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
PIK3AP1	118788	broad.mit.edu	36	10	98395238	98395238	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:98395238C>G	uc001kmq.1	-	c.1357G>C	c.(1357-1359)GCT>CCT	p.A453P	PIK3AP1_uc001kmp.1_Missense_Mutation_p.A275P	NM_152309	NP_689522	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	453						cytoplasm|plasma membrane				ovary(1)	1		Colorectal(252;0.0442)												0.263158	6.831915	7.827102	5	14	CC		KEEP	---	---	---	---	capture		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)	Missense_Mutation	SNP	98395238	98395238	12332	10	C	G	G	28	28	PIK3AP1	G	3	3
TMPRSS4	56649	broad.mit.edu	36	11	117491091	117491091	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:117491091G>A	uc009yzt.1	+	c.1038G>A	c.(1036-1038)GCG>GCA	p.A346A	TMPRSS4_uc001psd.2_Silent_p.A341A|TMPRSS4_uc009yzu.1_Intron|TMPRSS4_uc009yzv.1_Silent_p.A321A	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4 isoform 1	346	Extracellular (Potential).|Peptidase S1.				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			large_intestine(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)												0.275862	19.687679	20.999425	8	21	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)	Silent	SNP	117491091	117491091	16790	11	G	A	A	40	40	TMPRSS4	A	1	1
TECTA	7007	broad.mit.edu	36	11	120504083	120504083	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:120504083C>T	uc001pxr.1	+	c.2187C>T	c.(2185-2187)TAC>TAT	p.Y729Y		NM_005422	NP_005413	O75443	TECTA_HUMAN	tectorin alpha precursor	729	VWFD 2.				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix				breast(6)|ovary(2)	8	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)												0.226087	117.881149	133.729238	52	178	CC		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)	Silent	SNP	120504083	120504083	16274	11	C	T	T	19	19	TECTA	T	1	1
OR52D1	390066	broad.mit.edu	36	11	5466798	5466798	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0789-01	TCGA-14-0789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr11:5466798T>A	uc001max.1	+	c.286T>A	c.(286-288)TCC>ACC	p.S96T	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	NM_001005163	NP_001005163	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D,	96	Extracellular (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			central_nervous_system(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)												0.278947	121.786711	130.143555	53	137	TT		KEEP	---	---	---	---	capture		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	Missense_Mutation	SNP	5466798	5466798	11524	11	T	A	A	62	62	OR52D1	A	4	4
SRRM4	84530	broad.mit.edu	36	12	118052871	118052871	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:118052871G>A	uc001txa.1	+	c.620G>A	c.(619-621)CGC>CAC	p.R207H		NM_194286	NP_919262	A7MD48	SRRM4_HUMAN	KIAA1853 protein	207	Ser-rich.				cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding	p.R207H(1)		ovary(2)	2														0.403846	59.076328	59.492654	21	31	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	118052871	118052871	15685	12	G	A	A	38	38	SRRM4	A	1	1
C12orf77	196415	broad.mit.edu	36	12	25040188	25040188	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:25040188C>T	uc001rgf.1	-	c.227G>A	c.(226-228)CGA>CAA	p.R76Q	C12orf77_uc009zjb.1_Missense_Mutation_p.R21Q	NM_001101339	NP_001094809	C9JDV5	CL097_HUMAN	hypothetical protein LOC196415	76											0														0.290698	65.544888	68.917678	25	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25040188	25040188	1763	12	C	T	T	31	31	C12orf77	T	1	1
ACVRL1	94	broad.mit.edu	36	12	50596190	50596190	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:50596190G>A	uc001rzj.1	+	c.1152G>A	c.(1150-1152)CAG>CAA	p.Q384Q	ACVRL1_uc001rzk.1_Silent_p.Q384Q	NM_000020	NP_001070869	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	384	Cytoplasmic (Potential).|Protein kinase.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|protein phosphorylation|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells	cell surface|integral to plasma membrane	activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity			lung(2)	2					Adenosine triphosphate(DB00171)					321				0.269006	115.066266	123.306502	46	125	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(357;0.0991)	Silent	SNP	50596190	50596190	226	12	G	A	A	33	33	ACVRL1	A	2	2
ESPL1	9700	broad.mit.edu	36	12	51973462	51973462	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr12:51973462C>T	uc001sck.2	+	c.6300C>T	c.(6298-6300)CCC>CCT	p.P2100P	ESPL1_uc001scj.2_Silent_p.P1775P|PFDN5_uc001scl.1_5'Flank|PFDN5_uc001scm.1_5'Flank|PFDN5_uc001scn.1_5'Flank|PFDN5_uc001sco.1_5'Flank	NM_012291	NP_036423	Q14674	ESPL1_HUMAN	extra spindle poles like 1	2100					apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding			lung(1)|kidney(1)	2						Colon(53;1069 1201 2587 5382)								0.204082	43.941871	51.909964	20	78	CC		KEEP	---	---	---	---	capture			Silent	SNP	51973462	51973462	5446	12	C	T	T	22	22	ESPL1	T	2	2
KCNC2	3747	broad.mit.edu	36	12	73887825	73887825	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr12:73887825G>A	uc001sxg.1	-	c.206C>T	c.(205-207)CCG>CTG	p.P69L	KCNC2_uc009zry.1_Missense_Mutation_p.P69L|KCNC2_uc001sxe.1_Missense_Mutation_p.P69L|KCNC2_uc001sxf.1_Missense_Mutation_p.P69L	NM_139137	NP_631875	Q96PR1	KCNC2_HUMAN	Shaw-related voltage-gated potassium channel	69	Gly/Pro-rich (insert).|Cytoplasmic (Potential).				energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	voltage-gated potassium channel activity			breast(2)|pancreas(2)|skin(1)|lung(1)	6														0.228571	17.784271	20.148212	8	27	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73887825	73887825	8320	12	G	A	A	39	39	KCNC2	A	1	1
PAN3	255967	broad.mit.edu	36	13	27692510	27692510	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:27692510C>T	uc001urz.1	+	c.557C>T	c.(556-558)GCG>GTG	p.A186V	PAN3_uc001urx.1_Missense_Mutation_p.A132V|PAN3_uc001ury.1_5'UTR	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	PABP1-dependent poly A-specific ribonuclease	186	Interaction with polyadenylate-binding protein.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening|protein phosphorylation	centrosome|cytosol	ATP binding|protein kinase activity			ovary(1)	1	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)												0.280654	275.090086	290.94923	103	264	CC		KEEP	---	---	---	---	capture	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)	Missense_Mutation	SNP	27692510	27692510	11832	13	C	T	T	27	27	PAN3	T	1	1
AKT1	207	broad.mit.edu	36	14	104312321	104312321	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr14:104312321G>A	uc001ypk.1	-	c.632C>T	c.(631-633)ACA>ATA	p.T211I	AKT1_uc001ypl.1_Missense_Mutation_p.T211I|AKT1_uc010axa.1_Missense_Mutation_p.T211I|AKT1_uc001ypm.1_Missense_Mutation_p.T211I|AKT1_uc001ypn.1_Missense_Mutation_p.T211I	NM_005163	NP_005154	P31749	AKT1_HUMAN	AKT1 kinase	211	Protein kinase.				activation of pro-apoptotic gene products|activation-induced cell death of T cells|endocrine pancreas development|G-protein coupled receptor protein signaling pathway|glucose metabolic process|glycogen biosynthetic process|induction of apoptosis by intracellular signals|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|mRNA metabolic process|negative regulation of fatty acid beta-oxidation|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|nitric oxide biosynthetic process|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of blood vessel endothelial cell migration|positive regulation of cell growth|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of establishment of protein localization in plasma membrane|positive regulation of fat cell differentiation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|positive regulation of nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein autophosphorylation|protein import into nucleus, translocation|regulation of neuron projection development|regulation of translation|response to fluid shear stress|response to heat|response to UV-A|T cell costimulation	cytosol|nucleoplasm|plasma membrane	ATP binding|enzyme binding|identical protein binding|nitric-oxide synthase regulator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein serine/threonine kinase activity			breast(77)|urinary_tract(12)|thyroid(10)|lung(7)|endometrium(5)|large_intestine(4)|skin(4)|prostate(3)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|NS(1)	125		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)			Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)			1		998				0.258065	74.83804	81.41975	32	92	GG		KEEP	---	---	---	---	capture	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Missense_Mutation	SNP	104312321	104312321	481	14	G	A	A	48	48	AKT1	A	2	2
