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
LDHA	3939	broad.mit.edu	36	11	18385294	18385294	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr11:18385294C>T	uc001mok.2	+	c.889C>T	c.(889-891)CAG>TAG	p.Q297*	LDHA_uc009yhn.1_Nonsense_Mutation_p.Q296*|LDHA_uc009yho.1_Nonsense_Mutation_p.Q124*|LDHA_uc001mol.2_3'UTR	NM_005566	NP_005557	P00338	LDHA_HUMAN	L-lactate dehydrogenase A isoform 1	297					glycolysis|oxidation-reduction process|pyruvate metabolic process	cytosol	L-lactate dehydrogenase activity|protein binding			central_nervous_system(3)	3					NADH(DB00157)					124				0.766667	394.589925	404.347413	115	35	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	18385294	18385294	9022	11	C	T	T	17	17	LDHA	T	5	2
PUS1	80324	broad.mit.edu	36	12	130991902	130991902	+	Silent	SNP	T	C	C			TCGA-14-0865-01	TCGA-14-0865-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:130991902T>C	uc001ujf.1	+	c.657T>C	c.(655-657)GAT>GAC	p.D219D	PUS1_uc001ujg.1_Silent_p.D191D|PUS1_uc001ujh.1_Silent_p.D191D|PUS1_uc001uji.1_Silent_p.D166D	NM_025215	NP_001002020	Q9Y606	TRUA_HUMAN	pseudouridylate synthase 1 isoform 1	219						mitochondrion	pseudouridine synthase activity|pseudouridylate synthase activity|RNA binding			breast(1)|central_nervous_system(1)	2	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.05e-08)|Epithelial(86;2.51e-07)|all cancers(50;2.94e-07)		Esophageal Squamous(102;671 2009 17384 45666)								0.222222	6.888854	8.168927	4	14	TT		KEEP	---	---	---	---	capture			Silent	SNP	130991902	130991902	13288	12	T	C	C	51	51	PUS1	C	4	4
HELB	92797	broad.mit.edu	36	12	65011674	65011674	+	Silent	SNP	T	C	C			TCGA-14-0865-01	TCGA-14-0865-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr12:65011674T>C	uc001sti.2	+	c.3144T>C	c.(3142-3144)AGT>AGC	p.S1048S	HELB_uc009zqt.1_Non-coding_Transcript	NM_033647	NP_387467	Q8NG08	HELB_HUMAN	helicase (DNA) B	1048					DNA replication, synthesis of RNA primer		ATP binding|ATP-dependent 5'-3' DNA helicase activity|single-stranded DNA-dependent ATP-dependent DNA helicase activity			central_nervous_system(1)|pancreas(1)	2			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)										0.182171	107.681939	132.152639	47	211	TT		KEEP	---	---	---	---	capture			Silent	SNP	65011674	65011674	7328	12	T	C	C	58	58	HELB	C	4	4
SUCLA2	8803	broad.mit.edu	36	13	47415549	47415549	+	Silent	SNP	C	A	A			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:47415549C>A	uc001vbs.1	-	c.1350G>T	c.(1348-1350)GCG>GCT	p.A450A		NM_003850	NP_003841	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit	450					succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|protein binding|succinate-CoA ligase (ADP-forming) activity			central_nervous_system(1)	1		all_cancers(8;1.13e-24)|all_epithelial(8;1.78e-13)|all_lung(13;2.85e-06)|Breast(56;0.000141)|Lung NSC(96;0.000226)|all_hematologic(8;0.000885)|Prostate(109;0.00132)|Acute lymphoblastic leukemia(8;0.0167)|Myeloproliferative disorder(33;0.039)|Hepatocellular(98;0.0556)|Lung SC(185;0.102)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(144;2.1e-06)	Succinic acid(DB00139)									0.88	236.10164	246.726245	66	9	CC		KEEP	---	---	---	---	capture			Silent	SNP	47415549	47415549	15883	13	C	A	A	31	31	SUCLA2	A	3	3
