).	regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(1)|central_nervous_system(1)	2	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)												0.333333	126.470137	129.417171	40	80	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)	Silent	SNP	132242352	132242352	18303	12	A	G	G	3	3	ZNF10	G	4	4
MLL2	8085	broad.mit.edu	36	12	47734589	47734589	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:47734589C>T	uc001rta.2	-	c.389G>A	c.(388-390)GGA>GAA	p.G130E		NM_003482	NP_003473	O14686	MLL2_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 2	130					chromatin silencing|histone H3-K4 methylation|oocyte growth|positive regulation of cell proliferation|positive regulation of estrogen receptor signaling pathway|positive regulation of gene-specific transcription from RNA polymerase II promoter|response to estrogen stimulus|transcription, DNA-dependent	histone methyltransferase complex	histone-lysine N-methyltransferase activity|promoter binding|protein binding|zinc ion binding			kidney(16)|lung(4)|skin(4)|ovary(3)|pancreas(2)	29														0.5	41.274585	41.274585	13	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47734589	47734589	10011	12	C	T	T	30	30	MLL2	T	2	2
ENO2	2026	broad.mit.edu	36	12	6897080	6897080	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:6897080C>G	uc001qru.1	+	c.385C>G	c.(385-387)CCC>GCC	p.P129A	ENO2_uc009zfi.1_Missense_Mutation_p.P129A|ENO2_uc001qrv.1_Missense_Mutation_p.P129A	NM_001975	NP_001966	P09104	ENOG_HUMAN	enolase 2	129					gluconeogenesis|glycolysis	phosphopyruvate hydratase complex|plasma membrane	magnesium ion binding|phosphopyruvate hydratase activity				0														0.462963	68.765631	68.845207	25	29	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6897080	6897080	5315	12	C	G	G	26	26	ENO2	G	3	3
LRRIQ1	84125	broad.mit.edu	36	12	84016400	84016400	+	Silent	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:84016400C>T	uc001tac.1	+	c.3024C>T	c.(3022-3024)GGC>GGT	p.G1008G	LRRIQ1_uc001tab.1_Silent_p.G1008G	NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1008	LRR 6.									ovary(4)|central_nervous_system(1)	5														0.366667	91.247594	92.655767	33	57	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(134;0.212)	Silent	SNP	84016400	84016400	9405	12	C	T	T	27	27	LRRIQ1	T	1	1
KERA	11081	broad.mit.edu	36	12	89974181	89974181	+	Silent	SNP	G	C	C			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:89974181G>C	uc001tbl.1	-	c.9C>G	c.(7-9)GGC>GGG	p.G3G		NM_007035	NP_008966	O60938	KERA_HUMAN	keratocan	3					response to stimulus|visual perception	proteinaceous extracellular matrix					0														0.238095	6.315985	7.60842	5	16	GG		KEEP	---	---	---	---	capture			Silent	SNP	89974181	89974181	8449	12	G	C	C	46	46	KERA	C	3	3
ADCY4	196883	broad.mit.edu	36	14	23870912	23870912	+	Silent	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:23870912G>A	uc001wov.1	-	c.591C>T	c.(589-591)CGC>CGT	p.R197R	ADCY4_uc001wow.1_Silent_p.R197R|ADCY4_uc001wox.1_Silent_p.R197R|ADCY4_uc001woy.1_Silent_p.R197R	NM_139247	NP_640340	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	197	Cytoplasmic (Potential).				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)|pancreas(1)	3										1				0.382979	46.526438	47.094405	18	29	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(265;0.0192)	Silent	SNP	23870912	23870912	297	14	G	A	A	38	38	ADCY4	A	1	1
SYT16	83851	broad.mit.edu	36	14	61617618	61617618	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:61617618G>A	uc001xfu.1	+	c.1307G>A	c.(1306-1308)CGC>CAC	p.R436H		NM_031914	NP_114120	Q17RD7	SYT16_HUMAN	synaptotagmin XIV-like	436	C2 1.									central_nervous_system(1)	1														0.452381	51.725035	51.806341	19	23	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)	Missense_Mutation	SNP	61617618	61617618	15993	14	G	A	A	38	38	SYT16	A	1	1
C15orf48	84419	broad.mit.edu	36	15	43510545	43510545	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:43510545G>A	uc001zvg.1	+	c.91G>A	c.(91-93)GCT>ACT	p.A31T	C15orf48_uc001zvh.1_Missense_Mutation_p.A31T	NM_197955	NP_922946	Q9C002	NMES1_HUMAN	hypothetical protein LOC84419	31						nucleus		p.A31P(1)		ovary(1)	1		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)												0.290476	151.894952	160.15365	61	149	GG		KEEP	---	---	---	---	capture		all cancers(107;1.67e-16)|GBM - Glioblastoma multiforme(94;1.71e-06)	Missense_Mutation	SNP	43510545	43510545	1849	15	G	A	A	38	38	C15orf48	A	1	1
CCDC33	80125	broad.mit.edu	36	15	72351117	72351117	+	Silent	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:72351117C>T	uc002axo.1	+	c.567C>T	c.(565-567)AAC>AAT	p.N189N	CCDC33_uc002axp.2_Silent_p.N11N	NM_025055	NP_079331	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33 isoform 1	392							protein binding			ovary(3)	3														0.267857	33.805788	36.530218	15	41	CC		KEEP	---	---	---	---	capture			Silent	SNP	72351117	72351117	2928	15	C	T	T	19	19	CCDC33	T	1	1
ITGAX	3687	broad.mit.edu	36	16	31281849	31281849	+	Silent	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:31281849C>T	uc002ebt.2	+	c.1452C>T	c.(1450-1452)TAC>TAT	p.Y484Y	ITGAX_uc002ebu.1_Silent_p.Y484Y	NM_000887	NP_000878	P20702	ITAX_HUMAN	integrin alpha X precursor	484	FG-GAP 5.|Extracellular (Potential).				blood coagulation|cell adhesion|integrin-mediated signaling pathway|leukocyte migration|organ morphogenesis	integrin complex	protein binding|receptor activity			ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.382609	121.074439	122.46274	44	71	CC		KEEP	---	---	---	---	capture			Silent	SNP	31281849	31281849	8193	16	C	T	T	19	19	ITGAX	T	1	1
MYLK3	91807	broad.mit.edu	36	16	45312588	45312588	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:45312588C>T	uc002eei.2	-	c.1933G>A	c.(1933-1935)GTC>ATC	p.V645I		NM_182493	NP_872299	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	645	Protein kinase.				cardiac myofibril assembly|cellular response to interleukin-1|positive regulation of sarcomere organization|protein phosphorylation|regulation of vascular permeability involved in acute inflammatory response|sarcomere organization|sarcomerogenesis	cytosol	ATP binding|calmodulin-dependent protein kinase activity|myosin light chain kinase activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)								207				0.307317	170.253449	177.03606	63	142	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	45312588	45312588	10453	16	C	T	T	19	19	MYLK3	T	1	1