NAA30	122830	broad.mit.edu	36	14	56927987	56927987	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:56927987C>G	uc001xcx.2	+	c.559C>G	c.(559-561)CTG>GTG	p.L187V	NAA30_uc010aow.1_Intron	NM_001011713	NP_001011713	Q147X3	NAA30_HUMAN	N-acetyltransferase 12	187						cytoplasm	peptide alpha-N-acetyltransferase activity				0														0.204545	10.647927	14.361991	9	35	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	56927987	56927987	10517	14	C	G	G	28	28	NAA30	G	3	3
TRIP11	9321	broad.mit.edu	36	14	91540434	91540434	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:91540434C>T	uc001xzy.2	-	c.3639G>A	c.(3637-3639)AAG>AAA	p.K1213K	TRIP11_uc010auf.1_Silent_p.K949K	NM_004239	NP_004230	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1213	Potential.				transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity	p.K1213N(1)		ovary(6)|kidney(2)|central_nervous_system(1)|breast(1)|skin(1)	11						Ovarian(84;609 1888 9852 42686)			p.K949N(HCC38-Tumor)	1481				0.236111	82.976637	92.14486	34	110	CC		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(157;0.223)	Silent	SNP	91540434	91540434	17105	14	C	T	T	20	20	TRIP11	T	2	2
PRIMA1	145270	broad.mit.edu	36	14	93273404	93273404	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:93273404C>T	uc001ybw.1	-	c.295G>A	c.(295-297)GTA>ATA	p.V99I	PRIMA1_uc001ybx.1_Non-coding_Transcript	NM_178013	NP_821092	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1 precursor	99	Helical; (Potential).				neurotransmitter catabolic process	cell junction|integral to membrane|synapse				large_intestine(1)	1		all_cancers(154;0.127)												0.227273	44.956226	50.963424	20	68	CC		KEEP	---	---	---	---	capture		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)	Missense_Mutation	SNP	93273404	93273404	12935	14	C	T	T	19	19	PRIMA1	T	1	1
GABRB3	2562	broad.mit.edu	36	15	24344255	24344255	+	Silent	SNP	G	T	T			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:24344255G>T	uc001zbb.1	-	c.1368C>A	c.(1366-1368)ATC>ATA	p.I456I	GABRB3_uc001zaz.1_Silent_p.I400I|GABRB3_uc001zba.1_Silent_p.I400I	NM_021912	NP_068712	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta	400	Cytoplasmic (Probable).				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity			ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	4		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)			Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)									0.256881	131.986152	143.612794	56	162	GG		KEEP	---	---	---	---	capture		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Silent	SNP	24344255	24344255	6419	15	G	T	T	41	41	GABRB3	T	3	3
OTUD7A	161725	broad.mit.edu	36	15	29564044	29564044	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:29564044C>T	uc001zfr.1	-	c.1547G>A	c.(1546-1548)CGC>CAC	p.R516H	OTUD7A_uc001zfq.1_Missense_Mutation_p.R509H	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN	OTU domain containing 7A	509	Nuclear localization signal (Potential).					cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding			pancreas(1)	1		all_lung(180;1.6e-09)												0.343284	62.83475	64.274095	23	44	CC		KEEP	---	---	---	---	capture		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)	Missense_Mutation	SNP	29564044	29564044	11731	15	C	T	T	27	27	OTUD7A	T	1	1
RYR3	6263	broad.mit.edu	36	15	31552966	31552966	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0789-01	TCGA-14-0789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr15:31552966T>A	uc001zhi.1	+	c.106T>A	c.(106-108)TTC>ATC	p.F36I	RYR3_uc010bar.1_Missense_Mutation_p.F36I	NM_001036	NP_001027	Q15413	RYR3_HUMAN	ryanodine receptor 3	36	Cytoplasmic (By similarity).				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(5)|central_nervous_system(4)|lung(1)	10		all_lung(180;7.18e-09)												0.245	105.601711	117.439612	49	151	TT		KEEP	---	---	---	---	capture		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	Missense_Mutation	SNP	31552966	31552966	14250	15	T	A	A	60	60	RYR3	A	4	4
CKMT1A	548596	broad.mit.edu	36	15	41778517	41778517	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:41778517C>T	uc001zsn.1	+	c.1192C>T	c.(1192-1194)CGG>TGG	p.R398W	CKMT1A_uc001zso.2_Missense_Mutation_p.R398W	NM_001015001	NP_066270	P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1A precursor	398	Phosphagen kinase C-terminal.				creatine metabolic process	mitochondrial inner membrane	ATP binding|creatine kinase activity				0		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)			Creatine(DB00148)									0.284585	188.407265	198.939632	72	181	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(94;3.56e-07)	Missense_Mutation	SNP	41778517	41778517	3585	15	C	T	T	19	19	CKMT1A	T	1	1
DUOX2	50506	broad.mit.edu	36	15	43173690	43173690	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:43173690C>T	uc010bea.1	-	c.4597G>A	c.(4597-4599)GTC>ATC	p.V1533I	DUOX2_uc001zun.1_Missense_Mutation_p.V1533I	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN	dual oxidase 2 precursor	1533	Cytoplasmic (Potential).				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|oxidation-reduction process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity			ovary(2)|pancreas(1)	3		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)												0.245283	62.411906	68.666649	26	80	CC		KEEP	---	---	---	---	capture		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)	Missense_Mutation	SNP	43173690	43173690	4986	15	C	T	T	19	19	DUOX2	T	1	1
COMMD4	54939	broad.mit.edu	36	15	73417770	73417770	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr15:73417770C>G	uc002azy.1	+	c.97C>G	c.(97-99)CTC>GTC	p.L33V	COMMD4_uc002azz.1_Missense_Mutation_p.L33V|COMMD4_uc002baa.1_Missense_Mutation_p.L33V	NM_017828	NP_060298	Q9H0A8	COMD4_HUMAN	COMM domain containing 4	33						cytoplasm	protein binding				0														0.555556	10.949094	10.9705	5	4	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	73417770	73417770	3856	15	C	G	G	28	28	COMMD4	G	3	3
CACNA1H	8912	broad.mit.edu	36	16	1202095	1202095	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1202095G>A	uc002cks.1	+	c.4715G>A	c.(4714-4716)CGG>CAG	p.R1572Q	CACNA1H_uc002ckt.1_Missense_Mutation_p.R1572Q|CACNA1H_uc002cku.1_Missense_Mutation_p.R278Q|CACNA1H_uc010brj.1_Missense_Mutation_p.R278Q|CACNA1H_uc002ckv.1_Missense_Mutation_p.R278Q	NM_021098	NP_066921	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type,	1572	Cytoplasmic (Potential).				axon guidance|muscle contraction|muscle organ development|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity			breast(2)	2		Hepatocellular(780;0.00369)			Flunarizine(DB04841)|Mibefradil(DB01388)									0.317757	93.310148	96.470412	34	73	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1202095	1202095	2661	16	G	A	A	39	39	CACNA1H	A	1	1
ZP2	7783	broad.mit.edu	36	16	21120967	21120967	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr16:21120967G>A	uc010bwn.1	-	c.1363C>T	c.(1363-1365)CGG>TGG	p.R455W	ZP2_uc002dii.2_Missense_Mutation_p.R416W	NM_003460	NP_003451	Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 preproprotein	416	Extracellular (Potential).|ZP.				binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity			ovary(1)|central_nervous_system(1)	2														0.242991	59.699134	66.143881	26	81	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(48;0.0573)	Missense_Mutation	SNP	21120967	21120967	18820	16	G	A	A	40	40	ZP2	A	1	1
