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	TCGAscape_Amplification_Peaks	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_judgement	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	dataset	Oncotatorv0393GAF20hg19Feb2011dbSNPbuild132UniProtRelease2011_6	type	classification	start	end	gene	chr	ref_allele	tum_allele1	tum_allele2	newbase	context_orig	context65	gene_name	categ	categ_ignoring_null_categ
SLC39A12	221074	broad.mit.edu	37	10	18270285	18270285	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr10:18270285G>T	uc001ipo.2	+	c.969G>T	c.(967-969)AAG>AAT	p.K323N	SLC39A12_uc001ipn.2_Missense_Mutation_p.K323N|SLC39A12_uc001ipp.2_Missense_Mutation_p.K323N|SLC39A12_uc010qck.1_Missense_Mutation_p.K189N	NM_001145195	NP_001138667	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter),	323	Cytoplasmic (Potential).				zinc ion transport	integral to membrane	metal ion transmembrane transporter activity			ovary(1)|breast(1)	2														0.09375	3.314975	13.920165	6	58	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	18270285	18270285	15112	10	G	T	T	T	451	35	SLC39A12	2	2
DDI1	414301	broad.mit.edu	37	11	103908104	103908104	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:103908104A>G	uc001phr.2	+	c.554A>G	c.(553-555)GAG>GGG	p.E185G	PDGFD_uc001php.2_Intron|PDGFD_uc001phq.2_Intron	NM_001001711	NP_001001711	Q8WTU0	DDI1_HUMAN	DDI1, DNA-damage inducible 1, homolog 1	185					proteolysis		aspartic-type endopeptidase activity			large_intestine(3)|pancreas(1)	4		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)										0.064103	-5.382164	10.034174	5	73	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	103908104	103908104	4499	11	A	G	G	G	143	11	DDI1	4	4
NTM	50863	broad.mit.edu	37	11	132180083	132180083	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:132180083G>A	uc010sci.1	+	c.739G>A	c.(739-741)GCA>ACA	p.A247T	NTM_uc001qgm.2_Missense_Mutation_p.A247T|NTM_uc010sch.1_Missense_Mutation_p.A238T|NTM_uc010scj.1_Missense_Mutation_p.A206T|NTM_uc001qgo.2_Missense_Mutation_p.A247T|NTM_uc001qgq.2_Missense_Mutation_p.A247T|NTM_uc001qgp.2_Missense_Mutation_p.A247T|NTM_uc001qgr.2_5'UTR	NM_001144058	NP_001137530	Q9P121	NTRI_HUMAN	neurotrimin isoform 3	247	Ig-like C2-type 3.				cell adhesion|neuron recognition	anchored to membrane|plasma membrane				ovary(4)|central_nervous_system(1)	5														0.079848	-1.178171	46.145443	21	242	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	132180083	132180083	11104	11	G	A	A	A	442	34	NTM	2	2
OR5D14	219436	broad.mit.edu	37	11	55563896	55563896	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:55563896C>A	uc010rim.1	+	c.865C>A	c.(865-867)CCT>ACT	p.P289T		NM_001004735	NP_001004735	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D,	289	Helical; Name=7; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)|central_nervous_system(1)	3		all_epithelial(135;0.196)												0.12766	6.299597	12.712026	6	41	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	55563896	55563896	11565	11	C	A	A	A	286	22	OR5D14	2	2
OR5T2	219464	broad.mit.edu	37	11	56000092	56000092	+	Silent	SNP	A	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56000092A>T	uc010rjc.1	-	c.570T>A	c.(568-570)GCT>GCA	p.A190A		NM_001004746	NP_001004746	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T,	190	Helical; Name=4; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(2)	2	Esophageal squamous(21;0.00448)													0.042169	-22.220575	15.148164	7	159	KEEP	---	---	---	---	capture		Silent	SNP	56000092	56000092	11592	11	A	T	T	T	80	7	OR5T2	3	3
OR5M9	390162	broad.mit.edu	37	11	56230509	56230509	+	Silent	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:56230509G>T	uc010rjj.1	-	c.369C>A	c.(367-369)GCC>GCA	p.A123A		NM_001004743	NP_001004743	Q8NGP3	OR5M9_HUMAN	olfactory receptor, family 5, subfamily M,	123	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(21;0.00448)													0.053571	-11.603807	11.920699	6	106	KEEP	---	---	---	---	capture		Silent	SNP	56230509	56230509	11587	11	G	T	T	T	496	39	OR5M9	1	1
OR4D6	219983	broad.mit.edu	37	11	59224942	59224942	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr11:59224942G>T	uc010rku.1	+	c.509G>T	c.(508-510)GGC>GTC	p.G170V		NM_001004708	NP_001004708	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D,	170	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)	1														0.090226	3.90933	26.432624	12	121	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	59224942	59224942	11465	11	G	T	T	T	546	42	OR4D6	2	2
CLEC12A	160364	broad.mit.edu	37	12	10124236	10124236	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:10124236A>G	uc001qwq.2	+	c.71A>G	c.(70-72)AAC>AGC	p.N24S	CLEC12A_uc001qwr.3_Missense_Mutation_p.N14S|CLEC12A_uc001qws.3_Missense_Mutation_p.N14S|CLEC12A_uc001qwt.2_5'UTR	NM_138337	NP_612210	Q5QGZ9	CL12A_HUMAN	myeloid inhibitory C-type lectin-like receptor	14	Cytoplasmic (Potential).					integral to membrane|plasma membrane	receptor activity|sugar binding				0						Melanoma(197;1487 2125 16611 22221 34855)								0.037736	-39.372633	21.891383	10	255	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10124236	10124236	3634	12	A	G	G	G	26	2	CLEC12A	4	4
