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
ITIH5	80760	broad.mit.edu	36	10	7719266	7719266	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:7719266C>T	uc001ijq.1	-	c.583G>A	c.(583-585)GCG>ACG	p.A195T	ITIH5_uc001ijr.1_Missense_Mutation_p.A195T	NM_030569	NP_085046	Q86UX2	ITIH5_HUMAN	inter-alpha trypsin inhibitor heavy chain	195					hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			ovary(2)|central_nervous_system(2)	4														0.847059	234.347369	244.144864	72	13	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	7719266	7719266	8211	10	C	T	T	27	27	ITIH5	T	1	1
TUBB8	347688	broad.mit.edu	36	10	83575	83575	+	Silent	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr10:83575G>A	uc001ifi.1	-	c.757C>T	c.(757-759)CTG>TTG	p.L253L	TUBB8_uc009xhe.1_Silent_p.L216L	NM_177987	NP_817124	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8	253					microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity			ovary(1)	1		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)				Pancreas(192;2041 3010 9013 18103)								0.25	10.393215	11.301575	4	12	GG		KEEP	---	---	---	---	capture		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)	Silent	SNP	83575	83575	17316	10	G	A	A	34	34	TUBB8	A	2	2
LIPN	643418	broad.mit.edu	36	10	90511951	90511951	+	Nonsense_Mutation	SNP	C	A	A			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr10:90511951C>A	uc009xtl.1	+	c.135C>A	c.(133-135)TAC>TAA	p.Y45*		NM_001102469	NP_001095939	Q5VXI9	LIPN_HUMAN	lipase-like, ab-hydrolase domain containing 4	45					lipid catabolic process	extracellular region	hydrolase activity				0		Colorectal(252;0.0161)												0.307692	6.475815	6.916698	4	9	CC		KEEP	---	---	---	---	capture		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)	Nonsense_Mutation	SNP	90511951	90511951	9156	10	C	A	A	18	18	LIPN	A	5	3
LDHAL6A	160287	broad.mit.edu	36	11	18443903	18443903	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18443903C>G	uc001mop.1	+	c.388C>G	c.(388-390)CAC>GAC	p.H130D	LDHAL6A_uc001moq.1_Missense_Mutation_p.H130D	NM_144972	NP_659409	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	130					glycolysis|oxidation-reduction process	cytoplasm	binding|L-lactate dehydrogenase activity				0					NADH(DB00157)									0.262673	171.774485	182.829884	57	160	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	18443903	18443903	9023	11	C	G	G	29	29	LDHAL6A	G	3	3
ANO5	203859	broad.mit.edu	36	11	22171641	22171641	+	Silent	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:22171641G>A	uc001mqi.1	+	c.27G>A	c.(25-27)GTG>GTA	p.V9V	ANO5_uc001mqj.1_Silent_p.V9V	NM_213599	NP_998764	Q75V66	ANO5_HUMAN	anoctamin 5 isoform a	9	Cytoplasmic (Potential).					chloride channel complex|endoplasmic reticulum membrane	chloride channel activity			central_nervous_system(3)|ovary(1)	4														0.608696	42.452888	42.690545	14	9	GG		KEEP	---	---	---	---	capture			Silent	SNP	22171641	22171641	708	11	G	A	A	48	48	ANO5	A	2	2
OR10V1	390201	broad.mit.edu	36	11	59237297	59237297	+	Silent	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr11:59237297G>A	uc001nof.1	-	c.598C>T	c.(598-600)CTG>TTG	p.L200L		NM_001005324	NP_001005324	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V,	200	Helical; Name=5; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0														0.396552	136.738881	137.820614	46	70	GG		KEEP	---	---	---	---	capture			Silent	SNP	59237297	59237297	11326	11	G	A	A	33	33	OR10V1	A	2	2
TMEM119	338773	broad.mit.edu	36	12	107510169	107510169	+	Silent	SNP	A	C	C			TCGA-14-0786-01	TCGA-14-0786-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr12:107510169A>C	uc001tng.1	-	c.120T>G	c.(118-120)GGT>GGG	p.G40G	TMEM119_uc001tnf.1_Non-coding_Transcript|TMEM119_uc009zuz.1_Silent_p.G40G	NM_181724	NP_859075	Q4V9L6	TM119_HUMAN	transmembrane protein 119	40	Extracellular (Potential).					integral to membrane				ovary(1)	1														0.333333	9.597117	9.891769	4	8	AA		KEEP	---	---	---	---	capture			Silent	SNP	107510169	107510169	16563	12	A	C	C	14	14	TMEM119	C	4	4
HOXC9	3225	broad.mit.edu	36	12	52680574	52680575	+	Missense_Mutation	DNP	GG	TA	TA			TCGA-14-0786-01	TCGA-14-0786-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:52680574_52680575GG>TA	uc001sep.1	+	c.335_336GG>TA	c.(334-336)GGG>GTA	p.G112V	HOXC9_uc001seq.1_Missense_Mutation_p.G112V	NM_006897	NP_008828	P31274	HXC9_HUMAN	homeobox C9	112					multicellular organismal development|regulation of transcription, DNA-dependent	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription activator activity			large_intestine(1)|pancreas(1)	2														0.428571	7.622666	7.654027	3	4	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	52680574	52680575	7609	12	GG	TA	TA	43	43	HOXC9	TA	3	3