CCDC144A	9720	broad.mit.edu	36	17	16606478	16606478	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:16606478C>A	uc002gqk.1	+	c.3793C>A	c.(3793-3795)CAA>AAA	p.Q1265K	LOC162632_uc010cpj.1_Non-coding_Transcript|CCDC144A_uc002gql.1_Missense_Mutation_p.Q781K	NM_014695	NP_055510	A2RUR9	C144A_HUMAN	coiled-coil domain containing 144A	1265	Potential.										0														0.5	8.324088	8.324088	3	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	16606478	16606478	2897	17	C	A	A	25	25	CCDC144A	A	3	3
SRR	63826	broad.mit.edu	36	17	2173770	2173770	+	Silent	SNP	T	G	G			TCGA-14-0789-01	TCGA-14-0789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:2173770T>G	uc002fue.1	+	c.876T>G	c.(874-876)GCT>GCG	p.A292A	SRR_uc002fui.1_Silent_p.A143A|TSR1_uc002fuj.1_3'UTR	NM_021947	NP_068766	Q9GZT4	SRR_HUMAN	serine racemase	292					D-serine biosynthetic process|L-serine metabolic process|protein homotetramerization|pyruvate biosynthetic process|response to lipopolysaccharide	cytoplasm|neuronal cell body|soluble fraction	ATP binding|calcium ion binding|D-serine ammonia-lyase activity|glycine binding|L-serine ammonia-lyase activity|magnesium ion binding|PDZ domain binding|protein homodimerization activity|pyridoxal phosphate binding|serine racemase activity|threonine racemase activity				0		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)			L-Serine(DB00133)|Pyridoxal Phosphate(DB00114)									0.157143	6.841689	14.973516	11	59	TT		KEEP	---	---	---	---	capture		COAD - Colon adenocarcinoma(228;3.24e-06)|READ - Rectum adenocarcinoma(1115;0.0649)	Silent	SNP	2173770	2173770	15680	17	T	G	G	55	55	SRR	G	4	4
NF1	4763	broad.mit.edu	36	17	26580607	26580607	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr17:26580607C>T	uc002hgg.1	+	c.2848C>T	c.(2848-2850)CAG>TAG	p.Q950*	NF1_uc002hgh.1_Nonsense_Mutation_p.Q950*|NF1_uc002hgi.1_5'UTR|NF1_uc010csn.1_Nonsense_Mutation_p.Q810*	NM_001042492	NP_001035957	P21359	NF1_HUMAN	neurofibromin isoform 1	950					actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.?(3)		soft_tissue(155)|central_nervous_system(56)|large_intestine(27)|lung(19)|haematopoietic_and_lymphoid_tissue(13)|ovary(12)|autonomic_ganglia(7)|skin(3)|stomach(2)|breast(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	300		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)								847	TCGA GBM(6;<1E-8)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			0.264865	117.881673	127.134142	49	136	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	Nonsense_Mutation	SNP	26580607	26580607	10756	17	C	T	T	17	17	NF1	T	5	2
MARCH10	162333	broad.mit.edu	36	17	58219644	58219644	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:58219644G>A	uc010dds.1	-	c.139C>T	c.(139-141)CGC>TGC	p.R47C	MARCH10_uc010ddr.1_Missense_Mutation_p.R47C|MARCH10_uc002jag.2_Missense_Mutation_p.R47C|MARCH10_uc002jah.2_Missense_Mutation_p.R47C	NM_152598	NP_689811	Q8NA82	MARHA_HUMAN	ring finger protein 190	47							ligase activity|zinc ion binding				0														0.277778	114.101915	121.242559	45	117	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	58219644	58219644	9682	17	G	A	A	40	40	MARCH10	A	1	1
GALK1	2584	broad.mit.edu	36	17	71265788	71265788	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0789-01	TCGA-14-0789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr17:71265788T>C	uc002jpk.1	-	c.1123A>G	c.(1123-1125)ACT>GCT	p.T375A		NM_000154	NP_000145	P51570	GALK1_HUMAN	galactokinase 1	375					galactose catabolic process	cytosol	ATP binding|galactokinase activity|galactose binding				0	all_cancers(13;1.5e-07)													0.285714	6.472895	7.065977	4	10	TT		KEEP	---	---	---	---	capture	all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		Missense_Mutation	SNP	71265788	71265788	6467	17	T	C	C	58	58	GALK1	C	4	4
ZNF532	55205	broad.mit.edu	36	18	54738734	54738734	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:54738734C>T	uc002lho.1	+	c.2235C>T	c.(2233-2235)GAC>GAT	p.D745D	ZNF532_uc002lhp.1_Silent_p.D743D|ZNF532_uc002lhq.1_Silent_p.D745D|ZNF532_uc002lhr.1_Silent_p.D743D|ZNF532_uc002lhs.1_Silent_p.D743D	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	745					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(1)	1														0.240964	46.160305	51.241098	20	63	CC		KEEP	---	---	---	---	capture			Silent	SNP	54738734	54738734	18566	18	C	T	T	18	18	ZNF532	T	2	2
ZNF516	9658	broad.mit.edu	36	18	72283324	72283324	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr18:72283324G>A	uc010dqx.1	-	c.675C>T	c.(673-675)ACC>ACT	p.T225T	ZNF516_uc002lme.2_Non-coding_Transcript	NM_014643	NP_055458	Q92618	ZN516_HUMAN	zinc finger protein 516	225					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1		Prostate(75;0.0869)|Esophageal squamous(42;0.129)												0.242857	38.737904	42.96193	17	53	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)	Silent	SNP	72283324	72283324	18554	18	G	A	A	39	39	ZNF516	A	1	1
LDLR	3949	broad.mit.edu	36	19	11085366	11085366	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:11085366G>C	uc002mqk.2	+	c.1514G>C	c.(1513-1515)GGC>GCC	p.G505A		NM_000527	NP_000518	P01130	LDLR_HUMAN	low density lipoprotein receptor precursor	505	Extracellular (Potential).|LDL-receptor class B 3.				cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity			ovary(2)	2		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)			Methyl aminolevulinate(DB00992)|Porfimer(DB00707)	GBM(18;201 575 7820 21545)				1109				0.170455	64.780921	82.831031	30	146	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Missense_Mutation	SNP	11085366	11085366	9028	19	G	C	C	42	42	LDLR	C	3	3
LPHN1	22859	broad.mit.edu	36	19	14135115	14135115	+	Silent	SNP	A	C	C			TCGA-14-0789-01	TCGA-14-0789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14135115A>C	uc002myg.1	-	c.513T>G	c.(511-513)GGT>GGG	p.G171G	LPHN1_uc002myh.1_Silent_p.G166G	NM_001008701	NP_001008701	O94910	LPHN1_HUMAN	latrophilin 1 isoform 1 precursor	171	Olfactomedin-like.|Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding			ovary(1)|central_nervous_system(1)	2														0.222222	8.182224	13.201119	14	49	AA		KEEP	---	---	---	---	capture			Silent	SNP	14135115	14135115	9288	19	A	C	C	6	6	LPHN1	C	4	4
GIPC1	10755	broad.mit.edu	36	19	14452540	14452540	+	Silent	SNP	C	G	G			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:14452540C>G	uc002myt.1	-	c.339G>C	c.(337-339)CTG>CTC	p.L113L	GIPC1_uc002myu.1_Silent_p.L113L|GIPC1_uc002myv.1_Silent_p.L16L|GIPC1_uc002myw.1_Silent_p.L16L|GIPC1_uc002myx.1_Silent_p.L113L|GIPC1_uc002myy.1_Silent_p.L16L	NM_005716	NP_974223	O14908	GIPC1_HUMAN	regulator of G-protein signalling 19 interacting	113					endothelial cell migration|G-protein coupled receptor protein signaling pathway|glutamate secretion|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|protein targeting|regulation of protein stability|regulation of synaptic plasticity|synaptic transmission	cell cortex|dendritic shaft|dendritic spine|membrane fraction|soluble fraction|synaptic vesicle|vesicle membrane	actin binding|myosin binding|protein homodimerization activity|receptor binding				0						Pancreas(33;78 923 2910 41023 52850)						OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.169435	103.964353	135.074552	51	250	CC		KEEP	---	---	---	---	capture			Silent	SNP	14452540	14452540	6660	19	C	G	G	21	21	GIPC1	G	3	3
TSKS	60385	broad.mit.edu	36	19	54934971	54934971	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54934971G>A	uc002ppm.1	-	c.1653C>T	c.(1651-1653)CAC>CAT	p.H551H		NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN	testis-specific kinase substrate	551							protein binding			large_intestine(1)	1		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)												0.190661	97.009029	120.02849	49	208	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)	Silent	SNP	54934971	54934971	17177	19	G	A	A	36	36	TSKS	A	2	2
