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
WNT8B	7479	broad.mit.edu	36	10	102212954	102212954	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:102212954C>A	uc001krb.1	+	c.39C>A	c.(37-39)TTC>TTA	p.F13L		NM_003393	NP_003384	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family,	13					anterior/posterior pattern formation|axis specification|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|determination of dorsal identity|endoderm development|eye development|gastrulation|hypothalamus development|negative regulation of anterior neural cell fate commitment of the neural plate by Wnt receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|otic placode formation|positive regulation of gene expression|response to estradiol stimulus|Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway, calcium modulating pathway	extracellular space|plasma membrane|proteinaceous extracellular matrix	G-protein-coupled receptor binding|signal transducer activity			large_intestine(1)|skin(1)	2		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)										0.107884	22.988206	59.734897	26	215	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	102212954	102212954	17971	10	C	A	A	29	29	WNT8B	A	3	3
C10orf46	143384	broad.mit.edu	36	10	120457068	120457068	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr10:120457068T>C	uc001lds.1	-	c.619A>G	c.(619-621)ATT>GTT	p.I207V	C10orf46_uc009xze.1_Non-coding_Transcript	NM_153810	NP_722517	Q86Y37	CJ046_HUMAN	chromosome 10 open reading frame 46	207					ubiquitin-dependent protein catabolic process	cullin-RING ubiquitin ligase complex	ubiquitin protein ligase binding				0		Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0131)										0.266667	6.387974	7.130428	4	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	120457068	120457068	1641	10	T	C	C	49	49	C10orf46	C	4	4
NRP1	8829	broad.mit.edu	36	10	33592652	33592652	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:33592652G>A	uc001iwx.2	-	c.586C>T	c.(586-588)CCT>TCT	p.P196S	NRP1_uc001iww.2_Missense_Mutation_p.P15S|NRP1_uc001iwv.2_Missense_Mutation_p.P196S|NRP1_uc009xlz.1_Missense_Mutation_p.P196S|NRP1_uc001iwy.2_Missense_Mutation_p.P196S|NRP1_uc001iwz.2_Missense_Mutation_p.P196S|NRP1_uc001ixa.2_Missense_Mutation_p.P196S|NRP1_uc001ixb.1_Missense_Mutation_p.P196S|NRP1_uc001ixc.1_Missense_Mutation_p.P196S	NM_003873	NP_003864	O14786	NRP1_HUMAN	neuropilin 1 isoform a	196	Extracellular (Potential).|CUB 2.				axon guidance|cell adhesion|cell-cell signaling|organ morphogenesis|positive regulation of cell proliferation	extracellular region|integral to membrane|plasma membrane	growth factor binding|heparin binding|metal ion binding|vascular endothelial growth factor receptor activity			central_nervous_system(2)|ovary(1)	3					Palifermin(DB00039)|Pegaptanib(DB04895)	Melanoma(104;886 1489 44640 45944 51153)								0.310345	15.252429	16.189101	9	20	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33592652	33592652	11065	10	G	A	A	42	42	NRP1	A	2	2
RET	5979	broad.mit.edu	36	10	42920494	42920495	+	Missense_Mutation	DNP	GC	AG	AG			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:42920494_42920495GC>AG	uc001jal.1	+	c.714_715GC>AG	c.(712-717)GAGCTG>GAAGTG	p.L239V	RET_uc001jak.1_Missense_Mutation_p.L239V	NM_020975	NP_066124	P07949	RET_HUMAN	ret proto-oncogene isoform a	239	Cadherin.|Extracellular (Potential).				homophilic cell adhesion|positive regulation of metanephric glomerulus development|positive regulation of transcription, DNA-dependent|posterior midgut development|protein phosphorylation	integral to membrane	ATP binding|calcium ion binding|transcription activator activity|transmembrane receptor protein tyrosine kinase activity			thyroid(381)|adrenal_gland(20)|lung(6)|large_intestine(5)|ovary(4)|central_nervous_system(3)|urinary_tract(1)	420		Ovarian(717;0.0423)			Sunitinib(DB01268)	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)		1		536				0.6	7.122926	7.166158	3	2	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	42920494	42920495	13705	10	GC	AG	AG	34	34	RET	AG	2	2
LRRC20	55222	broad.mit.edu	36	10	71753785	71753785	+	Silent	SNP	G	A	A	rs35118383	unknown	TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:71753785G>A	uc001jqx.1	-	c.240C>T	c.(238-240)CAC>CAT	p.H80H	LRRC20_uc001jqy.1_Intron|LRRC20_uc001jqz.1_Silent_p.H30H	NM_207119	NP_997002	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20 isoform 1	80	LRR 2.										0														0.423077	32.521542	32.655445	11	15	GG		KEEP	---	---	---	---	capture			Silent	SNP	71753785	71753785	9351	10	G	A	A	44	44	LRRC20	A	2	2
CDH23	64072	broad.mit.edu	36	10	73076265	73076265	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr10:73076265A>G	uc001jrx.2	+	c.1334A>G	c.(1333-1335)AAG>AGG	p.K445R	CDH23_uc001jrw.2_Missense_Mutation_p.K445R|CDH23_uc001jrz.2_Missense_Mutation_p.K61R|CDH23_uc001jry.2_Missense_Mutation_p.K61R	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	445	Cadherin 4.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11														0.138889	7.710319	16.797413	10	62	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73076265	73076265	3237	10	A	G	G	3	3	CDH23	G	4	4
TM9SF3	56889	broad.mit.edu	36	10	98326529	98326529	+	Silent	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:98326529G>T	uc001kmm.2	-	c.150C>A	c.(148-150)CCC>CCA	p.P50P		NM_020123	NP_064508	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	50						integral to membrane	binding				0		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)										0.230769	16.352806	19.830639	12	40	GG		KEEP	---	---	---	---	capture			Silent	SNP	98326529	98326529	16509	10	G	T	T	35	35	TM9SF3	T	3	3
TRAPPC4	51399	broad.mit.edu	36	11	118394745	118394745	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118394745C>G	uc001puo.1	+	c.30C>G	c.(28-30)AAC>AAG	p.N10K	RPS25_uc001pun.1_5'Flank|TRAPPC4_uc001pup.1_Non-coding_Transcript	NM_016146	NP_057230	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4	10					dendrite development|ER to Golgi vesicle-mediated transport	cis-Golgi network|dendrite|endoplasmic reticulum|Golgi stack|synaptic vesicle	protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)										0.166667	8.241855	13.947077	9	45	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118394745	118394745	17005	11	C	G	G	17	17	TRAPPC4	G	3	3
TRAPPC4	51399	broad.mit.edu	36	11	118396115	118396115	+	Silent	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:118396115A>G	uc001puo.1	+	c.396A>G	c.(394-396)TCA>TCG	p.S132S	RPS25_uc001pun.1_5'Flank|TRAPPC4_uc001pup.1_Intron	NM_016146	NP_057230	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4	132					dendrite development|ER to Golgi vesicle-mediated transport	cis-Golgi network|dendrite|endoplasmic reticulum|Golgi stack|synaptic vesicle	protein binding				0	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)										0.205882	9.206349	11.939809	7	27	AA		KEEP	---	---	---	---	capture			Silent	SNP	118396115	118396115	17005	11	A	G	G	7	7	TRAPPC4	G	4	4
CRTAM	56253	broad.mit.edu	36	11	122226017	122226017	+	Silent	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:122226017C>A	uc001pyj.1	+	c.78C>A	c.(76-78)ATC>ATA	p.I26I		NM_019604	NP_062550	O95727	CRTAM_HUMAN	class-I MHC-restricted T cell associated	26	Ig-like V-type.|Extracellular (Potential).				cell recognition|detection of tumor cell|positive regulation of cytokine secretion|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	integral to membrane|plasma membrane	receptor binding			ovary(1)	1		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.28e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)										0.16129	8.29503	15.096643	10	52	CC		KEEP	---	---	---	---	capture			Silent	SNP	122226017	122226017	4036	11	C	A	A	29	29	CRTAM	A	3	3
SAA2	6289	broad.mit.edu	36	11	18226120	18226120	+	Silent	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18226120C>T	uc001mnz.2	-	c.15G>A	c.(13-15)ACG>ACA	p.T5T	SAA2_uc009yhj.1_Silent_p.T5T	NM_030754	NP_110381	P02735	SAA_HUMAN	serum amyloid A2 isoform a	5					acute-phase response|elevation of cytosolic calcium ion concentration|innate immune response|lymphocyte chemotaxis|macrophage chemotaxis|negative regulation of inflammatory response|neutrophil chemotaxis|platelet activation|positive regulation of cell adhesion|positive regulation of interleukin-1 secretion	high-density lipoprotein particle	G-protein-coupled receptor binding				0					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)									0.786517	237.984079	244.733298	70	19	CC		KEEP	---	---	---	---	capture			Silent	SNP	18226120	18226120	14279	11	C	T	T	23	23	SAA2	T	1	1
DBX1	120237	broad.mit.edu	36	11	20138156	20138156	+	Silent	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:20138156A>T	uc001mpw.1	-	c.291T>A	c.(289-291)ACT>ACA	p.T97T		NM_001029865	NP_001025036	A6NMT0	DBX1_HUMAN	developing brain homeobox 1	97					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity			ovary(1)	1														0.714286	22.941599	23.516236	10	4	AA		KEEP	---	---	---	---	capture			Silent	SNP	20138156	20138156	4430	11	A	T	T	7	7	DBX1	T	4	4
PHRF1	57661	broad.mit.edu	36	11	598100	598100	+	Missense_Mutation	SNP	T	A	A			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:598100T>A	uc001lqe.1	+	c.2644T>A	c.(2644-2646)TAC>AAC	p.Y882N	PHRF1_uc009ybz.1_Missense_Mutation_p.Y672N|PHRF1_uc009yca.1_Non-coding_Transcript	NM_020901	NP_065952	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	882							RNA polymerase binding|zinc ion binding				0														0.4	10.29725	10.384781	4	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	598100	598100	12285	11	T	A	A	53	53	PHRF1	A	4	4
NXF1	10482	broad.mit.edu	36	11	62320588	62320588	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:62320588G>A	uc009yog.1	-	c.1335C>T	c.(1333-1335)GAC>GAT	p.D445D	NXF1_uc001nvf.1_Silent_p.D402D|NXF1_uc001nvg.1_3'UTR	NM_006362	NP_006353	Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1 isoform 1	402	NTF2.				gene expression|interspecies interaction between organisms	cytosol|nuclear speck	nucleotide binding|protein binding			skin(1)	1														0.24359	28.268299	32.964972	19	59	GG		KEEP	---	---	---	---	capture			Silent	SNP	62320588	62320588	11187	11	G	A	A	44	44	NXF1	A	2	2
CATSPER1	117144	broad.mit.edu	36	11	65545543	65545543	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:65545543C>G	uc001ogt.1	-	c.1691G>C	c.(1690-1692)AGC>ACC	p.S564T		NM_053054	NP_444282	Q8NEC5	CTSR1_HUMAN	sperm-associated cation channel 1	564	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	cilium|flagellar membrane|integral to membrane	protein binding			ovary(2)	2														0.6	7.324074	7.367827	3	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	65545543	65545543	2806	11	C	G	G	24	24	CATSPER1	G	3	3
SHANK2	22941	broad.mit.edu	36	11	70009925	70009925	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:70009925G>C	uc001opz.1	-	c.2336C>G	c.(2335-2337)ACC>AGC	p.T779S	SHANK2_uc001opy.1_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	995					intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)											0.277778	8.261685	9.066276	5	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70009925	70009925	14757	11	G	C	C	44	44	SHANK2	C	3	3
PNPLA2	57104	broad.mit.edu	36	11	812566	812566	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:812566T>G	uc001lrt.1	+	c.656T>G	c.(655-657)CTC>CGC	p.L219R	PNPLA2_uc009ycl.1_5'Flank	NM_020376	NP_065109	Q96AD5	PLPL2_HUMAN	patatin-like phospholipase domain containing 2	219	Lumenal (Potential).		L -> F.		negative regulation of sequestering of triglyceride|positive regulation of triglyceride catabolic process	integral to membrane|lipid particle|plasma membrane	triglyceride lipase activity				0		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)										0.444444	8.193633	8.21841	4	5	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	812566	812566	12592	11	T	G	G	54	54	PNPLA2	G	4	4
FZD4	8322	broad.mit.edu	36	11	86340100	86340100	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:86340100G>A	uc001pce.1	-	c.1346C>T	c.(1345-1347)ACG>ATG	p.T449M	PRSS23_uc001pcc.1_Non-coding_Transcript	NM_012193	NP_036325	Q9ULV1	FZD4_HUMAN	frizzled 4	449	Helical; Name=6; (Potential).				canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|negative regulation of cell-substrate adhesion|neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription, DNA-dependent|progesterone secretion|regulation of gene-specific transcription from RNA polymerase II promoter|regulation of vascular endothelial growth factor receptor signaling pathway|substrate adhesion-dependent cell spreading|vasculogenesis|Wnt receptor signaling pathway, calcium modulating pathway	cell projection|cell surface|cytoplasm|integral to plasma membrane	cytokine binding|G-protein coupled receptor activity|PDZ domain binding|protein heterodimerization activity|protein homodimerization activity|Wnt receptor activity|Wnt-protein binding			large_intestine(1)	1		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)												0.895349	1341.325607	1408.173807	385	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86340100	86340100	6383	11	G	A	A	40	40	FZD4	A	1	1
C11orf54	28970	broad.mit.edu	36	11	93130149	93130149	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr11:93130149A>T	uc001peh.1	+	c.527A>T	c.(526-528)AAA>ATA	p.K176I	C11orf54_uc001pee.1_Missense_Mutation_p.K117I|C11orf54_uc001pef.1_Intron|C11orf54_uc009ywi.1_Missense_Mutation_p.K176I|C11orf54_uc001peg.1_Missense_Mutation_p.K176I|C11orf54_uc001pei.1_Missense_Mutation_p.K157I|C11orf54_uc001pej.1_Missense_Mutation_p.K157I|C11orf54_uc001pek.1_Missense_Mutation_p.K65I	NM_014039	NP_054758	Q9H0W9	CK054_HUMAN	hypothetical protein LOC28970	176						nucleus	hydrolase activity, acting on ester bonds|protein binding|zinc ion binding				0		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)												0.222222	11.17329	13.740409	8	28	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	93130149	93130149	1688	11	A	T	T	1	1	C11orf54	T	4	4
OLR1	4973	broad.mit.edu	36	12	10210627	10210627	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:10210627G>A	uc001qxo.1	-	c.375C>T	c.(373-375)CAC>CAT	p.H125H		NM_002543	NP_002534	P78380	OLR1_HUMAN	oxidized low density lipoprotein (lectin-like)	125	Extracellular (Potential).|Neck.				blood circulation|blood coagulation|inflammatory response|leukocyte migration|proteolysis	extracellular region|integral to plasma membrane|membrane fraction	sugar binding			ovary(1)	1														0.674267	675.170023	683.42984	207	100	GG		KEEP	---	---	---	---	capture			Silent	SNP	10210627	10210627	11268	12	G	A	A	44	44	OLR1	A	2	2
POLR3B	55703	broad.mit.edu	36	12	105296236	105296236	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:105296236G>T	uc001tlp.1	+	c.558G>T	c.(556-558)AAG>AAT	p.K186N	POLR3B_uc001tlq.1_Missense_Mutation_p.K128N	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	186					innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding			ovary(1)|central_nervous_system(1)	2														0.152632	56.382424	78.297491	29	161	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	105296236	105296236	12657	12	G	T	T	33	33	POLR3B	T	3	3
BTBD11	121551	broad.mit.edu	36	12	106553241	106553241	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:106553241G>A	uc001tmk.1	+	c.2681G>A	c.(2680-2682)GGG>GAG	p.G894E	BTBD11_uc009zut.1_Missense_Mutation_p.G775E|BTBD11_uc001tmj.2_Missense_Mutation_p.G894E|BTBD11_uc001tml.1_Missense_Mutation_p.G431E|BTBD11_uc001tmm.1_5'UTR	NM_001018072	NP_001018082	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11 isoform a	894						integral to membrane	DNA binding			ovary(1)	1														0.238245	198.745132	218.649085	76	243	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106553241	106553241	1571	12	G	A	A	43	43	BTBD11	A	2	2
MPHOSPH9	10198	broad.mit.edu	36	12	122211716	122211717	+	Missense_Mutation	DNP	CA	AG	AG			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:122211716_122211717CA>AG	uc001uel.1	-	c.2844_2845TG>CT	c.(2842-2847)AATGAT>AACTAT	p.D949Y	MPHOSPH9_uc001uem.1_Missense_Mutation_p.D403Y	NM_022782	NP_073619	Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	949					M phase of mitotic cell cycle	Golgi membrane					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)										0.174603	9.087665	15.413512	11	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	122211716	122211717	10120	12	CA	AG	AG	29	29	MPHOSPH9	AG	3	3
TMEM132D	121256	broad.mit.edu	36	12	128750741	128750742	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:128750741_128750742CC>AA	uc009zyl.1	-	c.534_535GG>TT	c.(532-537)GAGGTG>GATTTG	p.178_179EV>DL		NM_133448	NP_597705	Q14C87	T132D_HUMAN	transmembrane protein 132D	178_179	Extracellular (Potential).					integral to membrane				ovary(10)|pancreas(2)	12	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)										0.875	16.098061	17.111323	7	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	128750741	128750742	16579	12	CC	AA	AA	18	18	TMEM132D	AA	3	3
LRTM2	654429	broad.mit.edu	36	12	1814114	1814114	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:1814114A>T	uc001qjt.1	+	c.1079A>T	c.(1078-1080)CAC>CTC	p.H360L	CACNA2D4_uc001qjp.1_Intron|CACNA2D4_uc009zds.1_Intron|CACNA2D4_uc009zdt.1_Intron|CACNA2D4_uc009zdr.1_Intron|LRTM2_uc001qju.1_Missense_Mutation_p.H360L|LRTM2_uc001qjv.1_Missense_Mutation_p.H122L	NM_001039029	NP_001034118	Q8N967	LRTM2_HUMAN	leucine-rich repeats and transmembrane domains	360	Cytoplasmic (Potential).					integral to membrane				large_intestine(1)	1	Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.000834)											0.25	8.628108	10.002149	6	18	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1814114	1814114	9421	12	A	T	T	6	6	LRTM2	T	4	4
FGF6	2251	broad.mit.edu	36	12	4424775	4424775	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:4424775C>G	uc001qmr.1	-	c.223G>C	c.(223-225)GAA>CAA	p.E75Q		NM_020996	NP_066276	P10767	FGF6_HUMAN	fibroblast growth factor 6 precursor	75					angiogenesis|cell proliferation|cell-cell signaling|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|positive regulation of cell division|positive regulation of cell proliferation	extracellular space	growth factor activity			ovary(1)	1			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)											0.174603	11.375072	17.693931	11	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	4424775	4424775	6093	12	C	G	G	30	30	FGF6	G	3	3