GPR133	283383	broad.mit.edu	37	12	131590330	131590330	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:131590330C>T	uc010tbm.1	+	c.1903C>T	c.(1903-1905)CAC>TAC	p.H635Y	GPR133_uc001uit.3_Missense_Mutation_p.H603Y|GPR133_uc009zyo.2_Intron|GPR133_uc001uiv.1_Missense_Mutation_p.H122Y|GPR133_uc009zyp.2_Non-coding_Transcript	NM_198827	NP_942122	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133 precursor	603	Helical; Name=2; (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity			pancreas(5)|ovary(3)	8	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)										0.136364	5.211145	8.02679	3	19	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	131590330	131590330	6917	12	C	T	T	T	273	21	GPR133	2	2
KCNA6	3742	broad.mit.edu	37	12	4919925	4919925	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:4919925C>T	uc001qng.2	+	c.718C>T	c.(718-720)CCT>TCT	p.P240S		NM_002235	NP_002226	P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related	240						voltage-gated potassium channel complex	voltage-gated potassium channel activity			ovary(1)|skin(1)	2														0.043011	-12.179411	8.647929	4	89	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	4919925	4919925	8312	12	C	T	T	T	286	22	KCNA6	2	2
CBX5	23468	broad.mit.edu	37	12	54635557	54635558	+	Missense_Mutation	DNP	TT	AA	AA			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:54635557_54635558TT>AA	uc001sfh.3	-	c.557_558AA>TT	c.(556-558)AAA>ATT	p.K186I	CBX5_uc001sfk.3_Missense_Mutation_p.K186I|CBX5_uc001sfi.3_Missense_Mutation_p.K185I|CBX5_uc001sfj.3_Missense_Mutation_p.K186I	NM_001127322	NP_001120794	P45973	CBX5_HUMAN	heterochromatin protein 1-alpha	186					blood coagulation|chromatin assembly or disassembly|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent	cytoplasm|histone deacetylase complex|histone methyltransferase complex|nuclear centromeric heterochromatin|nuclear envelope|nucleolus|transcriptional repressor complex	general transcriptional repressor activity|methylated histone residue binding|protein binding, bridging|repressing transcription factor binding				0						Colon(153;588 2459 18334 48613)								0.041096	-21.579906	11.505427	6	140	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	54635557	54635558	2840	12	TT	AA	AA	AA	725	56	CBX5	3	3
PABPC3	5042	broad.mit.edu	37	13	25671011	25671011	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:25671011T>A	uc001upy.2	+	c.675T>A	c.(673-675)GAT>GAA	p.D225E		NM_030979	NP_112241	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	225	RRM 3.				mRNA metabolic process	cytoplasm	nucleotide binding|poly(A) RNA binding			ovary(3)|skin(1)	4		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.0071)|Epithelial(112;0.0398)|OV - Ovarian serous cystadenocarcinoma(117;0.151)|GBM - Glioblastoma multiforme(144;0.222)|Lung(94;0.241)										0.105882	10.414186	23.526774	9	76	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	25671011	25671011	11780	13	T	A	A	A	660	51	PABPC3	3	3
FOXO1	2308	broad.mit.edu	37	13	41134917	41134917	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr13:41134917C>A	uc001uxl.3	-	c.711G>T	c.(709-711)TGG>TGT	p.W237C	FOXO1_uc010acc.1_Missense_Mutation_p.W52C	NM_002015	NP_002006	Q12778	FOXO1_HUMAN	forkhead box O1	237					anti-apoptosis|blood vessel development|embryo development|endocrine pancreas development|insulin receptor signaling pathway|negative regulation of gene-specific transcription from RNA polymerase II promoter|negative regulation of stress-activated MAPK cascade|nerve growth factor receptor signaling pathway|pattern specification process|phosphatidylinositol-mediated signaling|positive regulation of transcription from RNA polymerase II promoter|regulation of cell proliferation|regulation of sequence-specific DNA binding transcription factor activity|response to DNA damage stimulus|tissue development	cytosol|transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|protein kinase 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		PAX3/FOXO1(749)|PAX7/FOXO1(197)	soft_tissue(946)|central_nervous_system(1)	947		Lung NSC(96;1.18e-05)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;7.32e-09)|Epithelial(112;2.87e-06)|OV - Ovarian serous cystadenocarcinoma(117;6.98e-05)|GBM - Glioblastoma multiforme(144;0.00394)|BRCA - Breast invasive adenocarcinoma(63;0.0815)						55				0.122449	11.74434	25.423	12	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	41134917	41134917	6269	13	C	A	A	A	390	30	FOXO1	2	2
RTN1	6252	broad.mit.edu	37	14	60213133	60213133	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr14:60213133G>C	uc001xen.1	-	c.308C>G	c.(307-309)TCG>TGG	p.S103W		NM_021136	NP_066959	Q16799	RTN1_HUMAN	reticulon 1 isoform A	103					neuron differentiation	integral to endoplasmic reticulum membrane	signal transducer activity			ovary(2)|central_nervous_system(2)	4				OV - Ovarian serous cystadenocarcinoma(108;0.0968)										0.045113	-14.846324	14.546843	6	127	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	60213133	60213133	14205	14	G	C	C	C	481	37	RTN1	3	3
LYSMD4	145748	broad.mit.edu	37	15	100271393	100271393	+	Silent	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:100271393C>T	uc002bvl.2	-	c.270G>A	c.(268-270)GTG>GTA	p.V90V	LYSMD4_uc002bvj.1_Intron|LYSMD4_uc010bou.1_Intron|LYSMD4_uc002bvk.2_Intron|LYSMD4_uc002bvm.2_Silent_p.*98*|LYSMD4_uc010bov.2_Intron	NM_152449	NP_689662	Q5XG99	LYSM4_HUMAN	LysM, putative peptidoglycan-binding, domain	256	Cytoplasmic (Potential).				cell wall macromolecule catabolic process	integral to membrane					0	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00162)|LUSC - Lung squamous cell carcinoma(107;0.17)|Lung(145;0.208)											0.061224	-3.514847	6.33325	3	46	KEEP	---	---	---	---	capture		Silent	SNP	100271393	100271393	9504	15	C	T	T	T	366	29	LYSMD4	2	2