CLEC11A	6320	broad.mit.edu	36	19	55920287	55920287	+	Silent	SNP	C	G	G			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:55920287C>G	uc002psy.1	+	c.723C>G	c.(721-723)GGC>GGG	p.G241G		NM_002975	NP_002966	Q9Y240	CLC11_HUMAN	stem cell growth factor precursor	241	C-type lectin.				positive regulation of cell proliferation	cytoplasm|extracellular region	growth factor activity|sugar binding			ovary(1)	1		all_neural(266;0.057)												0.291667	7.236589	8.235745	7	17	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)	Silent	SNP	55920287	55920287	3633	19	C	G	G	27	27	CLEC11A	G	3	3
ACTL9	284382	broad.mit.edu	36	19	8668821	8668821	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:8668821C>T	uc002mkl.1	-	c.1231G>A	c.(1231-1233)GTG>ATG	p.V411M		NM_178525	NP_848620	Q8TC94	ACTL9_HUMAN	hypothetical protein LOC284382	411						cytoplasm|cytoskeleton				large_intestine(2)|pancreas(1)	3														0.178082	103.431204	131.916498	52	240	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	8668821	8668821	204	19	C	T	T	19	19	ACTL9	T	1	1
GPSM2	29899	broad.mit.edu	36	1	109273985	109273985	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:109273985G>C	uc001dwd.2	+	c.1934G>C	c.(1933-1935)AGA>ACA	p.R645T	CLCC1_uc001dwe.1_3'UTR|CLCC1_uc001dwg.1_3'UTR|CLCC1_uc001dwf.1_3'UTR	NM_013296	NP_037428	P81274	GPSM2_HUMAN	LGN protein	652					G-protein coupled receptor protein signaling pathway	cell cortex|nucleus	GTPase activator activity|identical protein binding			central_nervous_system(1)	1		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)												0.234899	100.048085	109.625921	35	114	GG		KEEP	---	---	---	---	capture		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)	Missense_Mutation	SNP	109273985	109273985	7011	1	G	C	C	33	33	GPSM2	C	3	3
ZNF697	90874	broad.mit.edu	36	1	119967000	119967000	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:119967000C>T	uc001ehy.1	-	c.1489G>A	c.(1489-1491)GAG>AAG	p.E497K		NM_001080470	NP_001073939	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	497	C2H2-type 10.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)												0.269231	18.513839	19.76307	7	19	CC		KEEP	---	---	---	---	capture		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)	Missense_Mutation	SNP	119967000	119967000	18695	1	C	T	T	31	31	ZNF697	T	1	1
LINGO4	339398	broad.mit.edu	36	1	150041019	150041019	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150041019G>A	uc001ezf.1	-	c.786C>T	c.(784-786)TGC>TGT	p.C262C	LINGO4_uc009wnc.1_Silent_p.C262C	NM_001004432	NP_001004432	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	262	Extracellular (Potential).|LRR 8.					integral to membrane				large_intestine(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)													0.260417	112.316783	122.334699	50	142	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.181)		Silent	SNP	150041019	150041019	9144	1	G	A	A	46	46	LINGO4	A	2	2
FLG2	388698	broad.mit.edu	36	1	150595720	150595720	+	Missense_Mutation	SNP	T	G	G			TCGA-14-0789-01	TCGA-14-0789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150595720T>G	uc001ezw.2	-	c.1166A>C	c.(1165-1167)CAG>CCG	p.Q389P		NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	filaggrin family member 2	389	Ser-rich.						calcium ion binding|structural molecule activity			ovary(9)|breast(1)	10	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)													0.258883	132.135708	142.509898	51	146	TT		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150595720	150595720	6161	1	T	G	G	55	55	FLG2	G	4	4
CRNN	49860	broad.mit.edu	36	1	150649805	150649805	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150649805G>A	uc001ezx.1	-	c.377C>T	c.(376-378)GCG>GTG	p.A126V		NM_016190	NP_057274	Q9UBG3	CRNN_HUMAN	cornulin	126					cell-cell adhesion|response to heat	cytoplasm|membrane	calcium ion binding			ovary(2)	2	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)													0.256198	338.011675	370.401825	155	450	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.206)		Missense_Mutation	SNP	150649805	150649805	4031	1	G	A	A	38	38	CRNN	A	1	1
S100A7A	338324	broad.mit.edu	36	1	151657284	151657284	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:151657284G>A	uc001fbt.1	+	c.102G>A	c.(100-102)ACG>ACA	p.T34T		NM_176823	NP_789793	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7-like 1	34	EF-hand 1.					cytoplasm	calcium ion binding			skin(1)	1	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)													0.215548	136.310855	157.454651	61	222	GG		KEEP	---	---	---	---	capture	LUSC - Lung squamous cell carcinoma(543;0.171)		Silent	SNP	151657284	151657284	14264	1	G	A	A	37	37	S100A7A	A	1	1
MRTO4	51154	broad.mit.edu	36	1	19457049	19457049	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:19457049C>T	uc001bbs.1	+	c.477C>T	c.(475-477)CCC>CCT	p.P159P		NM_016183	NP_057267	Q9UKD2	MRT4_HUMAN	ribosomal protein P0-like protein	159					ribosome biogenesis	nuclear membrane|nucleolus					0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)				GBM(192;2418 3032 7540 48714)								0.234043	70.532067	79.641304	33	108	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Silent	SNP	19457049	19457049	10245	1	C	T	T	21	21	MRTO4	T	2	2
HHIPL2	79802	broad.mit.edu	36	1	220780116	220780116	+	Nonsense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:220780116G>A	uc001hnh.1	-	c.1309C>T	c.(1309-1311)CGA>TGA	p.R437*		NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	437					carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding			ovary(1)	1														0.28934	156.065401	163.860297	57	140	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(131;0.0185)	Nonsense_Mutation	SNP	220780116	220780116	7378	1	G	A	A	39	39	HHIPL2	A	5	1
MAP7D1	55700	broad.mit.edu	36	1	36410676	36410676	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0789-01	TCGA-14-0789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36410676A>G	uc001bzz.1	+	c.485A>G	c.(484-486)GAG>GGG	p.E162G	MAP7D1_uc001caa.1_Missense_Mutation_p.E162G|MAP7D1_uc001cab.1_Missense_Mutation_p.E162G|MAP7D1_uc001cac.1_5'UTR	NM_018067	NP_060537	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	162	Potential.					cytoplasm|spindle				ovary(3)|breast(2)	5		Myeloproliferative disorder(586;0.0393)												0.24	9.050279	10.588017	6	19	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	36410676	36410676	9650	1	A	G	G	11	11	MAP7D1	G	4	4
LRRC47	57470	broad.mit.edu	36	1	3690484	3690484	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3690484G>C	uc001akx.1	-	c.1246C>G	c.(1246-1248)CTG>GTG	p.L416V		NM_020710	NP_065761	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	416	Potential.				translation		phenylalanine-tRNA ligase activity|RNA binding			large_intestine(1)|ovary(1)	2	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)												0.285714	6.974135	7.566132	4	10	GG		KEEP	---	---	---	---	capture		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)	Missense_Mutation	SNP	3690484	3690484	9379	1	G	C	C	34	34	LRRC47	C	3	3
HPCAL4	51440	broad.mit.edu	36	1	39922381	39922381	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:39922381C>T	uc001cdr.1	-	c.193G>A	c.(193-195)GCG>ACG	p.A65T		NM_016257	NP_057341	Q9UM19	HPCL4_HUMAN	hippocalcin-like protein 4	65	EF-hand 2.				central nervous system development	intracellular	calcium ion binding			central_nervous_system(1)	1	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)												0.36	76.207448	77.500168	27	48	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		Missense_Mutation	SNP	39922381	39922381	7623	1	C	T	T	27	27	HPCAL4	T	1	1