KRT74	121391	broad.mit.edu	36	12	51247145	51247145	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51247145C>A	uc001sap.1	-	c.1465G>T	c.(1465-1467)GCA>TCA	p.A489S		NM_175053	NP_778223	Q7RTS7	K2C74_HUMAN	keratin 6 irs4	489	Tail.					keratin filament	structural molecule activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(357;0.191)										0.333333	12.003488	12.527387	7	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51247145	51247145	8802	12	C	A	A	26	26	KRT74	A	3	3
ERBB3	2065	broad.mit.edu	36	12	54774547	54774547	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:54774547T>G	uc001sjh.1	+	c.1799T>G	c.(1798-1800)ATC>AGC	p.I600S	ERBB3_uc009zoj.1_Intron|ERBB3_uc009zok.1_Missense_Mutation_p.I42S|ERBB3_uc001sjk.1_5'Flank	NM_001982	NP_001973	P21860	ERBB3_HUMAN	erbB-3 isoform 1 precursor	600	Extracellular (Potential).				cranial nerve development|heart development|negative regulation of cell adhesion|negative regulation of neuron apoptosis|negative regulation of secretion|negative regulation of signal transduction|neuron apoptosis|phosphatidylinositol 3-kinase cascade|positive regulation of phosphatidylinositol 3-kinase cascade|protein phosphorylation|regulation of cell proliferation|Schwann cell differentiation|transmembrane receptor protein tyrosine kinase signaling pathway|wound healing	basolateral plasma membrane|extracellular space|integral to plasma membrane|receptor complex	ATP binding|growth factor binding|protein heterodimerization activity|protein homodimerization activity|protein tyrosine kinase activator activity|receptor signaling protein tyrosine kinase activity|transmembrane receptor protein tyrosine kinase activity			lung(3)|central_nervous_system(2)|stomach(1)|ovary(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)							322				0.22549	35.555377	42.639239	23	79	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54774547	54774547	5401	12	T	G	G	50	50	ERBB3	G	4	4
LRRIQ1	84125	broad.mit.edu	36	12	84150609	84150609	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:84150609C>A	uc001tac.1	+	c.4960C>A	c.(4960-4962)CAC>AAC	p.H1654N		NM_001079910	NP_001073379	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1654										ovary(4)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(134;0.212)										0.104651	6.72063	20.109592	9	77	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84150609	84150609	9405	12	C	A	A	29	29	LRRIQ1	A	3	3
FGD6	55785	broad.mit.edu	36	12	94010674	94010674	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:94010674T>G	uc001tdp.2	-	c.3679A>C	c.(3679-3681)ATG>CTG	p.M1227L	FGD6_uc009zsx.1_Missense_Mutation_p.M360L|FGD6_uc001tdq.1_Missense_Mutation_p.M263L	NM_018351	NP_060821	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	1227	FYVE-type.				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding			ovary(2)|breast(1)	3														0.354167	50.786086	51.674678	17	31	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94010674	94010674	6074	12	T	G	G	52	52	FGD6	G	4	4
USP44	84101	broad.mit.edu	36	12	94451158	94451158	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:94451158C>G	uc001teg.1	-	c.1006G>C	c.(1006-1008)GAA>CAA	p.E336Q	USP44_uc009zte.1_Missense_Mutation_p.E333Q|USP44_uc001teh.1_Missense_Mutation_p.E336Q	NM_001042403	NP_115523	Q9H0E7	UBP44_HUMAN	ubiquitin specific protease 44	336					anaphase|cell division|mitosis|negative regulation of mitotic anaphase-promoting complex activity|protein deubiquitination|regulation of spindle checkpoint|ubiquitin-dependent protein catabolic process	nucleus	protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(1)	1														0.10989	10.500543	24.197815	10	81	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	94451158	94451158	17639	12	C	G	G	29	29	USP44	G	3	3
FREM2	341640	broad.mit.edu	36	13	38322215	38322215	+	Silent	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:38322215C>T	uc001uwv.1	+	c.6420C>T	c.(6418-6420)AGC>AGT	p.S2140S	FREM2_uc001uww.2_Silent_p.S226S	NM_207361	NP_997244	Q5SZK8	FREM2_HUMAN	FRAS1-related extracellular matrix protein 2	2140	Extracellular (Potential).|Calx-beta 4.				cell communication|homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(7)|haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)|pancreas(1)	10		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)										0.399038	243.991705	245.841612	83	125	CC		KEEP	---	---	---	---	capture			Silent	SNP	38322215	38322215	6292	13	C	T	T	27	27	FREM2	T	1	1
MRPS31	10240	broad.mit.edu	36	13	40229133	40229133	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr13:40229133A>G	uc001uxm.2	-	c.616T>C	c.(616-618)TCA>CCA	p.S206P		NM_005830	NP_005821	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31	206						mitochondrion|ribosome	protein domain specific binding				0		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)										0.3	11.040963	11.757112	6	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	40229133	40229133	10234	13	A	G	G	12	12	MRPS31	G	4	4
PCDH8	5100	broad.mit.edu	36	13	52320366	52320366	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr13:52320366G>C	uc001vhi.1	-	c.207C>G	c.(205-207)TTC>TTG	p.F69L	PCDH8_uc001vhj.1_Missense_Mutation_p.F69L	NM_002590	NP_002581	O95206	PCDH8_HUMAN	protocadherin 8 isoform 1 precursor	69	Extracellular (Potential).|Cadherin 1.				cell-cell signaling|homophilic cell adhesion	cell junction|dendrite|integral to plasma membrane|postsynaptic membrane|presynaptic membrane	calcium ion binding			breast(1)	1		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		GBM(36;25 841 9273 49207)								0.258065	13.378143	15.029818	8	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52320366	52320366	11937	13	G	C	C	45	45	PCDH8	C	3	3
HSP90AA1	3320	broad.mit.edu	36	14	101620824	101620824	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:101620824C>T	uc001ykv.2	-	c.1294G>A	c.(1294-1296)GGA>AGA	p.G432R	HSP90AA1_uc001yku.2_Missense_Mutation_p.G310R|HSP90AA1_uc001ykw.1_Missense_Mutation_p.G131R|HSP90AA1_uc001ykx.1_Missense_Mutation_p.G299R	NM_001017963	NP_005339	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic),	310					axon guidance|cellular chaperone-mediated protein complex assembly|G2/M transition of mitotic cell cycle|nitric oxide metabolic process|positive regulation of nitric oxide biosynthetic process|protein import into mitochondrial outer membrane|protein refolding|regulation of nitric-oxide synthase activity|response to unfolded protein|signal transduction	cytosol|melanosome|plasma membrane	ATP binding|ATPase activity|nitric-oxide synthase regulator activity|protein homodimerization activity|TPR domain binding|unfolded protein binding			ovary(2)|central_nervous_system(2)	4					Rifabutin(DB00615)					7				0.186275	41.790475	51.181323	19	83	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101620824	101620824	7700	14	C	T	T	23	23	HSP90AA1	T	1	1
CHD8	57680	broad.mit.edu	36	14	20946824	20946824	+	Missense_Mutation	SNP	T	A	A			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:20946824T>A	uc001was.1	-	c.1528A>T	c.(1528-1530)AAT>TAT	p.N510Y	CHD8_uc001war.1_Missense_Mutation_p.N406Y|CHD8_uc001wav.1_5'UTR	NM_020920	NP_065971	Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	789	Chromo 2.				ATP-dependent chromatin remodeling|canonical Wnt receptor signaling pathway|chromatin assembly or disassembly|negative regulation of Wnt receptor signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase III promoter|transcription, DNA-dependent	chromatin|MLL1 complex	ATP binding|beta-catenin binding|chromatin binding|DNA binding|DNA helicase activity|DNA-dependent ATPase activity|methylated histone residue binding|p53 binding|transcription activator activity|transcription repressor activity			ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|breast(1)|skin(1)	10	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)						886				0.333333	7.690895	7.988657	4	8	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20946824	20946824	3465	14	T	A	A	62	62	CHD8	A	4	4
PTGER2	5732	broad.mit.edu	36	14	51863692	51863692	+	Missense_Mutation	SNP	T	A	A			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr14:51863692T>A	uc001wzr.1	+	c.847T>A	c.(847-849)TTT>ATT	p.F283I		NM_000956	NP_000947	P43116	PE2R2_HUMAN	prostaglandin E receptor 2 (subtype EP2), 53kDa	283	Helical; Name=6; (Potential).					integral to plasma membrane	prostaglandin E receptor activity				0	Breast(41;0.0639)|all_epithelial(31;0.0729)				Alprostadil(DB00770)|Iloprost(DB01088)									0.307692	8.493384	8.923184	4	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	51863692	51863692	13198	14	T	A	A	64	64	PTGER2	A	4	4
PELI2	57161	broad.mit.edu	36	14	55833244	55833244	+	Silent	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:55833244C>G	uc001xch.1	+	c.870C>G	c.(868-870)ACC>ACG	p.T290T		NM_021255	NP_067078	Q9HAT8	PELI2_HUMAN	pellino 2	290					innate immune response|MyD88-dependent toll-like receptor signaling pathway|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of MAPKKK cascade|positive regulation of protein phosphorylation|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	protein binding			ovary(1)	1														0.416667	21.336154	21.483455	10	14	CC		KEEP	---	---	---	---	capture			Silent	SNP	55833244	55833244	12143	14	C	G	G	22	22	PELI2	G	3	3
SYNE2	23224	broad.mit.edu	36	14	63520332	63520333	+	Missense_Mutation	DNP	CT	TA	TA			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:63520332_63520333CT>TA	uc001xgl.1	+	c.2126_2127CT>TA	c.(2125-2127)CCT>CTA	p.P709L	SYNE2_uc001xgm.1_Missense_Mutation_p.P709L	NM_182914	NP_878918	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	709	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)										0.5	7.021848	7.021848	3	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	63520332	63520333	15967	14	CT	TA	TA	24	24	SYNE2	TA	2	2
DCAF5	8816	broad.mit.edu	36	14	68591604	68591604	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:68591604G>A	uc001xkp.1	-	c.1552C>T	c.(1552-1554)CGC>TGC	p.R518C	DCAF5_uc001xkq.1_Missense_Mutation_p.R517C	NM_003861	NP_003852	Q96JK2	DCAF5_HUMAN	WD repeat domain 22	518					protein ubiquitination	CUL4 RING ubiquitin ligase complex				ovary(1)|central_nervous_system(1)	2														0.444444	23.898369	23.946536	8	10	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	68591604	68591604	4444	14	G	A	A	38	38	DCAF5	A	1	1
HERC2	8924	broad.mit.edu	36	15	26035599	26035599	+	Silent	SNP	A	C	C			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:26035599A>C	uc001zbj.1	-	c.13416T>G	c.(13414-13416)GGT>GGG	p.G4472G	HERC2_uc001zbi.1_Silent_p.G161G	NM_004667	NP_004658	O95714	HERC2_HUMAN	hect domain and RLD 2	4472	HECT.				DNA repair|intracellular protein transport|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|regulation of mitotic metaphase/anaphase transition	anaphase-promoting complex	guanyl-nucleotide exchange factor activity|heme binding|protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(4)|lung(4)|skin(2)|central_nervous_system(1)	11		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)						1580				0.333333	7.492174	7.789297	4	8	AA		KEEP	---	---	---	---	capture			Silent	SNP	26035599	26035599	7341	15	A	C	C	6	6	HERC2	C	4	4
KIAA1370	56204	broad.mit.edu	36	15	50688694	50688695	+	Missense_Mutation	DNP	TT	GA	GA			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:50688694_50688695TT>GA	uc002acg.2	-	c.1708_1709AA>TC	c.(1708-1710)AAT>TCT	p.N570S	KIAA1370_uc002ach.2_Non-coding_Transcript|KIAA1370_uc010bfg.1_Missense_Mutation_p.N482S	NM_019600	NP_062546	Q32MH5	K1370_HUMAN	hypothetical protein LOC56204	570											0				all cancers(107;0.0803)										0.307692	8.693959	9.123347	4	9	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	50688694	50688695	8535	15	TT	GA	GA	52	52	KIAA1370	GA	4	4
ANP32A	8125	broad.mit.edu	36	15	66866858	66866858	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:66866858T>C	uc002arl.1	-	c.275A>G	c.(274-276)CAT>CGT	p.H92R		NM_006305	NP_006296	P39687	AN32A_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32	92	LRR 4.				intracellular signal transduction|mRNA metabolic process|nucleocytoplasmic transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	endoplasmic reticulum|nucleoplasm|perinuclear region of cytoplasm	protein binding				0														0.258065	39.24538	44.194132	24	69	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	66866858	66866858	713	15	T	C	C	51	51	ANP32A	C	4	4
PML	5371	broad.mit.edu	36	15	72112060	72112060	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:72112060A>T	uc002awv.1	+	c.1349A>T	c.(1348-1350)CAC>CTC	p.H450L	PML_uc002awj.1_Intron|PML_uc002awk.1_Missense_Mutation_p.H450L|PML_uc002awl.1_Intron|PML_uc002awm.1_Missense_Mutation_p.H450L|PML_uc002awn.1_Missense_Mutation_p.H450L|PML_uc002awo.1_Intron|PML_uc002awp.1_Intron|PML_uc002awq.1_Missense_Mutation_p.H450L|PML_uc002awr.1_Missense_Mutation_p.H450L|PML_uc002aws.1_Intron|PML_uc002awt.1_Intron|PML_uc002awu.1_Intron|PML_uc002awx.1_Intron|PML_uc002awy.1_Intron	NM_033238	NP_150241	P29590	PML_HUMAN	promyelocytic leukemia protein isoform 1	450					cell cycle arrest|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 resulting in induction of apoptosis|endoplasmic reticulum calcium ion homeostasis|induction of apoptosis|interferon-gamma-mediated signaling pathway|interspecies interaction between organisms|maintenance of protein location in nucleus|negative regulation of angiogenesis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of mitotic cell cycle|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|negative regulation of telomerase activity|negative regulation of telomere maintenance via telomerase|negative regulation of transcription, DNA-dependent|negative regulation of translation in response to oxidative stress|PML body organization|PML body organization|positive regulation of defense response to virus by host|positive regulation of histone deacetylation|protein complex assembly|protein stabilization|protein targeting|regulation of calcium ion transport into cytosol|regulation of protein phosphorylation|response to hypoxia|response to virus|transcription, DNA-dependent	cytoplasm|cytosol|early endosome membrane|extrinsic to endoplasmic reticulum membrane|insoluble fraction|nuclear matrix|nuclear membrane|nucleolus|nucleus|PML body	cobalt ion binding|DNA binding|protein binding|protein binding|protein heterodimerization activity|protein homodimerization activity|SUMO binding|transcription coactivator activity|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding|zinc ion binding			central_nervous_system(2)|kidney(2)	4										214				0.26087	19.574114	21.962426	12	34	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72112060	72112060	12561	15	A	T	T	6	6	PML	T	4	4
TMC3	342125	broad.mit.edu	36	15	79412130	79412130	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:79412130C>G	uc002bgo.1	-	c.2988G>C	c.(2986-2988)TGG>TGC	p.W996C	TMC3_uc010blr.1_Non-coding_Transcript	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	996	Cytoplasmic (Potential).					integral to membrane				ovary(1)|liver(1)	2														0.545455	13.54341	13.562573	6	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79412130	79412130	16516	15	C	G	G	30	30	TMC3	G	3	3
TMC3	342125	broad.mit.edu	36	15	79420882	79420882	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:79420882G>A	uc002bgo.1	-	c.1748C>T	c.(1747-1749)GCG>GTG	p.A583V	TMC3_uc010blr.1_Non-coding_Transcript|TMC3_uc002bgp.2_Missense_Mutation_p.A583V	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN	transmembrane channel-like 3	583	Helical; (Potential).					integral to membrane				ovary(1)|liver(1)	2														0.206897	12.836653	15.144306	6	23	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	79420882	79420882	16516	15	G	A	A	38	38	TMC3	A	1	1
WDR93	56964	broad.mit.edu	36	15	88059214	88059214	+	Splice_Site_SNP	SNP	G	C	C			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:88059214G>C	uc002boj.1	+	c.e6_splice_site			WDR93_uc010bnr.1_Splice_Site_SNP	NM_020212	NP_064597			WD repeat domain 93						electron transport chain	mitochondrial inner membrane	oxidoreductase activity, acting on NADH or NADPH			ovary(2)	2	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)											0.25	6.79081	7.702042	4	12	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	88059214	88059214	17914	15	G	C	C	35	35	WDR93	C	5	3
MAN2A2	4122	broad.mit.edu	36	15	89251057	89251057	+	Missense_Mutation	SNP	A	C	C			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr15:89251057A>C	uc010bnz.1	+	c.919A>C	c.(919-921)ACC>CCC	p.T307P	MAN2A2_uc002bqa.1_Non-coding_Transcript|MAN2A2_uc002bqb.1_Non-coding_Transcript|MAN2A2_uc002bqc.1_Missense_Mutation_p.T307P|MAN2A2_uc010boa.1_Missense_Mutation_p.T349P	NM_006122	NP_006113	P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	307	Lumenal (Potential).				mannose metabolic process|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-mannosidase activity|carbohydrate binding|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity|zinc ion binding			large_intestine(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)											0.227273	6.867268	8.370624	5	17	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	89251057	89251057	9598	15	A	C	C	6	6	MAN2A2	C	4	4
HDDC3	374659	broad.mit.edu	36	15	89275937	89275937	+	Splice_Site_SNP	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:89275937C>T	uc002bqf.2	-	c.e3_splice_site			UNC45A_uc002bqd.1_Intron|HDDC3_uc002bqe.2_Splice_Site_SNP	NM_198527	NP_940929			HD domain containing 3								guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity|metal ion binding			ovary(1)	1	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)									OREG0023475	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.725166	734.026253	747.819452	219	83	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	89275937	89275937	7300	15	C	T	T	18	18	HDDC3	T	5	2