MYOCD	93649	broad.mit.edu	36	17	12607560	12607560	+	Silent	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:12607560G>A	uc002gno.1	+	c.2835G>A	c.(2833-2835)CCG>CCA	p.P945P	MYOCD_uc002gnn.1_Silent_p.P897P|MYOCD_uc002gnq.1_Silent_p.P621P	NM_153604	NP_705832	Q8IZQ8	MYCD_HUMAN	myocardin	897					cardiac cell differentiation|positive regulation of gene-specific transcription from RNA polymerase II promoter|positive regulation of smooth muscle contraction|regulation of smooth muscle cell differentiation|transcription, DNA-dependent	nucleus	nucleic acid binding|transcription factor binding			central_nervous_system(2)|ovary(1)	3														0.512821	104.745725	104.757072	40	38	GG		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)	Silent	SNP	12607560	12607560	10482	17	G	A	A	38	38	MYOCD	A	1	1
SLC13A5	284111	broad.mit.edu	36	17	6538202	6538202	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:6538202G>T	uc002gdj.1	-	c.1094C>A	c.(1093-1095)ACC>AAC	p.T365N	SLC13A5_uc002gdk.1_Missense_Mutation_p.T348N|SLC13A5_uc010clq.1_Missense_Mutation_p.T322N	NM_177550	NP_808218	Q86YT5	S13A5_HUMAN	solute carrier family 13, member 5 isoform a	365	Helical; (Potential).					integral to membrane	citrate transmembrane transporter activity				0														0.21875	12.141972	14.466149	7	25	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6538202	6538202	14890	17	G	T	T	44	44	SLC13A5	T	3	3
SLC2A4	6517	broad.mit.edu	36	17	7128421	7128421	+	Silent	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7128421G>A	uc002gfp.1	+	c.726G>A	c.(724-726)AAG>AAA	p.K242K	SLC2A4_uc002gfo.1_Silent_p.K242K|SLC2A4_uc010cmd.1_Non-coding_Transcript	NM_001042	NP_001033	P14672	GTR4_HUMAN	glucose transporter 4	242	Cytoplasmic (Potential).				carbohydrate metabolic process|glucose homeostasis|glucose import	external side of plasma membrane|integral to plasma membrane|perinuclear region of cytoplasm	D-glucose transmembrane transporter activity|protein binding				0														0.34	45.657301	46.789925	17	33	GG		KEEP	---	---	---	---	capture			Silent	SNP	7128421	7128421	15043	17	G	A	A	33	33	SLC2A4	A	2	2
RHBDF2	79651	broad.mit.edu	36	17	71984660	71984660	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71984660C>T	uc002jrq.1	-	c.1049G>A	c.(1048-1050)GGC>GAC	p.G350D	RHBDF2_uc002jrp.1_Missense_Mutation_p.G321D|RHBDF2_uc002jrr.1_Missense_Mutation_p.G202D|RHBDF2_uc002jrs.1_Missense_Mutation_p.G345D	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1	350	Cytoplasmic (Potential).				negative regulation of protein secretion	endoplasmic reticulum membrane|integral to membrane	serine-type endopeptidase activity				0														0.390071	149.889016	151.382157	55	86	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71984660	71984660	13795	17	C	T	T	26	26	RHBDF2	T	2	2
POLI	11201	broad.mit.edu	36	18	50063322	50063322	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:50063322G>A	uc002lfj.2	+	c.914G>A	c.(913-915)CGT>CAT	p.R305H	POLI_uc002lfk.2_Missense_Mutation_p.R202H|POLI_uc010dpg.1_5'UTR|POLI_uc002lfl.1_Missense_Mutation_p.R237H	NM_007195	NP_009126	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	305					DNA repair|DNA replication	nucleoplasm	damaged DNA binding|DNA-directed DNA polymerase activity|metal ion binding|protein binding			ovary(2)|kidney(1)	3														0.25	10.392645	11.301377	4	12	GG		KEEP	---	---	---	---	capture		Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)	Missense_Mutation	SNP	50063322	50063322	12631	18	G	A	A	40	40	POLI	A	1	1
WIZ	58525	broad.mit.edu	36	19	15396725	15396725	+	Silent	SNP	C	G	G			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:15396725C>G	uc002nba.2	-	c.1851G>C	c.(1849-1851)TCG>TCC	p.S617S	WIZ_uc002nbb.2_Silent_p.S576S	NM_021241	NP_067064	O95785	WIZ_HUMAN	widely-interspaced zinc finger motifs	1433						nucleus	zinc ion binding				0														0.5	6.895354	6.895354	4	4	CC		KEEP	---	---	---	---	capture			Silent	SNP	15396725	15396725	17949	19	C	G	G	27	27	WIZ	G	3	3
DDX49	54555	broad.mit.edu	36	19	18891579	18891579	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18891579C>T	uc002nkq.1	+	c.29C>T	c.(28-30)TCA>TTA	p.S10L	COPE_uc002nkk.1_5'Flank|COPE_uc002nkl.1_5'Flank|COPE_uc002nkm.1_5'Flank|COPE_uc002nkn.1_5'Flank|HOMER3_uc002nkp.1_Intron|HOMER3_uc002nko.1_Intron|DDX49_uc002nkr.1_Non-coding_Transcript|DDX49_uc002nks.1_5'UTR|DDX49_uc002nkt.1_5'Flank	NM_019070	NP_061943	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	10	Q motif.						ATP binding|ATP-dependent helicase activity|RNA binding			ovary(1)	1														0.333333	53.780179	55.256128	20	40	CC		KEEP	---	---	---	---	capture	Epithelial(12;0.0289)		Missense_Mutation	SNP	18891579	18891579	4537	19	C	T	T	29	29	DDX49	T	2	2
SERTAD1	29950	broad.mit.edu	36	19	45620818	45620818	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:45620818C>G	uc002ont.2	-	c.476G>C	c.(475-477)GGC>GCC	p.G159A		NM_013376	NP_037508	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	159					positive regulation of cell proliferation|regulation of cyclin-dependent protein kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent						0														0.333333	6.463085	6.664574	3	6	CC		KEEP	---	---	---	---	capture	Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Missense_Mutation	SNP	45620818	45620818	14608	19	C	G	G	26	26	SERTAD1	G	3	3
SH2D3A	10045	broad.mit.edu	36	19	6711704	6711704	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6711704G>A	uc002mft.1	-	c.364C>T	c.(364-366)CGC>TGC	p.R122C		NM_005490	NP_005481	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	122					JNK cascade|small GTPase mediated signal transduction	intracellular	guanyl-nucleotide exchange factor activity|SH3/SH2 adaptor activity			breast(2)	2														0.396226	59.968929	60.466513	21	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6711704	6711704	14724	19	G	A	A	40	40	SH2D3A	A	1	1