C15orf2	23742	broad.mit.edu	37	15	24923774	24923774	+	Silent	SNP	A	C	C			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:24923774A>C	uc001ywo.2	+	c.2760A>C	c.(2758-2760)GCA>GCC	p.A920A		NM_018958	NP_061831	Q9NZP6	CO002_HUMAN	hypothetical protein LOC23742	920					cell differentiation|multicellular organismal development|spermatogenesis					ovary(2)|large_intestine(2)|kidney(1)|central_nervous_system(1)	6		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)						443				0.058824	-5.454814	8.410525	4	64	KEEP	---	---	---	---	capture		Silent	SNP	24923774	24923774	1834	15	A	C	C	C	54	5	C15orf2	4	4
MYO5A	4644	broad.mit.edu	37	15	52700338	52700338	+	Splice_Site_SNP	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:52700338C>T	uc002aby.2	-	c.757_splice	c.e7-1	p.A253_splice	MYO5A_uc002abx.3_Splice_Site_SNP_p.A253_splice|MYO5A_uc010uge.1_Splice_Site_SNP_p.A122_splice	NM_000259	NP_000250			myosin VA isoform 1						actin filament-based movement|transport	cytoplasm|growth cone|myosin complex|ruffle	actin binding|ATP binding|calmodulin binding|microfilament motor activity			ovary(3)|central_nervous_system(1)	4				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)										0.070588	-1.922351	14.247648	6	79	KEEP	---	---	---	---	capture		Splice_Site_SNP	SNP	52700338	52700338	10473	15	C	T	T	T	312	24	MYO5A	5	2
ODF3L1	161753	broad.mit.edu	37	15	76019833	76019833	+	Missense_Mutation	SNP	C	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr15:76019833C>G	uc002bax.1	+	c.777C>G	c.(775-777)ATC>ATG	p.I259M		NM_175881	NP_787077	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	259	DUF1309 2.										0														0.073171	0.192494	7.871602	3	38	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	76019833	76019833	11236	15	C	G	G	G	369	29	ODF3L1	3	3
BBS2	583	broad.mit.edu	37	16	56544822	56544822	+	Silent	SNP	G	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:56544822G>A	uc002ejd.2	-	c.483C>T	c.(481-483)GAC>GAT	p.D161D	BBS2_uc010ccg.2_Silent_p.D161D	NM_031885	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2 protein	161					adult behavior|brain morphogenesis|cerebral cortex development|cilium morphogenesis|fat cell differentiation|hippocampus development|melanosome transport|negative regulation of multicellular organism growth|photoreceptor cell maintenance|protein localization to organelle|regulation of cilium beat frequency involved in ciliary motility|sperm axoneme assembly|striatum development	BBSome|cilium membrane|microtubule basal body|motile cilium	protein binding			ovary(1)	1														0.085106	0.963196	17.346053	8	86	KEEP	---	---	---	---	capture		Silent	SNP	56544822	56544822	1359	16	G	A	A	A	620	48	BBS2	2	2
STAT3	6774	broad.mit.edu	37	17	40475149	40475149	+	Silent	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:40475149G>T	uc002hzl.1	-	c.1761C>A	c.(1759-1761)GGC>GGA	p.G587G	STAT3_uc002hzk.1_Silent_p.G587G|STAT3_uc002hzm.1_Silent_p.G587G|STAT3_uc010wgh.1_Silent_p.G489G|STAT3_uc002hzn.1_Silent_p.G587G	NM_139276	NP_644805	P40763	STAT3_HUMAN	signal transducer and activator of transcription	587	SH2.				cellular component movement|eating behavior|eye photoreceptor cell differentiation|glucose homeostasis|interleukin-6-mediated signaling pathway|interspecies interaction between organisms|JAK-STAT cascade involved in growth hormone signaling pathway|negative regulation of transcription from RNA polymerase II promoter|nerve growth factor receptor signaling pathway|protein import into nucleus|response to estradiol stimulus|sexual reproduction|temperature homeostasis	cytosol|nucleus|plasma membrane	calcium ion binding|protein dimerization activity|protein kinase binding|sequence-specific DNA binding transcription factor activity|signal transducer activity|transcription activator activity|transcription factor binding			ovary(1)|lung(1)|central_nervous_system(1)	3		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)						793		OREG0024421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.036585	-26.723135	11.399019	6	158	KEEP	---	---	---	---	capture		Silent	SNP	40475149	40475149	15786	17	G	T	T	T	431	34	STAT3	2	2
KCND3	3752	broad.mit.edu	37	1	112524699	112524699	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:112524699G>A	uc001ebu.1	-	c.650C>T	c.(649-651)CCG>CTG	p.P217L	KCND3_uc001ebv.1_Missense_Mutation_p.P217L	NM_004980	NP_004971	Q9UK17	KCND3_HUMAN	potassium voltage-gated channel, Shal-related	217						sarcolemma|voltage-gated potassium channel complex	A-type (transient outward) potassium channel activity|metal ion binding			ovary(2)|large_intestine(1)	3		all_cancers(81;8.52e-06)|all_epithelial(167;5.65e-06)|all_lung(203;2.72e-05)|Lung NSC(69;4.56e-05)		all cancers(265;0.056)|Lung(183;0.0576)|Colorectal(144;0.1)|Epithelial(280;0.104)|COAD - Colon adenocarcinoma(174;0.222)|LUSC - Lung squamous cell carcinoma(189;0.231)										0.111111	3.906642	7.942046	3	24	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	112524699	112524699	8325	1	G	A	A	A	507	39	KCND3	1	1