DIS3	22894	broad.mit.edu	36	13	72244401	72244401	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr13:72244401C>T	uc001vix.2	-	c.1400G>A	c.(1399-1401)CGA>CAA	p.R467Q	DIS3_uc001viy.2_Missense_Mutation_p.R437Q|DIS3_uc001viz.2_Non-coding_Transcript	NM_014953	NP_055768	Q9Y2L1	RRP44_HUMAN	DIS3 mitotic control isoform b	467					CUT catabolic process|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|rRNA catabolic process|rRNA processing	cytosol|exosome (RNase complex)|nucleolus|nucleoplasm	3'-5'-exoribonuclease activity|endonuclease activity|guanyl-nucleotide exchange factor activity|protein binding|RNA binding				0		Breast(118;0.0074)|Acute lymphoblastic leukemia(28;0.0195)		GBM - Glioblastoma multiforme(99;0.000181)							Multiple Myeloma(4;0.011)			0.625	16.876399	16.985972	5	3	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	72244401	72244401	4714	13	C	T	T	31	31	DIS3	T	1	1
YLPM1	56252	broad.mit.edu	36	14	74334244	74334244	+	Nonsense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:74334244C>T	uc001xqj.2	+	c.2491C>T	c.(2491-2493)CGA>TGA	p.R831*	YLPM1_uc001xql.2_Non-coding_Transcript	NM_019589	NP_062535	P49750	YLPM1_HUMAN	YLP motif containing 1	636					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear speck				ovary(2)|pancreas(1)	3			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)										0.676364	609.309114	616.894265	186	89	CC		KEEP	---	---	---	---	capture			Nonsense_Mutation	SNP	74334244	74334244	18069	14	C	T	T	31	31	YLPM1	T	5	1
DICER1	23405	broad.mit.edu	36	14	94632312	94632312	+	Silent	SNP	C	G	G			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr14:94632312C>G	uc001ydw.2	-	c.4698G>C	c.(4696-4698)CTG>CTC	p.L1566L	DICER1_uc010avh.1_Silent_p.L464L|DICER1_uc001ydv.2_Silent_p.L1556L|DICER1_uc001ydx.2_Silent_p.L1566L|DICER1_uc001ydy.1_Silent_p.L418L	NM_030621	NP_803187	Q9UPY3	DICER_HUMAN	dicer1	1566					negative regulation of Schwann cell proliferation|negative regulation of transcription from RNA polymerase II promoter|nerve development|neuron projection morphogenesis|peripheral nervous system myelin formation|positive regulation of myelination|positive regulation of Schwann cell differentiation|pre-microRNA processing|production of siRNA involved in RNA interference|targeting of mRNA for destruction involved in RNA interference	cytosol|RNA-induced silencing complex	ATP binding|ATP-dependent helicase activity|double-stranded RNA binding|metal ion binding|protein binding|ribonuclease III activity			ovary(1)|pancreas(1)|lung(1)|skin(1)	4		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)						741				0.434084	433.378581	434.556176	135	176	CC		KEEP	---	---	---	---	capture			Silent	SNP	94632312	94632312	4700	14	C	G	G	25	25	DICER1	G	3	3
IL16	3603	broad.mit.edu	36	15	79379353	79379353	+	Silent	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr15:79379353G>A	uc002bgh.2	+	c.2631G>A	c.(2629-2631)AAG>AAA	p.K877K	IL16_uc010blq.1_Silent_p.K831K|IL16_uc002bge.2_Non-coding_Transcript|IL16_uc002bgg.1_Silent_p.K877K|IL16_uc002bgi.1_Silent_p.K267K|IL16_uc002bgj.1_Silent_p.K371K|IL16_uc002bgk.1_Silent_p.K176K|IL16_uc002bgl.1_Silent_p.K176K	NM_172217	NP_757366	Q14005	IL16_HUMAN	interleukin 16 isoform 2	877					immune response|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|extracellular space|nucleus|plasma membrane	cytokine activity			ovary(2)|lung(1)|skin(1)	4														0.5	83.51301	83.51301	27	27	GG		KEEP	---	---	---	---	capture			Silent	SNP	79379353	79379353	7934	15	G	A	A	34	34	IL16	A	2	2
RPL3L	6123	broad.mit.edu	36	16	1935930	1935930	+	Silent	SNP	A	C	C			TCGA-14-0865-01	TCGA-14-0865-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr16:1935930A>C	uc002cnh.1	-	c.954T>G	c.(952-954)GGT>GGG	p.G318G	SEPX1_uc002cng.1_5'Flank	NM_005061	NP_005052	Q92901	RL3L_HUMAN	ribosomal protein L3-like	318					endocrine pancreas development|translational elongation|translational termination|viral transcription	cytosol|ribosome	RNA binding|structural constituent of ribosome				0														0.166667	6.924459	10.725075	6	30	AA		KEEP	---	---	---	---	capture			Silent	SNP	1935930	1935930	14073	16	A	C	C	6	6	RPL3L	C	4	4