LRRK1	79705	broad.mit.edu	36	15	99423383	99423383	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:99423383G>A	uc002bwr.1	+	c.5218G>A	c.(5218-5220)GTG>ATG	p.V1740M	LRRK1_uc002bws.1_Non-coding_Transcript	NM_024652	NP_078928	Q38SD2	LRRK1_HUMAN	leucine-rich repeat kinase 1	1740					protein phosphorylation|small GTPase mediated signal transduction	mitochondrion	ATP binding|GTP binding|metal ion binding|protein binding|protein serine/threonine kinase activity			ovary(4)|lung(4)|central_nervous_system(3)|large_intestine(1)	12	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)							1100				0.352941	15.963182	16.279119	6	11	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99423383	99423383	9408	15	G	A	A	40	40	LRRK1	A	1	1
TSC2	7249	broad.mit.edu	36	16	2062904	2062905	+	Missense_Mutation	DNP	CA	AG	AG			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:2062904_2062905CA>AG	uc002con.1	+	c.2274_2275CA>AG	c.(2272-2277)TCCAGA>TCAGGA	p.R759G	TSC2_uc010bsd.1_Missense_Mutation_p.R759G|TSC2_uc002coo.1_Missense_Mutation_p.R759G|TSC2_uc002cop.1_Missense_Mutation_p.R559G	NM_000548	NP_000539	P49815	TSC2_HUMAN	tuberous sclerosis 2 isoform 1	759					cell cycle arrest|endocytosis|heart development|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|negative regulation of phosphatidylinositol 3-kinase cascade|negative regulation of protein kinase B signaling cascade|negative regulation of TOR signaling cascade|negative regulation of Wnt receptor signaling pathway|nerve growth factor receptor signaling pathway|neural tube closure|phosphatidylinositol 3-kinase cascade|phosphatidylinositol-mediated signaling|positive chemotaxis|protein import into nucleus|protein kinase B signaling cascade|regulation of endocytosis|regulation of insulin receptor signaling pathway|regulation of small GTPase mediated signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm|TSC1-TSC2 complex	GTPase activator activity|protein homodimerization activity			central_nervous_system(4)|lung(3)|ovary(2)|pancreas(1)	10		Hepatocellular(780;0.0202)								1098				0.5	8.595099	8.595099	4	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	2062904	2062905	17157	16	CA	AG	AG	21	21	TSC2	AG	3	3
E4F1	1877	broad.mit.edu	36	16	2225463	2225465	+	Missense_Mutation	TNP	GGC	CTG	CTG			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:2225463_2225465GGC>CTG	uc002cpm.1	+	c.2244_2246GGC>CTG	c.(2242-2247)CAGGCC>CACTGC	p.748_749QA>HC	DNASE1L2_uc002cpn.1_5'Flank|DNASE1L2_uc002cpo.1_5'Flank|DNASE1L2_uc002cpp.1_5'Flank|DNASE1L2_uc002cpq.1_5'Flank|E4F1_uc010bsi.1_3'UTR|E4F1_uc010bsj.1_Missense_Mutation_p.571_572QA>HC	NM_004424	NP_004415	Q66K89	E4F1_HUMAN	p120E4F	748_749					cell division|cell proliferation|interspecies interaction between organisms|mitosis|regulation of growth|regulation of transcription, DNA-dependent	cytoplasm|nucleoplasm	DNA binding|ligase activity|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity|zinc ion binding			ovary(1)	1														0.944444	46.275939	48.805438	17	1	GG		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	2225463	2225465	5060	16	GGC	CTG	CTG	35	35	E4F1	CTG	3	3
SPN	6693	broad.mit.edu	36	16	29582775	29582775	+	Silent	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:29582775C>A	uc002dtm.1	+	c.225C>A	c.(223-225)TCC>TCA	p.S75S	BOLA2_uc010bzb.1_Intron|BOLA2_uc010bzc.1_Intron|SPN_uc002dtn.1_Silent_p.S75S|SPN_uc010bzd.1_Non-coding_Transcript|SPN_uc010bze.1_Silent_p.S75S	NM_001030288	NP_003114	P16150	LEUK_HUMAN	sialophorin	75	Extracellular (Potential).				blood coagulation|cellular defense response|chemotaxis|defense response to bacterium|establishment or maintenance of cell polarity|immune response|leukocyte migration|negative regulation of cell adhesion|positive regulation of tumor necrosis factor biosynthetic process	extracellular space|integral to plasma membrane	bacterial cell surface binding|transmembrane receptor activity			central_nervous_system(2)	2														0.162866	93.785953	126.940152	50	257	CC		KEEP	---	---	---	---	capture			Silent	SNP	29582775	29582775	15586	16	C	A	A	22	22	SPN	A	3	3
ZNF646	9726	broad.mit.edu	36	16	30998174	30998174	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30998174G>C	uc002eap.1	+	c.3028G>C	c.(3028-3030)GAC>CAC	p.D1010H		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	1010					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2														0.150943	6.557823	12.765599	8	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30998174	30998174	18657	16	G	C	C	41	41	ZNF646	C	3	3
ZNF646	9726	broad.mit.edu	36	16	30998416	30998416	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:30998416C>A	uc002eap.1	+	c.3270C>A	c.(3268-3270)AAC>AAA	p.N1090K		NM_014699	NP_055514	O15015	ZN646_HUMAN	zinc finger protein 646	1090	C2H2-type 19.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding			breast(2)	2														0.173913	9.088227	13.701613	8	38	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30998416	30998416	18657	16	C	A	A	18	18	ZNF646	A	3	3
CREBBP	1387	broad.mit.edu	36	16	3800738	3800738	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:3800738C>G	uc002cvv.1	-	c.842G>C	c.(841-843)AGT>ACT	p.S281T	CREBBP_uc002cvw.1_Missense_Mutation_p.S281T	NM_004380	NP_004371	Q92793	CBP_HUMAN	CREB binding protein isoform a	281	Interaction with SRCAP.				cellular lipid metabolic process|homeostatic process|interspecies interaction between organisms|N-terminal peptidyl-lysine acetylation|protein complex assembly|response to hypoxia	cytoplasm|nuclear body	histone acetyltransferase activity|MyoD binding|p53 binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription coactivator activity|zinc ion binding			ovary(6)|skin(2)|pancreas(1)|lung(1)	10		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)						748				0.148936	9.672952	20.834382	14	80	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	3800738	3800738	4000	16	C	G	G	20	20	CREBBP	G	3	3
PIGQ	9091	broad.mit.edu	36	16	573278	573278	+	Silent	SNP	T	A	A			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:573278T>A	uc002cho.1	+	c.1926T>A	c.(1924-1926)CTT>CTA	p.L642L	PIGQ_uc010bqw.1_3'UTR|PIGQ_uc002chn.1_3'UTR|PIGQ_uc002chp.1_Silent_p.L212L	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	642					C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)												0.36	16.960023	17.394285	9	16	TT		KEEP	---	---	---	---	capture			Silent	SNP	573278	573278	12320	16	T	A	A	62	62	PIGQ	A	4	4
ADAMTS18	170692	broad.mit.edu	36	16	75933187	75933187	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr16:75933187T>G	uc002ffc.2	-	c.1625A>C	c.(1624-1626)AAA>ACA	p.K542T	ADAMTS18_uc010chc.1_Missense_Mutation_p.K130T|ADAMTS18_uc002ffe.1_Missense_Mutation_p.K238T	NM_199355	NP_955387	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1	542	Disintegrin.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			large_intestine(4)|kidney(4)|skin(2)|pancreas(1)|ovary(1)	12										1451				0.266667	7.192077	7.931331	4	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	75933187	75933187	264	16	T	G	G	64	64	ADAMTS18	G	4	4
ELAC2	60528	broad.mit.edu	36	17	12839754	12839754	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:12839754T>G	uc002gnz.2	-	c.1799A>C	c.(1798-1800)CAC>CCC	p.H600P	ELAC2_uc002gnv.2_Missense_Mutation_p.H228P|ELAC2_uc002gnw.2_Missense_Mutation_p.H258P|ELAC2_uc002gnx.2_Missense_Mutation_p.H360P|ELAC2_uc002gny.2_Missense_Mutation_p.H566P|ELAC2_uc002goa.2_Missense_Mutation_p.H584P|ELAC2_uc002gnu.2_5'UTR	NM_018127	NP_060597	Q9BQ52	RNZ2_HUMAN	elaC homolog 2	600					tRNA processing	nucleus	endonuclease activity|metal ion binding|protein binding				0														0.192308	7.357984	9.661815	5	21	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	12839754	12839754	5238	17	T	G	G	59	59	ELAC2	G	4	4
FLII	2314	broad.mit.edu	36	17	18093376	18093376	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:18093376G>C	uc002gsr.1	-	c.1848C>G	c.(1846-1848)CAC>CAG	p.H616Q	FLII_uc002gsq.1_Missense_Mutation_p.H487Q|FLII_uc010cpy.1_Missense_Mutation_p.H605Q|FLII_uc002gss.1_Missense_Mutation_p.H615Q	NM_002018	NP_002009	Q13045	FLII_HUMAN	flightless I homolog	616	Interaction with ACTL6A.				multicellular organismal development|muscle contraction|regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|nucleus	actin binding			central_nervous_system(1)	1	all_neural(463;0.228)													0.176471	6.422147	9.790435	6	28	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18093376	18093376	6163	17	G	C	C	36	36	FLII	C	3	3
AP2B1	163	broad.mit.edu	36	17	31008861	31008861	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:31008861C>A	uc002hjq.1	+	c.1927C>A	c.(1927-1929)CCA>ACA	p.P643T	AP2B1_uc002hjr.1_Missense_Mutation_p.P643T|AP2B1_uc002hjs.1_Missense_Mutation_p.P586T|AP2B1_uc002hjt.1_Missense_Mutation_p.P643T|AP2B1_uc010ctv.1_Missense_Mutation_p.P643T	NM_001030006	NP_001025177	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1	643	Pro-rich (stalk region).				axon guidance|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of epidermal growth factor receptor signaling pathway|nerve growth factor receptor signaling pathway|regulation of defense response to virus by virus|synaptic transmission|vesicle-mediated transport|viral reproduction	clathrin adaptor complex|coated pit|cytosol|endocytic vesicle membrane|plasma membrane	clathrin binding|protein transporter activity			ovary(1)	1		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)										0.101351	14.632531	38.082687	15	133	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	31008861	31008861	751	17	C	A	A	26	26	AP2B1	A	3	3
KRT9	3857	broad.mit.edu	36	17	36977981	36977981	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:36977981G>A	uc002hxe.2	-	c.1353C>T	c.(1351-1353)ATC>ATT	p.I451I		NM_000226	NP_000217	P35527	K1C9_HUMAN	keratin 9	451	Rod.|Coil 2.				intermediate filament organization|skin development		protein binding|structural constituent of cytoskeleton			ovary(1)|central_nervous_system(1)|pancreas(1)	3		Breast(137;0.000307)												0.259259	33.690425	36.483909	14	40	GG		KEEP	---	---	---	---	capture			Silent	SNP	36977981	36977981	8816	17	G	A	A	37	37	KRT9	A	1	1
CDC27	996	broad.mit.edu	36	17	42576250	42576250	+	Missense_Mutation	SNP	T	C	C	rs1064545	by-cluster,by-hapmap	TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:42576250T>C	uc002ile.2	-	c.1186A>G	c.(1186-1188)AAG>GAG	p.K396E	CDC27_uc002ild.2_Missense_Mutation_p.K390E|CDC27_uc002ilf.2_Missense_Mutation_p.K390E	NM_001114091	NP_001107563	P30260	CDC27_HUMAN	cell division cycle protein 27 isoform 1	390					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|cell proliferation|mitotic cell cycle spindle assembly checkpoint|mitotic metaphase/anaphase transition|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein K11-linked ubiquitination	anaphase-promoting complex|centrosome|cytosol|nucleoplasm|spindle microtubule	protein binding			lung(2)|breast(2)|ovary(1)	5														0.214286	7.724606	9.849378	6	22	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42576250	42576250	3194	17	T	C	C	63	63	CDC27	C	4	4
TTLL6	284076	broad.mit.edu	36	17	44222371	44222372	+	Missense_Mutation	DNP	TT	CC	CC			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:44222371_44222372TT>CC	uc002ioe.1	-	c.861_862AA>GG	c.(859-864)GAAAGC>GAGGGC	p.S288G	TTLL6_uc002iob.1_Missense_Mutation_p.S119G|TTLL6_uc010dbi.1_Non-coding_Transcript|TTLL6_uc002ioc.1_Missense_Mutation_p.S194G|TTLL6_uc002iod.1_Missense_Mutation_p.S288G	NM_173623	NP_775894	Q8N841	TTLL6_HUMAN	tubulin tyrosine ligase-like family, member 6	393	TTL.					cilium|microtubule basal body	ATP binding|tubulin binding|tubulin-tyrosine ligase activity				0														0.190476	10.473081	14.243716	8	34	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	44222371	44222372	17286	17	TT	CC	CC	56	56	TTLL6	CC	4	4
DHX40	79665	broad.mit.edu	36	17	55005373	55005373	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr17:55005373A>T	uc002ixn.1	+	c.541A>T	c.(541-543)ACT>TCT	p.T181S	DHX40_uc002ixo.1_Missense_Mutation_p.T82S	NM_024612	NP_078888	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	181	Helicase ATP-binding.						ATP binding|ATP-dependent helicase activity|nucleic acid binding				0	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)													0.314815	29.534275	31.194635	17	37	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55005373	55005373	4691	17	A	T	T	2	2	DHX40	T	4	4
QRICH2	84074	broad.mit.edu	36	17	71800531	71800531	+	Silent	SNP	T	A	A			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71800531T>A	uc002jrd.1	-	c.1374A>T	c.(1372-1374)GGA>GGT	p.G458G	QRICH2_uc010dgw.1_Intron	NM_032134	NP_115510	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	458	Gln-rich.						protein binding			ovary(1)|lung(1)|central_nervous_system(1)|pancreas(1)	4														0.25	11.973859	13.803273	8	24	TT		KEEP	---	---	---	---	capture			Silent	SNP	71800531	71800531	13338	17	T	A	A	62	62	QRICH2	A	4	4
AMAC1L3	643664	broad.mit.edu	36	17	7326635	7326635	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7326635T>C	uc010cmj.1	+	c.608T>C	c.(607-609)CTG>CCG	p.L203P	POLR2A_uc002ghe.2_5'Flank|POLR2A_uc002ghf.2_5'Flank|ZBTB4_uc002ghc.2_5'Flank|ZBTB4_uc002ghd.2_Intron	NM_001102614	NP_001096084	P0C7Q6	AMCL3_HUMAN	acyl-malonyl condensing enzyme 1-like 3	203	Helical; (Potential).					integral to membrane					0		Prostate(122;0.173)												0.168317	14.468126	25.083273	17	84	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7326635	7326635	564	17	T	C	C	55	55	AMAC1L3	C	4	4
PER1	5187	broad.mit.edu	36	17	7986434	7986434	+	Silent	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:7986434C>G	uc002gkd.1	-	c.3327G>C	c.(3325-3327)GGG>GGC	p.G1109G	PER1_uc010cns.1_5'Flank	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	1109					circadian rhythm|entrainment of circadian clock|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			breast(2)|ovary(1)|large_intestine(1)|kidney(1)|skin(1)	6										239				0.916667	28.73819	30.33509	11	1	CC		KEEP	---	---	---	---	capture			Silent	SNP	7986434	7986434	12150	17	C	G	G	22	22	PER1	G	3	3
PER1	5187	broad.mit.edu	36	17	7986436	7986437	+	Missense_Mutation	DNP	CA	TT	TT			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:7986436_7986437CA>TT	uc002gkd.1	-	c.3324_3325TG>AA	c.(3322-3327)GCTGGG>GCAAGG	p.G1109R	PER1_uc010cns.1_5'Flank	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	1109					circadian rhythm|entrainment of circadian clock|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			breast(2)|ovary(1)|large_intestine(1)|kidney(1)|skin(1)	6										239				0.888889	19.359951	20.635789	8	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	7986436	7986437	12150	17	CA	TT	TT	21	21	PER1	TT	2	2
C18orf34	374864	broad.mit.edu	36	18	29049566	29049566	+	Nonsense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:29049566A>T	uc002kxn.2	-	c.2024T>A	c.(2023-2025)TTA>TAA	p.L675*	C18orf34_uc010dme.1_Nonsense_Mutation_p.L189*|C18orf34_uc010dmf.1_Intron|C18orf34_uc002kxo.2_Nonsense_Mutation_p.L637*|C18orf34_uc002kxp.2_Nonsense_Mutation_p.L675*	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN	hypothetical protein LOC374864 isoform 1	675	Potential.									ovary(1)	1														0.285714	9.094757	9.671515	4	10	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	29049566	29049566	1963	18	A	T	T	13	13	C18orf34	T	5	4
LAMA1	284217	broad.mit.edu	36	18	6975397	6975397	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:6975397G>A	uc002knm.1	-	c.5499C>T	c.(5497-5499)CAC>CAT	p.H1833H		NM_005559	NP_005550	P25391	LAMA1_HUMAN	laminin, alpha 1 precursor	1833	Domain II and I.				axon guidance|cell adhesion|cell surface receptor linked signaling pathway|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	extracellular space|laminin-1 complex|laminin-3 complex	extracellular matrix structural constituent|receptor binding			ovary(8)|large_intestine(4)|breast(2)|pancreas(2)|central_nervous_system(1)	17		Colorectal(10;0.172)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)					1597				0.866142	731.216641	764.254232	220	34	GG		KEEP	---	---	---	---	capture			Silent	SNP	6975397	6975397	8928	18	G	A	A	36	36	LAMA1	A	2	2
ANKRD12	23253	broad.mit.edu	36	18	9244712	9244712	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr18:9244712A>G	uc002knv.2	+	c.1447A>G	c.(1447-1449)AAA>GAA	p.K483E	ANKRD12_uc002knw.2_Missense_Mutation_p.K460E|ANKRD12_uc002knx.2_Missense_Mutation_p.K460E|ANKRD12_uc010dkx.1_Missense_Mutation_p.K190E	NM_015208	NP_056023	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12 isoform 1	483						nucleus				ovary(2)|central_nervous_system(1)	3														0.533333	26.802709	26.817481	8	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9244712	9244712	643	18	A	G	G	13	13	ANKRD12	G	4	4
GDF15	9518	broad.mit.edu	36	19	18360198	18360198	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:18360198T>G	uc002niv.2	+	c.380T>G	c.(379-381)CTG>CGG	p.L127R		NM_004864	NP_004855	Q99988	GDF15_HUMAN	growth differentiation factor 15	127					cell-cell signaling|transforming growth factor beta receptor signaling pathway	extracellular space	cytokine activity|growth factor activity			central_nervous_system(1)	1												OREG0025363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.4	9.094259	9.182618	4	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18360198	18360198	6581	19	T	G	G	55	55	GDF15	G	4	4
TLE6	79816	broad.mit.edu	36	19	2945039	2945039	+	Silent	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:2945039A>G	uc010dtg.1	+	c.1560A>G	c.(1558-1560)GGA>GGG	p.G520G	TLE6_uc002lwt.1_Silent_p.G397G|TLE6_uc002lwu.1_Silent_p.G397G|TLE6_uc002lwv.1_Silent_p.G301G	NM_024760	NP_079036	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6 isoform 2	397	WD 6.					nucleus				ovary(1)	1				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)										0.363636	8.092676	8.274251	4	7	AA		KEEP	---	---	---	---	capture			Silent	SNP	2945039	2945039	16472	19	A	G	G	9	9	TLE6	G	4	4
EML2	24139	broad.mit.edu	36	19	50829560	50829560	+	Nonsense_Mutation	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50829560G>T	uc002pcq.1	-	c.792C>A	c.(790-792)TAC>TAA	p.Y264*	EML2_uc002pcn.1_Nonsense_Mutation_p.Y63*|EML2_uc002pco.1_Non-coding_Transcript|EML2_uc002pcp.1_Intron|EML2_uc010ekj.1_Nonsense_Mutation_p.Y63*|EML2_uc010ekk.1_5'Flank	NM_012155	NP_036287	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like	63					sensory perception of sound|visual perception	cytoplasm|intracellular membrane-bounded organelle|microtubule|microtubule associated complex	catalytic activity|protein binding			large_intestine(1)|ovary(1)	2		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)										0.333333	7.421656	7.643234	3	6	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	50829560	50829560	5289	19	G	T	T	44	44	EML2	T	5	3