ATP1A2	477	broad.mit.edu	37	1	160105300	160105300	+	Missense_Mutation	SNP	T	A	A	rs28933400		TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:160105300T>A	uc001fvc.2	+	c.2192T>A	c.(2191-2193)ATG>AAG	p.M731K	ATP1A2_uc001fvb.2_Missense_Mutation_p.M731K|ATP1A2_uc001fvd.2_Missense_Mutation_p.M467K	NM_000702	NP_000693	P50993	AT1A2_HUMAN	Na+/K+ -ATPase alpha 2 subunit proprotein	731	Cytoplasmic (Potential).				ATP biosynthetic process	sodium:potassium-exchanging ATPase complex	ATP binding|metal ion binding|sodium:potassium-exchanging ATPase activity			ovary(2)|central_nervous_system(2)	4	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)											0.052174	-12.220701	12.142704	6	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	160105300	160105300	1148	1	T	A	A	A	663	51	ATP1A2	3	3
RYR2	6262	broad.mit.edu	37	1	237806708	237806708	+	Missense_Mutation	SNP	G	C	C			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:237806708G>C	uc001hyl.1	+	c.7303G>C	c.(7303-7305)GTT>CTT	p.V2435L		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	2435	Cytoplasmic (By similarity).|4 X approximate repeats.				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)											0.058394	-8.603529	19.382989	8	129	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	237806708	237806708	14249	1	G	C	C	C	520	40	RYR2	3	3
KRTAP10-6	386674	broad.mit.edu	37	21	46011808	46011808	+	Nonsense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr21:46011808G>T	uc002zfm.2	-	c.558C>A	c.(556-558)TGC>TGA	p.C186*	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198688	NP_941961	P60371	KR106_HUMAN	keratin associated protein 10-6	186	16.|29 X 5 AA repeats of C-C-X(3).					keratin filament					0														0.064815	-14.840148	27.60352	14	202	KEEP	---	---	---	---	capture		Nonsense_Mutation	SNP	46011808	46011808	8828	21	G	T	T	T	438	34	KRTAP10-6	5	2
TRIOBP	11078	broad.mit.edu	37	22	38119527	38119527	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr22:38119527G>A	uc003atr.2	+	c.964G>A	c.(964-966)GCC>ACC	p.A322T	TRIOBP_uc003atu.2_Missense_Mutation_p.A150T|TRIOBP_uc003atq.1_Missense_Mutation_p.A322T|TRIOBP_uc003ats.1_Missense_Mutation_p.A150T	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	322					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)													0.086294	-0.514459	33.621018	17	180	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38119527	38119527	17103	22	G	A	A	A	546	42	TRIOBP	2	2
CNTNAP5	129684	broad.mit.edu	37	2	125555845	125555845	+	Silent	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:125555845C>A	uc010flu.2	+	c.3165C>A	c.(3163-3165)CTC>CTA	p.L1055L	CNTNAP5_uc002tno.2_Silent_p.L1054L	NM_130773	NP_570129	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5 precursor	1054	Extracellular (Potential).|Laminin G-like 4.				cell adhesion|signal transduction	integral to membrane	receptor binding			ovary(10)	10				BRCA - Breast invasive adenocarcinoma(221;0.248)										0.055046	-10.626662	12.083412	6	103	KEEP	---	---	---	---	capture		Silent	SNP	125555845	125555845	3788	2	C	A	A	A	405	32	CNTNAP5	2	2
POTEF	728378	broad.mit.edu	37	2	130832776	130832776	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:130832776C>T	uc010fmh.2	-	c.2269G>A	c.(2269-2271)GAG>AAG	p.E757K		NM_001099771	NP_001093241	A5A3E0	POTEF_HUMAN	prostate, ovary, testis expressed protein on	757	Actin-like.					cell cortex	ATP binding			ovary(2)|skin(1)	3														0.066667	-2.948714	8.729782	4	56	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	130832776	130832776	12695	2	C	T	T	T	390	30	POTEF	2	2
LRP1B	53353	broad.mit.edu	37	2	141598496	141598496	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:141598496G>T	uc002tvj.1	-	c.5105C>A	c.(5104-5106)CCA>CAA	p.P1702Q		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	1702	Extracellular (Potential).|LDL-receptor class B 15.				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding			lung(17)|ovary(10)|pancreas(3)|central_nervous_system(2)|liver(1)|kidney(1)	34		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.095238	4.39985	14.76052	6	57	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	141598496	141598496	9328	2	G	T	T	T	611	47	LRP1B	2	2
XIRP2	129446	broad.mit.edu	37	2	168108168	168108168	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:168108168G>T	uc002udx.2	+	c.10266G>T	c.(10264-10266)ATG>ATT	p.M3422I	XIRP2_uc010fpn.2_Intron|XIRP2_uc010fpo.2_Intron|XIRP2_uc010fpp.2_Intron|XIRP2_uc002udy.2_Missense_Mutation_p.M3247I|XIRP2_uc010fpq.2_Missense_Mutation_p.M3200I|XIRP2_uc010fpr.2_Intron	NM_152381	NP_689594	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2 isoform 1	3247					actin cytoskeleton organization	cell junction	actin binding			ovary(6)|pancreas(1)|skin(1)	8														0.046053	-18.30867	15.120701	7	145	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	168108168	168108168	18011	2	G	T	T	T	611	47	XIRP2	2	2
UBE2E3	10477	broad.mit.edu	37	2	181927579	181927579	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:181927579G>T	uc002unq.1	+	c.588G>T	c.(586-588)AGG>AGT	p.R196S	UBE2E3_uc002unr.1_Missense_Mutation_p.R196S|UBE2E3_uc010fri.1_Missense_Mutation_p.R196S	NM_182678	NP_872619	Q969T4	UB2E3_HUMAN	ubiquitin-conjugating enzyme E2E 3	196					post-translational protein modification|protein K11-linked ubiquitination|protein K48-linked ubiquitination|protein K63-linked ubiquitination|regulation of growth	cytoplasm|nucleolus	ATP binding|protein binding|ubiquitin-protein ligase activity			ovary(1)	1														0.055046	-11.208117	11.487717	6	103	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	181927579	181927579	17411	2	G	T	T	T	529	41	UBE2E3	2	2