USP15	9958	broad.mit.edu	36	12	61064221	61064221	+	Silent	SNP	T	C	C			TCGA-14-0786-01	TCGA-14-0786-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:61064221T>C	uc001src.1	+	c.1344T>C	c.(1342-1344)TGT>TGC	p.C448C	USP15_uc001srb.1_Silent_p.C419C	NM_006313	NP_006304	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	448					protein deubiquitination|ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			ovary(2)	2						Melanoma(181;615 2041 39364 49691 50001)								0.433824	200.200043	200.719843	59	77	TT		KEEP	---	---	---	---	capture	GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)	Silent	SNP	61064221	61064221	17608	12	T	C	C	58	58	USP15	C	4	4
ADAM21	8747	broad.mit.edu	36	14	69996072	69996072	+	Silent	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:69996072C>T	uc001xmd.1	+	c.2103C>T	c.(2101-2103)GTC>GTT	p.V701V		NM_003813	NP_003804	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21 preproprotein	701	Helical; (Potential).				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			pancreas(1)	1														0.456647	238.805641	239.088782	79	94	CC		KEEP	---	---	---	---	capture		all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)	Silent	SNP	69996072	69996072	244	14	C	T	T	31	31	ADAM21	T	1	1
ZDHHC1	29800	broad.mit.edu	36	16	65986522	65986522	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0786-01	TCGA-14-0786-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:65986522A>T	uc002etc.1	-	c.1114T>A	c.(1114-1116)TCG>ACG	p.S372T	TPPP3_uc002eta.1_5'Flank|TPPP3_uc002etb.1_5'Flank	NM_013304	NP_037436	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	372						integral to membrane	DNA binding|zinc ion binding				0		Ovarian(137;0.223)												0.333333	27.947271	28.742803	11	22	AA		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)	Missense_Mutation	SNP	65986522	65986522	18188	16	A	T	T	11	11	ZDHHC1	T	4	4
ASB16	92591	broad.mit.edu	36	17	39611221	39611221	+	Silent	SNP	G	C	C			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr17:39611221G>C	uc002ifl.1	+	c.1299G>C	c.(1297-1299)CGG>CGC	p.R433R	ASB16_uc002ifm.1_Non-coding_Transcript|C17orf65_uc002ifn.1_Intron|C17orf65_uc010czr.1_5'Flank	NM_080863	NP_543139	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box-containing protein	433	SOCS box.				intracellular signal transduction		protein binding			kidney(2)	2		Breast(137;0.00765)|Prostate(33;0.0313)												0.25	6.38488	7.517777	5	15	GG		KEEP	---	---	---	---	capture		BRCA - Breast invasive adenocarcinoma(366;0.114)	Silent	SNP	39611221	39611221	1038	17	G	C	C	42	42	ASB16	C	3	3
MEGF8	1954	broad.mit.edu	36	19	47547722	47547722	+	Missense_Mutation	SNP	T	G	G			TCGA-14-0786-01	TCGA-14-0786-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47547722T>G	uc002otl.2	+	c.2869T>G	c.(2869-2871)TGT>GGT	p.C957G	MEGF8_uc002otm.2_Missense_Mutation_p.C565G	NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1024	Extracellular (Potential).					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)												0.6	7.723928	7.767319	3	2	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47547722	47547722	9852	19	T	G	G	59	59	MEGF8	G	4	4
PPM1N	147699	broad.mit.edu	36	19	50695046	50695046	+	Splice_Site_SNP	SNP	G	C	C			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:50695046G>C	uc002pce.1	+	c.940_splice	c.e2-1	p.G314_splice	RTN2_uc002pcb.1_5'Flank|RTN2_uc002pcc.1_5'Flank|RTN2_uc002pcd.1_5'Flank|PPM1N_uc010ekh.1_Splice_Site_SNP|PPM1N_uc002pcf.1_Splice_Site_SNP	NM_001080401	NP_001073870			hypothetical protein LOC147699								magnesium ion binding|manganese ion binding|phosphoprotein phosphatase activity				0														0.416667	15.272807	15.345587	5	7	GG		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	50695046	50695046	12781	19	G	C	C	35	35	PPM1N	C	5	3
ZSCAN5B	342933	broad.mit.edu	36	19	61393235	61393235	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:61393235C>T	uc002qmp.1	-	c.1117G>A	c.(1117-1119)GCC>ACC	p.A373T		NM_001080456	NP_001073925	A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	421	C2H2-type 3.				regulation of transcription, DNA-dependent|viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1														0.447368	96.381309	96.556494	34	42	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	61393235	61393235	18843	19	C	T	T	27	27	ZSCAN5B	T	1	1