FBN3	84467	broad.mit.edu	36	19	8060483	8060483	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8060483G>A	uc002mjf.1	-	c.6322C>T	c.(6322-6324)CGC>TGC	p.R2108C	FBN3_uc002mje.1_5'UTR	NM_032447	NP_115823	Q75N90	FBN3_HUMAN	fibrillin 3 precursor	2108	EGF-like 33; calcium-binding.					proteinaceous extracellular matrix	calcium ion binding|extracellular matrix structural constituent			ovary(6)|central_nervous_system(1)|pancreas(1)	8														0.347458	237.870284	242.721196	82	154	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8060483	8060483	5940	19	G	A	A	39	39	FBN3	A	1	1
TXNIP	10628	broad.mit.edu	36	1	144152266	144152266	+	Silent	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:144152266C>T	uc001enn.2	+	c.996C>T	c.(994-996)CCC>CCT	p.P332P	TXNIP_uc001enm.1_Intron	NM_006472	NP_006463	Q9H3M7	TXNIP_HUMAN	thioredoxin interacting protein	332					cell cycle|keratinocyte differentiation|transcription, DNA-dependent		ubiquitin protein ligase binding			ovary(2)	2	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)													0.281457	244.04697	257.00829	85	217	CC		KEEP	---	---	---	---	capture			Silent	SNP	144152266	144152266	17359	1	C	T	T	24	24	TXNIP	T	2	2
FLG	2312	broad.mit.edu	36	1	150545479	150545479	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150545479C>T	uc001ezu.1	-	c.8507G>A	c.(8506-8508)AGT>AAT	p.S2836N		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2836	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)	9	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.156522	186.925189	264.651187	108	582	CC		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150545479	150545479	6160	1	C	T	T	20	20	FLG	T	2	2
CELA3A	10136	broad.mit.edu	36	1	22206010	22206010	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:22206010G>A	uc001bfl.1	+	c.415G>A	c.(415-417)GTC>ATC	p.V139I		NM_005747	NP_005738	P09093	CEL3A_HUMAN	elastase 3A, pancreatic preproprotein	139	Peptidase S1.				cholesterol metabolic process|digestion|proteolysis		serine-type endopeptidase activity				0														0.390728	160.496532	162.072857	59	92	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	22206010	22206010	3346	1	G	A	A	40	40	CELA3A	A	1	1
EPB41	2035	broad.mit.edu	36	1	29217438	29217438	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:29217438G>A	uc001brm.1	+	c.1021G>A	c.(1021-1023)GAC>AAC	p.D341N	EPB41_uc001brg.1_Missense_Mutation_p.D132N|EPB41_uc001brh.1_Missense_Mutation_p.D132N|EPB41_uc001bri.1_Missense_Mutation_p.D306N|EPB41_uc001brj.1_Missense_Mutation_p.D132N|EPB41_uc009vtk.1_Missense_Mutation_p.D306N|EPB41_uc001brk.2_Missense_Mutation_p.D341N|EPB41_uc001brl.1_Missense_Mutation_p.D341N|EPB41_uc009vtl.1_Missense_Mutation_p.D132N|EPB41_uc009vtm.1_5'UTR	NM_203342	NP_976217	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	341	FERM.				blood circulation|cortical actin cytoskeleton organization|positive regulation of protein binding	extrinsic to membrane|Golgi apparatus|nucleus|plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	1-phosphatidylinositol binding|actin binding|spectrin binding|structural constituent of cytoskeleton			ovary(1)	1		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)												0.340807	212.83433	217.827878	76	147	GG		KEEP	---	---	---	---	capture		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)	Missense_Mutation	SNP	29217438	29217438	5344	1	G	A	A	37	37	EPB41	A	1	1
EIF2C3	192669	broad.mit.edu	36	1	36278023	36278023	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36278023G>A	uc001bzp.1	+	c.1888G>A	c.(1888-1890)GTA>ATA	p.V630I	EIF2C3_uc001bzq.1_Missense_Mutation_p.V396I	NM_024852	NP_803171	Q9H9G7	AGO3_HUMAN	eukaryotic translation initiation factor 2C, 3	630	Piwi.				mRNA catabolic process|negative regulation of translation involved in gene silencing by miRNA	cytoplasmic mRNA processing body|cytosol	protein binding|RNA binding				0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				Colon(144;60 2363 31043 40539)								0.380952	152.170634	153.73686	48	78	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36278023	36278023	5196	1	G	A	A	36	36	EIF2C3	A	2	2
EPHA10	284656	broad.mit.edu	36	1	37969762	37969762	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:37969762C>T	uc009vvi.1	-	c.1571G>A	c.(1570-1572)CGC>CAC	p.R524H	EPHA10_uc009vvh.1_Non-coding_Transcript|EPHA10_uc001cbu.2_Non-coding_Transcript|EPHA10_uc001cbv.1_Non-coding_Transcript	NM_001099439	NP_001092909	Q5JZY3	EPHAA_HUMAN	EPH receptor A10 isofom 3	524	Fibronectin type-III 2.|Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular region|integral to membrane|integral to plasma membrane	ATP binding|ephrin receptor activity|protein binding|transmembrane-ephrin receptor activity			breast(3)|stomach(1)	4	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)								328				0.380734	218.142737	220.870976	83	135	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37969762	37969762	5359	1	C	T	T	27	27	EPHA10	T	1	1
GBP1	2633	broad.mit.edu	36	1	89298492	89298492	+	Silent	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:89298492G>A	uc001dmx.2	-	c.294C>T	c.(292-294)ACC>ACT	p.T98T		NM_002053	NP_002044	P32455	GBP1_HUMAN	guanylate binding protein 1,	98	GTP.				interferon-gamma-mediated signaling pathway	plasma membrane	GTP binding|GTPase activity			ovary(1)	1		Lung NSC(277;0.123)												0.428571	373.400785	374.599597	117	156	GG		KEEP	---	---	---	---	capture		all cancers(265;0.0156)|Epithelial(280;0.0291)	Silent	SNP	89298492	89298492	6539	1	G	A	A	39	39	GBP1	A	1	1