PKD1L2	114780	broad.mit.edu	36	16	79790162	79790162	+	Silent	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr16:79790162C>T	uc002fgh.1	-	c.1149G>A	c.(1147-1149)GTG>GTA	p.V383V	PKD1L2_uc002fgj.1_Silent_p.V383V	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN	polycystin 1-like 2 isoform a	383	Extracellular (Potential).				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding			ovary(1)|central_nervous_system(1)|pancreas(1)	3														0.135593	12.759042	20.35008	8	51	CC		KEEP	---	---	---	---	capture			Silent	SNP	79790162	79790162	12389	16	C	T	T	29	29	PKD1L2	T	2	2
PPP4R1	9989	broad.mit.edu	36	18	9585119	9585119	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr18:9585119C>T	uc002koe.1	-	c.85G>A	c.(85-87)GTG>ATG	p.V29M	PPP4R1_uc002kod.1_Intron	NM_001042388	NP_001035847	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	29	HEAT 2.				protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity				0						Melanoma(188;1232 2082 5061 11948 35994)								0.4625	220.917744	221.115049	74	86	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9585119	9585119	12839	18	C	T	T	17	17	PPP4R1	T	2	2
RYR1	6261	broad.mit.edu	36	19	43726263	43726264	+	Missense_Mutation	DNP	GG	CA	CA			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:43726263_43726264GG>CA	uc002oit.1	+	c.11920_11921GG>CA	c.(11920-11922)GGG>CAG	p.G3974Q	RYR1_uc002oiu.1_Missense_Mutation_p.G3969Q|RYR1_uc002oiv.1_Non-coding_Transcript	NM_000540	NP_000531	P21817	RYR1_HUMAN	skeletal muscle ryanodine receptor isoform 1	3974					muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity			ovary(7)|pancreas(2)|breast(1)	10	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Dantrolene(DB01219)									0.409091	21.074902	21.232034	9	13	GG		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	43726263	43726264	14248	19	GG	CA	CA	39	39	RYR1	CA	3	3
CIC	23152	broad.mit.edu	36	19	47487667	47487667	+	Missense_Mutation	SNP	G	C	C			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr19:47487667G>C	uc002otf.1	+	c.2816G>C	c.(2815-2817)GGC>GCC	p.G939A		NM_015125	NP_055940	Q96RK0	CIC_HUMAN	capicua homolog	939	Pro-rich.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding			ovary(4)|breast(4)	8		Prostate(69;0.00682)								241				0.25	6.817779	7.501033	3	9	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47487667	47487667	3558	19	G	C	C	42	42	CIC	C	3	3
SCAF1	58506	broad.mit.edu	36	19	54846144	54846144	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0865-01	TCGA-14-0865-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr19:54846144A>G	uc002poq.1	+	c.686A>G	c.(685-687)GAC>GGC	p.D229G	SCAF1_uc002por.1_Missense_Mutation_p.D229G	NM_021228	NP_067051	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	229	Pro-rich.				mRNA processing|RNA splicing	nucleus	RNA binding				0		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)										0.333333	7.285383	7.698525	5	10	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54846144	54846144	14349	19	A	G	G	10	10	SCAF1	G	4	4
TCHH	7062	broad.mit.edu	36	1	150350736	150350736	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr1:150350736C>G	uc001ezp.2	-	c.1581G>C	c.(1579-1581)AGG>AGC	p.R527S	TCHH_uc009wne.1_Missense_Mutation_p.R527S	NM_007113	NP_009044	Q07283	TRHY_HUMAN	trichohyalin	527	9 X 28 AA approximate tandem repeats.				keratinization	cytoskeleton	calcium ion binding			ovary(3)|kidney(1)|central_nervous_system(1)	5	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)											0.492063	93.23048	93.235072	31	32	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	150350736	150350736	16226	1	C	G	G	26	26	TCHH	G	3	3