ABCA7	10347	broad.mit.edu	36	19	993173	993173	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr19:993173C>T	uc002lqw.2	+	c.413C>T	c.(412-414)ACG>ATG	p.T138M	ABCA7_uc010dsa.1_Missense_Mutation_p.T138M|ABCA7_uc010dsb.1_5'Flank	NM_019112	NP_061985	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A, member 7	138	Extracellular (By similarity).				phagocytosis|transmembrane transport	ATP-binding cassette (ABC) transporter complex|endosome membrane|Golgi membrane|integral to membrane|plasma membrane	ATP binding|ATPase activity|transporter activity			pancreas(7)|ovary(1)|central_nervous_system(1)	9		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)												0.225806	16.311852	18.450227	7	24	CC		KEEP	---	---	---	---	capture		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Missense_Mutation	SNP	993173	993173	38	19	C	T	T	19	19	ABCA7	T	1	1
GJA8	2703	broad.mit.edu	36	1	145846970	145846970	+	Silent	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:145846970G>A	uc001epu.1	+	c.264G>A	c.(262-264)CCG>CCA	p.P88P	NBPF11_uc009wjd.1_Intron|NBPF11_uc009wje.1_Intron|GJA8_uc009wjl.1_Silent_p.P88P	NM_005267	NP_005258	P48165	CXA8_HUMAN	connexin 50	88	Helical; (Potential).		P -> S (in CZP1).		cell communication|visual perception	connexon complex|integral to plasma membrane	channel activity			ovary(2)|large_intestine(2)|breast(1)	5	all_hematologic(923;0.0276)					Melanoma(76;1255 1795 8195 52096)								0.527273	172.147629	172.21938	58	52	GG		KEEP	---	---	---	---	capture			Silent	SNP	145846970	145846970	6673	1	G	A	A	40	40	GJA8	A	1	1
RYR2	6262	broad.mit.edu	36	1	235840754	235840754	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235840754C>T	uc001hyl.1	+	c.4753C>T	c.(4753-4755)CGC>TGC	p.R1585C		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1585	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)												0.625	30.552192	30.771393	10	6	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		Missense_Mutation	SNP	235840754	235840754	14249	1	C	T	T	27	27	RYR2	T	1	1
WDR8	49856	broad.mit.edu	36	1	3537953	3537953	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:3537953C>T	uc001ako.1	-	c.1177G>A	c.(1177-1179)GGA>AGA	p.G393R	WDR8_uc001akn.2_Missense_Mutation_p.G393R	NM_017818	NP_060288	Q9P2S5	WRP73_HUMAN	WD repeat domain 8 protein	393	WD 6.					cytoplasm	protein binding				0	all_cancers(77;0.0128)|all_epithelial(69;0.00526)|Ovarian(185;0.0634)|Lung NSC(156;0.162)|all_lung(157;0.172)	all_epithelial(116;7.37e-22)|all_lung(118;8.23e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)												0.419355	38.868745	39.044914	13	18	CC		KEEP	---	---	---	---	capture		Epithelial(90;4.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.16e-22)|GBM - Glioblastoma multiforme(42;1.05e-14)|Colorectal(212;1.19e-05)|BRCA - Breast invasive adenocarcinoma(365;2.67e-05)|COAD - Colon adenocarcinoma(227;5.82e-05)|Kidney(185;0.000364)|KIRC - Kidney renal clear cell carcinoma(229;0.00223)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)	Missense_Mutation	SNP	3537953	3537953	17902	1	C	T	T	22	22	WDR8	T	2	2
KIF2C	11004	broad.mit.edu	36	1	45005103	45005103	+	Nonsense_Mutation	SNP	G	T	T			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:45005103G>T	uc001cmg.2	+	c.1990G>T	c.(1990-1992)GAG>TAG	p.E664*	KIF2C_uc001cmh.2_Nonsense_Mutation_p.E610*	NM_006845	NP_006836	Q99661	KIF2C_HUMAN	kinesin family member 2C	664					blood coagulation|cell division|cell proliferation|chromosome segregation|establishment or maintenance of microtubule cytoskeleton polarity|microtubule depolymerization|microtubule-based movement|mitotic prometaphase|regulation of chromosome segregation	condensed chromosome kinetochore|cytosol|kinesin complex|microtubule|nucleus	ATP binding|centromeric DNA binding|microtubule motor activity|microtubule plus-end binding			ovary(1)	1	Acute lymphoblastic leukemia(166;0.155)													0.212121	6.381731	9.077794	7	26	GG		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	45005103	45005103	8610	1	G	T	T	45	45	KIF2C	T	5	3