WDR75	84128	broad.mit.edu	37	2	190339976	190339976	+	Missense_Mutation	SNP	G	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:190339976G>A	uc002uql.1	+	c.2326G>A	c.(2326-2328)GAA>AAA	p.E776K	WDR75_uc002uqm.1_Missense_Mutation_p.E712K|WDR75_uc002uqn.1_Missense_Mutation_p.E554K|WDR75_uc002uqo.1_Missense_Mutation_p.E554K	NM_032168	NP_115544	Q8IWA0	WDR75_HUMAN	WD repeat domain 75	776						nucleolus				ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.00105)|Epithelial(96;0.0129)|all cancers(119;0.0456)											0.061538	-3.755689	9.285169	4	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	190339976	190339976	17898	2	G	A	A	A	429	33	WDR75	2	2
PIKFYVE	200576	broad.mit.edu	37	2	209195289	209195290	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:209195289_209195290GG>TT	uc002vcz.2	+	c.3834_3835GG>TT	c.(3832-3837)ATGGTA>ATTTTA	p.1278_1279MV>IL	PIKFYVE_uc002vcy.1_Missense_Mutation_p.1222_1223MV>IL	NM_015040	NP_055855	Q9Y2I7	FYV1_HUMAN	phosphatidylinositol-3-phosphate 5-kinase type	1278_1279					cellular protein metabolic process|intracellular signal transduction|protein localization to nucleus|retrograde transport, endosome to Golgi	early endosome membrane|membrane raft	1-phosphatidylinositol-3-phosphate 5-kinase activity|1-phosphatidylinositol-4-phosphate 5-kinase activity|ATP binding|protein binding|zinc ion binding			ovary(5)|kidney(2)|central_nervous_system(1)|pancreas(1)	9										756				0.047733	-51.493965	39.936284	20	399	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	209195289	209195290	12348	2	GG	TT	TT	TT	611	47	PIKFYVE	2	2
VWA3B	200403	broad.mit.edu	37	2	98744812	98744812	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr2:98744812C>A	uc002syo.2	+	c.813C>A	c.(811-813)AAC>AAA	p.N271K	VWA3B_uc010yvh.1_Missense_Mutation_p.N121K|VWA3B_uc002syj.2_Non-coding_Transcript|VWA3B_uc002syk.1_Non-coding_Transcript|VWA3B_uc002syl.1_Intron|VWA3B_uc002sym.2_Missense_Mutation_p.N271K|VWA3B_uc002syn.1_Non-coding_Transcript	NM_144992	NP_659429	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	271										ovary(3)|large_intestine(2)	5														0.036458	-29.052321	15.598497	7	185	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	98744812	98744812	17810	2	C	A	A	A	246	19	VWA3B	1	1
SLC6A11	6538	broad.mit.edu	37	3	10967754	10967754	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:10967754G>T	uc003bvz.2	+	c.1185G>T	c.(1183-1185)TGG>TGT	p.W395C		NM_014229	NP_055044	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter	395	Helical; Name=8; (Potential).				neurotransmitter secretion	integral to plasma membrane	gamma-aminobutyric acid:sodium symporter activity|neurotransmitter:sodium symporter activity			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(96;0.229)										0.070652	-23.525877	81.087096	39	513	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	10967754	10967754	15171	3	G	T	T	T	559	43	SLC6A11	2	2
SLC6A6	6533	broad.mit.edu	37	3	14489271	14489271	+	Silent	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:14489271C>A	uc010heg.2	+	c.546C>A	c.(544-546)GTC>GTA	p.V182V	SLC6A6_uc003byp.2_Silent_p.V182V|SLC6A6_uc010hef.1_Non-coding_Transcript|SLC6A6_uc003byq.2_Silent_p.V182V|SLC6A6_uc003byr.2_Non-coding_Transcript	NM_001134367	NP_001127839	P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter	182	Extracellular (Potential).				cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity			ovary(1)	1														0.109091	2.896311	11.264585	6	49	KEEP	---	---	---	---	capture		Silent	SNP	14489271	14489271	15185	3	C	A	A	A	405	32	SLC6A6	2	2
DCLK3	85443	broad.mit.edu	37	3	36763132	36763132	+	Missense_Mutation	SNP	T	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:36763132T>G	uc003cgi.2	-	c.1471A>C	c.(1471-1473)AAA>CAA	p.K491Q		NM_033403	NP_208382	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	491	Protein kinase.				protein phosphorylation	cytoplasm|nucleus	ATP binding|protein serine/threonine kinase activity			lung(3)|large_intestine(2)|ovary(1)|breast(1)|kidney(1)	8										128				0.089286	5.563163	24.679767	10	102	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	36763132	36763132	4464	3	T	G	G	G	819	63	DCLK3	4	4
OR5H14	403273	broad.mit.edu	37	3	97868848	97868848	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:97868848C>A	uc003dsg.1	+	c.619C>A	c.(619-621)CAA>AAA	p.Q207K		NM_001005514	NP_001005514	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H,	207	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.08	0.058295	9.057781	4	46	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	97868848	97868848	11570	3	C	A	A	A	377	29	OR5H14	2	2
DNAJB14	79982	broad.mit.edu	37	4	100822261	100822261	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:100822261C>T	uc003hvl.2	-	c.1064G>A	c.(1063-1065)CGA>CAA	p.R355Q	DNAJB14_uc003hvk.2_Missense_Mutation_p.R270Q|DNAJB14_uc010ili.2_Missense_Mutation_p.R288Q	NM_001031723	NP_001026893	Q8TBM8	DJB14_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 14	355					protein folding	integral to membrane	heat shock protein binding|unfolded protein binding				0				OV - Ovarian serous cystadenocarcinoma(123;4.59e-09)										0.055556	-7.694583	11.004083	5	85	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	100822261	100822261	4802	4	C	T	T	T	403	31	DNAJB14	1	1