SPTA1	6708	broad.mit.edu	36	1	156899327	156899327	+	Silent	SNP	T	C	C			TCGA-14-0865-01	TCGA-14-0865-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:156899327T>C	uc001fst.1	-	c.2253A>G	c.(2251-2253)GCA>GCG	p.A751A		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	751	Spectrin 8.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|breast(1)	5	all_hematologic(112;0.0378)													0.457143	53.998359	54.0541	16	19	TT		KEEP	---	---	---	---	capture			Silent	SNP	156899327	156899327	15630	1	T	C	C	51	51	SPTA1	C	4	4
NADK	65220	broad.mit.edu	36	1	1686684	1686684	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0865-01	TCGA-14-0865-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:1686684T>C	uc001aie.1	-	c.22A>G	c.(22-24)ATG>GTG	p.M8V	NADK_uc009vkw.1_Missense_Mutation_p.M8V|NADK_uc001aic.1_Missense_Mutation_p.M8V|NADK_uc001aid.2_Missense_Mutation_p.M8V|NADK_uc009vkx.1_5'UTR	NM_023018	NP_075394	O95544	NADK_HUMAN	NAD kinase	8					ATP metabolic process|NAD metabolic process|water-soluble vitamin metabolic process	cytosol	ATP binding|metal ion binding|NAD+ kinase activity|protein binding				0	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)										0.25	7.25768	8.402193	5	15	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1686684	1686684	10533	1	T	C	C	52	52	NADK	C	4	4
TNNT2	7139	broad.mit.edu	36	1	199599051	199599051	+	Missense_Mutation	SNP	T	A	A			TCGA-14-0865-01	TCGA-14-0865-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr1:199599051T>A	uc001gwf.1	-	c.596A>T	c.(595-597)CAG>CTG	p.Q199L	TNNT2_uc009wzn.1_5'Flank|TNNT2_uc009wzo.1_5'Flank|TNNT2_uc009wzp.1_5'Flank|TNNT2_uc009wzq.1_Missense_Mutation_p.Q189L|TNNT2_uc001gwg.1_Missense_Mutation_p.Q189L|TNNT2_uc001gwh.1_Missense_Mutation_p.Q184L|TNNT2_uc001gwi.1_Missense_Mutation_p.Q159L|TNNT2_uc009wzr.1_Missense_Mutation_p.Q130L|TNNT2_uc001gwj.1_Non-coding_Transcript|TNNT2_uc009wzs.1_Missense_Mutation_p.Q164L|TNNT2_uc001gwk.1_Missense_Mutation_p.Q130L|TNNT2_uc009wzt.1_Missense_Mutation_p.Q189L	NM_000364	NP_000355	P45379	TNNT2_HUMAN	troponin T type 2, cardiac isoform 1	199					ATP catabolic process|muscle filament sliding|negative regulation of ATPase activity|positive regulation of ATPase activity|regulation of heart contraction|response to calcium ion|response to calcium ion|ventricular cardiac muscle tissue morphogenesis	cytosol|troponin complex	actin binding|tropomyosin binding|troponin C binding|troponin I binding				0														0.404453	659.120817	663.427301	218	321	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	199599051	199599051	16872	1	T	A	A	55	55	TNNT2	A	4	4
RYR2	6262	broad.mit.edu	36	1	235847329	235847329	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:235847329G>A	uc001hyl.1	+	c.5836G>A	c.(5836-5838)GAA>AAA	p.E1946K		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1946	Cytoplasmic (By similarity).|4 X approximate repeats.				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding			ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)											0.282812	480.302764	507.425292	181	459	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	235847329	235847329	14249	1	G	A	A	37	37	RYR2	A	1	1