SLC13A3	64849	broad.mit.edu	36	20	44650124	44650124	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr20:44650124C>G	uc002xsf.1	-	c.1102G>C	c.(1102-1104)GCC>CCC	p.A368P	SLC13A3_uc002xsg.1_Missense_Mutation_p.A321P|SLC13A3_uc010gho.1_Intron|SLC13A3_uc010ghn.1_Missense_Mutation_p.A337P	NM_022829	NP_073740	Q8WWT9	S13A3_HUMAN	solute carrier family 13 member 3 isoform a	368	Extracellular (Potential).					integral to membrane|plasma membrane	high affinity sodium:dicarboxylate symporter activity			ovary(1)	1		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)									0.241379	7.569213	9.333618	7	22	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44650124	44650124	14888	20	C	G	G	26	26	SLC13A3	G	3	3
KRTAP19-2	337969	broad.mit.edu	36	21	30781506	30781506	+	Missense_Mutation	SNP	G	T	T			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:30781506G>T	uc002yof.1	-	c.33C>A	c.(31-33)AGC>AGA	p.S11R		NM_181608	NP_853639	Q3LHN2	KR192_HUMAN	keratin associated protein 19-2	11						intermediate filament					0														0.390728	154.370313	155.953548	59	92	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30781506	30781506	8844	21	G	T	T	34	34	KRTAP19-2	T	3	3
TMPRSS3	64699	broad.mit.edu	36	21	42676306	42676306	+	Silent	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr21:42676306G>A	uc002zbb.1	-	c.687C>T	c.(685-687)CCC>CCT	p.P229P	TMPRSS3_uc002zay.1_5'UTR|TMPRSS3_uc002zaz.1_Silent_p.P102P|TMPRSS3_uc002zba.1_Silent_p.P102P|TMPRSS3_uc002zbc.1_Silent_p.P229P|TMPRSS3_uc002zbd.1_Silent_p.P229P	NM_024022	NP_115780	P57727	TMPS3_HUMAN	transmembrane protease, serine 3 isoform 1	229	Peptidase S1.|Extracellular (Potential).				cellular sodium ion homeostasis|proteolysis	endoplasmic reticulum membrane|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity|sodium channel regulator activity			ovary(2)|breast(1)	3														0.362319	69.628477	70.790135	25	44	GG		KEEP	---	---	---	---	capture			Silent	SNP	42676306	42676306	16789	21	G	A	A	35	35	TMPRSS3	A	2	2
C22orf24	25775	broad.mit.edu	36	22	30664001	30664001	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0786-01	TCGA-14-0786-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr22:30664001T>C	uc003aly.1	-	c.52A>G	c.(52-54)ACC>GCC	p.T18A	C22orf24_uc003alx.1_Non-coding_Transcript	NM_015372	NP_056187	Q9Y442	CV024_HUMAN	hypothetical protein LOC25775	18						integral to membrane				central_nervous_system(1)	1														0.436019	609.73554	611.256806	184	238	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	30664001	30664001	2218	22	T	C	C	58	58	C22orf24	C	4	4
ST6GAL2	84620	broad.mit.edu	36	2	106826636	106826636	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:106826636C>T	uc002tdr.1	-	c.230G>A	c.(229-231)CGC>CAC	p.R77H	ST6GAL2_uc002tds.2_Missense_Mutation_p.R77H	NM_032528	NP_115917	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide	77	Lumenal (Potential).				growth|multicellular organismal development|oligosaccharide metabolic process|protein glycosylation	Golgi cisterna membrane|integral to Golgi membrane	beta-galactoside alpha-2,6-sialyltransferase activity			pancreas(6)|ovary(3)	9														0.364865	76.730591	77.908431	27	47	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	106826636	106826636	15740	2	C	T	T	27	27	ST6GAL2	T	1	1
PPIG	9360	broad.mit.edu	36	2	170201346	170201346	+	Missense_Mutation	SNP	A	C	C			TCGA-14-0786-01	TCGA-14-0786-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr2:170201346A>C	uc002uez.1	+	c.1332A>C	c.(1330-1332)AAA>AAC	p.K444N	PPIG_uc010fpx.1_Missense_Mutation_p.K429N|PPIG_uc010fpy.1_Missense_Mutation_p.K437N|PPIG_uc002ufb.1_Missense_Mutation_p.K444N|PPIG_uc002ufd.1_Missense_Mutation_p.K441N	NM_004792	NP_004783	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G	444					protein folding|RNA splicing	nuclear matrix|nuclear speck	cyclosporin A binding|peptidyl-prolyl cis-trans isomerase activity			ovary(2)|central_nervous_system(1)	3					L-Proline(DB00172)									0.471698	75.269065	75.306152	25	28	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	170201346	170201346	12759	2	A	C	C	3	3	PPIG	C	4	4