ABCE1	6059	broad.mit.edu	37	4	146031567	146031567	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:146031567A>G	uc003ijx.2	+	c.584A>G	c.(583-585)AAG>AGG	p.K195R	ABCE1_uc003ijy.2_Missense_Mutation_p.K195R|ABCE1_uc010iot.2_Non-coding_Transcript	NM_001040876	NP_001035809	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E, member 1	195	ABC transporter 1.				interspecies interaction between organisms|response to virus|RNA catabolic process	mitochondrion	ATP binding|ATPase activity|electron carrier activity|iron-sulfur cluster binding|ribonuclease inhibitor activity				0	all_hematologic(180;0.151)													0.067961	-6.866017	13.075463	7	96	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	146031567	146031567	65	4	A	G	G	G	39	3	ABCE1	4	4
MFAP3L	9848	broad.mit.edu	37	4	170913452	170913452	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:170913452G>T	uc003isp.3	-	c.307C>A	c.(307-309)CAA>AAA	p.Q103K	MFAP3L_uc003isn.3_5'UTR	NM_021647	NP_067679	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like isoform	103	Extracellular (Potential).|Ig-like C2-type.					integral to membrane|plasma membrane				ovary(1)	1		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)										0.125	12.042369	21.91929	9	63	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	170913452	170913452	9906	4	G	T	T	T	598	46	MFAP3L	2	2
ADAM29	11086	broad.mit.edu	37	4	175897502	175897502	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:175897502A>G	uc003iuc.2	+	c.826A>G	c.(826-828)AAC>GAC	p.N276D	ADAM29_uc003iud.2_Missense_Mutation_p.N276D|ADAM29_uc010irr.2_Missense_Mutation_p.N276D|ADAM29_uc011cki.1_Missense_Mutation_p.N276D	NM_014269	NP_055084	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29 preproprotein	276	Peptidase M12B.|Extracellular (Potential).				proteolysis|spermatogenesis	integral to plasma membrane	metalloendopeptidase activity|zinc ion binding			ovary(3)|large_intestine(2)|central_nervous_system(2)|skin(2)|pancreas(1)	10		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		Ovarian(140;1727 1835 21805 25838 41440)				106				0.088235	4.760641	28.279052	12	124	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	175897502	175897502	248	4	A	G	G	G	117	9	ADAM29	4	4
GABRG1	2565	broad.mit.edu	37	4	46043195	46043195	+	Missense_Mutation	SNP	C	A	A	rs17852913		TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:46043195C>A	uc003gxb.2	-	c.1208G>T	c.(1207-1209)GGG>GTG	p.G403V		NM_173536	NP_775807	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid A receptor, gamma 1	403	Cytoplasmic (Probable).				gamma-aminobutyric acid signaling pathway	cell junction|chloride channel complex|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity			ovary(2)	2				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)										0.054348	-10.300814	8.964898	5	87	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	46043195	46043195	6422	4	C	A	A	A	286	22	GABRG1	2	2
C4orf6	10141	broad.mit.edu	37	4	5527967	5527967	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:5527967C>A	uc003gii.2	+	c.191C>A	c.(190-192)ACA>AAA	p.T64K		NM_005750	NP_005741	Q99440	CD006_HUMAN	chromosome 4 open reading frame 6	64					nervous system development						0														0.115942	6.085539	16.083319	8	61	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	5527967	5527967	2376	4	C	A	A	A	221	17	C4orf6	2	2
PRKG2	5593	broad.mit.edu	37	4	82074851	82074851	+	Missense_Mutation	SNP	T	C	C			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:82074851T>C	uc003hmh.2	-	c.937A>G	c.(937-939)ATC>GTC	p.I313V	PRKG2_uc011ccf.1_5'UTR|PRKG2_uc011ccg.1_5'UTR|PRKG2_uc011cch.1_Missense_Mutation_p.I313V	NM_006259	NP_006250	Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	313	cGMP 2.				platelet activation|protein phosphorylation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7										728				0.121212	3.675751	8.322103	4	29	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	82074851	82074851	12966	4	T	C	C	C	663	51	PRKG2	4	4
MAN2A1	4124	broad.mit.edu	37	5	109117165	109117165	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:109117165G>T	uc003kou.1	+	c.1443G>T	c.(1441-1443)AAG>AAT	p.K481N		NM_002372	NP_002363	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	481	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			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)										0.065217	-2.514484	6.517613	3	43	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	109117165	109117165	9597	5	G	T	T	T	451	35	MAN2A1	2	2
PCDH12	51294	broad.mit.edu	37	5	141325368	141325368	+	Silent	SNP	G	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr5:141325368G>A	uc003llx.2	-	c.3133C>T	c.(3133-3135)CTG>TTG	p.L1045L		NM_016580	NP_057664	Q9NPG4	PCD12_HUMAN	protocadherin 12 precursor	1045	Cytoplasmic (Potential).				neuron recognition	integral to plasma membrane	calcium ion binding			ovary(3)	3		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)											0.12	3.207248	6.749452	3	22	KEEP	---	---	---	---	capture		Silent	SNP	141325368	141325368	11930	5	G	A	A	A	425	33	PCDH12	2	2