ZNF417	147687	broad.mit.edu	36	19	63111834	63111834	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:63111834G>T	uc002qqq.1	-	c.1624C>A	c.(1624-1626)CAC>AAC	p.H542N	ZNF417_uc002qqr.1_Missense_Mutation_p.H541N	NM_152475	NP_689688	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	542	C2H2-type 12.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)										0.191083	326.779153	396.825862	150	635	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	63111834	63111834	18487	19	G	T	T	45	45	ZNF417	T	3	3
C3	718	broad.mit.edu	36	19	6630479	6630479	+	Silent	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:6630479C>T	uc002mfm.1	-	c.4485G>A	c.(4483-4485)CCG>CCA	p.P1495P	C3_uc002mfl.1_Silent_p.P231P	NM_000064	NP_000055	P01024	CO3_HUMAN	complement component 3 precursor	1495					complement activation, alternative pathway|complement activation, classical pathway|G-protein coupled receptor protein signaling pathway|inflammatory response|positive regulation vascular endothelial growth factor production	extracellular space	endopeptidase inhibitor activity|receptor binding			ovary(1)|pancreas(1)	2				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)										0.43573	619.456624	621.101488	200	259	CC		KEEP	---	---	---	---	capture			Silent	SNP	6630479	6630479	2296	19	C	T	T	23	23	C3	T	1	1
MTHFR	4524	broad.mit.edu	36	1	11776580	11776580	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11776580C>G	uc001atb.1	-	c.1570G>C	c.(1570-1572)GGC>CGC	p.G524R	MTHFR_uc001atc.1_Missense_Mutation_p.G501R	NM_005957	NP_005948	P42898	MTHR_HUMAN	5,10-methylenetetrahydrofolate reductase	501					blood circulation|folic acid metabolic process|oxidation-reduction process	cytosol	methylenetetrahydrofolate reductase (NADPH) activity|protein binding				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)|Raltitrexed(DB00293)|Riboflavin(DB00140)|S-Adenosylmethionine(DB00118)|Tetrahydrofolic acid(DB00116)									0.222222	7.197576	8.472272	4	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11776580	11776580	10324	1	C	G	G	22	22	MTHFR	G	3	3
CLCN6	1185	broad.mit.edu	36	1	11788977	11788977	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:11788977G>T	uc001ate.2	+	c.71G>T	c.(70-72)CGC>CTC	p.R24L	CLCN6_uc009vne.1_Missense_Mutation_p.R24L|CLCN6_uc009vnf.1_Missense_Mutation_p.R24L|CLCN6_uc009vng.1_Missense_Mutation_p.R24L|CLCN6_uc009vnh.1_Missense_Mutation_p.R24L|MTHFR_uc001atb.1_5'Flank|MTHFR_uc001atc.1_5'Flank|MTHFR_uc001atd.1_5'Flank|MTHFR_uc009vnd.1_5'Flank	NM_001286	NP_001277	P51797	CLCN6_HUMAN	chloride channel 6 isoform ClC-6a	24	Cytoplasmic (By similarity).				cell volume homeostasis|signal transduction	endosome membrane|integral to membrane	antiporter activity|ATP binding|voltage-gated chloride channel activity				0	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)										0.130435	6.966557	12.958415	6	40	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	11788977	11788977	3603	1	G	T	T	38	38	CLCN6	T	3	3
PI4KB	5298	broad.mit.edu	36	1	149549357	149549357	+	Splice_Site_SNP	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:149549357T>G	uc001exr.2	-	c.e3_splice_site			PI4KB_uc001exs.2_Intron|PI4KB_uc001ext.2_Splice_Site_SNP|PI4KB_uc001exu.2_Intron	NM_002651	NP_002642			phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process|phosphatidylinositol-mediated signaling|receptor-mediated endocytosis	endosome|Golgi apparatus|mitochondrial outer membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum membrane	1-phosphatidylinositol 4-kinase activity|ATP binding|protein binding			ovary(2)|skin(1)	3	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			Colon(154;765 1838 9854 28443 37492)				342				0.307692	7.19174	7.622577	4	9	TT		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	149549357	149549357	12298	1	T	G	G	55	55	PI4KB	G	5	4
HRNR	388697	broad.mit.edu	36	1	150452403	150452403	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150452403C>T	uc001ezt.1	-	c.8326G>A	c.(8326-8328)GGG>AGG	p.G2776R		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	2776	30.				keratinization		calcium ion binding|protein binding			ovary(1)	1	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.190476	7.862285	11.650509	8	34	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150452403	150452403	7653	1	C	T	T	23	23	HRNR	T	1	1
HRNR	388697	broad.mit.edu	36	1	150452483	150452483	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150452483C>T	uc001ezt.1	-	c.8246G>A	c.(8245-8247)CGT>CAT	p.R2749H		NM_001009931	NP_001009931	Q86YZ3	HORN_HUMAN	hornerin	2749	30.				keratinization		calcium ion binding|protein binding			ovary(1)	1	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.6	6.521361	6.564498	3	2	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150452483	150452483	7653	1	C	T	T	19	19	HRNR	T	1	1
NUP210L	91181	broad.mit.edu	36	1	152262262	152262262	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:152262262A>T	uc001fdw.1	-	c.4258T>A	c.(4258-4260)TTC>ATC	p.F1420I	NUP210L_uc009woq.1_Missense_Mutation_p.F329I|NUP210L_uc009wop.1_Missense_Mutation_p.F383I	NM_207308	NP_997191	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1420						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)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)											0.181818	12.339994	18.65374	12	54	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	152262262	152262262	11166	1	A	T	T	4	4	NUP210L	T	4	4
DCST1	149095	broad.mit.edu	36	1	153273618	153273618	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:153273618G>A	uc001fgn.1	+	c.145G>A	c.(145-147)GCT>ACT	p.A49T	DCST2_uc001fgm.1_5'Flank|DCST2_uc009wpb.1_5'Flank	NM_152494	NP_689707	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1 isoform 1	49	Helical; (Potential).					integral to membrane	zinc ion binding			ovary(1)	1	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)											0.372549	37.385894	38.122512	19	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	153273618	153273618	4473	1	G	A	A	46	46	DCST1	A	2	2
ARHGAP30	257106	broad.mit.edu	36	1	159285662	159285662	+	Silent	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:159285662C>T	uc001fxl.1	-	c.1773G>A	c.(1771-1773)CTG>CTA	p.L591L	ARHGAP30_uc001fxk.1_Silent_p.L591L|ARHGAP30_uc001fxm.1_Silent_p.L437L|ARHGAP30_uc009wtx.1_Silent_p.L264L|ARHGAP30_uc001fxn.1_Silent_p.L437L	NM_001025598	NP_001020769	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30 isoform 1	591					regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity			ovary(2)	2	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)											0.315789	40.988943	43.276601	24	52	CC		KEEP	---	---	---	---	capture			Silent	SNP	159285662	159285662	891	1	C	T	T	21	21	ARHGAP30	T	2	2
ABL2	27	broad.mit.edu	36	1	177357590	177357590	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:177357590C>G	uc001gmj.2	-	c.723G>C	c.(721-723)TTG>TTC	p.L241F	ABL2_uc001gmi.2_Missense_Mutation_p.L226F|ABL2_uc001gmh.2_Missense_Mutation_p.L205F|ABL2_uc001gmg.2_Missense_Mutation_p.L226F|ABL2_uc009wxe.1_Missense_Mutation_p.L220F|ABL2_uc009wxf.1_Missense_Mutation_p.L226F|ABL2_uc001gmk.2_Missense_Mutation_p.L205F	NM_007314	NP_009298	P42684	ABL2_HUMAN	arg tyrosine kinase isoform b	241	SH2.				axon guidance|cell adhesion|peptidyl-tyrosine phosphorylation|positive regulation of oxidoreductase activity|signal transduction	cytoskeleton|cytosol	ATP binding|magnesium ion binding|manganese ion binding|non-membrane spanning protein tyrosine kinase activity|protein binding			lung(4)|ovary(2)|breast(2)|central_nervous_system(1)	9					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)					285				0.287671	35.924567	38.892625	21	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	177357590	177357590	94	1	C	G	G	21	21	ABL2	G	3	3
TP53BP2	7159	broad.mit.edu	36	1	222061217	222061217	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:222061217C>T	uc001hod.1	-	c.41G>A	c.(40-42)CGC>CAC	p.R14H	TP53BP2_uc001hoe.1_Missense_Mutation_p.R14H	NM_005426	NP_005417	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein, 2 isoform 2	137	Gln-rich.				apoptosis|cell cycle|induction of apoptosis|negative regulation of cell cycle|signal transduction	nucleus|perinuclear region of cytoplasm	NF-kappaB binding|protein binding|SH3 domain binding|SH3/SH2 adaptor activity			ovary(2)|lung(1)	3				GBM - Glioblastoma multiforme(131;0.0958)										0.3125	64.06984	66.561721	25	55	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	222061217	222061217	16926	1	C	T	T	27	27	TP53BP2	T	1	1
ABCB10	23456	broad.mit.edu	36	1	227749937	227749937	+	Missense_Mutation	SNP	A	C	C			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:227749937A>C	uc001htp.2	-	c.853T>G	c.(853-855)TCA>GCA	p.S285A		NM_012089	NP_036221	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B, member 10	285	Mitochondrial intermembrane (Potential).|Mitochondrial intermembrane (Potential).|ABC transmembrane type-1.					integral to mitochondrial membrane|mitochondrial inner membrane	ATP binding|oligopeptide-transporting ATPase activity			breast(2)	2	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)												0.179487	7.290336	11.078824	7	32	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	227749937	227749937	42	1	A	C	C	11	11	ABCB10	C	4	4
PCNXL2	80003	broad.mit.edu	36	1	231203922	231203925	+	Missense	Complex_substitution	GNCA	ANAT	ANAT			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:231203922G>A	uc001hvl.2	-	c.5081C>T	c.(5080-5082)TCC>TTC	p.S1694F	PCNXL2_uc001hvk.1_Missense_Mutation_p.S346F|PCNXL2_uc001hvm.1_Non-coding_Transcript	NM_014801	NP_055616	A6NKB5	PCX2_HUMAN	pecanex-like 2	1694						integral to membrane				central_nervous_system(1)|pancreas(1)	2		all_cancers(173;0.0347)|Prostate(94;0.137)												0.75	6.722362	6.946612	3	1	GG		KEEP	---	---	---	---	capture			Missense	Complex_substitution	231203922	231203925	12012	1	GNCA	ANAT	ANAT	41	41	PCNXL2	ANAT	5	5
RYR2	6262	broad.mit.edu	36	1	236014798	236014798	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:236014798G>T	uc001hyl.1	+	c.13163G>T	c.(13162-13164)GGA>GTA	p.G4388V		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	4388					cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.173913	7.153816	11.80441	8	38	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	236014798	236014798	14249	1	G	T	T	41	41	RYR2	T	3	3
C1orf201	90529	broad.mit.edu	36	1	24568864	24568864	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:24568864C>T	uc001bja.1	-	c.483G>A	c.(481-483)ATG>ATA	p.M161I	C1orf201_uc001bjb.1_Missense_Mutation_p.M116I|C1orf201_uc001bjc.1_Missense_Mutation_p.M208I|C1orf201_uc001bjd.1_Missense_Mutation_p.M208I|C1orf201_uc001bje.1_Missense_Mutation_p.M161I|C1orf201_uc001bjf.2_Missense_Mutation_p.M76I	NM_178122	NP_835223	Q5TH74	CA201_HUMAN	hypothetical protein LOC90529	208										ovary(1)|breast(1)	2		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.0191)|all_lung(284;0.0251)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.056)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.48e-25)|Colorectal(126;7.29e-08)|COAD - Colon adenocarcinoma(152;3.85e-06)|GBM - Glioblastoma multiforme(114;0.000399)|BRCA - Breast invasive adenocarcinoma(304;0.00107)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00393)|READ - Rectum adenocarcinoma(331;0.0672)|Lung(427;0.145)										0.193548	14.166834	19.613244	12	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	24568864	24568864	2095	1	C	T	T	17	17	C1orf201	T	2	2
KIAA1522	57648	broad.mit.edu	36	1	33009401	33009401	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:33009401G>A	uc001bvu.1	+	c.2034G>A	c.(2032-2034)AGG>AGA	p.R678R	KIAA1522_uc001bvv.1_Silent_p.R619R	NM_020888	NP_065939	Q9P206	K1522_HUMAN	hypothetical protein LOC57648	619	Pro-rich.										0		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)												0.333333	9.464679	9.836352	5	10	GG		KEEP	---	---	---	---	capture			Silent	SNP	33009401	33009401	8547	1	G	A	A	41	41	KIAA1522	A	2	2
MRPS15	64960	broad.mit.edu	36	1	36702383	36702383	+	Silent	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36702383G>T	uc001cas.2	-	c.81C>A	c.(79-81)GGC>GGA	p.G27G		NM_031280	NP_112570	P82914	RT15_HUMAN	mitochondrial ribosomal protein S15	27				GGGSAKFPFNQWGLQPRSLLLQAARGYVVRKPAQSRLDDDP PPSTLLKDYQNV -> AVGAPSFLSTSGACSLEVSSSRPRA DMSSGNQPSLGWMMTHLLLRCSKTTRMS (in Ref. 2; AAG44697).	translation	mitochondrial small ribosomal subunit|nuclear membrane	structural constituent of ribosome			ovary(1)	1		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)								2				0.204545	10.639984	14.22268	9	35	GG		KEEP	---	---	---	---	capture			Silent	SNP	36702383	36702383	10218	1	G	T	T	38	38	MRPS15	T	3	3
PLK3	1263	broad.mit.edu	36	1	45042748	45042748	+	Nonsense_Mutation	SNP	C	A	A	rs17880829	unknown	TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:45042748C>A	uc001cmn.1	+	c.1493C>A	c.(1492-1494)TCG>TAG	p.S498*	PLK3_uc001cmo.1_Non-coding_Transcript	NM_004073	NP_004064	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	498	POLO box 1.				protein phosphorylation	membrane	ATP binding|protein binding|protein serine/threonine kinase activity				0	Acute lymphoblastic leukemia(166;0.155)									186				0.225806	11.301375	13.45234	7	24	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	45042748	45042748	12523	1	C	A	A	31	31	PLK3	A	5	3
SPTLC3	55304	broad.mit.edu	36	20	13038839	13038839	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:13038839C>A	uc002wod.1	+	c.907C>A	c.(907-909)CTC>ATC	p.L303I		NM_018327	NP_060797	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base	303					sphingoid biosynthetic process	integral to membrane|serine C-palmitoyltransferase complex	pyridoxal phosphate binding|serine C-palmitoyltransferase activity|transferase activity, transferring nitrogenous groups				0					Pyridoxal Phosphate(DB00114)									0.25	10.80205	12.402445	7	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	13038839	13038839	15639	20	C	A	A	32	32	SPTLC3	A	3	3
MAFB	9935	broad.mit.edu	36	20	38750237	38750237	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:38750237T>G	uc002xji.1	-	c.668A>C	c.(667-669)GAG>GCG	p.E223A		NM_005461	NP_005452	Q9Y5Q3	MAFB_HUMAN	transcription factor MAFB	223					negative regulation of erythrocyte differentiation		sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding				0		Myeloproliferative disorder(115;0.00878)								12				0.833333	11.573123	12.19812	5	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	38750237	38750237	9535	20	T	G	G	54	54	MAFB	G	4	4
BCAS1	8537	broad.mit.edu	36	20	52078903	52078903	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:52078903C>A	uc002xws.2	-	c.158G>T	c.(157-159)AGT>ATT	p.S53I	BCAS1_uc002xwt.2_Missense_Mutation_p.S53I|BCAS1_uc010gil.1_Missense_Mutation_p.S53I|BCAS1_uc010gim.1_5'UTR	NM_003657	NP_003648	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	53						cytoplasm	protein binding			ovary(2)|central_nervous_system(1)	3	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)											0.229665	129.896561	143.895841	48	161	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52078903	52078903	1371	20	C	A	A	20	20	BCAS1	A	3	3
SRMS	6725	broad.mit.edu	36	20	61643140	61643140	+	Missense_Mutation	SNP	T	A	A			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr20:61643140T>A	uc002yfi.1	-	c.1133A>T	c.(1132-1134)GAC>GTC	p.D378V		NM_080823	NP_543013	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory	378	Protein kinase.				protein phosphorylation		ATP binding|non-membrane spanning protein tyrosine kinase activity			lung(1)	1	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;9.69e-09)|all cancers(9;5.84e-08)|BRCA - Breast invasive adenocarcinoma(10;3.63e-06)							557				0.76	43.093797	44.621264	19	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61643140	61643140	15666	20	T	A	A	58	58	SRMS	A	4	4
MYT1	4661	broad.mit.edu	36	20	62334173	62334175	+	Missense_Mutation	TNP	CCC	AAG	AAG			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:62334173_62334175CCC>AAG	uc002yii.1	+	c.2888_2890CCC>AAG	c.(2887-2892)ACCCAC>AAAGAC	p.963_964TH>KD	MYT1_uc002yij.1_Missense_Mutation_p.622_623TH>KD	NM_004535	NP_004526	Q01538	MYT1_HUMAN	myelin transcription factor 1	963_964	C2HC-type 7.				cell differentiation|nervous system development|regulation of transcription, DNA-dependent	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					GBM(59;481 1041 20555 21139 33705)				1819				0.909091	22.933384	24.270447	10	1	CC		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	62334173	62334175	10501	20	CCC	AAG	AAG	18	18	MYT1	AAG	3	3
ATP5O	539	broad.mit.edu	36	21	34201576	34201576	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:34201576G>T	uc002ytl.1	-	c.380C>A	c.(379-381)GCC>GAC	p.A127D	DONSON_uc002ysn.1_5'UTR	NM_001697	NP_001688	P48047	ATPO_HUMAN	mitochondrial ATP synthase, O subunit precursor	127					ATP catabolic process|mitochondrial ATP synthesis coupled proton transport|respiratory electron transport chain	mitochondrial proton-transporting ATP synthase complex|plasma membrane|proton-transporting ATP synthase complex, catalytic core F(1)	drug binding|hydrogen ion transporting ATP synthase activity, rotational mechanism			ovary(1)	1														0.118616	84.761281	171.379246	72	535	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34201576	34201576	1181	21	G	T	T	42	42	ATP5O	T	3	3
HIRA	7290	broad.mit.edu	36	22	17764403	17764403	+	Silent	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:17764403T>C	uc002zpf.1	-	c.561A>G	c.(559-561)AAA>AAG	p.K187K	HIRA_uc010grn.1_Silent_p.K187K|HIRA_uc010gro.1_Silent_p.K143K|HIRA_uc010grp.1_Silent_p.K143K	NM_003325	NP_003316	P54198	HIRA_HUMAN	HIR histone cell cycle regulation defective	187	WD 4.				chromatin modification|regulation of transcription from RNA polymerase II promoter	PML body	chromatin binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|transcription regulator activity			ovary(1)	1	Colorectal(54;0.0993)													0.285714	9.329623	10.203748	6	15	TT		KEEP	---	---	---	---	capture			Silent	SNP	17764403	17764403	7405	22	T	C	C	52	52	HIRA	C	4	4