CHD5	26038	broad.mit.edu	36	1	6111620	6111620	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:6111620C>A	uc001amb.1	-	c.3484G>T	c.(3484-3486)GCC>TCC	p.A1162S	CHD5_uc001alz.1_Missense_Mutation_p.A19S|CHD5_uc001ama.1_Non-coding_Transcript|CHD5_uc001amc.1_Non-coding_Transcript|CHD5_uc009vlx.1_Non-coding_Transcript	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN	chromodomain helicase DNA binding protein 5	1162	Helicase C-terminal.				chromatin assembly or disassembly|chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromatin|nucleus	ATP binding|ATP-dependent helicase activity|chromatin binding|DNA binding|zinc ion binding			breast(3)|central_nervous_system(3)|ovary(1)|lung(1)|pancreas(1)	9	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)								2304				0.280374	72.701099	77.344599	30	77	CC		KEEP	---	---	---	---	capture		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)	Missense_Mutation	SNP	6111620	6111620	3462	1	C	A	A	26	26	CHD5	A	3	3
PTPRA	5786	broad.mit.edu	36	20	2917091	2917091	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr20:2917091G>A	uc002whj.1	+	c.709G>A	c.(709-711)GAC>AAC	p.D237N	PTPRA_uc002whk.1_Missense_Mutation_p.D228N|PTPRA_uc002whl.1_Missense_Mutation_p.D228N|PTPRA_uc002whm.1_Missense_Mutation_p.D4N|PTPRA_uc002whn.1_Missense_Mutation_p.D228N|PTPRA_uc002who.1_5'UTR	NM_002836	NP_002827	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	237	Cytoplasmic (Potential).				axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity				0														0.255474	84.244132	91.690186	35	102	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	2917091	2917091	13252	20	G	A	A	37	37	PTPRA	A	1	1
RBPJL	11317	broad.mit.edu	36	20	43370228	43370228	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:43370228C>A	uc002xns.1	+	c.54C>A	c.(52-54)CAC>CAA	p.H18Q	MATN4_uc002xnn.1_5'Flank|MATN4_uc002xno.1_5'Flank|MATN4_uc002xnp.1_5'Flank|MATN4_uc002xnq.1_Intron|MATN4_uc002xnr.1_Splice_Site_SNP|RBPJL_uc002xnt.1_Missense_Mutation_p.H18Q	NM_014276	NP_055091	Q9UBG7	RBPJL_HUMAN	recombining binding protein L	18					regulation of transcription, DNA-dependent|signal transduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)												0.237179	85.652324	95.464761	37	119	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	43370228	43370228	13631	20	C	A	A	18	18	RBPJL	A	3	3
NCOA5	57727	broad.mit.edu	36	20	44132371	44132371	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:44132371C>T	uc002xrd.1	-	c.250G>A	c.(250-252)GTG>ATG	p.V84M	NCOA5_uc002xrc.1_De_novo_Start_InFrame|NCOA5_uc002xre.1_Missense_Mutation_p.V84M	NM_020967	NP_066018	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	84	Arg/Asp-rich (mixed charge).|Transcription repression.				regulation of transcription, DNA-dependent|transcription, DNA-dependent|translation	nucleus	aminoacyl-tRNA ligase activity|ATP binding			central_nervous_system(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)												0.292237	162.810121	171.277415	64	155	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44132371	44132371	10631	20	C	T	T	19	19	NCOA5	T	1	1
SIM2	6493	broad.mit.edu	36	21	37035984	37035984	+	Missense_Mutation	SNP	A	C	C			TCGA-14-0789-01	TCGA-14-0789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr21:37035984A>C	uc002yvr.1	+	c.947A>C	c.(946-948)AAC>ACC	p.N316T	SIM2_uc002yvq.1_Missense_Mutation_p.N316T	NM_005069	NP_005060	Q14190	SIM2_HUMAN	single-minded homolog 2 long isoform	316	PAC.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1														0.461538	7.228084	7.264527	6	7	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37035984	37035984	14819	21	A	C	C	2	2	SIM2	C	4	4
LRP1B	53353	broad.mit.edu	36	2	140798000	140798000	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0789-01	TCGA-14-0789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr2:140798000T>C	uc002tvj.1	-	c.12446A>G	c.(12445-12447)GAG>GGG	p.E4149G		NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN	low density lipoprotein-related protein 1B	4149	Extracellular (Potential).				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)				Colon(99;50 2074 2507 20106)				2546	TSP Lung(27;0.18)			0.2875	70.592729	73.832102	23	57	TT		KEEP	---	---	---	---	capture		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)	Missense_Mutation	SNP	140798000	140798000	9328	2	T	C	C	54	54	LRP1B	C	4	4
SGOL2	151246	broad.mit.edu	36	2	201146219	201146219	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:201146219G>A	uc002uvw.1	+	c.2905G>A	c.(2905-2907)GAA>AAA	p.E969K		NM_152524	NP_689737	Q562F6	SGOL2_HUMAN	shugoshin-like 2	969					cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding			ovary(2)	2														0.262295	38.7682	41.889412	16	45	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	201146219	201146219	14708	2	G	A	A	45	45	SGOL2	A	2	2
SP140	11262	broad.mit.edu	36	2	230818018	230818018	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0789-01	TCGA-14-0789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:230818018A>T	uc002vql.1	+	c.643A>T	c.(643-645)AGC>TGC	p.S215C	SP140_uc002vqk.1_Missense_Mutation_p.S215C|SP140_uc002vqm.1_Missense_Mutation_p.S215C|SP140_uc010fxl.1_Missense_Mutation_p.S215C|SP140_uc002vqn.1_Missense_Mutation_p.S215C	NM_007237	NP_009168	Q13342	LY10_HUMAN	SP140 nuclear body protein isoform 1	215					defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)								802				0.219048	52.461545	60.106534	23	82	AA		KEEP	---	---	---	---	capture		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)	Missense_Mutation	SNP	230818018	230818018	15462	2	A	T	T	7	7	SP140	T	4	4
UGT1A10	54575	broad.mit.edu	36	2	234209934	234209934	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:234209934C>T	uc002vur.1	+	c.27C>T	c.(25-27)CCC>CCT	p.P9P	UGT1A8_uc002vup.1_Intron|UGT1A10_uc002vuq.2_Silent_p.P9P	NM_019075	NP_061948	Q9HAW8	UD110_HUMAN	UDP glycosyltransferase 1 family, polypeptide	9				MARAGWTSPVPLCVCLLLTCGFA -> MAPRRVDQPRSFMC VSTADLWLC (in Ref. 1).	flavone metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding			ovary(2)	2		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)												0.251534	104.208544	113.342639	41	122	CC		KEEP	---	---	---	---	capture		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Silent	SNP	234209934	234209934	17503	2	C	T	T	23	23	UGT1A10	T	1	1
PLB1	151056	broad.mit.edu	36	2	28614708	28614708	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:28614708G>A	uc002rmb.1	+	c.574G>A	c.(574-576)GGC>AGC	p.G192S	PLB1_uc010ezj.1_Missense_Mutation_p.G203S	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN	phospholipase B1	192	4 X 308-326 AA approximate repeats.|Extracellular (Potential).|1.				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity			ovary(4)|large_intestine(2)|breast(1)	7	Acute lymphoblastic leukemia(172;0.155)													0.241379	33.841676	37.368682	14	44	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	28614708	28614708	12450	2	G	A	A	39	39	PLB1	A	1	1
PIK3CB	5291	broad.mit.edu	36	3	139900549	139900549	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:139900549C>T	uc003esu.1	-	c.1660G>A	c.(1660-1662)GAA>AAA	p.E554K	PIK3CB_uc010huh.1_5'UTR	NM_006219	NP_006210	P42338	PK3CB_HUMAN	phosphoinositide-3-kinase, catalytic, beta	554					activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity			ovary(1)|skin(1)	2										330				0.288889	129.014692	136.214171	52	128	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	139900549	139900549	12338	3	C	T	T	29	29	PIK3CB	T	2	2
HES1	3280	broad.mit.edu	36	3	195338344	195338344	+	Silent	SNP	G	C	C			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:195338344G>C	uc003ftq.1	+	c.471G>C	c.(469-471)GGG>GGC	p.G157G		NM_005524	NP_005515	Q14469	HES1_HUMAN	hairy and enhancer of split 1	157	Pro-rich.				endocrine pancreas development|Notch signaling pathway	nucleus	histone deacetylase binding|sequence-specific DNA binding transcription factor activity|transcription repressor activity			ovary(1)|lung(1)	2	all_cancers(143;7.3e-09)|Ovarian(172;0.0634)													0.217391	9.668226	15.211881	15	54	GG		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(49;3.65e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.48e-05)	Silent	SNP	195338344	195338344	7348	3	G	C	C	42	42	HES1	C	3	3