NUDT3	11165	broad.mit.edu	37	6	34261308	34261308	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr6:34261308T>A	uc003ojl.2	-	c.260A>T	c.(259-261)CAG>CTG	p.Q87L		NM_006703	NP_006694	O95989	NUDT3_HUMAN	nudix-type motif 3	87	Nudix hydrolase.				cell-cell signaling|diadenosine polyphosphate catabolic process|diphosphoinositol polyphosphate catabolic process	cytoplasm	diphosphoinositol-polyphosphate diphosphatase activity|magnesium ion binding				0						GBM(96;1206 1939 18658 39482)								0.076923	0.387201	14.679294	6	72	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	34261308	34261308	11145	6	T	A	A	A	715	55	NUDT3	3	3
PTPRN2	5799	broad.mit.edu	37	7	157959914	157959914	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:157959914C>A	uc011kwa.1	-	c.688G>T	c.(688-690)GGG>TGG	p.G230W	PTPRN2_uc003wno.2_Missense_Mutation_p.G207W|PTPRN2_uc003wnp.2_Missense_Mutation_p.G190W|PTPRN2_uc003wnq.2_Missense_Mutation_p.G207W|PTPRN2_uc003wnr.2_Missense_Mutation_p.G169W	NM_002847	NP_002838	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N	207	Extracellular (Potential).					integral to plasma membrane	protein binding|transmembrane receptor protein tyrosine phosphatase activity			ovary(4)|large_intestine(1)|pleura(1)	6	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)										0.155172	16.727389	23.243264	9	49	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	157959914	157959914	13265	7	C	A	A	A	299	23	PTPRN2	1	1
DNAH11	8701	broad.mit.edu	37	7	21723542	21723542	+	Silent	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:21723542G>T	uc003svc.2	+	c.5622G>T	c.(5620-5622)GTG>GTT	p.V1874V		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1874	AAA 1 (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.036269	-34.048439	11.000446	7	186	KEEP	---	---	---	---	capture		Silent	SNP	21723542	21723542	4781	7	G	T	T	T	574	45	DNAH11	2	2
VPS41	27072	broad.mit.edu	37	7	38816338	38816338	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:38816338C>A	uc003tgy.2	-	c.823G>T	c.(823-825)GCA>TCA	p.A275S	VPS41_uc003tgz.2_Missense_Mutation_p.A250S|VPS41_uc010kxn.2_Missense_Mutation_p.A186S	NM_014396	NP_055211	P49754	VPS41_HUMAN	vacuolar protein sorting 41 isoform 1	275					Golgi vesicle transport|intracellular protein transport|vesicle-mediated transport	cytosol|Golgi-associated vesicle|HOPS complex|membrane fraction	zinc ion binding			central_nervous_system(1)	1														0.074074	-1.205445	13.878755	6	75	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	38816338	38816338	17777	7	C	A	A	A	325	25	VPS41	2	2
ZNF92	168374	broad.mit.edu	37	7	64864055	64864055	+	Missense_Mutation	SNP	G	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:64864055G>T	uc003ttz.2	+	c.1028G>T	c.(1027-1029)TGT>TTT	p.C343F	ZNF92_uc003tua.2_Missense_Mutation_p.C274F|ZNF92_uc010kzu.2_Missense_Mutation_p.C311F|ZNF92_uc003tub.2_Missense_Mutation_p.C267F	NM_152626	NP_689839	Q03936	ZNF92_HUMAN	zinc finger protein 92 isoform 2	343	C2H2-type 8.				regulation of transcription, DNA-dependent	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Lung NSC(55;0.159)												0.056338	-6.155785	8.52965	4	67	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	64864055	64864055	18805	7	G	T	T	T	624	48	ZNF92	2	2
ZFHX4	79776	broad.mit.edu	37	8	77765686	77765686	+	Missense_Mutation	SNP	T	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:77765686T>A	uc003yav.2	+	c.6394T>A	c.(6394-6396)TTT>ATT	p.F2132I	ZFHX4_uc003yau.1_Missense_Mutation_p.F2177I|ZFHX4_uc003yaw.1_Missense_Mutation_p.F2132I	NM_024721	NP_078997	Q86UP3	ZFHX4_HUMAN	zinc finger homeodomain 4	2132	Homeobox 1.				regulation of transcription, DNA-dependent	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription regulator activity|zinc ion binding			ovary(8)|large_intestine(4)|breast(2)|lung(1)	15			BRCA - Breast invasive adenocarcinoma(89;0.0895)											0.050459	-26.24538	20.477193	11	207	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77765686	77765686	18223	8	T	A	A	A	780	60	ZFHX4	3	3
DCAF4L2	138009	broad.mit.edu	37	8	88885169	88885169	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:88885169C>A	uc003ydz.2	-	c.1031G>T	c.(1030-1032)CGT>CTT	p.R344L		NM_152418	NP_689631	Q8NA75	DC4L2_HUMAN	WD repeat domain 21C	344	WD 2.									ovary(1)	1														0.166667	11.05995	14.216872	5	25	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	88885169	88885169	4443	8	C	A	A	A	247	19	DCAF4L2	1	1
DCX	1641	broad.mit.edu	37	X	110574146	110574147	+	Missense_Mutation	DNP	CC	AA	AA			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:110574146_110574147CC>AA	uc011msv.1	-	c.1174_1175GG>TT	c.(1174-1176)GGT>TTT	p.G392F	DCX_uc004epd.2_Splice_Site_DNP_p.A392_splice|DCX_uc004epe.2_Splice_Site_DNP_p.A311_splice|DCX_uc004epf.2_Missense_Mutation_p.G311F|DCX_uc004epg.2_Splice_Site_DNP_p.A311_splice	NM_178152	NP_835365	O43602	DCX_HUMAN	doublecortin isoform b	391	Pro/Ser-rich.				axon guidance|central nervous system development|intracellular signal transduction	cytosol|microtubule associated complex	microtubule binding			central_nervous_system(2)|lung(1)|skin(1)	4														0.103343	24.757894	76.221134	34	295	KEEP	---	---	---	---	capture		Missense_Mutation	DNP	110574146	110574147	4489	23	CC	AA	AA	AA	234	18	DCX	2	2