MN1	4330	broad.mit.edu	36	22	26524148	26524148	+	Missense_Mutation	SNP	T	A	A			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:26524148T>A	uc003adj.1	-	c.2384A>T	c.(2383-2385)CAG>CTG	p.Q795L		NM_002430	NP_002421	Q10571	MN1_HUMAN	meningioma  1	795							binding			central_nervous_system(3)|large_intestine(1)|ovary(1)	5										140				0.75	7.236815	7.450162	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	26524148	26524148	10064	22	T	A	A	55	55	MN1	A	4	4
AP1B1	162	broad.mit.edu	36	22	28085940	28085941	+	Missense_Mutation	DNP	AA	TC	TC			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:28085940_28085941AA>TC	uc003afj.1	-	c.151_152TT>GA	c.(151-153)TTC>GAC	p.F51D	AP1B1_uc003afi.1_Missense_Mutation_p.F51D|AP1B1_uc003afk.1_Missense_Mutation_p.F51D|AP1B1_uc003afl.1_Missense_Mutation_p.F51D	NM_001127	NP_001118	Q10567	AP1B1_HUMAN	adaptor-related protein complex 1 beta 1 subunit	51					endocytosis|intracellular protein transport|post-Golgi vesicle-mediated transport|regulation of defense response to virus by virus|viral reproduction	clathrin adaptor complex|clathrin coated vesicle membrane|cytosol|Golgi membrane|lysosomal membrane	protein binding|protein transporter activity			ovary(1)	1												OREG0026449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.3	10.536213	11.255171	6	14	AA		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	28085940	28085941	741	22	AA	TC	TC	9	9	AP1B1	TC	4	4
SMTN	6525	broad.mit.edu	36	22	29826886	29826886	+	Silent	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr22:29826886C>T	uc003ajm.1	+	c.2619C>T	c.(2617-2619)TGC>TGT	p.C873C	SMTN_uc003ajk.1_Silent_p.C873C|SMTN_uc003ajl.1_Intron|SMTN_uc003ajn.1_Silent_p.C896C|SMTN_uc003ajo.1_Silent_p.C396C|SMTN_uc010gwe.1_Silent_p.C253C|SMTN_uc003ajp.1_5'Flank	NM_134270	NP_599032	P53814	SMTN_HUMAN	smoothelin isoform a	873	CH.				muscle organ development|smooth muscle contraction	actin cytoskeleton|cytoplasm	actin binding|structural constituent of muscle			large_intestine(2)|pancreas(1)	3														0.444444	8.595455	8.619984	4	5	CC		KEEP	---	---	---	---	capture			Silent	SNP	29826886	29826886	15314	22	C	T	T	26	26	SMTN	T	2	2
SH3BP1	23616	broad.mit.edu	36	22	36391708	36391708	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:36391708A>T	uc003atj.1	+	c.1702A>T	c.(1702-1704)ACA>TCA	p.T568S	PDXP_uc003atm.1_Missense_Mutation_p.T259S			Q9Y3L3	3BP1_HUMAN	cDNA FLJ44925 fis, clone BRAMY3014613, highly similar to Homo sapiens SH3-domain binding protein 1 (SH3BP1).	Error:Variant_position_missing_in_Q9Y3L3_after_alignment					signal transduction	cytoplasm	GTPase activator activity|SH3 domain binding			central_nervous_system(1)	1	Melanoma(58;0.0574)													0.181818	12.649701	18.953388	12	54	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36391708	36391708	14735	22	A	T	T	6	6	SH3BP1	T	4	4
SYNGR1	9145	broad.mit.edu	36	22	38107849	38107851	+	Missense_Mutation	TNP	AGT	TTA	TTA			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:38107849_38107851AGT>TTA	uc003axq.2	+	c.686_688AGT>TTA	c.(685-690)CAGTCG>CTTACG	p.229_230QS>LT	TAB1_uc003axr.1_Intron	NM_004711	NP_004702	O43759	SNG1_HUMAN	synaptogyrin 1 isoform 1a	229_230					regulation of long-term neuronal synaptic plasticity|regulation of short-term neuronal synaptic plasticity	cell junction|integral to plasma membrane|melanosome					0	Melanoma(58;0.04)													1	22.502323	22.498368	8	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	38107849	38107851	15969	22	AGT	TTA	TTA	7	7	SYNGR1	TTA	4	4
TNRC6B	23112	broad.mit.edu	36	22	39026508	39026508	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr22:39026508A>T	uc003ayn.2	+	c.3482A>T	c.(3481-3483)CAG>CTG	p.Q1161L	TNRC6B_uc003aym.1_Missense_Mutation_p.Q467L|TNRC6B_uc003ayo.2_Missense_Mutation_p.Q1018L	NM_015088	NP_055903	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B isoform 1	1271					gene silencing by RNA|regulation of translation	cytoplasmic mRNA processing body	nucleotide binding|RNA binding				0										794				0.307692	7.290063	7.721802	4	9	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	39026508	39026508	16882	22	A	T	T	7	7	TNRC6B	T	4	4
FAM109B	150368	broad.mit.edu	36	22	40803950	40803951	+	Missense_Mutation	DNP	TG	AT	AT			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:40803950_40803951TG>AT	uc003bbz.1	+	c.707_708TG>AT	c.(706-708)GTG>GAT	p.V236D	FAM109B_uc010gyt.1_Missense_Mutation_p.V236D|C22orf32_uc003bca.1_5'Flank	NM_001002034	NP_001002034	Q6ICB4	SESQ2_HUMAN	hypothetical protein LOC150368	236						clathrin-coated vesicle|early endosome|Golgi apparatus|recycling endosome					0														0.75	7.524822	7.750172	3	1	TT		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	40803950	40803951	5592	22	TG	AT	AT	59	59	FAM109B	AT	4	4
PARVB	29780	broad.mit.edu	36	22	42726839	42726839	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr22:42726839G>C	uc003bem.1	+	c.164G>C	c.(163-165)GGC>GCC	p.G55A		NM_001003828	NP_001003828	Q9HBI1	PARVB_HUMAN	parvin, beta isoform a	Error:Variant_position_missing_in_Q9HBI1_after_alignment					cell adhesion|cell junction assembly	cytoskeleton|cytosol|focal adhesion	actin binding				0		Ovarian(80;0.0246)|all_neural(38;0.0423)												0.227273	14.711172	17.733927	10	34	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42726839	42726839	11886	22	G	C	C	42	42	PARVB	C	3	3
MBD5	55777	broad.mit.edu	36	2	148943035	148943035	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:148943035A>T	uc002twm.2	+	c.1053A>T	c.(1051-1053)TTA>TTT	p.L351F	MBD5_uc010fns.1_Missense_Mutation_p.L351F|MBD5_uc002twn.1_5'Flank	NM_018328	NP_060798	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	351	Pro-rich.					chromosome|nucleus	chromatin binding|DNA binding			ovary(2)	2				BRCA - Breast invasive adenocarcinoma(221;0.0569)										0.176471	9.343505	14.389876	9	42	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	148943035	148943035	9735	2	A	T	T	13	13	MBD5	T	4	4
CRYGD	1421	broad.mit.edu	36	2	208697152	208697152	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:208697152C>A	uc002vcn.2	-	c.181G>T	c.(181-183)GGC>TGC	p.G61C		NM_006891	NP_008822	P07320	CRGD_HUMAN	crystallin, gamma D	61	Beta/gamma crystallin 'Greek key' 2.				cellular response to reactive oxygen species|visual perception	soluble fraction	protein binding|structural constituent of eye lens				0				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.0858)|Lung(261;0.133)										0.285714	9.449416	10.060878	4	10	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	208697152	208697152	4056	2	C	A	A	23	23	CRYGD	A	3	3
SCG2	7857	broad.mit.edu	36	2	224171533	224171533	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:224171533T>C	uc002vnm.1	-	c.712A>G	c.(712-714)AAC>GAC	p.N238D	SCG2_uc010fwv.1_Missense_Mutation_p.N238D	NM_003469	NP_003460	P13521	SCG2_HUMAN	secretogranin II precursor	238					angiogenesis|endothelial cell migration|eosinophil chemotaxis|induction of positive chemotaxis|inflammatory response|MAPKKK cascade|negative regulation of apoptosis|negative regulation of endothelial cell proliferation|positive regulation of endothelial cell proliferation|protein secretion	extracellular space	chemoattractant activity|cytokine activity			ovary(1)	1		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)										0.625	592.302977	596.038745	170	102	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	224171533	224171533	14372	2	T	C	C	61	61	SCG2	C	4	4
SPHKAP	80309	broad.mit.edu	36	2	228591954	228591954	+	Silent	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:228591954G>T	uc002vpq.1	-	c.1860C>A	c.(1858-1860)CTC>CTA	p.L620L	SPHKAP_uc002vpp.1_Silent_p.L620L	NM_030623	NP_085126	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	620						cytoplasm	protein binding			ovary(4)|lung(1)	5		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)										0.208333	6.358549	8.256653	5	19	GG		KEEP	---	---	---	---	capture			Silent	SNP	228591954	228591954	15560	2	G	T	T	45	45	SPHKAP	T	3	3
B3GNT7	93010	broad.mit.edu	36	2	231971276	231971276	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:231971276G>A	uc002vrs.1	+	c.602G>A	c.(601-603)GGC>GAC	p.G201D		NM_145236	NP_660279	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal	201	Lumenal (Potential).				protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity				0		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)										0.238095	7.056676	8.381344	5	16	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	231971276	231971276	1283	2	G	A	A	42	42	B3GNT7	A	2	2
TRIM54	57159	broad.mit.edu	36	2	27382619	27382619	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27382619C>T	uc002rjn.1	+	c.1027C>T	c.(1027-1029)CGG>TGG	p.R343W	TRIM54_uc002rjo.1_Missense_Mutation_p.R301W	NM_032546	NP_115935	Q9BYV2	TRI54_HUMAN	ring finger protein 30 isoform 1	301	COS.				cell differentiation|microtubule-based process|multicellular organismal development|negative regulation of microtubule depolymerization	microtubule|sarcomere	signal transducer activity|zinc ion binding			ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)													0.444444	7.711508	7.73264	4	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27382619	27382619	17074	2	C	T	T	27	27	TRIM54	T	1	1
FAM179A	165186	broad.mit.edu	36	2	29111998	29111998	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:29111998C>T	uc010ezl.1	+	c.2390C>T	c.(2389-2391)ACG>ATG	p.T797M	FAM179A_uc002rmr.2_Missense_Mutation_p.T324M|FAM179A_uc002rms.1_Missense_Mutation_p.T95M	NM_199280	NP_954974	Q6ZUX3	F179A_HUMAN	hypothetical protein LOC165186	797							binding			ovary(3)|skin(1)	4														0.633333	61.530504	62.0005	19	11	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	29111998	29111998	5711	2	C	T	T	19	19	FAM179A	T	1	1
POLR1A	25885	broad.mit.edu	36	2	86150757	86150757	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:86150757G>A	uc002sqs.1	-	c.1761C>T	c.(1759-1761)GCC>GCT	p.A587A		NM_015425	NP_056240	O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	587					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	DNA-directed RNA polymerase I complex|nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|protein binding|zinc ion binding			ovary(2)	2														0.184211	8.498749	12.064127	7	31	GG		KEEP	---	---	---	---	capture			Silent	SNP	86150757	86150757	12637	2	G	A	A	39	39	POLR1A	A	1	1
STARD7	56910	broad.mit.edu	36	2	96224864	96224864	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:96224864C>G	uc002svm.2	-	c.441G>C	c.(439-441)AAG>AAC	p.K147N	STARD7_uc002svl.1_5'UTR	NM_020151	NP_064536	Q9NQZ5	STAR7_HUMAN	START domain containing 7	147	START.					mitochondrion					0														0.217391	7.057351	8.758375	5	18	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	96224864	96224864	15781	2	C	G	G	32	32	STARD7	G	3	3
COL8A1	1295	broad.mit.edu	36	3	100995787	100995787	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:100995787G>A	uc003dti.1	+	c.355G>A	c.(355-357)GGG>AGG	p.G119R	COL8A1_uc003dtg.1_Missense_Mutation_p.G118R|COL8A1_uc003dth.1_Missense_Mutation_p.G118R	NM_020351	NP_065084	P27658	CO8A1_HUMAN	alpha 1 type VIII collagen precursor	118	Triple-helical region (COL1).				angiogenesis|cell adhesion	basement membrane|collagen type VIII					0														0.834979	2025.574955	2101.059423	592	117	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100995787	100995787	3843	3	G	A	A	35	35	COL8A1	A	2	2
MYLK	4638	broad.mit.edu	36	3	124820296	124820296	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:124820296G>C	uc003ego.1	-	c.5380C>G	c.(5380-5382)CAA>GAA	p.Q1794E	MYLK_uc003egp.1_Missense_Mutation_p.Q1725E|MYLK_uc003egq.1_Missense_Mutation_p.Q1743E|MYLK_uc003egr.1_Missense_Mutation_p.Q1674E|MYLK_uc003egs.1_Missense_Mutation_p.Q1618E|MYLK_uc003egl.1_Missense_Mutation_p.Q34E|MYLK_uc003egm.1_Missense_Mutation_p.Q33E|MYLK_uc010hrr.1_Missense_Mutation_p.Q229E|MYLK_uc003egn.1_Missense_Mutation_p.Q984E	NM_053025	NP_444253	Q15746	MYLK_HUMAN	myosin light chain kinase isoform 1	1794					aorta smooth muscle tissue morphogenesis|muscle contraction|protein phosphorylation	cytosol	actin binding|ATP binding|calmodulin binding|metal ion binding|myosin light chain kinase activity			ovary(6)	6		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)						766				0.170732	7.590589	11.810993	7	34	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	124820296	124820296	10451	3	G	C	C	47	47	MYLK	C	3	3
ZDHHC19	131540	broad.mit.edu	36	3	197420769	197420769	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:197420769C>G	uc003fwc.1	-	c.283G>C	c.(283-285)GGC>CGC	p.G95R	ZDHHC19_uc010hzz.1_Non-coding_Transcript|ZDHHC19_uc010iaa.1_Non-coding_Transcript|ZDHHC19_uc010iab.1_Non-coding_Transcript	NM_001039617	NP_001034706	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC domain containing 19	95						integral to membrane	acyltransferase activity|zinc ion binding			ovary(3)	3	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)										1	8.442862	8.32449	3	0	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	197420769	197420769	18197	3	C	G	G	22	22	ZDHHC19	G	3	3
MST1R	4486	broad.mit.edu	36	3	49903037	49903037	+	Missense_Mutation	SNP	T	A	A			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:49903037T>A	uc003cxy.2	-	c.3695A>T	c.(3694-3696)GAC>GTC	p.D1232V		NM_002447	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor precursor	1232	Cytoplasmic (Potential).|Protein kinase.				cellular component movement|defense response|multicellular organismal development|positive regulation of cell proliferation|protein phosphorylation|single fertilization|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|macrophage colony-stimulating factor receptor activity|protein binding			ovary(5)|lung(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)						205				0.307692	12.974591	13.841617	8	18	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	49903037	49903037	10284	3	T	A	A	58	58	MST1R	A	4	4
IQCF2	389123	broad.mit.edu	36	3	51872075	51872075	+	Silent	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:51872075A>T	uc003dbt.1	+	c.144A>T	c.(142-144)GTA>GTT	p.V48V	IQCF1_uc003dbq.2_Intron|IQCF2_uc003dbu.1_Non-coding_Transcript	NM_203424	NP_982248	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	48	IQ 1.										0				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)										0.15	16.979642	33.465555	21	119	AA		KEEP	---	---	---	---	capture			Silent	SNP	51872075	51872075	8109	3	A	T	T	13	13	IQCF2	T	4	4
ACTR8	93973	broad.mit.edu	36	3	53877828	53877828	+	Silent	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:53877828A>G	uc003dhd.1	-	c.1833T>C	c.(1831-1833)TTT>TTC	p.F611F	ACTR8_uc003dhb.1_Silent_p.F316F|ACTR8_uc003dhc.1_Silent_p.F500F	NM_022899	NP_075050	Q9H981	ARP8_HUMAN	actin-related protein 8	611					cell division|mitosis	chromosome|nucleus				ovary(1)|central_nervous_system(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)										0.230769	8.932104	10.665739	6	20	AA		KEEP	---	---	---	---	capture			Silent	SNP	53877828	53877828	218	3	A	G	G	5	5	ACTR8	G	4	4
ROBO2	6092	broad.mit.edu	36	3	77754108	77754108	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:77754108C>G	uc003dpy.2	+	c.3595C>G	c.(3595-3597)CCA>GCA	p.P1199A		NM_002942	NP_002933	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2	1199	Cytoplasmic (Potential).				apoptosis involved in luteolysis|axon midline choice point recognition|cellular response to hormone stimulus|homophilic cell adhesion|metanephros development|negative regulation of negative chemotaxis|negative regulation of synaptogenesis|olfactory bulb interneuron development|positive regulation of axonogenesis|retinal ganglion cell axon guidance|ureteric bud development	axolemma|cell surface|integral to membrane	axon guidance receptor activity|identical protein binding			lung(5)|ovary(1)|large_intestine(1)|liver(1)	8				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)						1049				0.122807	13.190051	21.121049	7	50	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77754108	77754108	13993	3	C	G	G	30	30	ROBO2	G	3	3
SCLT1	132320	broad.mit.edu	36	4	130086690	130086690	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:130086690A>T	uc003igp.2	-	c.1361T>A	c.(1360-1362)CTG>CAG	p.L454Q	SCLT1_uc003igq.2_Intron|SCLT1_uc010iob.1_Intron|SCLT1_uc003ign.2_Missense_Mutation_p.L118Q|SCLT1_uc003igo.2_Missense_Mutation_p.L64Q	NM_144643	NP_653244	Q96NL6	SCLT1_HUMAN	sodium channel associated protein 1	454	Potential.					cytoplasm				ovary(3)|central_nervous_system(1)	4														0.206897	8.732844	11.046548	6	23	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	130086690	130086690	14388	4	A	T	T	7	7	SCLT1	T	4	4
LRBA	987	broad.mit.edu	36	4	151992592	151992592	+	Silent	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:151992592C>T	uc010ipj.1	-	c.3720G>A	c.(3718-3720)AAG>AAA	p.K1240K	LRBA_uc003ilu.2_Silent_p.K1240K|LRBA_uc003ilt.2_5'Flank	NM_006726	NP_006717	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and	1240						endoplasmic reticulum|Golgi apparatus|integral to membrane|lysosome|plasma membrane	protein binding			ovary(3)|breast(3)	6	all_hematologic(180;0.151)													0.232283	140.687353	157.372335	59	195	CC		KEEP	---	---	---	---	capture			Silent	SNP	151992592	151992592	9304	4	C	T	T	32	32	LRBA	T	2	2
NAF1	92345	broad.mit.edu	36	4	164307261	164307261	+	Silent	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:164307261A>G	uc003iqj.1	-	c.69T>C	c.(67-69)GTT>GTC	p.V23V	NAF1_uc010iqw.1_Silent_p.V23V|NAF1_uc003iqk.1_Non-coding_Transcript	NM_138386	NP_612395	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 homolog isoform a	23					rRNA processing	box H/ACA snoRNP complex|cytoplasm	protein binding|pseudouridine synthase activity|snoRNA binding			ovary(2)	2	all_hematologic(180;0.166)	Prostate(90;0.109)												0.357143	9.465012	9.719053	5	9	AA		KEEP	---	---	---	---	capture			Silent	SNP	164307261	164307261	10536	4	A	G	G	5	5	NAF1	G	4	4
STOX2	56977	broad.mit.edu	36	4	185168960	185168960	+	Nonsense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:185168960A>T	uc003ivz.1	+	c.1975A>T	c.(1975-1977)AAA>TAA	p.K659*	STOX2_uc003iwa.1_Nonsense_Mutation_p.K348*	NM_020225	NP_064610	Q9P2F5	STOX2_HUMAN	storkhead box 2	659					embryo development|maternal placenta development						0		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)										0.785714	25.614615	26.664448	11	3	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	185168960	185168960	15840	4	A	T	T	1	1	STOX2	T	5	4