CHL1	10752	broad.mit.edu	36	3	380060	380060	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0789-01	TCGA-14-0789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:380060A>T	uc003bot.1	+	c.1579A>T	c.(1579-1581)ATT>TTT	p.I527F	CHL1_uc003bou.1_Missense_Mutation_p.I511F|CHL1_uc003bow.1_Missense_Mutation_p.I511F	NM_006614	NP_006605	O00533	CHL1_HUMAN	cell adhesion molecule with homology to L1CAM	511	Extracellular (Potential).				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix				central_nervous_system(4)|large_intestine(2)|ovary(1)	7		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)								659				0.244094	80.967907	88.542261	31	96	AA		KEEP	---	---	---	---	capture		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)	Missense_Mutation	SNP	380060	380060	3483	3	A	T	T	16	16	CHL1	T	4	4
CACNA2D3	55799	broad.mit.edu	36	3	54905889	54905889	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:54905889G>A	uc003dhf.1	+	c.2320G>A	c.(2320-2322)GCT>ACT	p.A774T	CACNA2D3_uc003dhg.1_Missense_Mutation_p.A680T|CACNA2D3_uc003dhh.1_Non-coding_Transcript	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha	774	Extracellular (Potential).					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity	p.A774T(1)		large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7														0.245	115.480764	127.324983	49	151	GG		KEEP	---	---	---	---	capture		KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Missense_Mutation	SNP	54905889	54905889	2666	3	G	A	A	38	38	CACNA2D3	A	1	1
FGA	2243	broad.mit.edu	36	4	155726747	155726747	+	Nonsense_Mutation	SNP	G	T	T			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:155726747G>T	uc003iod.1	-	c.1284C>A	c.(1282-1284)TAC>TAA	p.Y428*	FGA_uc003ioe.1_Nonsense_Mutation_p.Y428*|FGA_uc003iof.1_Intron	NM_000508	NP_000499	P02671	FIBA_HUMAN	fibrinogen, alpha polypeptide isoform alpha-E	428	By similarity.				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding			ovary(2)|breast(1)	3	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	NSCLC(143;340 1922 20892 22370 48145)								0.223913	247.237103	279.430507	103	357	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	155726747	155726747	6067	4	G	T	T	44	44	FGA	T	5	3
COX18	285521	broad.mit.edu	36	4	74154166	74154166	+	Missense_Mutation	SNP	T	G	G			TCGA-14-0789-01	TCGA-14-0789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:74154166T>G	uc003hgm.1	-	c.65A>C	c.(64-66)GAC>GCC	p.D22A	COX18_uc003hgn.1_5'UTR|COX18_uc010iih.1_Missense_Mutation_p.T56P	NM_173827	NP_776188	Q8N8Q8	COX18_HUMAN	mitochondrial COX18	22					protein insertion into mitochondrial membrane|respiratory chain complex IV assembly	integral to mitochondrial inner membrane	protein transporter activity				0	Breast(15;0.00096)													0.333333	8.021233	8.243023	3	6	TT		KEEP	---	---	---	---	capture	Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)		Missense_Mutation	SNP	74154166	74154166	3905	4	T	G	G	58	58	COX18	G	4	4
CCDC158	339965	broad.mit.edu	36	4	77523900	77523900	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:77523900C>T	uc003hkb.2	-	c.742G>A	c.(742-744)GAA>AAA	p.E248K	CCDC158_uc010ijg.1_Non-coding_Transcript|CCDC158_uc003hkd.2_Missense_Mutation_p.E248K	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN	hypothetical protein LOC339965	248	Potential.									ovary(2)|pancreas(1)	3														0.251969	75.84133	82.937358	32	95	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	77523900	77523900	2912	4	C	T	T	29	29	CCDC158	T	2	2
IDUA	3425	broad.mit.edu	36	4	985507	985507	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:985507C>T	uc003gby.1	+	c.630C>T	c.(628-630)CGC>CGT	p.R210R	IDUA_uc003gbz.1_Non-coding_Transcript|IDUA_uc003gca.1_Silent_p.R163R	NM_000203	NP_000194	P35475	IDUA_HUMAN	alpha-L-iduronidase precursor	210					disaccharide metabolic process	lysosome	cation binding|L-iduronidase activity				0					Laronidase(DB00090)									0.25	15.223104	16.806719	7	21	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(23;0.0158)		Silent	SNP	985507	985507	7804	4	C	T	T	27	27	IDUA	T	1	1
HARS	3035	broad.mit.edu	36	5	140034087	140034087	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140034087C>T	uc003lgv.1	-	c.1469G>A	c.(1468-1470)CGA>CAA	p.R490Q	DND1_uc003lgt.1_5'Flank|HARS_uc003lgu.1_Missense_Mutation_p.R421Q|HARS_uc003lgw.1_Missense_Mutation_p.R470Q|HARS_uc010jfu.1_Missense_Mutation_p.R402Q	NM_002109	NP_002100	P12081	SYHC_HUMAN	histidyl-tRNA synthetase	490					histidyl-tRNA aminoacylation	cytosol	ATP binding|histidine-tRNA ligase activity			ovary(1)	1					L-Histidine(DB00117)									0.178218	35.596053	45.436506	18	83	CC		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Missense_Mutation	SNP	140034087	140034087	7241	5	C	T	T	31	31	HARS	T	1	1
PCDHA2	56146	broad.mit.edu	36	5	140154934	140154934	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140154934G>A	uc003lhd.1	+	c.201G>A	c.(199-201)GCG>GCA	p.A67A	PCDHA1_uc003lha.1_Intron|PCDHA1_uc003lhb.1_Intron|PCDHA2_uc003lhc.1_Silent_p.A67A	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2 isoform 1 precursor	67	Extracellular (Potential).|Cadherin 1.				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(4)	4														0.283871	208.954746	221.974822	88	222	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Silent	SNP	140154934	140154934	11944	5	G	A	A	40	40	PCDHA2	A	1	1
PCDHB4	56131	broad.mit.edu	36	5	140483655	140483655	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr5:140483655G>A	uc003lip.1	+	c.1891G>A	c.(1891-1893)GAG>AAG	p.E631K		NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4 precursor	631	Cadherin 6.|Extracellular (Potential).				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding			ovary(1)	1														0.307087	99.381034	103.593296	39	88	GG		KEEP	---	---	---	---	capture	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		Missense_Mutation	SNP	140483655	140483655	11964	5	G	A	A	37	37	PCDHB4	A	1	1
THBS4	7060	broad.mit.edu	36	5	79414697	79414697	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0789-01	TCGA-14-0789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr5:79414697A>G	uc003kgh.1	+	c.2863A>G	c.(2863-2865)AAT>GAT	p.N955D		NM_003248	NP_003239	P35443	TSP4_HUMAN	thrombospondin 4 precursor	955					endothelial cell-cell adhesion|myoblast migration|negative regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation	basement membrane|extracellular space	calcium ion binding|heparin binding|integrin binding|structural molecule activity				0		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)										OREG0016685	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	0.256944	105.113712	112.821186	37	107	AA		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)	Missense_Mutation	SNP	79414697	79414697	16384	5	A	G	G	9	9	THBS4	G	4	4
GPRC6A	222545	broad.mit.edu	36	6	117234782	117234782	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:117234782C>T	uc003pxj.1	-	c.779G>A	c.(778-780)CGG>CAG	p.R260Q	GPRC6A_uc003pxk.1_Missense_Mutation_p.R260Q|GPRC6A_uc003pxl.1_Missense_Mutation_p.R260Q	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, family C, group 6,	260	Extracellular (Potential).				response to amino acid stimulus		G-protein coupled receptor activity			ovary(4)	4		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)												0.22561	90.891689	102.230861	37	127	CC		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)	Missense_Mutation	SNP	117234782	117234782	7004	6	C	T	T	23	23	GPRC6A	T	1	1