CAD	790	broad.mit.edu	36	2	27319289	27319289	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:27319289C>A	uc002rji.1	+	c.6424C>A	c.(6424-6426)CTC>ATC	p.L2142I	CAD_uc010eyw.1_Missense_Mutation_p.L2079I	NM_004341	NP_004332	P27708	PYR1_HUMAN	carbamoylphosphate synthetase 2/aspartate	2142	ATCase (Aspartate transcarbamylase).				'de novo' pyrimidine base biosynthetic process|glutamine metabolic process|peptidyl-threonine phosphorylation|protein autophosphorylation|pyrimidine nucleoside biosynthetic process|pyrimidine nucleotide biosynthetic process	cytosol|nuclear matrix	aspartate binding|aspartate carbamoyltransferase activity|ATP binding|carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity|dihydroorotase activity|enzyme binding|metal ion binding|protein kinase activity			ovary(4)|large_intestine(2)|kidney(2)|lung(1)|pancreas(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				L-Aspartic Acid(DB00128)|L-Glutamine(DB00130)					653				0.439394	85.682032	85.889748	29	37	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	27319289	27319289	2681	2	C	A	A	28	28	CAD	A	3	3
PRKD3	23683	broad.mit.edu	36	2	37355320	37355320	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:37355320G>C	uc002rqd.1	-	c.1399C>G	c.(1399-1401)CGC>GGC	p.R467G	PRKD3_uc002rqe.1_Missense_Mutation_p.R67G|PRKD3_uc002rqf.1_Missense_Mutation_p.R467G	NM_005813	NP_005804	O94806	KPCD3_HUMAN	protein kinase D3	467	PH.				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|intracellular signal transduction|protein phosphorylation	cytoplasm|membrane|nucleus	ATP binding|metal ion binding|protein binding|protein kinase C activity			lung(2)|ovary(1)|central_nervous_system(1)	4		all_hematologic(82;0.21)				Melanoma(80;621 1355 8613 11814 51767)			p.R467C(BL70-Tumor)	569				0.472527	124.112793	124.172838	43	48	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	37355320	37355320	12963	2	G	C	C	39	39	PRKD3	C	3	3
CCDC54	84692	broad.mit.edu	36	3	108579926	108579926	+	Missense_Mutation	SNP	T	A	A	rs34430473	unknown	TCGA-14-0786-01	TCGA-14-0786-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:108579926T>A	uc003dwi.1	+	c.802T>A	c.(802-804)TTA>ATA	p.L268I		NM_032600	NP_115989	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	268											0														0.441048	300.345386	301.038351	101	128	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	108579926	108579926	2947	3	T	A	A	60	60	CCDC54	A	4	4
HSPBAP1	79663	broad.mit.edu	36	3	123942632	123942632	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:123942632G>A	uc003efu.1	-	c.844C>T	c.(844-846)CGG>TGG	p.R282W	HSPBAP1_uc003eft.1_5'UTR	NM_024610	NP_078886	Q96EW2	HBAP1_HUMAN	Hspb associated protein 1	282	JmjC.					cytoplasm				ovary(1)|lung(1)	2														0.488189	203.845219	203.860514	62	65	GG		KEEP	---	---	---	---	capture		GBM - Glioblastoma multiforme(114;0.0531)	Missense_Mutation	SNP	123942632	123942632	7725	3	G	A	A	39	39	HSPBAP1	A	1	1
C3orf20	84077	broad.mit.edu	36	3	14777987	14777987	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0786-01	TCGA-14-0786-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr3:14777987T>A	uc003byy.1	+	c.2356T>A	c.(2356-2358)TTT>ATT	p.F786I	C3orf20_uc003byz.1_Missense_Mutation_p.F664I|C3orf20_uc003bza.1_Missense_Mutation_p.F664I|C3orf20_uc003bzb.1_Missense_Mutation_p.F287I	NM_032137	NP_115513	Q8ND61	CC020_HUMAN	hypothetical protein LOC84077	786	Helical; (Potential).					cytoplasm|integral to membrane				ovary(3)	3														0.454545	148.839939	149.037362	50	60	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	14777987	14777987	2306	3	T	A	A	60	60	C3orf20	A	4	4
NR2C2	7182	broad.mit.edu	36	3	15054605	15054605	+	Silent	SNP	C	G	G			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr3:15054605C>G	uc003bzi.1	+	c.1524C>G	c.(1522-1524)GGC>GGG	p.G508G	NR2C2_uc003bzj.2_Silent_p.G489G	NM_003298	NP_003289	P49116	NR2C2_HUMAN	nuclear receptor subfamily 2, group C, member 2	489	Ligand-binding (By similarity).				cell differentiation|nervous system development|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|spermatogenesis	nucleoplasm	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription coactivator activity|zinc ion binding				0														0.405882	221.487177	222.789711	69	101	CC		KEEP	---	---	---	---	capture			Silent	SNP	15054605	15054605	11028	3	C	G	G	28	28	NR2C2	G	3	3
BANK1	55024	broad.mit.edu	36	4	103165637	103165637	+	Silent	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:103165637G>A	uc003hvy.2	+	c.1542G>A	c.(1540-1542)CCG>CCA	p.P514P	BANK1_uc003hvx.2_Silent_p.P499P|BANK1_uc010ill.1_Silent_p.P381P|BANK1_uc003hvz.2_Silent_p.P484P	NM_017935	NP_001077376	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	514					B cell activation					ovary(2)	2		Hepatocellular(203;0.217)												0.378378	76.492857	77.448805	28	46	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)	Silent	SNP	103165637	103165637	1330	4	G	A	A	38	38	BANK1	A	1	1