ODZ1	10178	broad.mit.edu	37	X	123680734	123680734	+	Missense_Mutation	SNP	A	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:123680734A>T	uc010nqy.2	-	c.2641T>A	c.(2641-2643)TTT>ATT	p.F881I	ODZ1_uc011muj.1_Missense_Mutation_p.F880I|ODZ1_uc004euj.2_Missense_Mutation_p.F881I	NM_001163278	NP_001156750	Q9UKZ4	TEN1_HUMAN	odz, odd Oz/ten-m homolog 1 isoform 1	881	Extracellular (Potential).				immune response|negative regulation of cell proliferation|nervous system development|signal transduction	extracellular region	heparin binding			ovary(11)|breast(4)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)	22										623				0.094737	5.100478	20.771608	9	86	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	123680734	123680734	11239	23	A	T	T	T	52	4	ODZ1	3	3
FAM47A	158724	broad.mit.edu	37	X	34149595	34149595	+	Silent	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:34149595C>T	uc004ddg.2	-	c.801G>A	c.(799-801)CTG>CTA	p.L267L		NM_203408	NP_981953	Q5JRC9	FA47A_HUMAN	hypothetical protein LOC158724	267										ovary(4)|central_nervous_system(1)	5														0.096774	2.035124	7.056633	3	28	KEEP	---	---	---	---	capture		Silent	SNP	34149595	34149595	5790	23	C	T	T	T	262	21	FAM47A	2	2
KIAA2022	340533	broad.mit.edu	37	X	73963452	73963452	+	Missense_Mutation	SNP	A	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:73963452A>G	uc004eby.2	-	c.940T>C	c.(940-942)TAT>CAT	p.Y314H		NM_001008537	NP_001008537	Q5QGS0	K2022_HUMAN	hypothetical protein LOC340533	314					base-excision repair, gap-filling|DNA replication proofreading|DNA replication, removal of RNA primer|nucleotide-excision repair, DNA gap filling|regulation of mitotic cell cycle|S phase of mitotic cell cycle	delta DNA polymerase complex	3'-5'-exodeoxyribonuclease activity|DNA-directed DNA polymerase activity			ovary(7)|large_intestine(4)|skin(2)|central_nervous_system(1)	14										126				0.048	-12.749381	14.412407	6	119	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	73963452	73963452	8580	23	A	G	G	G	208	16	KIAA2022	4	4
ATP7A	538	broad.mit.edu	37	X	77245190	77245190	+	Missense_Mutation	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:77245190C>T	uc004ecx.3	+	c.1072C>T	c.(1072-1074)CCC>TCC	p.P358S	ATP7A_uc004ecw.2_Missense_Mutation_p.P358S	NM_000052	NP_000043	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	358	Poly-Ser.|Cytoplasmic (Potential).				ATP biosynthetic process|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|T-helper cell differentiation|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity				0														0.091667	4.729955	24.889005	11	109	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	77245190	77245190	1209	23	C	T	T	T	390	30	ATP7A	2	2
PCDH11X	27328	broad.mit.edu	37	X	91134023	91134023	+	Silent	SNP	C	T	T			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:91134023C>T	uc004efk.1	+	c.2784C>T	c.(2782-2784)TTC>TTT	p.F928F	PCDH11X_uc004efl.1_Silent_p.F928F|PCDH11X_uc004efo.1_Silent_p.F928F|PCDH11X_uc010nmv.1_Silent_p.F928F|PCDH11X_uc004efm.1_Silent_p.F928F|PCDH11X_uc004efn.1_Silent_p.F928F|PCDH11X_uc004efh.1_Silent_p.F928F|PCDH11X_uc004efj.1_Silent_p.F928F	NM_032968	NP_116750	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked isoform c	928	Cytoplasmic (Potential).				homophilic cell adhesion	integral to plasma membrane	calcium ion binding			large_intestine(2)	2						NSCLC(38;925 1092 2571 38200 45895)								0.0625	-6.58229	9.374194	5	75	KEEP	---	---	---	---	capture		Silent	SNP	91134023	91134023	11928	23	C	T	T	T	376	29	PCDH11X	2	2
PCDH19	57526	broad.mit.edu	37	X	99663117	99663117	+	Missense_Mutation	SNP	C	A	A			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:99663117C>A	uc010nmz.2	-	c.479G>T	c.(478-480)AGC>ATC	p.S160I	PCDH19_uc004efw.3_Missense_Mutation_p.S160I|PCDH19_uc004efx.3_Missense_Mutation_p.S160I	NM_020766	NP_001098713	Q8TAB3	PCD19_HUMAN	protocadherin 19 isoform b	160	Cadherin 2.|Extracellular (Potential).				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)|breast(2)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	7														0.25	12.166595	13.302112	5	15	KEEP	---	---	---	---	capture		Missense_Mutation	SNP	99663117	99663117	11934	23	C	A	A	A	364	28	PCDH19	2	2
PYGO2	90780	broad.mit.edu	37	1	154932096	154932097	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:154932096_154932097insG	uc001fft.2	-	c.379_380insC	c.(379-381)CAGfs	p.Q127fs		NM_138300	NP_612157	Q9BRQ0	PYGO2_HUMAN	pygopus homolog 2	127	Pro-rich.				Wnt receptor signaling pathway	nucleus	protein binding|zinc ion binding				0	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			NSCLC(87;357 1460 1955 21029 23522)								0.50			3	3		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	154932096	154932097	13322	1	-	G	G	G	715	55	PYGO2	5	5
TJP2	9414	broad.mit.edu	37	9	71835952	71835953	+	Frame_Shift_Ins	INS	-	G	G			TCGA-17-Z009-01	TCGA-17-Z009-01										Phase_I	Unspecified				Illumina GAIIx	g.chr9:71835952_71835953insG	uc011lrv.1	+	c.558_559insG	c.(556-561)CATGGGfs	p.H186fs	TJP2_uc011lrs.1_Frame_Shift_Ins_p.H141fs|TJP2_uc004ahb.1_Frame_Shift_Ins_p.H141fs|TJP2_uc011lrt.1_Frame_Shift_Ins_p.H141fs|TJP2_uc004ahd.2_Frame_Shift_Ins_p.H164fs|TJP2_uc004ahe.2_Frame_Shift_Ins_p.H164fs|TJP2_uc004ahf.2_Frame_Shift_Ins_p.H164fs|TJP2_uc011lru.1_Frame_Shift_Ins_p.H168fs	NM_004817	NP_004808	Q9UDY2	ZO2_HUMAN	tight junction protein 2 (zona occludens 2)	164_165					cellular component disassembly involved in apoptosis	adherens junction|cytoplasm|nucleus|tight junction	guanylate kinase activity|protein binding				0														0.33			2	4		---	---	---	---	capture_indel		Frame_Shift_Ins	INS	71835952	71835953	16459	9	-	G	G	G	660	51	TJP2	5	5