LPA	4018	broad.mit.edu	36	6	160940521	160940521	+	Splice_Site_SNP	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:160940521C>T	uc003qtl.1	-	c.3287_splice	c.e21+1	p.A1096_splice		NM_005577	NP_005568			lipoprotein Lp(a) precursor						blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity			ovary(3)|pancreas(1)	4		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)			Aminocaproic Acid(DB00513)									0.217514	347.97905	400.063927	154	554	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Splice_Site_SNP	SNP	160940521	160940521	9276	6	C	T	T	19	19	LPA	T	5	1
PRRT1	80863	broad.mit.edu	36	6	32226138	32226138	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:32226138G>A	uc003nzs.1	-	c.666C>T	c.(664-666)GTC>GTT	p.V222V	PRRT1_uc003nzt.1_Silent_p.V181V|PRRT1_uc003nzu.1_Silent_p.L74L	NM_030651	NP_085154	Q99946	PRRT1_HUMAN	NG5 protein	181					response to biotic stimulus	integral to membrane				breast(1)	1														0.234568	45.682089	50.904491	19	62	GG		KEEP	---	---	---	---	capture			Silent	SNP	32226138	32226138	13058	6	G	A	A	33	33	PRRT1	A	2	2
ITPR3	3710	broad.mit.edu	36	6	33741600	33741600	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:33741600C>T	uc010jvc.1	+	c.1420C>T	c.(1420-1422)CAG>TAG	p.Q474*		NM_002224	NP_002215	Q14573	ITPR3_HUMAN	inositol 1,4,5-triphosphate receptor, type 3	474	Cytoplasmic (Potential).				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding			central_nervous_system(5)|ovary(3)|lung(1)|kidney(1)	10														0.235294	58.441907	64.985701	24	78	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	33741600	33741600	8226	6	C	T	T	21	21	ITPR3	T	5	2
VEGFA	7422	broad.mit.edu	36	6	43856457	43856457	+	Nonsense_Mutation	SNP	C	T	T	rs45533131	unknown	TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:43856457C>T	uc003owh.1	+	c.973C>T	c.(973-975)CGA>TGA	p.R325*	VEGFA_uc003owd.1_Intron|VEGFA_uc003owe.1_Intron|VEGFA_uc003owg.1_Nonsense_Mutation_p.R325*|VEGFA_uc003owf.1_Nonsense_Mutation_p.R325*|VEGFA_uc003owi.1_Intron|VEGFA_uc003owj.1_Intron|VEGFA_uc010jyx.1_Intron|VEGFA_uc003owk.1_Intron	NM_001025366	NP_001020537	P15692	VEGFA_HUMAN	vascular endothelial growth factor A isoform a	145					basophil chemotaxis|cellular response to hypoxia|induction of positive chemotaxis|induction of positive chemotaxis|platelet activation|platelet degranulation|platelet-derived growth factor receptor signaling pathway|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cell division|positive regulation of endothelial cell proliferation|positive regulation of leukocyte migration|positive regulation of mast cell chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|positive regulation of vascular permeability|regulation of cell shape|vascular endothelial growth factor receptor signaling pathway|vasculogenesis	cell surface|extracellular space|membrane|platelet alpha granule lumen	cell surface binding|chemoattractant activity|cytokine activity|extracellular matrix binding|fibronectin binding|growth factor activity|heparin binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity|vascular endothelial growth factor receptor 1 binding|vascular endothelial growth factor receptor 2 binding|vascular endothelial growth factor receptor binding			ovary(1)	1	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)				Atorvastatin(DB01076)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Simvastatin(DB00641)					359				0.237569	102.440488	113.82591	43	138	CC		KEEP	---	---	---	---	capture	all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		Nonsense_Mutation	SNP	43856457	43856457	17717	6	C	T	T	31	31	VEGFA	T	5	1
ASB15	142685	broad.mit.edu	36	7	123056282	123056282	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0789-01	TCGA-14-0789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr7:123056282A>G	uc003vku.1	+	c.998A>G	c.(997-999)GAT>GGT	p.D333G	ASB15_uc003vkw.1_Missense_Mutation_p.D333G	NM_080928	NP_563616	Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box-containing 15	333	ANK 6.				intracellular signal transduction					lung(1)	1														0.20678	159.720517	183.217879	61	234	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	123056282	123056282	1037	7	A	G	G	12	12	ASB15	G	4	4
KIAA1549	57670	broad.mit.edu	36	7	138244370	138244370	+	Silent	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:138244370G>A	uc003vuk.2	-	c.3033C>T	c.(3031-3033)TTC>TTT	p.F1011F	KIAA1549_uc003vul.2_5'Flank	NM_020910	NP_065961	Q9HCM3	K1549_HUMAN	hypothetical protein LOC57670	1061						integral to membrane			KIAA1549/BRAF(211)	central_nervous_system(211)|pancreas(1)	212						NSCLC(119;1534 1718 44213 46230 50068)				967				0.235294	11.072476	13.373939	8	26	GG		KEEP	---	---	---	---	capture			Silent	SNP	138244370	138244370	8553	7	G	A	A	33	33	KIAA1549	A	2	2
EGFR	1956	broad.mit.edu	36	7	55206364	55206364	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55206364G>A	uc003tqk.1	+	c.1883G>A	c.(1882-1884)TGC>TAC	p.C628Y	EGFR_uc010kzg.1_Missense_Mutation_p.C583Y	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	628	Extracellular (Potential).				activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(8200)|central_nervous_system(103)|upper_aerodigestive_tract(37)|prostate(32)|ovary(31)|thyroid(23)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|stomach(6)|urinary_tract(6)|skin(5)|adrenal_gland(5)|kidney(4)|soft_tissue(4)|bone(3)|NS(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)|pancreas(1)	8515	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)				Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)			8		608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.100451	43.550948	184.889238	89	797	GG		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Missense_Mutation	SNP	55206364	55206364	5156	7	G	A	A	46	46	EGFR	A	2	2
CALN1	83698	broad.mit.edu	36	7	70890787	70890787	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:70890787C>T	uc003twb.2	-	c.695G>A	c.(694-696)CGG>CAG	p.R232Q	CALN1_uc003twa.2_Missense_Mutation_p.R190Q|CALN1_uc003twc.2_Missense_Mutation_p.R190Q	NM_031468	NP_113656	Q9BXU9	CABP8_HUMAN	calneuron 1 isoform 1	190	Cytoplasmic (Potential).					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding				0		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)												0.208054	72.86933	84.612288	31	118	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	70890787	70890787	2708	7	C	T	T	23	23	CALN1	T	1	1
GRM3	2913	broad.mit.edu	36	7	86253591	86253591	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86253591C>T	uc003uid.1	+	c.547C>T	c.(547-549)CGC>TGC	p.R183C	GRM3_uc010lef.1_Missense_Mutation_p.R181C|GRM3_uc010leg.1_Missense_Mutation_p.R55C|GRM3_uc010leh.1_Intron	NM_000840	NP_000831	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3 precursor	183	Extracellular (Potential).				synaptic transmission	integral to plasma membrane				ovary(3)|central_nervous_system(2)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)				Acamprosate(DB00659)|Nicotine(DB00184)	GBM(52;969 1098 3139 52280)								0.242353	245.446164	271.152798	103	322	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	86253591	86253591	7077	7	C	T	T	27	27	GRM3	T	1	1
ABCB4	5244	broad.mit.edu	36	7	86930080	86930080	+	Silent	SNP	G	T	T			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:86930080G>T	uc003uiv.1	-	c.216C>A	c.(214-216)CCC>CCA	p.P72P	ABCB4_uc003uiw.1_Silent_p.P72P|ABCB4_uc003uix.1_Silent_p.P72P|ABCB4_uc003uiy.1_Silent_p.P72P	NM_018849	NP_061337	P21439	MDR3_HUMAN	ATP-binding cassette, subfamily B, member 4	72	ABC transmembrane type-1 1.|Helical; (By similarity).			IMAIAHGSGLP -> RGSSRVDLQAC (in Ref. 5; CAA84542).	cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity			ovary(4)|pancreas(1)	5	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)													0.185841	41.605626	52.061755	21	92	GG		KEEP	---	---	---	---	capture			Silent	SNP	86930080	86930080	44	7	G	T	T	43	43	ABCB4	T	3	3