TGM2	7052	broad.mit.edu	36	20	36209824	36209824	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2564-01	TCGA-06-2564-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr20:36209824A>G	uc002xhr.1	-	c.634T>C	c.(634-636)TCC>CCC	p.S212P	TGM2_uc002xhs.1_Missense_Mutation_p.S188P|TGM2_uc002xht.1_Missense_Mutation_p.S212P|TGM2_uc002xhu.2_Missense_Mutation_p.S212P	NM_004613	NP_004604	P21980	TGM2_HUMAN	transglutaminase 2 isoform a	212					apoptotic cell clearance|peptide cross-linking|positive regulation of cell adhesion		acyltransferase activity|metal ion binding|protein binding|protein-glutamine gamma-glutamyltransferase activity			large_intestine(1)|lung(1)|ovary(1)	3		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)									0.266667	6.670053	7.428539	4	11	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36209824	36209824	16358	20	A	G	G	11	11	TGM2	G	4	4
CSE1L	1434	broad.mit.edu	36	20	47122372	47122372	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:47122372C>T	uc002xty.1	+	c.911C>T	c.(910-912)ACG>ATG	p.T304M	CSE1L_uc010ghx.1_Intron|CSE1L_uc010ghy.1_De_novo_Start_InFrame	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein	304					apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)	1														0.306452	152.794936	159.015281	57	129	CC		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)		Missense_Mutation	SNP	47122372	47122372	4071	20	C	T	T	19	19	CSE1L	T	1	1
UCKL1	54963	broad.mit.edu	36	20	62042240	62042240	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:62042240C>T	uc010gkn.1	-	c.1345G>A	c.(1345-1347)GTG>ATG	p.V449M	UCKL1_uc002yhj.1_Missense_Mutation_p.V92M|UCKL1_uc010gkm.1_Missense_Mutation_p.V58M	NM_017859	NP_060329	Q9NWZ5	UCKL1_HUMAN	uridine-cytidine kinase 1-like 1	449					interspecies interaction between organisms	endoplasmic reticulum|nucleus	ATP binding|phosphotransferase activity, alcohol group as acceptor|protein binding|uridine kinase activity				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)													0.307692	20.696611	21.550344	8	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	62042240	62042240	17483	20	C	T	T	19	19	UCKL1	T	1	1
CACNA1I	8911	broad.mit.edu	36	22	38410309	38410309	+	Nonsense_Mutation	SNP	G	T	T			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:38410309G>T	uc003ayc.1	+	c.5887G>T	c.(5887-5889)GAG>TAG	p.E1963*	CACNA1I_uc003ayd.1_Nonsense_Mutation_p.E1928*|CACNA1I_uc003aye.2_Nonsense_Mutation_p.E1878*|CACNA1I_uc003ayf.2_Nonsense_Mutation_p.E1843*	NM_021096	NP_066919	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type,	1963	Cytoplasmic (Potential).				axon guidance|signal transduction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity|protein binding			breast(1)|central_nervous_system(1)	2	Melanoma(58;0.0749)				Flunarizine(DB04841)|Paramethadione(DB00617)|Verapamil(DB00661)									0.366667	30.916358	31.385543	11	19	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	38410309	38410309	2662	22	G	T	T	37	37	CACNA1I	T	5	3
TBC1D8	11138	broad.mit.edu	36	2	101016605	101016605	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:101016605C>G	uc010fiv.1	-	c.1606G>C	c.(1606-1608)GTG>CTG	p.V536L	TBC1D8_uc002tau.2_Missense_Mutation_p.V293L	NM_001102426	NP_001095896	O95759	TBCD8_HUMAN	TBC1 domain family, member 8	536	Rab-GAP TBC.				blood circulation|positive regulation of cell proliferation	intracellular|membrane	calcium ion binding|Rab GTPase activator activity			ovary(3)	3														0.333333	77.654159	79.497195	25	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101016605	101016605	16151	2	C	G	G	18	18	TBC1D8	G	3	3
SAP130	79595	broad.mit.edu	36	2	128423917	128423917	+	Silent	SNP	G	C	C			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:128423917G>C	uc010fmd.1	-	c.2871C>G	c.(2869-2871)GTC>GTG	p.V957V	SAP130_uc002tpn.1_Silent_p.V682V|SAP130_uc002tpo.1_Silent_p.V702V|SAP130_uc002tpp.1_Silent_p.V922V	NM_024545	NP_078821	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	922	Interactions with SIN3A and HDAC1.				histone H3 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	STAGA complex	transcription coactivator activity			ovary(2)	2	Colorectal(110;0.1)													0.222222	63.095407	70.122834	22	77	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(221;0.0771)	Silent	SNP	128423917	128423917	14311	2	G	C	C	45	45	SAP130	C	3	3
TTN	7273	broad.mit.edu	36	2	179128062	179128062	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:179128062G>A	uc002umr.1	-	c.80666C>T	c.(80665-80667)TCT>TTT	p.S26889F	TTN_uc002ums.1_Missense_Mutation_p.S20584F|TTN_uc010frc.1_Missense_Mutation_p.S20517F|TTN_uc010frd.1_Missense_Mutation_p.S20392F	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	27816										ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153										8722				0.375	117.997752	119.424869	39	65	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		Missense_Mutation	SNP	179128062	179128062	17290	2	G	A	A	33	33	TTN	A	2	2
PLCL1	5334	broad.mit.edu	36	2	198674288	198674288	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:198674288C>T	uc010fsp.1	+	c.2954C>T	c.(2953-2955)GCG>GTG	p.A985V	PLCL1_uc002uuv.2_Missense_Mutation_p.A906V|PLCL1_uc002uuw.2_Missense_Mutation_p.A887V	NM_001114661	NP_001108133	Q15111	PLCL1_HUMAN	phospholipase C-like 1 isoform a	985					intracellular signal transduction|lipid metabolic process	cytoplasm	calcium ion binding|phosphatidylinositol phospholipase C activity|signal transducer activity			ovary(1)	1					Quinacrine(DB01103)									0.357955	180.582917	183.70727	63	113	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	198674288	198674288	12465	2	C	T	T	27	27	PLCL1	T	1	1
DNAJB2	3300	broad.mit.edu	36	2	219857693	219857693	+	Missense_Mutation	SNP	A	C	C			TCGA-06-2564-01	TCGA-06-2564-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:219857693A>C	uc002vkx.1	+	c.715A>C	c.(715-717)ACC>CCC	p.T239P	DNAJB2_uc002vkw.1_Missense_Mutation_p.T239P|DNAJB2_uc002vky.1_Missense_Mutation_p.T55P	NM_006736	NP_006727	P25686	DNJB2_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 2	239					ER-associated protein catabolic process|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of inclusion body assembly|negative regulation of protein deubiquitination|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of protein ubiquitination|protein folding|response to unfolded protein	inclusion body	heat shock protein binding|Hsp70 protein binding|polyubiquitin binding|proteasome binding|protein binding|unfolded protein binding				0		Renal(207;0.0474)												0.227273	9.614739	12.878918	10	34	AA		KEEP	---	---	---	---	capture		Epithelial(149;1.97e-06)|all cancers(144;0.00028)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Missense_Mutation	SNP	219857693	219857693	4803	2	A	C	C	10	10	DNAJB2	C	4	4