SLC10A4	201780	broad.mit.edu	36	4	48180897	48180897	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:48180897C>A	uc003gyc.1	+	c.562C>A	c.(562-564)CTG>ATG	p.L188M		NM_152679	NP_689892	Q96EP9	NTCP4_HUMAN	solute carrier family 10 (sodium/bile acid	188	Cytoplasmic (Potential).					integral to membrane	bile acid:sodium symporter activity			central_nervous_system(1)	1														0.3	10.635937	11.355105	6	14	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48180897	48180897	14871	4	C	A	A	24	24	SLC10A4	A	3	3
MATR3	9782	broad.mit.edu	36	5	138686185	138686185	+	Splice_Site_SNP	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:138686185G>T	uc003ldw.1	+	c.e13_splice_site			MATR3_uc010jfb.1_Splice_Site_SNP|MATR3_uc003ldu.1_Splice_Site_SNP|MATR3_uc003ldx.1_Splice_Site_SNP|MATR3_uc010jfc.1_Splice_Site_SNP|MATR3_uc003ldy.1_Splice_Site_SNP|MATR3_uc003ldz.1_Splice_Site_SNP|MATR3_uc003lea.1_Splice_Site_SNP|MATR3_uc003leb.1_Splice_Site_SNP|MATR3_uc003lec.1_Splice_Site_SNP	NM_199189	NP_954659			matrin 3							nuclear inner membrane|nuclear matrix	nucleotide binding|protein binding|RNA binding|structural molecule activity|zinc ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)											0.384615	13.369713	13.522059	5	8	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	138686185	138686185	9721	5	G	T	T	33	33	MATR3	T	5	3
HARS	3035	broad.mit.edu	36	5	140037153	140037153	+	Nonsense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140037153C>A	uc003lgv.1	-	c.766G>T	c.(766-768)GAG>TAG	p.E256*	HARS_uc003lgu.1_Nonsense_Mutation_p.E187*|HARS_uc003lgw.1_Nonsense_Mutation_p.E236*|HARS_uc010jfu.1_Nonsense_Mutation_p.E256*	NM_002109	NP_002100	P12081	SYHC_HUMAN	histidyl-tRNA synthetase	256					histidyl-tRNA aminoacylation	cytosol	ATP binding|histidine-tRNA ligase activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		L-Histidine(DB00117)									0.213333	36.656253	42.354319	16	59	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	140037153	140037153	7241	5	C	A	A	32	32	HARS	A	5	3
PCDHB7	56129	broad.mit.edu	36	5	140534235	140534235	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140534235G>A	uc003lit.1	+	c.1635G>A	c.(1633-1635)GCG>GCA	p.A545A		NM_018940	NP_061763	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7 precursor	545	Extracellular (Potential).|Cadherin 5.				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(3)|central_nervous_system(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)											0.375	11.237039	11.45944	6	10	GG		KEEP	---	---	---	---	capture			Silent	SNP	140534235	140534235	11967	5	G	A	A	38	38	PCDHB7	A	1	1
PCDHB14	56122	broad.mit.edu	36	5	140585220	140585220	+	Silent	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140585220G>T	uc003ljb.1	+	c.1959G>T	c.(1957-1959)TCG>TCT	p.S653S		NM_018934	NP_061757	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14 precursor	653	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			Ovarian(141;50 1831 27899 33809 37648)								0.619048	27.359291	27.619318	13	8	GG		KEEP	---	---	---	---	capture			Silent	SNP	140585220	140585220	11959	5	G	T	T	39	39	PCDHB14	T	3	3
PPP2R2B	5521	broad.mit.edu	36	5	145998110	145998110	+	Silent	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:145998110C>T	uc003loi.2	-	c.696G>A	c.(694-696)GAG>GAA	p.E232E	PPP2R2B_uc003loe.1_Silent_p.E229E|PPP2R2B_uc010jgm.1_Silent_p.E218E|PPP2R2B_uc003log.2_Silent_p.E229E|PPP2R2B_uc003lof.2_Silent_p.E229E|PPP2R2B_uc003loh.2_Silent_p.E229E|PPP2R2B_uc003loj.2_Silent_p.E209E|PPP2R2B_uc003lok.2_Silent_p.E218E	NM_181676	NP_858062	Q00005	2ABB_HUMAN	beta isoform of regulatory subunit B55, protein	229	WD 4.				apoptosis|signal transduction	cytoskeleton|mitochondrial outer membrane|protein phosphatase type 2A complex	protein binding|protein phosphatase type 2A regulator activity			ovary(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.181818	27.203985	34.532252	14	63	CC		KEEP	---	---	---	---	capture			Silent	SNP	145998110	145998110	12821	5	C	T	T	20	20	PPP2R2B	T	2	2
TCOF1	6949	broad.mit.edu	36	5	149749728	149749728	+	Missense_Mutation	SNP	G	C	C			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:149749728G>C	uc003lry.1	+	c.3132G>C	c.(3130-3132)AAG>AAC	p.K1044N	TCOF1_uc003lrx.1_Missense_Mutation_p.K967N|TCOF1_uc003lrz.1_Missense_Mutation_p.K1044N|TCOF1_uc003lsa.1_Missense_Mutation_p.K967N	NM_001008657	NP_001008657	Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1044					skeletal system development	nucleolus	protein binding|transporter activity			ovary(2)|large_intestine(1)	3		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)											0.333333	7.590889	7.888654	4	8	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	149749728	149749728	16234	5	G	C	C	35	35	TCOF1	C	3	3
PDZD2	23037	broad.mit.edu	36	5	32124552	32124552	+	Nonsense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:32124552C>G	uc003jhl.1	+	c.5241C>G	c.(5239-5241)TAC>TAG	p.Y1747*	PDZD2_uc003jhm.1_Nonsense_Mutation_p.Y1747*	NM_178140	NP_835260	O15018	PDZD2_HUMAN	PDZ domain containing 2	1747					cell adhesion	cell-cell junction|endoplasmic reticulum|extracellular region|nucleus				central_nervous_system(4)|ovary(2)|large_intestine(1)	7														0.181818	7.787751	10.889441	6	27	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	32124552	32124552	12122	5	C	G	G	19	19	PDZD2	G	5	3
ENC1	8507	broad.mit.edu	36	5	73966972	73966972	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:73966972G>A	uc003kdc.2	-	c.1095C>T	c.(1093-1095)CAC>CAT	p.H365H	ENC1_uc010izg.1_Silent_p.H365H	NM_003633	NP_003624	O14682	ENC1_HUMAN	ectodermal-neural cortex (with BTB-like domain)	365	Kelch 2.				nervous system development	cytoplasm|cytoskeleton|nuclear matrix	actin binding			ovary(1)|pancreas(1)|skin(1)	3		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)										0.177083	16.708734	26.177772	17	79	GG		KEEP	---	---	---	---	capture			Silent	SNP	73966972	73966972	5306	5	G	A	A	40	40	ENC1	A	1	1
BHMT	635	broad.mit.edu	36	5	78447466	78447466	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:78447466C>T	uc003kfu.2	+	c.154C>T	c.(154-156)CAC>TAC	p.H52Y		NM_001713	NP_001704	Q93088	BHMT1_HUMAN	betaine-homocysteine methyltransferase	52	Hcy-binding.				protein methylation|regulation of homocysteine metabolic process	cytoplasm	betaine-homocysteine S-methyltransferase activity|homocysteine S-methyltransferase activity|zinc ion binding			ovary(1)	1		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;1.88e-45)|Epithelial(54;8.07e-41)|all cancers(79;3.51e-36)	L-Methionine(DB00134)									0.347826	15.082641	15.55728	8	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	78447466	78447466	1450	5	C	T	T	25	25	BHMT	T	2	2
PRDM13	59336	broad.mit.edu	36	6	100161764	100161764	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:100161764C>G	uc003pqg.1	+	c.133C>G	c.(133-135)CCT>GCT	p.P45A		NM_021620	NP_067633	Q9H4Q3	PRD13_HUMAN	PR domain containing 13	45	SET.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0598)										0.357143	10.567031	10.82026	5	9	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	100161764	100161764	12896	6	C	G	G	26	26	PRDM13	G	3	3
RFX6	222546	broad.mit.edu	36	6	117355264	117355264	+	Missense_Mutation	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:117355264G>T	uc003pxm.1	+	c.2267G>T	c.(2266-2268)AGC>ATC	p.S756I		NM_173560	NP_775831	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	756					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														0.181818	7.628951	10.774603	6	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117355264	117355264	13739	6	G	T	T	34	34	RFX6	T	3	3
TIAM2	26230	broad.mit.edu	36	6	155613825	155613825	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:155613825G>A	uc003qqb.1	+	c.4038G>A	c.(4036-4038)AAG>AAA	p.K1346K	TIAM2_uc003qqd.1_Silent_p.K1346K|TIAM2_uc003qqe.1_Silent_p.K1346K|TIAM2_uc010kjj.1_Silent_p.K908K|TIAM2_uc003qqf.1_Silent_p.K722K|TIAM2_uc003qqg.1_Silent_p.K658K|TIAM2_uc003qqh.1_Silent_p.K271K	NM_012454	NP_036586	Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1346					apoptosis|cellular lipid metabolic process|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol|filopodium|growth cone|lamellipodium	receptor signaling protein activity|Rho guanyl-nucleotide exchange factor activity			ovary(3)|breast(1)	4		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)										0.715278	714.19156	726.154387	206	82	GG		KEEP	---	---	---	---	capture			Silent	SNP	155613825	155613825	16419	6	G	A	A	35	35	TIAM2	A	2	2
THBS2	7058	broad.mit.edu	36	6	169368296	169368296	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:169368296A>T	uc003qwt.1	-	c.2442T>A	c.(2440-2442)AAT>AAA	p.N814K		NM_003247	NP_003238	P35442	TSP2_HUMAN	thrombospondin 2 precursor	814	TSP type-3 4.				cell adhesion	extracellular region	calcium ion binding|heparin binding|protein binding|structural molecule activity			ovary(4)	4		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		Esophageal Squamous(91;219 1934 18562 44706)								0.181818	6.623885	9.775318	6	27	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	169368296	169368296	16382	6	A	T	T	4	4	THBS2	T	4	4
HIST1H3H	8357	broad.mit.edu	36	6	27885950	27885950	+	Silent	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr6:27885950T>C	uc003njm.1	+	c.120T>C	c.(118-120)CAT>CAC	p.H40H	HIST1H2BL_uc003njl.1_5'Flank	NM_003536	NP_066298	P68431	H31_HUMAN	histone cluster 1, H3h	40					blood coagulation|nucleosome assembly|regulation of gene silencing|S phase	nucleoplasm|nucleosome	DNA binding|protein binding			ovary(1)	1														0.169811	8.735397	14.223661	9	44	TT		KEEP	---	---	---	---	capture			Silent	SNP	27885950	27885950	7447	6	T	C	C	50	50	HIST1H3H	C	4	4
BTNL2	56244	broad.mit.edu	36	6	32472121	32472121	+	Missense_Mutation	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32472121G>A	uc003obg.1	-	c.751C>T	c.(751-753)CCT>TCT	p.P251S	BTNL2_uc010jty.1_5'UTR|BTNL2_uc010jtz.1_Non-coding_Transcript|BTNL2_uc010jua.1_Missense_Mutation_p.P41S	NM_019602	NP_062548	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2	251	Extracellular (Potential).|Ig-like V-type 3.					integral to membrane				central_nervous_system(1)	1														0.181818	6.434962	9.578709	6	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	32472121	32472121	1599	6	G	A	A	44	44	BTNL2	A	2	2
C6orf126	389383	broad.mit.edu	36	6	35855176	35855176	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:35855176A>T	uc010jvz.1	+	c.274A>T	c.(274-276)ATG>TTG	p.M92L	C6orf126_uc003olc.1_Missense_Mutation_p.D118V|C6orf127_uc003old.2_5'Flank	NM_207409	NP_997292	Q6UWE3	CF126_HUMAN	hypothetical protein LOC389383	92					digestion|lipid catabolic process	extracellular region	enzyme activator activity				0														0.6	6.922642	6.965971	3	2	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	35855176	35855176	2428	6	A	T	T	12	12	C6orf126	T	4	4
RPL7L1	285855	broad.mit.edu	36	6	42956608	42956608	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:42956608C>G	uc003osq.1	+	c.46C>G	c.(46-48)CTC>GTC	p.L16V	RPL7L1_uc010jxw.1_Intron|RPL7L1_uc003osr.1_De_novo_Start_OutOfFrame|RPL7L1_uc003oss.1_Intron|RPL7L1_uc003ost.2_Missense_Mutation_p.L16V|RPL7L1_uc003osu.1_Non-coding_Transcript	NM_198486	NP_940888	Q6DKI1	RL7L_HUMAN	ribosomal protein L7-like 1	16					translation	large ribosomal subunit	protein binding|structural constituent of ribosome|transcription regulator activity				0	Colorectal(47;0.196)		Colorectal(64;0.00237)|all cancers(41;0.00288)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.088)											0.222222	7.730478	9.65659	6	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	42956608	42956608	14080	6	C	G	G	32	32	RPL7L1	G	3	3
COL21A1	81578	broad.mit.edu	36	6	56030585	56030587	+	Missense_Mutation	TNP	AGG	CAC	CAC			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:56030585_56030587AGG>CAC	uc003pcs.1	-	c.2701_2703CCT>GTG	c.(2701-2703)CCT>GTG	p.P901V	COL21A1_uc003pcr.1_Missense_Mutation_p.P258V|COL21A1_uc010jzy.1_Missense_Mutation_p.P267V	NM_030820	NP_110447	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1 precursor	901					cell adhesion	collagen|cytoplasm	structural molecule activity			ovary(2)	2	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)											1	11.862519	11.801582	4	0	AA		KEEP	---	---	---	---	capture			Missense_Mutation	TNP	56030585	56030587	3818	6	AGG	CAC	CAC	7	7	COL21A1	CAC	4	4
MDN1	23195	broad.mit.edu	36	6	90454612	90454612	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:90454612A>T	uc003pnn.1	-	c.11261T>A	c.(11260-11262)CTC>CAC	p.L3754H		NM_014611	NP_055426	Q9NU22	MDN1_HUMAN	MDN1, midasin homolog	3754					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)										0.186667	15.285876	22.22013	14	61	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	90454612	90454612	9804	6	A	T	T	11	11	MDN1	T	4	4
SPAM1	6677	broad.mit.edu	36	7	123380988	123380988	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:123380988T>C	uc003vle.1	+	c.128T>C	c.(127-129)GTT>GCT	p.V43A	SPAM1_uc003vld.1_Missense_Mutation_p.V43A|SPAM1_uc003vlf.2_Missense_Mutation_p.V43A|SPAM1_uc010lku.1_Missense_Mutation_p.V43A	NM_003117	NP_003108	P38567	HYALP_HUMAN	sperm adhesion molecule 1 isoform 1	43					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			ovary(3)|kidney(1)	4					Hyaluronidase(DB00070)									0.129032	13.262316	21.568231	8	54	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123380988	123380988	15489	7	T	C	C	60	60	SPAM1	C	4	4
NOBOX	135935	broad.mit.edu	36	7	143727439	143727439	+	Silent	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:143727439A>T	uc003wen.1	-	c.1224T>A	c.(1222-1224)CCT>CCA	p.P408P		NM_001080413	NP_001073882			NOBOX oogenesis homeobox											ovary(1)	1	Melanoma(164;0.14)													0.333333	7.621644	7.843229	3	6	AA		KEEP	---	---	---	---	capture			Silent	SNP	143727439	143727439	10915	7	A	T	T	11	11	NOBOX	T	4	4
PRKAG2	51422	broad.mit.edu	36	7	151109386	151109386	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:151109386C>A	uc003wkk.1	-	c.251G>T	c.(250-252)CGG>CTG	p.R84L	PRKAG2_uc003wkj.1_Missense_Mutation_p.R40L|PRKAG2_uc010lqe.1_Non-coding_Transcript|PRKAG2_uc003wkm.1_Missense_Mutation_p.R84L	NM_016203	NP_077747	Q9UGJ0	AAKG2_HUMAN	AMP-activated protein kinase gamma2 subunit	84					ATP biosynthetic process|carnitine shuttle|cell cycle arrest|fatty acid biosynthetic process|glycogen metabolic process|insulin receptor signaling pathway|intracellular protein kinase cascade|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein kinase activity|regulation of fatty acid biosynthetic process|regulation of fatty acid oxidation|regulation of glucose import|regulation of glycolysis|sterol biosynthetic process	AMP-activated protein kinase complex|cytosol|nucleoplasm	ADP binding|ATP binding|cAMP-dependent protein kinase inhibitor activity|cAMP-dependent protein kinase regulator activity|phosphorylase kinase regulator activity|protein kinase activator activity|protein kinase binding			kidney(1)	1	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)										0.363636	7.594412	7.775169	4	7	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	151109386	151109386	12944	7	C	A	A	23	23	PRKAG2	A	3	3
AMPH	273	broad.mit.edu	36	7	38442487	38442488	+	Missense_Mutation	DNP	CT	AA	AA			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:38442487_38442488CT>AA	uc003tgu.1	-	c.1043_1044AG>TT	c.(1042-1044)GAG>GTT	p.E348V	AMPH_uc003tgt.1_Missense_Mutation_p.E101V|AMPH_uc003tgv.1_Missense_Mutation_p.E348V	NM_001635	NP_001626	P49418	AMPH_HUMAN	amphiphysin isoform 1	348					endocytosis|synaptic transmission	actin cytoskeleton|cell junction|synaptic vesicle membrane				ovary(3)|liver(1)	4														0.188235	18.830713	26.599356	16	69	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	38442487	38442488	591	7	CT	AA	AA	24	24	AMPH	AA	3	3