FHDC1	85462	broad.mit.edu	36	4	154117285	154117285	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:154117285G>A	uc003inf.2	+	c.3392G>A	c.(3391-3393)CGG>CAG	p.R1131Q		NM_033393	NP_203751	Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	1131					actin cytoskeleton organization		actin binding			large_intestine(1)|ovary(1)	2	all_hematologic(180;0.093)													0.444444	12.999858	13.023875	4	5	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	154117285	154117285	6114	4	G	A	A	39	39	FHDC1	A	1	1
SLIT2	9353	broad.mit.edu	36	4	20150293	20150293	+	Missense_Mutation	SNP	C	A	A			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:20150293C>A	uc003gpr.1	+	c.1964C>A	c.(1963-1965)TCT>TAT	p.S655Y	SLIT2_uc003gps.1_Missense_Mutation_p.S647Y	NM_004787	NP_004778	O94813	SLIT2_HUMAN	slit homolog 2	655					apoptosis involved in luteolysis|axon extension involved in axon guidance|branching morphogenesis of a tube|cell migration involved in sprouting angiogenesis|cellular response to heparin|cellular response to hormone stimulus|chemorepulsion involved in postnatal olfactory bulb interneuron migration|corticospinal neuron axon guidance through spinal cord|induction of negative chemotaxis|initiation of Roundabout signal transduction|motor axon guidance|negative regulation of actin filament polymerization|negative regulation of cell growth|negative regulation of cellular response to growth factor stimulus|negative regulation of chemokine-mediated signaling pathway|negative regulation of endothelial cell migration|negative regulation of lamellipodium assembly|negative regulation of mononuclear cell migration|negative regulation of neutrophil chemotaxis|negative regulation of protein phosphorylation|negative regulation of retinal ganglion cell axon guidance|negative regulation of small GTPase mediated signal transduction|negative regulation of smooth muscle cell chemotaxis|negative regulation of vascular permeability|positive regulation of apoptosis|positive regulation of axonogenesis|response to cortisol stimulus|retinal ganglion cell axon guidance|ureteric bud development	cell surface|cytoplasm|extracellular space|plasma membrane	calcium ion binding|GTPase inhibitor activity|heparin binding|laminin-1 binding|protein homodimerization activity|proteoglycan binding|Roundabout binding			central_nervous_system(4)|ovary(3)	7														0.408759	160.06734	161.065597	56	81	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	20150293	20150293	15238	4	C	A	A	32	32	SLIT2	A	3	3
EEF1A1	1915	broad.mit.edu	36	6	74285917	74285917	+	Missense_Mutation	SNP	A	C	C			TCGA-14-0786-01	TCGA-14-0786-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr6:74285917A>C	uc003phi.1	-	c.188T>G	c.(187-189)CTG>CGG	p.L63R	EEF1A1_uc003phd.1_5'Flank|EEF1A1_uc003phe.1_Missense_Mutation_p.L63R|EEF1A1_uc003phf.1_Missense_Mutation_p.L63R|EEF1A1_uc003phg.1_Missense_Mutation_p.L63R|EEF1A1_uc003phh.1_Intron|EEF1A1_uc003phj.1_Missense_Mutation_p.L63R|EEF1A1_uc003phk.1_Missense_Mutation_p.L63R|EEF1A1_uc003phl.2_Missense_Mutation_p.L63R|EEF1A1_uc003phm.1_Intron	NM_001402	NP_001393	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha	63						cytosol|eukaryotic translation elongation factor 1 complex	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0												OREG0003890	type=REGULATORY REGION|Gene=LOC477388|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	0.401869	256.15408	257.969391	86	128	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	74285917	74285917	5110	6	A	C	C	7	7	EEF1A1	C	4	4
HBP1	26959	broad.mit.edu	36	7	106617029	106617029	+	Silent	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106617029C>T	uc003vdy.1	+	c.822C>T	c.(820-822)GGC>GGT	p.G274G	HBP1_uc003vdz.1_Silent_p.G274G|HBP1_uc003vea.2_Silent_p.G274G|HBP1_uc003veb.1_Silent_p.G274G	NM_012257	NP_036389	O60381	HBP1_HUMAN	HMG-box transcription factor 1	274	AXH.				cell cycle arrest|regulation of transcription, DNA-dependent|transcription, DNA-dependent|Wnt receptor signaling pathway	nucleus	DNA binding				0														0.288618	185.047596	194.889002	71	175	CC		KEEP	---	---	---	---	capture			Silent	SNP	106617029	106617029	7267	7	C	T	T	27	27	HBP1	T	1	1