COL4A4	1286	broad.mit.edu	36	2	227580329	227580329	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:227580329G>A	uc010fxd.1	-	c.5029C>T	c.(5029-5031)CGC>TGC	p.R1677C	COL4A4_uc010fxe.1_Missense_Mutation_p.R1677C	NM_000092	NP_000083	P53420	CO4A4_HUMAN	alpha 4 type IV collagen precursor	1677	Collagen IV NC1.				axon guidance|glomerular basement membrane development	basal lamina|collagen type IV	extracellular matrix structural constituent|protein binding			ovary(5)|central_nervous_system(3)|breast(1)|pancreas(1)	10		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)												0.386423	820.720328	829.374271	296	470	GG		KEEP	---	---	---	---	capture		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)	Missense_Mutation	SNP	227580329	227580329	3831	2	G	A	A	40	40	COL4A4	A	1	1
ATP2B2	491	broad.mit.edu	36	3	10362792	10362792	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:10362792G>A	uc003bvt.1	-	c.2434C>T	c.(2434-2436)CGG>TGG	p.R812W	ATP2B2_uc003bvv.1_Missense_Mutation_p.R767W|ATP2B2_uc003bvw.1_Missense_Mutation_p.R767W|ATP2B2_uc010hdo.1_Missense_Mutation_p.R517W|ATP2B2_uc003bvu.1_Missense_Mutation_p.R767W	NM_001001331	NP_001001331	Q01814	AT2B2_HUMAN	plasma membrane calcium ATPase 2 isoform 1	812	Cytoplasmic (Potential).				ATP biosynthetic process|cytosolic calcium ion homeostasis|platelet activation	integral to membrane|plasma membrane	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|calcium-transporting ATPase activity|calmodulin binding|calmodulin binding|metal ion binding|PDZ domain binding|protein C-terminus binding			ovary(3)|central_nervous_system(1)	4						Ovarian(125;1619 1709 15675 19819 38835)								0.34	43.459619	44.591101	17	33	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	10362792	10362792	1159	3	G	A	A	38	38	ATP2B2	A	1	1
GHSR	2693	broad.mit.edu	36	3	173648691	173648691	+	Silent	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:173648691C>T	uc003fib.1	-	c.207G>A	c.(205-207)TCG>TCA	p.S69S	GHSR_uc003fic.1_Silent_p.S69S	NM_198407	NP_940799	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor isoform 1a	69	Cytoplasmic (Potential).				actin polymerization or depolymerization|adult feeding behavior|decidualization|growth hormone secretion|hormone-mediated signaling pathway|negative regulation of inflammatory response|negative regulation of interleukin-1 beta production|negative regulation of interleukin-6 biosynthetic process|negative regulation of tumor necrosis factor biosynthetic process|positive regulation of appetite|positive regulation of multicellular organism growth	cell surface|integral to membrane|membrane raft|neuron projection|plasma membrane	growth hormone secretagogue receptor activity|growth hormone-releasing hormone receptor activity			ovary(1)|central_nervous_system(1)	2	Ovarian(172;0.00143)|Breast(254;0.197)					Esophageal Squamous(93;641 1401 20883 29581 34638)								0.480769	70.494047	70.508969	25	27	CC		KEEP	---	---	---	---	capture	Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)		Silent	SNP	173648691	173648691	6643	3	C	T	T	27	27	GHSR	T	1	1
SLC6A20	54716	broad.mit.edu	36	3	45789094	45789094	+	Silent	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:45789094C>T	uc003cou.1	-	c.600G>A	c.(598-600)GCG>GCA	p.A200A	SLC6A20_uc003cov.1_Intron|SLC6A20_uc003cow.1_5'Flank	NM_020208	NP_064593	Q9NP91	S6A20_HUMAN	solute carrier family 6, member 20 isoform 1	200	Helical; Name=5; (Potential).				cellular nitrogen compound metabolic process|glycine transport|proline transport	apical plasma membrane|integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity			ovary(2)	2														0.320755	46.962485	48.471901	17	36	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(193;0.01)|KIRC - Kidney renal clear cell carcinoma(197;0.0225)|Kidney(197;0.0267)	Silent	SNP	45789094	45789094	15181	3	C	T	T	19	19	SLC6A20	T	1	1
SULT1B1	27284	broad.mit.edu	36	4	70634503	70634503	+	Silent	SNP	A	G	G			TCGA-06-2564-01	TCGA-06-2564-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:70634503A>G	uc003hen.1	-	c.444T>C	c.(442-444)AAT>AAC	p.N148N		NM_014465	NP_055280	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member	148					3'-phosphoadenosine 5'-phosphosulfate metabolic process|cellular biogenic amine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|thyroid hormone metabolic process|xenobiotic metabolic process	cytosol					0														0.378378	46.138579	46.619621	14	23	AA		KEEP	---	---	---	---	capture			Silent	SNP	70634503	70634503	15896	4	A	G	G	4	4	SULT1B1	G	4	4
SEPT11	55752	broad.mit.edu	36	4	78168870	78168870	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:78168870G>A	uc003hkj.1	+	c.1018G>A	c.(1018-1020)GAA>AAA	p.E340K	SEPT11_uc010ijh.1_Missense_Mutation_p.E332K	NM_018243	NP_060713	Q9NVA2	SEP11_HUMAN	septin 11	340	Potential.				cell cycle|cell division|protein heterooligomerization	axon|cell junction|dendritic spine|septin complex|stress fiber|synapse	GTP binding|protein binding				0														0.4	162.618594	163.800647	54	81	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78168870	78168870	14547	4	G	A	A	33	33	SEPT11	A	2	2
FSTL4	23105	broad.mit.edu	36	5	132680061	132680061	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:132680061C>T	uc003kyn.1	-	c.592G>A	c.(592-594)GAA>AAA	p.E198K		NM_015082	NP_055897	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	198	Potential.|EF-hand.					extracellular region	calcium ion binding			central_nervous_system(1)	1		all_cancers(142;0.244)												0.383838	105.8069	106.983784	38	61	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Missense_Mutation	SNP	132680061	132680061	6330	5	C	T	T	31	31	FSTL4	T	1	1