AZGP1	563	broad.mit.edu	36	7	99407562	99407562	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:99407562C>T	uc003ush.1	-	c.80G>A	c.(79-81)CGT>CAT	p.R27H		NM_001185	NP_001176	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc	27					antigen processing and presentation|cell adhesion|immune response|lipid catabolic process|negative regulation of cell proliferation	extracellular region|MHC class I protein complex	fatty acid binding|protein transmembrane transporter activity|ribonuclease activity			ovary(1)|central_nervous_system(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)													0.198718	66.745817	79.918733	31	125	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	99407562	99407562	1260	7	C	T	T	19	19	AZGP1	T	1	1
ZNF706	51123	broad.mit.edu	36	8	102283137	102283137	+	Silent	SNP	A	G	G			TCGA-14-0789-01	TCGA-14-0789-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr8:102283137A>G	uc003yka.1	-	c.9T>C	c.(7-9)CGT>CGC	p.R3R	ZNF706_uc003ykb.1_Silent_p.R3R	NM_001042510	NP_057180	Q9Y5V0	ZN706_HUMAN	HSPC038 protein	3						intracellular	zinc ion binding			ovary(2)	2	all_cancers(14;3.3e-07)|all_epithelial(15;3.47e-09)|Lung NSC(17;3.44e-05)|all_lung(17;0.000117)													0.155556	11.297388	16.39624	7	38	AA		KEEP	---	---	---	---	capture	Epithelial(11;8.57e-11)|all cancers(13;1.43e-08)|OV - Ovarian serous cystadenocarcinoma(57;1.43e-05)		Silent	SNP	102283137	102283137	18706	8	A	G	G	6	6	ZNF706	G	4	4
OLFML2A	169611	broad.mit.edu	36	9	126606198	126606198	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:126606198C>T	uc004bov.1	+	c.924C>T	c.(922-924)AAC>AAT	p.N308N	OLFML2A_uc004bow.1_Silent_p.N94N|OLFML2A_uc010mwr.1_Silent_p.N272N	NM_182487	NP_872293	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	308											0														0.266667	50.07935	53.759587	20	55	CC		KEEP	---	---	---	---	capture			Silent	SNP	126606198	126606198	11262	9	C	T	T	17	17	OLFML2A	T	2	2
DBH	1621	broad.mit.edu	36	9	135497302	135497302	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135497302C>T	uc004cel.1	+	c.639C>T	c.(637-639)ACC>ACT	p.T213T		NM_000787	NP_000778	P09172	DOPO_HUMAN	dopamine beta-hydroxylase precursor	213	Intragranular (Potential).				hormone biosynthetic process|oxidation-reduction process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding			ovary(2)|central_nervous_system(2)	4					Dopamine(DB00988)|Vitamin C(DB00126)									0.269231	50.134258	53.887594	21	57	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Silent	SNP	135497302	135497302	4421	9	C	T	T	21	21	DBH	T	2	2
ALDH1A1	216	broad.mit.edu	36	9	74757720	74757720	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:74757720G>A	uc004ajd.1	-	c.17C>T	c.(16-18)ACG>ATG	p.T6M		NM_000689	NP_000680	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1A1	6					cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity			ovary(3)|lung(1)	4					NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)									0.242718	59.830827	66.042721	25	78	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74757720	74757720	493	9	G	A	A	40	40	ALDH1A1	A	1	1
TLR7	51284	broad.mit.edu	36	X	12814202	12814202	+	Silent	SNP	C	T	T			TCGA-14-0789-01	TCGA-14-0789-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:12814202C>T	uc004cvc.1	+	c.654C>T	c.(652-654)GCC>GCT	p.A218A		NM_016562	NP_057646	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	218	Extracellular (Potential).|LRR 7.				cellular response to mechanical stimulus|defense response to virus|I-kappaB phosphorylation|inflammatory response|innate immune response|positive regulation of chemokine production|positive regulation of inflammatory response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus	early phagosome|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosome|plasma membrane	double-stranded RNA binding|single-stranded RNA binding|siRNA binding|transmembrane receptor activity			ovary(1)	1					Imiquimod(DB00724)					69				0.442857	94.92126	95.119288	31	39	CC		KEEP	---	---	---	---	capture			Silent	SNP	12814202	12814202	16486	23	C	T	T	23	23	TLR7	T	1	1
ZRSR2	8233	broad.mit.edu	36	X	15750892	15750892	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0789-01	TCGA-14-0789-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:15750892G>A	uc004cxg.2	+	c.1055G>A	c.(1054-1056)CGG>CAG	p.R352Q		NM_005089	NP_005080	Q15696	U2AFM_HUMAN	U2 small nuclear RNA auxiliary factor 1-like 2	352					spliceosome assembly	U12-type spliceosomal complex	nucleotide binding|pre-mRNA 3'-splice site binding|protein binding|zinc ion binding			breast(3)	3	Hepatocellular(33;0.183)					NSCLC(197;1631 3042 5741 31152)								0.485714	161.821078	161.839688	51	54	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	15750892	15750892	18829	23	G	A	A	39	39	ZRSR2	A	1	1
POF1B	79983	broad.mit.edu	36	X	84520983	84520983	+	Missense_Mutation	SNP	T	G	G			TCGA-14-0789-01	TCGA-14-0789-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:84520983T>G	uc004ees.2	-	c.133A>C	c.(133-135)AAA>CAA	p.K45Q	POF1B_uc004eer.2_Missense_Mutation_p.K45Q	NM_024921	NP_079197	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	45							actin binding				0														0.454545	85.27159	85.37022	25	30	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	84520983	84520983	12610	23	T	G	G	64	64	POF1B	G	4	4
LGI4	163175	broad.mit.edu	36	19	40309478	40309479	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-0789-01	TCGA-14-0789-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:40309478_40309479insC	uc002nxx.2	-	c.834_835insG	c.(832-837)CCGAGCfs	p.P278fs	LGI4_uc002nxy.1_Frame_Shift_Ins_p.P106fs|LGI4_uc002nxz.1_Frame_Shift_Ins_p.P106fs	NM_139284	NP_644813	Q8N135	LGI4_HUMAN	leucine-rich repeat LGI family, member 4	278_279						extracellular region				pancreas(1)	1	all_lung(56;7.56e-09)|Lung NSC(56;1.1e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.54e-20)|OV - Ovarian serous cystadenocarcinoma(14;1.33e-18)|all cancers(14;4.27e-17)|LUSC - Lung squamous cell carcinoma(66;0.0849)											0.31			5	11				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	40309478	40309479	9080	19	-	C	C	54	54	LGI4	C	5	5
MUC4	4585	broad.mit.edu	36	3	196996768	196996769	+	In_Frame_Ins	INS	-	GAT	GAT			TCGA-14-0789-01	TCGA-14-0789-01										Phase_I	Unspecified				Illumina GAIIx	g.chr3:196996768_196996769insGAT	uc010hzt.1	-	c.6077_6078insATC	c.(6076-6078)TCC>TCATCC	p.2026_2026S>SS	MUC4_uc003fvo.1_Intron|MUC4_uc003fvp.1_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	798	Ser-rich.				cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)										0.33			2	4				---	---	---	---	capture_indel			In_Frame_Ins	INS	196996768	196996769	10372	3	-	GAT	GAT	47	47	MUC4	GAT	5	5
THOC2	57187	broad.mit.edu	36	X	122575699	122575701	+	In_Frame_Del	DEL	GGA	-	-			TCGA-14-0789-01	TCGA-14-0789-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:122575699_122575701delGGA	uc004etu.1	-	c.4332_4334delTCC	c.(4330-4335)CCTCCA>CCA	p.1444_1445PP>P	THOC2_uc004ett.1_In_Frame_Del_p.1329_1330PP>P|THOC2_uc010nqt.1_Non-coding_Transcript|THOC2_uc004etw.1_In_Frame_Del_p.265_266PP>P	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN	THO complex 2 isoform 1	1444_1445	Lys-rich.				intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding			ovary(3)	3														0.47			28	32				---	---	---	---	capture_indel			In_Frame_Del	DEL	122575699	122575701	16393	23	GGA	-	-	47	47	THOC2	-	5	5
STAG2	10735	broad.mit.edu	36	X	123004151	123004152	+	Frame_Shift_Ins	INS	-	A	A			TCGA-14-0789-01	TCGA-14-0789-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:123004151_123004152insA	uc004eua.1	+	c.437_438insA	c.(436-438)CGAfs	p.R146fs	STAG2_uc004etz.2_Frame_Shift_Ins_p.R146fs|STAG2_uc004eub.1_Frame_Shift_Ins_p.R146fs|STAG2_uc004euc.1_Frame_Shift_Ins_p.R146fs|STAG2_uc004eud.1_Frame_Shift_Ins_p.R146fs|STAG2_uc004eue.1_Frame_Shift_Ins_p.R146fs	NM_001042749	NP_001036215	Q8N3U4	STAG2_HUMAN	stromal antigen 2 isoform a	146					cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding			ovary(4)|skin(1)	5														0.45			35	43				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	123004151	123004152	15761	23	-	A	A	37	37	STAG2	A	5	5