EGFR	1956	broad.mit.edu	36	7	55189316	55189316	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:55189316C>T	uc003tqk.1	+	c.866C>T	c.(865-867)GCC>GTC	p.A289V	EGFR_uc003tqh.1_Missense_Mutation_p.A289V|EGFR_uc003tqi.1_Missense_Mutation_p.A289V|EGFR_uc003tqj.1_Missense_Mutation_p.A289V|EGFR_uc010kzg.1_Missense_Mutation_p.A244V	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a	289	Approximate.|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	p.A289V(20)|p.V30_R297>G(10)|p.A289D(3)		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	p.A289V(HEC6-Tumor)|p.A289D(HS683-Tumor)|p.A289V(RL952-Tumor)	608	TCGA GBM(3;<1E-8)|TSP Lung(4;<1E-8)			0.833506	2591.068196	2693.128761	806	161	CC		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	55189316	55189316	5156	7	C	T	T	26	26	EGFR	T	2	2
ZNF706	51123	broad.mit.edu	36	8	102283137	102283137	+	Silent	SNP	A	G	G			TCGA-14-0786-01	TCGA-14-0786-01	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)													0.163636	13.922346	19.871437	9	46	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
SLC30A8	169026	broad.mit.edu	36	8	118239226	118239226	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr8:118239226G>A	uc003yoh.1	+	c.534G>A	c.(532-534)ATG>ATA	p.M178I	SLC30A8_uc010mcz.1_Missense_Mutation_p.M129I|SLC30A8_uc003yog.1_Missense_Mutation_p.M129I|SLC30A8_uc003yoi.1_Missense_Mutation_p.M129I	NM_173851	NP_776250	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 member 8	178	Helical; (Potential).				insulin secretion|positive regulation of insulin secretion|regulation of sequestering of zinc ion|regulation of vesicle-mediated transport|response to glucose stimulus|sequestering of zinc ion	integral to membrane|plasma membrane|secretory granule membrane|transport vesicle membrane	protein homodimerization activity|zinc ion binding|zinc ion transmembrane transporter activity			ovary(2)|skin(1)	3	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)					Ovarian(162;1202 1922 6011 16223 52092)								0.364055	216.753725	220.286527	79	138	GG		KEEP	---	---	---	---	capture	STAD - Stomach adenocarcinoma(47;0.203)		Missense_Mutation	SNP	118239226	118239226	15058	8	G	A	A	45	45	SLC30A8	A	2	2
FLJ43860	389690	broad.mit.edu	36	8	142555326	142555326	+	Missense_Mutation	SNP	T	G	G			TCGA-14-0786-01	TCGA-14-0786-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr8:142555326T>G	uc003ywi.2	-	c.1549A>C	c.(1549-1551)ACC>CCC	p.T517P	FLJ43860_uc010meu.1_Intron	NM_207414	NP_997297	Q6ZUA9	Q6ZUA9_HUMAN	hypothetical protein LOC389690	517							binding				0	all_cancers(97;7.79e-15)|all_epithelial(106;4.52e-13)|Lung NSC(106;2.07e-05)|all_lung(105;2.89e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)													0.285714	8.892545	9.470708	4	10	TT		KEEP	---	---	---	---	capture	BRCA - Breast invasive adenocarcinoma(115;0.0493)		Missense_Mutation	SNP	142555326	142555326	6170	8	T	G	G	59	59	FLJ43860	G	4	4
NFKBIL2	4796	broad.mit.edu	36	8	145632821	145632821	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:145632821C>T	uc003zcu.2	-	c.1465G>A	c.(1465-1467)GAC>AAC	p.D489N		NM_013432	NP_038460	Q96HA7	TONSL_HUMAN	NF-kappa-B inhibitor-like protein 2	648					cytoplasmic sequestering of transcription factor|double-strand break repair via homologous recombination|replication fork processing	cytoplasm|nuclear replication fork	histone binding|transcription corepressor activity				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)													0.376471	87.875655	89.014862	32	53	CC		KEEP	---	---	---	---	capture	OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)		Missense_Mutation	SNP	145632821	145632821	10782	8	C	T	T	30	30	NFKBIL2	T	2	2
ABO	28	broad.mit.edu	36	9	135126552	135126552	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr9:135126552G>A	uc004cda.1	-	c.145C>T	c.(145-147)CGG>TGG	p.R49W	ABO_uc010naf.1_De_novo_Start_InFrame|ABO_uc010nag.1_Intron	NM_020469	NP_065202	P16442	BGAT_HUMAN	ABO blood group (transferase A, alpha	49	Helical; Signal-anchor for type II membrane protein; (Potential).				protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	fucosylgalactoside 3-alpha-galactosyltransferase activity|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity|metal ion binding				0														0.5	18.049497	18.049497	6	6	GG		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)	Missense_Mutation	SNP	135126552	135126552	98	9	G	A	A	40	40	ABO	A	1	1