NPM1	4869	broad.mit.edu	36	5	170752374	170752374	+	Missense_Mutation	SNP	A	C	C			TCGA-06-2564-01	TCGA-06-2564-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:170752374A>C	uc003mbi.1	+	c.408A>C	c.(406-408)TTA>TTC	p.L136F	NPM1_uc003mbh.1_Missense_Mutation_p.L136F|NPM1_uc003mbj.1_Missense_Mutation_p.L136F	NM_002520	NP_002511	P06748	NPM_HUMAN	nucleophosmin 1 isoform 1	136	Required for interaction with SENP3.				anti-apoptosis|cell aging|CenH3-containing nucleosome assembly at centromere|centrosome cycle|DNA repair|interspecies interaction between organisms|intracellular protein transport|negative regulation of cell proliferation|negative regulation of centrosome duplication|nucleocytoplasmic transport|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|regulation of endodeoxyribonuclease activity|regulation of endoribonuclease activity|ribosome assembly|signal transduction	nucleolus|nucleoplasm|ribonucleoprotein complex|spindle pole centrosome	histone binding|NF-kappaB binding|protein binding|protein heterodimerization activity|protein homodimerization activity|ribosomal large subunit binding|ribosomal small subunit binding|RNA binding|Tat protein binding|transcription coactivator activity|unfolded protein binding		NPM1/ALK(632)	haematopoietic_and_lymphoid_tissue(3087)|skin(1)	3088	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)								244				0.328638	227.698239	233.232985	70	143	AA		KEEP	---	---	---	---	capture	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Missense_Mutation	SNP	170752374	170752374	10992	5	A	C	C	13	13	NPM1	C	4	4
MICAL1	64780	broad.mit.edu	36	6	109874055	109874055	+	Missense_Mutation	SNP	C	G	G			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:109874055C>G	uc003ptj.1	-	c.2558G>C	c.(2557-2559)GGC>GCC	p.G853A	MICAL1_uc003ptk.1_Missense_Mutation_p.G853A|MICAL1_uc010kdr.1_Missense_Mutation_p.G767A	NM_022765	NP_073602	Q8TDZ2	MICA1_HUMAN	microtubule associated monoxygenase, calponin	853					cytoskeleton organization|oxidation-reduction process|signal transduction	cytoplasm|intermediate filament	SH3 domain binding|zinc ion binding			breast(2)|ovary(1)	3		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)												0.259259	8.865411	10.265345	7	20	CC		KEEP	---	---	---	---	capture		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)	Missense_Mutation	SNP	109874055	109874055	9959	6	C	G	G	26	26	MICAL1	G	3	3
FRK	2444	broad.mit.edu	36	6	116370352	116370352	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:116370352G>A	uc003pwi.1	-	c.1436C>T	c.(1435-1437)ACA>ATA	p.T479I		NM_002031	NP_002022	P42685	FRK_HUMAN	fyn-related kinase	479	Protein kinase.				negative regulation of cell proliferation|protein phosphorylation	cytoplasm|nucleus	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding			ovary(3)|lung(3)	6		all_cancers(87;0.00559)|all_epithelial(87;0.00738)|Colorectal(196;0.0465)								355				0.337423	147.163683	150.979532	55	108	GG		KEEP	---	---	---	---	capture		all cancers(137;0.0128)|OV - Ovarian serous cystadenocarcinoma(136;0.0209)|GBM - Glioblastoma multiforme(226;0.0459)|Epithelial(106;0.0625)	Missense_Mutation	SNP	116370352	116370352	6298	6	G	A	A	48	48	FRK	A	2	2
NUP153	9972	broad.mit.edu	36	6	17737336	17737336	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:17737336C>T	uc003ncd.1	-	c.3073G>A	c.(3073-3075)GGT>AGT	p.G1025S	NUP153_uc010jpl.1_Missense_Mutation_p.G983S	NM_005124	NP_005115	P49790	NU153_HUMAN	nucleoporin 153kDa	1025					carbohydrate metabolic process|glucose transport|interspecies interaction between organisms|mRNA transport|protein transport|regulation of glucose transport|transmembrane transport|viral reproduction	cytoplasm|nuclear membrane|nuclear pore|nucleolus|nucleoplasm	DNA binding|protein binding|transporter activity|zinc ion binding			lung(2)|ovary(1)|skin(1)	4	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)								1004				0.353293	167.872939	171.043204	59	108	CC		KEEP	---	---	---	---	capture	all cancers(50;0.0981)|Epithelial(50;0.112)		Missense_Mutation	SNP	17737336	17737336	11160	6	C	T	T	21	21	NUP153	T	2	2
SLC26A8	116369	broad.mit.edu	36	6	36031037	36031037	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:36031037G>A	uc003olm.1	-	c.2102C>T	c.(2101-2103)GCG>GTG	p.A701V	SLC26A8_uc003olk.1_Missense_Mutation_p.A283V|SLC26A8_uc003oln.1_Missense_Mutation_p.A701V|SLC26A8_uc003oll.1_Missense_Mutation_p.A596V|SLC26A8_uc010jwa.1_Non-coding_Transcript	NM_052961	NP_443193	Q96RN1	S26A8_HUMAN	solute carrier family 26, member 8 isoform a	701	Interaction with RACGAP1.|STAS.|Cytoplasmic (Potential).				cell differentiation|meiosis|multicellular organismal development|spermatogenesis	integral to membrane|plasma membrane	anion:anion antiporter activity|chloride channel activity|oxalate transmembrane transporter activity|protein binding|sulfate transmembrane transporter activity			ovary(2)	2														0.37037	139.911374	141.905893	50	85	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36031037	36031037	15020	6	G	A	A	38	38	SLC26A8	A	1	1
PRIM2	5558	broad.mit.edu	36	6	57606994	57606994	+	Silent	SNP	T	C	C	rs61753605	unknown	TCGA-06-2564-01	TCGA-06-2564-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:57606994T>C	uc003pdx.1	+	c.1299T>C	c.(1297-1299)AAT>AAC	p.N433N		NM_000947	NP_000938	P49643	PRI2_HUMAN	DNA primase polypeptide 2	433					DNA replication, synthesis of RNA primer|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	alpha DNA polymerase:primase complex|nucleoplasm	4 iron, 4 sulfur cluster binding|DNA binding|DNA primase activity|metal ion binding				0														0.285714	10.494349	11.071156	4	10	TT		KEEP	---	---	---	---	capture		Colorectal(6;0.041)|READ - Rectum adenocarcinoma(7;0.193)	Silent	SNP	57606994	57606994	12934	6	T	C	C	51	51	PRIM2	C	4	4
NRF1	4899	broad.mit.edu	36	7	129144376	129144376	+	Missense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:129144376G>A	uc003vpa.1	+	c.1147G>A	c.(1147-1149)GCA>ACA	p.A383T	NRF1_uc003voz.1_Missense_Mutation_p.A383T|NRF1_uc003vpb.1_Missense_Mutation_p.A383T	NM_005011	NP_005002	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	383	Required for transcriptional activation.				generation of precursor metabolites and energy|regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)	1														0.237569	93.838865	105.230272	43	138	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	129144376	129144376	11051	7	G	A	A	42	42	NRF1	A	2	2