CYP3A4	1576	broad.mit.edu	36	7	99203916	99203916	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99203916T>C	uc003urv.1	-	c.667A>G	c.(667-669)ATA>GTA	p.I223V	CYP3A4_uc003urw.1_Missense_Mutation_p.I223V	NM_017460	NP_059488	P08684	CP3A4_HUMAN	cytochrome P450, subfamily IIIA, polypeptide 4	223					alkaloid catabolic process|androgen metabolic process|exogenous drug catabolic process|heterocycle metabolic process|monoterpenoid metabolic process|oxidative demethylation|steroid catabolic process|vitamin D metabolic process|xenobiotic metabolic process	cell surface|endoplasmic reticulum membrane|integral to membrane|microsome	albendazole monooxygenase activity|caffeine oxidase activity|electron carrier activity|enzyme binding|heme binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen|oxygen binding|quinine 3-monooxygenase activity|steroid binding|taurochenodeoxycholate 6alpha-hydroxylase activity|testosterone 6-beta-hydroxylase activity|vitamin D 24-hydroxylase activity|vitamin D3 25-hydroxylase activity			central_nervous_system(3)|ovary(1)	4	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Albendazole(DB00518)|Alclometasone(DB00240)|Alfentanil(DB00802)|Alfuzosin(DB00346)|Aliskiren(DB01258)|Almotriptan(DB00918)|Alosetron(DB00969)|Alprazolam(DB00404)|Amlodipine(DB00381)|Amprenavir(DB00701)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Benazepril(DB00542)|Bepridil(DB01244)|Betamethasone(DB00443)|Bexarotene(DB00307)|Bortezomib(DB00188)|Bosentan(DB00559)|Bromocriptine(DB01200)|Budesonide(DB01222)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Buspirone(DB00490)|Busulfan(DB01008)|Carbamazepine(DB00564)|Cevimeline(DB00185)|Chlorpheniramine(DB01114)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cinacalcet(DB01012)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clindamycin(DB01190)|Clofibrate(DB00636)|Clonazepam(DB01068)|Clopidogrel(DB00758)|Cocaine(DB00907)|Conivaptan(DB00872)|Conjugated Estrogens(DB00286)|Cyproterone(DB04839)|Darifenacin(DB00496)|Darunavir(DB01264)|Dasatinib(DB01254)|Delavirdine(DB00705)|Desogestrel(DB00304)|Dexamethasone(DB01234)|Diazepam(DB00829)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dofetilide(DB00204)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Doxorubicin(DB00997)|Drospirenone(DB01395)|Dutasteride(DB01126)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enalapril(DB00584)|Epirubicin(DB00445)|Eplerenone(DB00700)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Ethosuximide(DB00593)|Etonogestrel(DB00294)|Etoposide(DB00773)|Etoricoxib(DB01628)|Exemestane(DB00990)|Felodipine(DB01023)|Fentanyl(DB00813)|Fexofenadine(DB00950)|Finasteride(DB01216)|Fluconazole(DB00196)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Fosamprenavir(DB01319)|Fulvestrant(DB00947)|Galantamine(DB00674)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Granisetron(DB00889)|Grepafloxacin(DB00365)|Halofantrine(DB01218)|Hydrocodone(DB00956)|Hydrocortamate(DB00769)|Hydrocortisone(DB00741)|Hydromorphone(DB00327)|Imatinib(DB00619)|Indinavir(DB00224)|Ipratropium(DB00332)|Irinotecan(DB00762)|Isosorbide Dinitrate(DB00883)|Isosorbide Mononitrate(DB01020)|Isradipine(DB00270)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Letrozole(DB01006)|Levobupivacaine(DB01002)|Levomethadyl Acetate(DB01227)|Levothyroxine(DB00451)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Maraviroc(DB04835)|Marinol(DB00470)|Mebendazole(DB00643)|Medroxyprogesterone(DB00603)|Methadone(DB00333)|Methylprednisolone(DB00959)|Metyrapone(DB01011)|Mibefradil(DB01388)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirtazapine(DB00370)|Modafinil(DB00745)|Mometasone(DB00764)|Montelukast(DB00471)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norgestrel(DB00506)|Nystatin(DB00646)|Ondansetron(DB00904)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Paricalcitol(DB00910)|Phenmetrazine(DB00830)|Pimecrolimus(DB00337)|Pimozide(DB01100)|Pioglitazone(DB01132)|Posaconazole(DB01263)|Pranlukast(DB01411)|Prednisolone(DB00860)|Prednisone(DB00635)|Prochlorperazine(DB00433)|Quetiapine(DB01224)|Quinapril(DB00881)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranolazine(DB00243)|Reboxetine(DB00234)|Retapamulin(DB01256)|Rifabutin(DB00615)|Rifampin(DB01045)|Rimonabant(DB06155)|Ritonavir(DB00503)|Rofecoxib(DB00533)|Roxithromycin(DB00778)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sertindole(DB06144)|Sibutramine(DB01105)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|Solifenacin(DB01591)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tadalafil(DB00820)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Terconazole(DB00251)|Terfenadine(DB00342)|Testosterone(DB00624)|Tiagabine(DB00906)|Ticlopidine(DB00208)|Tinidazole(DB00911)|Tiotropium(DB01409)|Tipranavir(DB00932)|Toremifene(DB00539)|Triazolam(DB00897)|Trimetrexate(DB01157)|Troglitazone(DB00197)|Valdecoxib(DB00580)|Vardenafil(DB00862)|Vinblastine(DB00570)|Vincristine(DB00541)|Vindesine(DB00309)|Vinorelbine(DB00361)|Voriconazole(DB00582)|Zaleplon(DB00962)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolpidem(DB00425)|Zonisamide(DB00909)					219				0.142857	7.692305	16.324177	10	60	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99203916	99203916	4343	7	T	C	C	52	52	CYP3A4	C	4	4
STAG3	10734	broad.mit.edu	36	7	99640944	99640944	+	Splice_Site_SNP	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99640944G>T	uc003utx.1	+	c.e29_splice_site			GATS_uc003uty.2_Intron|GATS_uc010lgt.1_Intron|GATS_uc003utz.2_Intron|GATS_uc003uua.2_Intron|STAG3_uc003uub.1_Splice_Site_SNP	NM_012447	NP_036579			stromal antigen 3						chromosome segregation|synaptonemal complex assembly	chromosome, centromeric region|meiotic cohesin complex|synaptonemal complex	binding			ovary(3)|skin(2)|lung(1)|kidney(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)									331				0.22807	18.128975	22.017755	13	44	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	99640944	99640944	15762	7	G	T	T	44	44	STAG3	T	5	3
SCRIB	23513	broad.mit.edu	36	8	144963037	144963037	+	Missense_Mutation	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:144963037C>A	uc003yzo.1	-	c.1845G>T	c.(1843-1845)AAG>AAT	p.K615N	SCRIB_uc003yzp.1_Missense_Mutation_p.K615N	NM_182706	NP_874365	Q14160	SCRIB_HUMAN	scribble isoform a	615	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity|apoptosis involved in morphogenesis|cell migration|cell proliferation|cell-cell adhesion|establishment of apical/basal cell polarity|interspecies interaction between organisms|mammary gland duct morphogenesis|negative regulation of mitotic cell cycle|positive chemotaxis|positive regulation of apoptosis|positive regulation of receptor recycling|protein localization to adherens junction	cell-cell adherens junction|Scrib-APC-beta-catenin complex	protein binding			urinary_tract(1)|ovary(1)|kidney(1)|central_nervous_system(1)|pancreas(1)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			Pancreas(51;966 1133 10533 14576 29674)				520				0.456522	67.078796	67.152985	21	25	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	144963037	144963037	14419	8	C	A	A	32	32	SCRIB	A	3	3
ZNF7	7553	broad.mit.edu	36	8	146037846	146037847	+	Missense_Mutation	DNP	CT	GA	GA			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:146037846_146037847CT>GA	uc010mge.1	+	c.583_584CT>GA	c.(583-585)CTT>GAT	p.L195D	ZNF7_uc003zeg.2_Missense_Mutation_p.L184D|ZNF7_uc003zeh.2_Intron|ZNF7_uc003zek.2_Missense_Mutation_p.L88D|COMMD5_uc003zel.1_Non-coding_Transcript	NM_003416	NP_003407	P17097	ZNF7_HUMAN	zinc finger protein 7	184					multicellular organismal development|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(3)	3	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)										0.245902	24.502042	28.089508	15	46	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	146037846	146037847	18697	8	CT	GA	GA	32	32	ZNF7	GA	3	3
ARHGEF10	9639	broad.mit.edu	36	8	1892809	1892809	+	Silent	SNP	C	A	A			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:1892809C>A	uc003wpr.1	+	c.4008C>A	c.(4006-4008)GTC>GTA	p.V1336V	ARHGEF10_uc003wps.1_Silent_p.V1298V|ARHGEF10_uc010lre.1_Silent_p.V987V	NM_014629	NP_055444	O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor 10	1361					regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			large_intestine(1)	1		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)						2844				0.25641	23.233788	25.331583	10	29	CC		KEEP	---	---	---	---	capture			Silent	SNP	1892809	1892809	908	8	C	A	A	32	32	ARHGEF10	A	3	3
KCNU1	157855	broad.mit.edu	36	8	36781876	36781876	+	Missense_Mutation	SNP	T	C	C			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:36781876T>C	uc010lvw.1	+	c.383T>C	c.(382-384)GTT>GCT	p.V128A	KCNU1_uc003xjw.2_Non-coding_Transcript	NM_001031836	NP_001027006	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	128	Extracellular (Potential).					voltage-gated potassium channel complex	binding|catalytic activity|large conductance calcium-activated potassium channel activity|voltage-gated potassium channel activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)										0.3125	10.865879	11.368578	5	11	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36781876	36781876	8398	8	T	C	C	60	60	KCNU1	C	4	4
ST18	9705	broad.mit.edu	36	8	53242035	53242035	+	Silent	SNP	G	A	A			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:53242035G>A	uc003xqz.1	-	c.1134C>T	c.(1132-1134)CAC>CAT	p.H378H	ST18_uc003xra.1_Silent_p.H378H|ST18_uc003xrb.1_Silent_p.H378H	NM_014682	NP_055497	O60284	ST18_HUMAN	suppression of tumorigenicity 18	378	C2HC-type 1.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(4)	4		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)												0.887324	820.446629	862.514246	252	32	GG		KEEP	---	---	---	---	capture			Silent	SNP	53242035	53242035	15730	8	G	A	A	40	40	ST18	A	1	1
MCPH1	79648	broad.mit.edu	36	8	6289488	6289488	+	Silent	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:6289488T>G	uc003wqi.1	+	c.837T>G	c.(835-837)TCT>TCG	p.S279S	MCPH1_uc003wqh.2_Silent_p.S279S	NM_024596	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin	279						microtubule organizing center				central_nervous_system(1)	1		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		Colon(95;1448 1467 8277 34473 35819)								0.206897	26.692867	33.636648	18	69	TT		KEEP	---	---	---	---	capture			Silent	SNP	6289488	6289488	9787	8	T	G	G	56	56	MCPH1	G	4	4
SVEP1	79987	broad.mit.edu	36	9	112210483	112210483	+	Nonsense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr9:112210483A>T	uc010mtz.1	-	c.7218T>A	c.(7216-7218)TAT>TAA	p.Y2406*	SVEP1_uc010mty.1_Nonsense_Mutation_p.Y332*	NM_153366	NP_699197	Q4LDE5	SVEP1_HUMAN	polydom	2406	Sushi 17.				cell adhesion	cytoplasm|extracellular region|membrane	calcium ion binding			ovary(7)	7														0.307692	6.589052	7.021538	4	9	AA		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	112210483	112210483	15940	9	A	T	T	4	4	SVEP1	T	5	4
RXRA	6256	broad.mit.edu	36	9	136440787	136440787	+	Splice_Site_SNP	SNP	G	T	T			TCGA-28-2506-01	TCGA-28-2506-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:136440787G>T	uc004cfb.1	+	c.e4_splice_site			RXRA_uc004cfc.1_Splice_Site_SNP	NM_002957	NP_002948			retinoid X receptor, alpha						cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of gene-specific transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)					303				0.444444	8.294758	8.319358	4	5	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	136440787	136440787	14243	9	G	T	T	44	44	RXRA	T	5	3
C9orf86	55684	broad.mit.edu	36	9	138846606	138846606	+	Missense_Mutation	SNP	T	G	G			TCGA-28-2506-01	TCGA-28-2506-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138846606T>G	uc004cjj.1	+	c.671T>G	c.(670-672)CTT>CGT	p.L224R	C9orf86_uc004cjh.1_Missense_Mutation_p.L223R|C9orf86_uc004cjk.1_Non-coding_Transcript|C9orf86_uc004cji.1_Missense_Mutation_p.L223R|C9orf86_uc010nbr.1_Missense_Mutation_p.L223R|C9orf86_uc004cjl.1_Non-coding_Transcript|C9orf86_uc010nbs.1_Missense_Mutation_p.L108R|C9orf86_uc004cjm.1_Missense_Mutation_p.L108R|C9orf86_uc004cjn.1_5'Flank	NM_024718	NP_078994	Q3YEC7	PARF_HUMAN	Rab-like GTP-binding protein 1	223	Small GTPase-like.				small GTPase mediated signal transduction	cytoplasm|nucleus	GTP binding|protein binding				0	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.61e-05)|Epithelial(140;0.000183)										0.291667	11.985319	12.939835	7	17	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	138846606	138846606	2618	9	T	G	G	56	56	C9orf86	G	4	4
UBAP2	55833	broad.mit.edu	36	9	33912814	33912814	+	Missense_Mutation	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:33912814C>G	uc003ztq.1	-	c.3135G>C	c.(3133-3135)TTG>TTC	p.L1045F	UBAP2_uc003ztn.1_Missense_Mutation_p.L284F|UBAP2_uc003zto.1_Missense_Mutation_p.L284F|UBAP2_uc003ztp.1_Missense_Mutation_p.L284F	NM_018449	NP_060919	Q5T6F2	UBAP2_HUMAN	ubiquitin associated protein 2	1045										ovary(3)	3			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)										0.30303	18.626036	19.776322	10	23	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	33912814	33912814	17394	9	C	G	G	21	21	UBAP2	G	3	3
TJP2	9414	broad.mit.edu	36	9	71041707	71041707	+	Nonsense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:71041707C>T	uc004ahe.1	+	c.2014C>T	c.(2014-2016)CAA>TAA	p.Q672*	TJP2_uc004ahd.2_Nonsense_Mutation_p.Q672*|TJP2_uc004ahf.1_Nonsense_Mutation_p.Q672*|TJP2_uc010mol.1_5'Flank	NM_004817	NP_004808	Q9UDY2	ZO2_HUMAN	tight junction protein 2 (zona occludens 2)	672					cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0														0.227848	28.492464	33.882118	18	61	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	71041707	71041707	16459	9	C	T	T	29	29	TJP2	T	5	2
CXorf57	55086	broad.mit.edu	36	X	105752584	105752584	+	Silent	SNP	A	C	C			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:105752584A>C	uc004emi.2	+	c.691A>C	c.(691-693)AGA>CGA	p.R231R	CXorf57_uc004emj.2_Silent_p.R231R|CXorf57_uc004emh.2_Silent_p.R231R	NM_018015	NP_060485	Q6NSI4	CX057_HUMAN	hypothetical protein LOC55086	231										ovary(1)|lung(1)|breast(1)	3														0.219178	40.459962	45.764336	16	57	AA		KEEP	---	---	---	---	capture			Silent	SNP	105752584	105752584	4277	23	A	C	C	7	7	CXorf57	C	4	4
DOCK11	139818	broad.mit.edu	36	X	117672596	117672596	+	Missense_Mutation	SNP	A	T	T			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:117672596A>T	uc004eqp.2	+	c.4699A>T	c.(4699-4701)ACT>TCT	p.T1567S	DOCK11_uc004eqq.2_Missense_Mutation_p.T1346S	NM_144658	NP_653259	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	1567	DHR-2.				blood coagulation	cytosol	GTP binding			ovary(3)	3														0.192982	11.682433	16.723585	11	46	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	117672596	117672596	4870	23	A	T	T	2	2	DOCK11	T	4	4
SMARCA1	6594	broad.mit.edu	36	X	128478090	128478090	+	Silent	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:128478090A>G	uc004eun.2	-	c.327T>C	c.(325-327)ATT>ATC	p.I109I	SMARCA1_uc004eup.2_Silent_p.I109I	NM_003069	NP_003060	P28370	SMCA1_HUMAN	SWI/SNF-related matrix-associated	109					ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of gene-specific transcription|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding|transcription regulator activity			ovary(3)|skin(1)	4														0.238281	155.147497	171.167228	61	195	AA		KEEP	---	---	---	---	capture			Silent	SNP	128478090	128478090	15266	23	A	G	G	9	9	SMARCA1	G	4	4
FAM47A	158724	broad.mit.edu	36	X	34060141	34060141	+	Missense_Mutation	SNP	C	T	T			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:34060141C>T	uc004ddg.1	-	c.176G>A	c.(175-177)CGC>CAC	p.R59H		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	59										ovary(4)|central_nervous_system(1)	5														0.666667	224.769064	227.351574	70	35	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34060141	34060141	5790	23	C	T	T	27	27	FAM47A	T	1	1
TRO	7216	broad.mit.edu	36	X	54972456	54972456	+	Silent	SNP	C	G	G			TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:54972456C>G	uc004dtq.1	+	c.2574C>G	c.(2572-2574)GGC>GGG	p.G858G	TRO_uc004dtr.1_Intron|TRO_uc004dts.1_Intron|TRO_uc004dtt.1_Intron|TRO_uc004dtu.1_Intron|TRO_uc004dtv.1_Intron|TRO_uc004dtw.1_Silent_p.G461G|TRO_uc004dtx.1_Silent_p.G241G	NM_001039705	NP_001034794	Q12816	TROP_HUMAN	trophinin isoform 5	858	62 X 10 AA approximate tandem repeats.				embryo implantation|homophilic cell adhesion	integral to plasma membrane				ovary(1)	1														0.2	10.069474	13.432373	8	32	CC		KEEP	---	---	---	---	capture			Silent	SNP	54972456	54972456	17125	23	C	G	G	28	28	TRO	G	3	3
FOXR2	139628	broad.mit.edu	36	X	55667297	55667297	+	Missense_Mutation	SNP	A	G	G			TCGA-28-2506-01	TCGA-28-2506-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:55667297A>G	uc004duo.1	+	c.428A>G	c.(427-429)AAG>AGG	p.K143R		NM_198451	NP_940853	Q6PJQ5	FOXR2_HUMAN	forkhead box R2	143					embryo development|negative regulation of gene-specific transcription from RNA polymerase II promoter|organ development|pattern specification process|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			lung(2)|central_nervous_system(1)	3														0.235294	32.600739	35.850754	12	39	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	55667297	55667297	6278	23	A	G	G	3	3	FOXR2	G	4	4
VCX	26609	broad.mit.edu	36	X	7771759	7771759	+	Missense_Mutation	SNP	C	G	G	rs5934293	unknown	TCGA-28-2506-01	TCGA-28-2506-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:7771759C>G	uc004crz.1	+	c.323C>G	c.(322-324)GCC>GGC	p.A108G	VCX_uc010ndn.1_Missense_Mutation_p.A108G	NM_013452	NP_038480	Q9H320	VCX1_HUMAN	variable charge, X chromosome	108	1.|10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				chromatin organization|ribosome assembly|spermatogenesis	nucleolus	chromatin binding				0		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)												0.166667	6.513961	8.409803	3	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7771759	7771759	17707	23	C	G	G	26	26	VCX	G	3	3
DNMBP	23268	broad.mit.edu	36	10	101633885	101633886	+	Frame_Shift_Ins	INS	-	A	A			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:101633885_101633886insA	uc001kqj.2	-	c.3869_3870insT	c.(3868-3870)TTCfs	p.F1290fs	DNMBP_uc001kqg.2_Frame_Shift_Ins_p.F578fs|DNMBP_uc001kqh.2_Frame_Shift_Ins_p.F922fs	NM_015221	NP_056036	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1290	SH3 5.				intracellular signal transduction|regulation of Rho protein signal transduction	cell junction|cytoskeleton|Golgi stack|synapse	protein binding|Rho guanyl-nucleotide exchange factor activity			ovary(5)	5		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)										0.51			68	65				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	101633885	101633886	4857	10	-	A	A	41	41	DNMBP	A	5	5
KIAA1598	57698	broad.mit.edu	36	10	118718172	118718172	+	Frame_Shift_Del	DEL	T	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:118718172_118718172delT	uc001lcx.2	-	c.153_153delA	c.(151-153)AAAfs	p.K51fs	KIAA1598_uc009xyw.1_Frame_Shift_Del_p.K51fs|KIAA1598_uc001lcz.2_Frame_Shift_Del_p.K51fs|KIAA1598_uc001lcy.2_Frame_Shift_Del_p.K21fs	NM_018330	NP_060800	A0MZ66	SHOT1_HUMAN	shootin1 isoform b	51	Potential.				axon guidance	axon					0				all cancers(201;0.00494)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	118718172	118718172	8555	10	T	-	-	60	60	KIAA1598	-	5	5
DDX10	1662	broad.mit.edu	36	11	108293884	108293884	+	Frame_Shift_Del	DEL	C	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:108293884_108293884delC	uc001pkm.1	+	c.2379_2379delC	c.(2377-2379)AGCfs	p.S793fs	DDX10_uc001pkl.1_Frame_Shift_Del_p.S793fs	NM_004398	NP_004389	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	793							ATP binding|ATP-dependent helicase activity|RNA binding|RNA helicase activity			breast(2)	2		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)						268				0.74			116	40				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	108293884	108293884	4513	11	C	-	-	25	25	DDX10	-	5	5
SHANK2	22941	broad.mit.edu	36	11	70011215	70011215	+	Frame_Shift_Del	DEL	A	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:70011215_70011215delA	uc001opz.1	-	c.1046_1046delT	c.(1045-1047)ATGfs	p.M349fs	SHANK2_uc001opy.1_Intron	NM_012309	NP_036441	Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	565					intracellular signal transduction	cell junction|cytoplasm|postsynaptic density|postsynaptic membrane	GKAP/Homer scaffold activity|ionotropic glutamate receptor binding|SH3 domain binding			ovary(2)|central_nervous_system(1)|pancreas(1)	4			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)											0.51			24	23				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	70011215	70011215	14757	11	A	-	-	8	8	SHANK2	-	5	5