C9orf86	55684	broad.mit.edu	36	9	138853337	138853337	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr9:138853337C>G	uc004cjj.1	+	c.1439C>G	c.(1438-1440)GCT>GGT	p.A480G	C9orf86_uc004cjk.1_Intron|C9orf86_uc004cji.1_Missense_Mutation_p.A479G|C9orf86_uc010nbr.1_Intron|C9orf86_uc004cjl.1_Non-coding_Transcript|C9orf86_uc010nbs.1_Missense_Mutation_p.A364G|C9orf86_uc004cjn.1_Missense_Mutation_p.A273G	NM_024718	NP_078994	Q3YEC7	PARF_HUMAN	Rab-like GTP-binding protein 1	479					small GTPase mediated signal transduction	cytoplasm|nucleus	GTP binding|protein binding				0	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0511)												0.235294	6.378467	7.48224	4	13	CC		KEEP	---	---	---	---	capture		OV - Ovarian serous cystadenocarcinoma(145;1.61e-05)|Epithelial(140;0.000183)	Missense_Mutation	SNP	138853337	138853337	2618	9	C	G	G	28	28	C9orf86	G	3	3
MAGEC2	51438	broad.mit.edu	36	X	141118922	141118922	+	Missense_Mutation	SNP	T	G	G			TCGA-14-0786-01	TCGA-14-0786-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chrX:141118922T>G	uc004fbu.1	-	c.518A>C	c.(517-519)AAG>ACG	p.K173T	MAGEC2_uc010nsm.1_Missense_Mutation_p.K173T	NM_016249	NP_057333	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	173	MAGE.					cytoplasm|nucleus				breast(2)	2	Acute lymphoblastic leukemia(192;6.56e-05)													0.38806	581.455356	587.375786	208	328	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	141118922	141118922	9562	23	T	G	G	56	56	MAGEC2	G	4	4
SSX3	10214	broad.mit.edu	36	X	48094502	48094502	+	Splice_Site_SNP	SNP	C	T	T			TCGA-14-0786-01	TCGA-14-0786-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48094502C>T	uc004djd.1	-	c.331_splice	c.e6-1	p.I111_splice	SSX3_uc004dje.1_Splice_Site_SNP_p.I111_splice	NM_021014	NP_066294			synovial sarcoma, X breakpoint 3 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding				0						Colon(37;227 826 19399 40970 48007)								0.42115	693.393214	696.323944	227	312	CC		KEEP	---	---	---	---	capture			Splice_Site_SNP	SNP	48094502	48094502	15723	23	C	T	T	32	32	SSX3	T	5	2
KCND1	3750	broad.mit.edu	36	X	48707509	48707509	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:48707509G>A	uc004dlx.1	-	c.1615C>T	c.(1615-1617)CGC>TGC	p.R539C	KCND1_uc004dlw.1_Missense_Mutation_p.R162C	NM_004979	NP_004970	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related	539	Cytoplasmic (Potential).					voltage-gated potassium channel complex	metal ion binding|voltage-gated potassium channel activity			ovary(2)|lung(1)	3														0.35	35.56146	36.344662	14	26	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	48707509	48707509	8323	23	G	A	A	38	38	KCND1	A	1	1
NLGN4X	57502	broad.mit.edu	36	X	5821156	5821156	+	Missense_Mutation	SNP	G	T	T			TCGA-14-0786-01	TCGA-14-0786-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chrX:5821156G>T	uc010ndi.1	-	c.2264C>A	c.(2263-2265)ACA>AAA	p.T755K	NLGN4X_uc004crp.1_Missense_Mutation_p.T738K|NLGN4X_uc010ndh.1_Missense_Mutation_p.T718K|NLGN4X_uc004crq.1_Missense_Mutation_p.T718K|NLGN4X_uc004crr.1_Missense_Mutation_p.T718K|NLGN4X_uc010ndj.1_Missense_Mutation_p.T718K	NM_181332	NP_851849	Q8N0W4	NLGNX_HUMAN	X-linked neuroligin 4	718	Cytoplasmic (Potential).				brainstem development|cell adhesion|cell-cell junction organization|cerebellum development|male courtship behavior|positive regulation of organ growth|regulation of excitatory postsynaptic membrane potential|regulation of synaptic transmission|social behavior|synapse assembly|territorial aggressive behavior|vocalization behavior	cell surface|dendrite|integral to plasma membrane|synapse	carboxylesterase activity|chloride ion binding|neurexin binding|protein homodimerization activity			large_intestine(1)|skin(1)	2														0.345324	136.555274	139.493109	48	91	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	5821156	5821156	10867	23	G	T	T	48	48	NLGN4X	T	3	3
ALPK1	80216	broad.mit.edu	36	4	113572547	113572547	+	Frame_Shift_Del	DEL	C	-	-			TCGA-14-0786-01	TCGA-14-0786-01										Phase_I	Unspecified				Illumina GAIIx	g.chr4:113572547_113572547delC	uc003ian.2	+	c.2395_2395delC	c.(2395-2397)CCCfs	p.P799fs	ALPK1_uc003iap.2_Frame_Shift_Del_p.P799fs|ALPK1_uc003iao.2_Intron|ALPK1_uc010imo.1_Frame_Shift_Del_p.P627fs	NM_001102406	NP_079420	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	799					protein phosphorylation		ATP binding|protein serine/threonine kinase activity			ovary(5)	5		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)						252				0.43			49	64				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	113572547	113572547	547	4	C	-	-	18	18	ALPK1	-	5	5