ZC3HC1	51530	broad.mit.edu	36	7	129449490	129449490	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:129449490C>T	uc003vpi.1	-	c.1345G>A	c.(1345-1347)GAT>AAT	p.D449N	ZC3HC1_uc003vph.1_Missense_Mutation_p.D293N|ZC3HC1_uc010lma.1_Missense_Mutation_p.D265N	NM_016478	NP_057562	Q86WB0	NIPA_HUMAN	zinc finger, C3HC type 1	449					cell division|mitosis	nucleus	protein kinase binding|zinc ion binding				0	Melanoma(18;0.0435)					Melanoma(115;540 1606 16325 28853 48167)								0.229947	103.018265	115.528374	43	144	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	129449490	129449490	18165	7	C	T	T	32	32	ZC3HC1	T	2	2
EPHA1	2041	broad.mit.edu	36	7	142807013	142807013	+	Missense_Mutation	SNP	T	C	C			TCGA-06-2564-01	TCGA-06-2564-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:142807013T>C	uc003wcz.1	-	c.688A>G	c.(688-690)ACC>GCC	p.T230A		NM_005232	NP_005223	P21709	EPHA1_HUMAN	ephrin receptor EphA1	230	Extracellular (Potential).|Cys-rich.				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			ovary(3)|lung(1)|breast(1)	5	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)								379				0.181818	6.414108	8.486753	4	18	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	142807013	142807013	5358	7	T	C	C	58	58	EPHA1	C	4	4
ABCF2	10061	broad.mit.edu	36	7	150552870	150552870	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:150552870G>A	uc003wjo.1	-	c.292C>T	c.(292-294)CAA>TAA	p.Q98*	ABCF2_uc003wjp.1_Nonsense_Mutation_p.Q98*	NM_005692	NP_005683	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F, member 2	98	ABC transporter 1.					ATP-binding cassette (ABC) transporter complex|mitochondrial envelope	ATP binding|ATPase activity|transporter activity			central_nervous_system(1)	1														0.230769	123.316776	138.871064	54	180	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Nonsense_Mutation	SNP	150552870	150552870	67	7	G	A	A	45	45	ABCF2	A	5	2
DFNA5	1687	broad.mit.edu	36	7	24708904	24708904	+	Silent	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:24708904C>T	uc010kus.1	-	c.1257G>A	c.(1255-1257)TTG>TTA	p.L419L	DFNA5_uc003swz.2_Silent_p.L255L|DFNA5_uc003sxa.1_Silent_p.L419L|DFNA5_uc010kut.1_Silent_p.L255L	NM_001127453	NP_001120925	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5 protein isoform	419					sensory perception of sound					ovary(1)	1						GBM(78;184 1250 20134 20900 23600)				312				0.2	130.007469	153.868604	57	228	CC		KEEP	---	---	---	---	capture			Silent	SNP	24708904	24708904	4633	7	C	T	T	21	21	DFNA5	T	2	2
TNS3	64759	broad.mit.edu	36	7	47406994	47406994	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:47406994C>T	uc003tnv.1	-	c.766G>A	c.(766-768)GTC>ATC	p.V256I	TNS3_uc003tnw.1_Missense_Mutation_p.V256I|TNS3_uc010kyo.1_3'UTR	NM_022748	NP_073585	Q68CZ2	TENS3_HUMAN	tensin 3	256	C2 tensin-type.					focal adhesion	protein binding			ovary(4)	4														0.230392	106.870911	120.428284	47	157	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47406994	47406994	16885	7	C	T	T	19	19	TNS3	T	1	1
TFPI2	7980	broad.mit.edu	36	7	93354084	93354084	+	Missense_Mutation	SNP	C	T	T	rs12669450	by-cluster,by-frequency,by-hapmap	TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:93354084C>T	uc003unb.1	-	c.710G>A	c.(709-711)CGG>CAG	p.R237Q	GNGT1_uc003umx.1_Intron|TFPI2_uc003umy.1_Missense_Mutation_p.R231Q|TFPI2_uc003umz.1_3'UTR|TFPI2_uc003una.1_Missense_Mutation_p.R220Q|TFPI2_uc010lfg.1_Missense_Mutation_p.R107Q	NM_006528	NP_006519	P48307	TFPI2_HUMAN	tissue factor pathway inhibitor 2	231					blood coagulation	proteinaceous extracellular matrix	extracellular matrix structural constituent|serine-type endopeptidase inhibitor activity			pancreas(1)	1	all_cancers(62;4.45e-10)|all_epithelial(64;2.92e-09)|Lung NSC(181;0.218)													0.174129	78.101311	98.243348	35	166	CC		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(171;0.000967)		Missense_Mutation	SNP	93354084	93354084	16337	7	C	T	T	23	23	TFPI2	T	1	1
IMPAD1	54928	broad.mit.edu	36	8	58041426	58041426	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:58041426C>T	uc003xte.2	-	c.686G>A	c.(685-687)CGC>CAC	p.R229H		NM_017813	NP_060283	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	229						Golgi apparatus|integral to membrane	inositol-1(or 4)-monophosphatase activity|metal ion binding			ovary(1)	1		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)												0.408805	184.537001	185.694069	65	94	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58041426	58041426	8026	8	C	T	T	27	27	IMPAD1	T	1	1
TRPA1	8989	broad.mit.edu	36	8	73131723	73131723	+	Nonsense_Mutation	SNP	G	A	A			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:73131723G>A	uc003xza.1	-	c.1177C>T	c.(1177-1179)CGA>TGA	p.R393*		NM_007332	NP_015628	O75762	TRPA1_HUMAN	ankyrin-like protein 1	393	Cytoplasmic (Potential).					integral to plasma membrane				ovary(4)|lung(1)|kidney(1)	6					Menthol(DB00825)									0.363636	46.892645	47.610538	16	28	GG		KEEP	---	---	---	---	capture	Epithelial(68;0.223)		Nonsense_Mutation	SNP	73131723	73131723	17128	8	G	A	A	38	38	TRPA1	A	5	1
MTDH	92140	broad.mit.edu	36	8	98804419	98804419	+	Missense_Mutation	SNP	A	G	G			TCGA-06-2564-01	TCGA-06-2564-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:98804419A>G	uc003yhz.1	+	c.1658A>G	c.(1657-1659)AAT>AGT	p.N553S	MTDH_uc010mbf.1_Non-coding_Transcript	NM_178812	NP_848927	Q86UE4	LYRIC_HUMAN	metadherin	553	Cytoplasmic (Potential).				lipopolysaccharide-mediated signaling pathway|negative regulation of apoptosis|negative regulation of transcription from RNA polymerase II promoter|positive regulation of angiogenesis|positive regulation of autophagy|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of protein kinase B signaling cascade	apical plasma membrane|endoplasmic reticulum membrane|integral to membrane|intercellular canaliculus|nuclear body|nuclear membrane|nucleolus|perinuclear region of cytoplasm|tight junction	NF-kappaB binding|RNA polymerase II transcription factor binding|transcription coactivator activity			liver(1)|central_nervous_system(1)	2	Breast(36;2.56e-06)													0.345794	238.778764	243.274898	74	140	AA		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(57;0.178)		Missense_Mutation	SNP	98804419	98804419	10310	8	A	G	G	4	4	MTDH	G	4	4