ACAD10	80724	broad.mit.edu	36	12	110634771	110634772	+	Frame_Shift_Ins	INS	-	T	T			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:110634771_110634772insT	uc009zvx.1	+	c.870_871insT	c.(868-873)GTGAAAfs	p.V290fs	ACAD10_uc001tso.2_Frame_Shift_Ins_p.V259fs|ACAD10_uc001tsp.1_Frame_Shift_Ins_p.V259fs|ACAD10_uc001tsq.1_Frame_Shift_Ins_p.V259fs|ACAD10_uc001tsr.2_5'UTR|ACAD10_uc001tss.1_5'Flank	NM_025247	NP_079523	Q6JQN1	ACD10_HUMAN	acyl-Coenzyme A dehydrogenase family, member 10	259_260					oxidation-reduction process		acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding|hydrolase activity			ovary(2)	2														0.30			236	542				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	110634771	110634772	109	12	-	T	T	45	45	ACAD10	T	5	5
MPHOSPH9	10198	broad.mit.edu	36	12	122252733	122252754	+	Frame_Shift_Del	DEL	TGTTTCAAACTATTTATTTCTG	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:122252733_122252754delTGTTTCAAACTATTTATTTCTG	uc001uel.1	-	c.1391_1412delCAGAAATAAATAGTTTGAAACA	c.(1390-1413)TCAGAAATAAATAGTTTGAAACAGfs	p.S464fs	MPHOSPH9_uc001uem.1_De_novo_Start_OutOfFrame	NM_022782	NP_073619	Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	464_471	Potential.				M phase of mitotic cell cycle	Golgi membrane					0	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)										0.42			102	142				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	122252733	122252754	10120	12	TGTTTCAAACTATTTATTTCTG	-	-	55	55	MPHOSPH9	-	5	5
STRN3	29966	broad.mit.edu	36	14	30564941	30564942	+	Frame_Shift_Ins	INS	-	C	C			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:30564941_30564942insC	uc001wqu.2	-	c.201_202insG	c.(199-204)GGGATAfs	p.G67fs	STRN3_uc001wqv.2_Frame_Shift_Ins_p.G67fs|AP4S1_uc001wqw.2_Intron|AP4S1_uc001wqx.2_Intron|AP4S1_uc010amh.1_Intron|AP4S1_uc001wqy.2_Intron|AP4S1_uc001wqz.2_Intron	NM_001083893	NP_001077362	Q13033	STRN3_HUMAN	nuclear autoantigen isoform 1	67_68					negative regulation of estrogen receptor signaling pathway|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|response to estradiol stimulus	cytoplasm|dendrite|Golgi apparatus|neuronal cell body|nucleoplasm|nucleus|plasma membrane|protein complex	armadillo repeat domain binding|calmodulin binding|protein complex binding|protein phosphatase 2A binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity				0	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)										0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	30564941	30564942	15850	14	-	C	C	50	50	STRN3	C	5	5
ARID4A	5926	broad.mit.edu	36	14	57866537	57866538	+	Frame_Shift_Ins	INS	-	A	A			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:57866537_57866538insA	uc001xdp.1	+	c.803_804insA	c.(802-804)ATAfs	p.I268fs	ARID4A_uc001xdo.1_Frame_Shift_Ins_p.I268fs|ARID4A_uc001xdq.1_Frame_Shift_Ins_p.I268fs|ARID4A_uc010apg.1_5'Flank	NM_002892	NP_002883	P29374	ARI4A_HUMAN	retinoblastoma-binding protein 1 isoform I	268					chromatin assembly or disassembly|negative regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	chromatin|transcriptional repressor complex	chromatin binding|DNA binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			ovary(3)|lung(1)	4														0.44			28	35				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	57866537	57866538	934	14	-	A	A	49	49	ARID4A	A	5	5
LACTB	114294	broad.mit.edu	36	15	61208804	61208810	+	Frame_Shift_Del	DEL	ATGTAAA	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:61208804_61208810delATGTAAA	uc002alw.1	+	c.1020_1026delATGTAAA	c.(1018-1026)GGATGTAAAfs	p.G340fs	LACTB_uc002alv.1_Frame_Shift_Del_p.G340fs	NM_032857	NP_116246	P83111	LACTB_HUMAN	lactamase, beta isoform a	340_342						mitochondrion	hydrolase activity				0						Melanoma(85;443 1381 6215 27308 35583)								0.50			53	53				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	61208804	61208810	8920	15	ATGTAAA	-	-	12	12	LACTB	-	5	5
SGK269	79834	broad.mit.edu	36	15	75194334	75194346	+	Frame_Shift_Del	DEL	TCAGGGCTTTTCC	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:75194334_75194346delTCAGGGCTTTTCC	uc002bcm.2	-	c.4448_4460delGGAAAAGCCCTGA	c.(4447-4461)GGGAAAAGCCCTGATfs	p.G1483fs		NM_024776	NP_079052	Q9H792	PEAK1_HUMAN	NKF3 kinase family member	1483_1487	Protein kinase.				cell migration|protein autophosphorylation|substrate adhesion-dependent cell spreading	actin cytoskeleton|cytoplasm|focal adhesion	ATP binding|non-membrane spanning protein tyrosine kinase activity|protein binding				0				STAD - Stomach adenocarcinoma(199;0.124)					p.D1487N(SNU407-Tumor)|p.D1487N(ME1-Tumor)	217				0.67			218	108				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	75194334	75194346	14702	15	TCAGGGCTTTTCC	-	-	50	50	SGK269	-	5	5
RNF151	146310	broad.mit.edu	36	16	1958886	1958898	+	Frame_Shift_Del	DEL	GAGGTGGTGGGGG	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:1958886_1958898delGAGGTGGTGGGGG	uc002cnt.1	+	c.697_709delGAGGTGGTGGGGG	c.(697-711)GAGGTGGTGGGGGAGfs	p.E233fs		NM_174903	NP_777563	Q2KHN1	RN151_HUMAN	ring finger protein 151	233_237					cell differentiation|spermatogenesis	cytoplasm|nucleus|ubiquitin ligase complex	ubiquitin-protein ligase activity|zinc ion binding				0														0.43			3	4				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	1958886	1958898	13929	16	GAGGTGGTGGGGG	-	-	45	45	RNF151	-	5	5
AARS	16	broad.mit.edu	36	16	68861061	68861063	+	In_Frame_Del	DEL	GCC	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:68861061_68861063delGCC	uc002eyn.1	-	c.921_923delGGC	c.(919-924)GTGGCA>GTA	p.A308del		NM_001605	NP_001596	P49588	SYAC_HUMAN	alanyl-tRNA synthetase	308					alanyl-tRNA aminoacylation|tRNA processing	cytosol|soluble fraction	alanine-tRNA ligase activity|ATP binding|metal ion binding|tRNA binding			pancreas(1)	1		Ovarian(137;0.0365)		BRCA - Breast invasive adenocarcinoma(221;0.161)	L-Alanine(DB00160)									0.32			547	1159				---	---	---	---	capture_indel			In_Frame_Del	DEL	68861061	68861063	20	16	GCC	-	-	46	46	AARS	-	5	5
ATP9B	374868	broad.mit.edu	36	18	75203354	75203356	+	Splice_Site_Del	DEL	GGT	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr18:75203354_75203356delGGT	uc002lmx.1	+	c.e20_splice_site			ATP9B_uc002lmw.1_Splice_Site_Del|ATP9B_uc002lmz.1_Splice_Site_Del|ATP9B_uc002lna.1_5'Flank	NM_198531	NP_940933			ATPase, class II, type 9B						ATP biosynthetic process	integral to membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)	3		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)										0.45			26	32				---	---	---	---	capture_indel			Splice_Site_Del	DEL	75203354	75203356	1218	18	GGT	-	-	35	35	ATP9B	-	5	5
ADCK4	79934	broad.mit.edu	36	19	45907840	45907841	+	Frame_Shift_Del	DEL	CC	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:45907840_45907841delCC	uc002oor.1	-	c.330_331delGG	c.(328-333)ATGGCTfs	p.M110fs	ADCK4_uc002ooq.1_Frame_Shift_Del_p.M110fs|ADCK4_uc002oos.1_Frame_Shift_Del_p.M110fs	NM_024876	NP_079152	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4 isoform a	110_111						integral to membrane	protein serine/threonine kinase activity				0			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)							88				0.38			113	187				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	45907840	45907841	291	19	CC	-	-	26	26	ADCK4	-	5	5
TMEM146	257062	broad.mit.edu	36	19	5705242	5705244	+	In_Frame_Del	DEL	TCC	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:5705242_5705244delTCC	uc002mda.1	+	c.1264_1266delTCC	c.(1264-1266)TCCdel	p.S422del	TMEM146_uc010duj.1_In_Frame_Del_p.S80del	NM_152784	NP_689997	Q86XM0	TM146_HUMAN	transmembrane protein 146	422	Extracellular (Potential).					integral to membrane				ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.49			151	155				---	---	---	---	capture_indel			In_Frame_Del	DEL	5705242	5705244	16592	19	TCC	-	-	50	50	TMEM146	-	5	5
PHF20	51230	broad.mit.edu	36	20	33950806	33950807	+	Frame_Shift_Ins	INS	-	AT	AT			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr20:33950806_33950807insAT	uc002xek.1	+	c.1383_1384insAT	c.(1381-1386)AAATTTfs	p.K461fs	PHF20_uc002xei.1_Frame_Shift_Ins_p.K461fs|PHF20_uc010gfo.1_Frame_Shift_Ins_p.K461fs|PHF20_uc002xej.1_Frame_Shift_Ins_p.K345fs	NM_016436	NP_057520	Q9BVI0	PHF20_HUMAN	PHD finger protein 20	461_462	C2H2-type.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	MLL1 complex	DNA binding|zinc ion binding			ovary(1)	1	Breast(12;0.00631)|all_lung(11;0.0145)													0.47			55	61				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	33950806	33950807	12254	20	-	AT	AT	4	4	PHF20	AT	5	5
TBC1D22A	25771	broad.mit.edu	36	22	45686745	45686757	+	Splice_Site_Del	DEL	ATAGGTAAGATTT	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:45686745_45686757delATAGGTAAGATTT	uc003bib.1	+	c.e8_splice_site			TBC1D22A_uc010haf.1_Splice_Site_Del|TBC1D22A_uc003bic.1_Splice_Site_Del|TBC1D22A_uc003bie.1_Splice_Site_Del|TBC1D22A_uc003bid.1_Splice_Site_Del|TBC1D22A_uc010hag.1_Splice_Site_Del|TBC1D22A_uc003bif.1_Splice_Site_Del	NM_014346	NP_055161			TBC1 domain family, member 22A							intracellular	protein homodimerization activity|Rab GTPase activator activity			ovary(1)	1		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)										0.42			120	166				---	---	---	---	capture_indel			Splice_Site_Del	DEL	45686745	45686757	16133	22	ATAGGTAAGATTT	-	-	8	8	TBC1D22A	-	5	5
HEATR5B	54497	broad.mit.edu	36	2	37152912	37152926	+	In_Frame_Del	DEL	TGTAGTTCTAGTAGA	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:37152912_37152926delTGTAGTTCTAGTAGA	uc002rpp.1	-	c.600_614delTCTACTAGAACTACA	c.(598-615)TGTCTACTAGAACTACAG>TGG	p.200_205CLLELQ>W		NM_019024	NP_061897	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	200_205							binding			ovary(5)|breast(1)	6		all_hematologic(82;0.21)												0.64			65	37				---	---	---	---	capture_indel			In_Frame_Del	DEL	37152912	37152926	7315	2	TGTAGTTCTAGTAGA	-	-	55	55	HEATR5B	-	5	5
GGCX	2677	broad.mit.edu	36	2	85631646	85631665	+	Frame_Shift_Del	DEL	ACATGTAGCAAGAAGGGCTA	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:85631646_85631665delACATGTAGCAAGAAGGGCTA	uc002sps.1	-	c.1782_1801delTAGCCCTTCTTGCTACATGT	c.(1780-1803)CCTAGCCCTTCTTGCTACATGTACfs	p.P594fs		NM_000821	NP_000812	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase isoform 1	594_601	Lumenal (Potential).				blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification	endoplasmic reticulum membrane|integral to membrane|membrane fraction	gamma-glutamyl carboxylase activity			ovary(1)	1					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|L-Glutamic Acid(DB00142)|Menadione(DB00170)|Phytonadione(DB01022)									0.43			164	221				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	85631646	85631665	6624	2	ACATGTAGCAAGAAGGGCTA	-	-	14	14	GGCX	-	5	5
KALRN	8997	broad.mit.edu	36	3	125466154	125466165	+	In_Frame_Del	DEL	CCCTCATCATTA	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:125466154_125466165delCCCTCATCATTA	uc003ehg.1	+	c.377_388delCCCTCATCATTA	c.(376-390)GCCCTCATCATTAAA>GAA	p.126_130ALIIK>E	KALRN_uc010hrv.1_In_Frame_Del_p.126_130ALIIK>E|KALRN_uc003ehf.1_In_Frame_Del_p.126_130ALIIK>E	NM_001024660	NP_001019831	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase isoform 1	126_130	CRAL-TRIO.				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|nervous system development|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|vesicle-mediated transport	actin cytoskeleton|cytosol	ATP binding|GTPase activator activity|metal ion binding|protein binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			large_intestine(2)|ovary(2)|central_nervous_system(1)	5										1865				0.46			46	55				---	---	---	---	capture_indel			In_Frame_Del	DEL	125466154	125466165	8279	3	CCCTCATCATTA	-	-	26	26	KALRN	-	5	5
EPHB3	2049	broad.mit.edu	36	3	185773359	185773364	+	In_Frame_Del	DEL	AGGCTG	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:185773359_185773364delAGGCTG	uc003foz.1	+	c.557_562delAGGCTG	c.(556-564)AAGGCTGGC>AGC	p.186_188KAG>S		NM_004443	NP_004434	P54753	EPHB3_HUMAN	ephrin receptor EphB3 precursor	186_188	Extracellular (Potential).				protein phosphorylation|transmembrane receptor protein tyrosine kinase signaling pathway	integral to plasma membrane	ATP binding|ephrin receptor activity			lung(2)|breast(2)|ovary(1)|skin(1)	6	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)							292				0.41			9	13				---	---	---	---	capture_indel			In_Frame_Del	DEL	185773359	185773364	5369	3	AGGCTG	-	-	3	3	EPHB3	-	5	5
TRIO	7204	broad.mit.edu	36	5	14535853	14535854	+	Frame_Shift_Del	DEL	CC	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:14535853_14535854delCC	uc003jff.1	+	c.6628_6629delCC	c.(6628-6630)CCGfs	p.P2210fs	TRIO_uc003jfg.1_Non-coding_Transcript|TRIO_uc003jfh.1_Frame_Shift_Del_p.P1859fs	NM_007118	NP_009049	O75962	TRIO_HUMAN	triple functional domain (PTPRF interacting)	2210	PH 2.				apoptosis|axon guidance|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|transmembrane receptor protein tyrosine phosphatase signaling pathway	cytosol	ATP binding|protein serine/threonine kinase activity|Rho guanyl-nucleotide exchange factor activity			skin(4)|central_nervous_system(3)|ovary(3)|large_intestine(2)|breast(2)|stomach(1)|kidney(1)	16	Lung NSC(4;0.000742)									1300				0.32			81	175				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	14535853	14535854	17102	5	CC	-	-	26	26	TRIO	-	5	5
CYFIP2	26999	broad.mit.edu	36	5	156721052	156721057	+	Splice_Site_Del	DEL	AGGGAT	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:156721052_156721057delAGGGAT	uc003lwq.1	+	c.e28_splice_site			CYFIP2_uc003lwr.1_Splice_Site_Del|CYFIP2_uc003lws.1_Splice_Site_Del|CYFIP2_uc003lwt.1_Splice_Site_Del	NM_001037333	NP_001032410			cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)											0.45			58	72				---	---	---	---	capture_indel			Splice_Site_Del	DEL	156721052	156721057	4303	5	AGGGAT	-	-	7	7	CYFIP2	-	5	5
VIP	7432	broad.mit.edu	36	6	153115025	153115025	+	Frame_Shift_Del	DEL	C	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:153115025_153115025delC	uc003qpe.1	+	c.20_20delC	c.(19-21)GCCfs	p.A7fs	VIP_uc003qpf.1_Frame_Shift_Del_p.A7fs|VIP_uc010kjd.1_Frame_Shift_Del_p.A7fs	NM_003381	NP_003372	P01282	VIP_HUMAN	vasoactive intestinal peptide isoform 1	7					body fluid secretion|G-protein coupled receptor protein signaling pathway|positive regulation of cell proliferation	extracellular region	neuropeptide hormone activity				0		Ovarian(120;0.0654)		OV - Ovarian serous cystadenocarcinoma(155;4.5e-11)|BRCA - Breast invasive adenocarcinoma(81;0.144)										0.46			51	61				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	153115025	153115025	17734	6	C	-	-	26	26	VIP	-	5	5
HBP1	26959	broad.mit.edu	36	7	106614047	106614051	+	Frame_Shift_Del	DEL	TAGTG	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:106614047_106614051delTAGTG	uc003vdy.1	+	c.546_550delTAGTG	c.(544-552)AATAGTGAGfs	p.N182fs	HBP1_uc003vdz.1_Frame_Shift_Del_p.N182fs|HBP1_uc003vea.2_Frame_Shift_Del_p.N182fs|HBP1_uc003veb.1_Frame_Shift_Del_p.N182fs	NM_012257	NP_036389	O60381	HBP1_HUMAN	HMG-box transcription factor 1	182_184					cell cycle arrest|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	DNA binding				0														0.41			143	207				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	106614047	106614051	7267	7	TAGTG	-	-	49	49	HBP1	-	5	5
TRYX3	136541	broad.mit.edu	36	7	141601471	141601478	+	Frame_Shift_Del	DEL	TTGATTAG	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:141601471_141601478delTTGATTAG	uc003vxb.1	-	c.310_317delCTAATCAA	c.(310-318)CTAATCAAGfs	p.L104fs	TRYX3_uc003vxc.2_Frame_Shift_Del_p.L104fs	NM_001001317	NP_001001317	Q8IYP2	PRS58_HUMAN	trypsin X3	104_106	Peptidase S1.				proteolysis	extracellular region	serine-type endopeptidase activity				0	Melanoma(164;0.0272)													0.49			267	279				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	141601471	141601478	17155	7	TTGATTAG	-	-	56	56	TRYX3	-	5	5
AKAP9	10142	broad.mit.edu	36	7	91468269	91468275	+	Frame_Shift_Del	DEL	CAAAAGA	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:91468269_91468275delCAAAAGA	uc003ulh.1	+	c.1138_1144delCAAAAGA	c.(1138-1146)CAAAAGAACfs	p.Q380fs	AKAP9_uc003ule.1_Frame_Shift_Del_p.Q380fs|AKAP9_uc003ulf.1_Frame_Shift_Del_p.Q368fs|AKAP9_uc003ulg.1_Frame_Shift_Del_p.Q368fs|AKAP9_uc003uli.1_5'UTR	NM_147171	NP_671700	Q99996	AKAP9_HUMAN	A-kinase anchor protein 9 (Protein kinase A-anchoring protein 9) (PRKA9) (A-kinase anchor protein 450 kDa) (AKAP 450) (A-kinase anchor protein 350 kDa) (AKAP 350) (hgAKAP 350) (AKAP 120-like protein) (Protein hyperion) (Protein yotiao) (Centrosome- and Golgi-localized PKN-associated protein) (CG-NAP).	380_382	Glu-rich.|Potential.				G2/M transition of mitotic cell cycle|signal transduction|synaptic transmission|transport	centrosome|cytosol|Golgi apparatus	receptor binding			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)	14	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)							807				0.50			3	3				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	91468269	91468275	462	7	CAAAAGA	-	-	25	25	AKAP9	-	5	5
PHF16	9767	broad.mit.edu	36	X	46802577	46802579	+	In_Frame_Del	DEL	GTT	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:46802577_46802579delGTT	uc004dgx.1	+	c.1626_1628delGTT	c.(1624-1629)AAGTTA>AAA	p.L543del	PHF16_uc004dgy.1_In_Frame_Del_p.L543del	NM_001077445	NP_055550	Q92613	JADE3_HUMAN	PHD finger protein 16	543					histone H3 acetylation|histone H4-K12 acetylation|histone H4-K5 acetylation|histone H4-K8 acetylation	histone acetyltransferase complex	zinc ion binding				0														0.57			405	304				---	---	---	---	capture_indel			In_Frame_Del	DEL	46802577	46802579	12250	23	GTT	-	-	36	36	PHF16	-	5	5
KIF4A	24137	broad.mit.edu	36	X	69543586	69543586	+	Frame_Shift_Del	DEL	A	-	-			TCGA-28-2506-01	TCGA-28-2506-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:69543586_69543586delA	uc004dyg.1	+	c.3191_3191delA	c.(3190-3192)GAGfs	p.E1064fs	KIF4A_uc010nkw.1_Frame_Shift_Del_p.E1064fs	NM_012310	NP_036442	O95239	KIF4A_HUMAN	kinesin family member 4	1064	Globular.|Interaction with PRC1.				anterograde axon cargo transport|axon guidance|blood coagulation|organelle organization	chromosome|cytosol|midbody|nuclear matrix|spindle microtubule	ATP binding|DNA binding|microtubule motor activity|protein binding			ovary(4)	4														0.52			23	21				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	69543586	69543586	8614	23	A	-	-	11	11	KIF4A	-	5	5