PALM2-AKAP2	445815	broad.mit.edu	36	9	111939968	111939968	+	Missense_Mutation	SNP	T	A	A			TCGA-06-2564-01	TCGA-06-2564-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:111939968T>A	uc004bei.2	+	c.3019T>A	c.(3019-3021)TTT>ATT	p.F1007I	PALM2-AKAP2_uc004bek.2_Missense_Mutation_p.F775I|PALM2-AKAP2_uc004bej.2_Missense_Mutation_p.F775I|PALM2-AKAP2_uc004bel.1_Missense_Mutation_p.F585I|AKAP2_uc004bem.1_Missense_Mutation_p.F633I|PALM2-AKAP2_uc010mtw.1_Missense_Mutation_p.F593I|PALM2-AKAP2_uc004ben.1_Missense_Mutation_p.F544I	NM_001004065	NP_001004065	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2 isoform 1	544							enzyme binding			ovary(3)|central_nervous_system(2)	5														0.4	245.45613	247.292287	84	126	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	111939968	111939968	11826	9	T	A	A	52	52	PALM2-AKAP2	A	4	4
SVEP1	79987	broad.mit.edu	36	9	112229733	112229733	+	Missense_Mutation	SNP	G	T	T			TCGA-06-2564-01	TCGA-06-2564-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:112229733G>T	uc010mtz.1	-	c.5934C>A	c.(5932-5934)AAC>AAA	p.N1978K	SVEP1_uc010mty.1_5'UTR	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	1978	Sushi 10.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7												OREG0019389	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.325733	288.892202	297.165031	100	207	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	112229733	112229733	15940	9	G	T	T	36	36	SVEP1	T	3	3
ZNF883	169834	broad.mit.edu	36	9	114799432	114799432	+	Missense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:114799432C>T	uc004bgl.2	-	c.929G>A	c.(928-930)CGA>CAA	p.R310Q		NM_001101338	NP_001094808	P0CG24	ZN883_HUMAN	hypothetical protein LOC169834	310	C2H2-type 11.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0														0.332203	271.065741	278.416392	98	197	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114799432	114799432	18802	9	C	T	T	31	31	ZNF883	T	1	1
NR5A1	2516	broad.mit.edu	36	9	126302670	126302670	+	Silent	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:126302670C>T	uc004boo.1	-	c.390G>A	c.(388-390)CCG>CCA	p.P130P		NM_004959	NP_004950	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	130					cell-cell signaling|male gonad development|positive regulation of transcription from RNA polymerase II promoter|primary sex determination|regulation of steroid biosynthetic process|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	nucleoplasm	enzyme binding|phospholipid binding|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0														0.530612	68.238806	68.278679	26	23	CC		KEEP	---	---	---	---	capture			Silent	SNP	126302670	126302670	11040	9	C	T	T	27	27	NR5A1	T	1	1
C9orf102	375748	broad.mit.edu	36	9	97709353	97709353	+	Nonsense_Mutation	SNP	T	G	G			TCGA-06-2564-01	TCGA-06-2564-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:97709353T>G	uc004avt.2	+	c.800T>G	c.(799-801)TTA>TGA	p.L267*	C9orf102_uc010mrx.1_Non-coding_Transcript|C9orf102_uc010mry.1_Intron|C9orf102_uc010mrz.1_Nonsense_Mutation_p.L78*	NM_001010895	NP_001010895	Q5T890	RAD26_HUMAN	RAD26L hypothetical protein	267	Helicase ATP-binding.				DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding				0		Acute lymphoblastic leukemia(62;0.0559)												0.361111	131.702039	133.533034	39	69	TT		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	97709353	97709353	2558	9	T	G	G	61	61	C9orf102	G	5	4
CT45A1	541466	broad.mit.edu	36	X	134684414	134684414	+	Nonsense_Mutation	SNP	C	T	T			TCGA-06-2564-01	TCGA-06-2564-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:134684414C>T	uc004eyy.1	+	c.523C>T	c.(523-525)CGA>TGA	p.R175*		NM_001017417	NP_001017417	Q5HYN5	CT451_HUMAN	hypothetical protein LOC541466	175											0														0.086553	13.147933	125.117658	56	591	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	134684414	134684414	4129	23	C	T	T	19	19	CT45A1	T	5	1
NACA	4666	broad.mit.edu	36	12	55398199	55398206	+	Frame_Shift_Del	DEL	TTGTGGGT	-	-			TCGA-06-2564-01	TCGA-06-2564-01										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				0.69			25	11				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	55398199	55398206	10528	12	TTGTGGGT	-	-	60	60	NACA	-	5	5
LRRIQ1	84125	broad.mit.edu	36	12	84070204	84070204	+	Frame_Shift_Del	DEL	G	-	-			TCGA-06-2564-01	TCGA-06-2564-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:84070204_84070204delG	uc001tac.1	+	c.4345_4345delG	c.(4345-4347)GAAfs	p.E1449fs		NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1449										ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(134;0.212)										0.31			18	40				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	84070204	84070204	9405	12	G	-	-	33	33	LRRIQ1	-	5	5
FAT1	2195	broad.mit.edu	36	4	187778176	187778177	+	Frame_Shift_Ins	INS	-	A	A			TCGA-06-2564-01	TCGA-06-2564-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:187778176_187778177insA	uc003izf.1	-	c.6557_6558insT	c.(6556-6558)TTCfs	p.F2186fs		NM_005245	NP_005236	Q14517	FAT1_HUMAN	FAT tumor suppressor 1 precursor	2186	Extracellular (Potential).|Cadherin 20.				actin filament organization|anatomical structure morphogenesis|cell migration|cell-cell signaling|establishment or maintenance of cell polarity|homophilic cell adhesion	cell-cell junction|integral to plasma membrane|nucleus|perinuclear region of cytoplasm	calcium ion binding|protein binding			ovary(10)|central_nervous_system(1)|pancreas(1)	12						Colon(197;1040 2055 4143 4984 49344)								0.37			76	129				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	187778176	187778177	5925	4	-	A	A	33	33	FAT1	A	5	5