OSCP1	127700	broad.mit.edu	36	1	36661556	36661556	+	Silent	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr1:36661556G>A	uc001cap.1	-	c.645C>T	c.(643-645)CTC>CTT	p.L215L	OSCP1_uc001caq.1_Silent_p.L205L	NM_145047	NP_659484	Q8WVF1	OSCP1_HUMAN	oxidored-nitro domain-containing protein isoform	215					transport	basal plasma membrane				ovary(2)|central_nervous_system(1)|pancreas(1)	4														0.179487	28.798866	36.341226	14	64	GG		KEEP	---	---	---	---	capture			Silent	SNP	36661556	36661556	11697	1	G	A	A	45	45	OSCP1	A	2	2
KRTAP10-7	386675	broad.mit.edu	36	21	44845848	44845848	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:44845848C>T	uc002zfn.2	+	c.884C>T	c.(883-885)CCG>CTG	p.P295L	C21orf29_uc002zfe.1_Intron|C21orf29_uc010gpv.1_Intron	NM_198689	NP_941962	P60409	KR107_HUMAN	keratin associated protein 10-7	300	30 X 5 AA repeats of C-C-X(3).					keratin filament					0														0.425532	125.188296	125.64163	40	54	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	44845848	44845848	8829	21	C	T	T	23	23	KRTAP10-7	T	1	1
TPTE	7179	broad.mit.edu	36	21	9955747	9955747	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr21:9955747C>T	uc002yip.1	-	c.1003G>A	c.(1003-1005)GCG>ACG	p.A335T	TPTE_uc002yiq.1_Missense_Mutation_p.A317T|TPTE_uc002yir.1_Missense_Mutation_p.A297T|TPTE_uc010gkv.1_Missense_Mutation_p.A197T|TPTE_uc002yis.1_Non-coding_Transcript	NM_199261	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	335	Phosphatase tensin-type.				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity			ovary(2)|lung(1)|breast(1)|skin(1)	5			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)										0.176147	204.557315	258.449112	96	449	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	9955747	9955747	16974	21	C	T	T	28	28	TPTE	T	2	2
RAD51AP2	729475	broad.mit.edu	36	2	17562947	17562947	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr2:17562947C>T	uc002rcl.1	-	c.217G>A	c.(217-219)GGA>AGA	p.G73R	RAD51AP2_uc010exn.1_Missense_Mutation_p.G64R	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	73										ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)													0.545455	18.549841	18.569506	6	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17562947	17562947	13447	2	C	T	T	22	22	RAD51AP2	T	2	2
CERKL	375298	broad.mit.edu	36	2	182176977	182176977	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:182176977G>A	uc002unx.1	-	c.313C>T	c.(313-315)CGG>TGG	p.R105W	CERKL_uc010frk.1_Non-coding_Transcript|CERKL_uc002uny.1_Missense_Mutation_p.R105W|CERKL_uc002unz.1_De_novo_Start_InFrame|CERKL_uc002uob.1_De_novo_Start_InFrame|CERKL_uc002uoa.1_Missense_Mutation_p.R105W|CERKL_uc002uoc.1_Missense_Mutation_p.R105W|CERKL_uc002uod.1_De_novo_Start_OutOfFrame|CERKL_uc002uoe.1_Missense_Mutation_p.R105W	NM_001030311	NP_001025482	Q49MI3	CERKL_HUMAN	ceramide kinase-like isoform b	105	Nuclear localization signal 2.			KRR->GGG: Only cytoplasmic.	activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|anti-apoptosis|visual perception	endoplasmic reticulum|endoplasmic reticulum|Golgi apparatus|Golgi apparatus|nucleolus|nucleolus	diacylglycerol kinase activity			ovary(2)|kidney(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(117;0.088)											0.448276	81.142762	81.277829	26	32	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	182176977	182176977	3401	2	G	A	A	40	40	CERKL	A	1	1
EPCAM	4072	broad.mit.edu	36	2	47454160	47454160	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr2:47454160G>A	uc002rvw.1	+	c.215G>A	c.(214-216)CGT>CAT	p.R72H	EPCAM_uc002rvx.1_Missense_Mutation_p.R44H	NM_002354	NP_002345	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule precursor	44	Extracellular (Potential).				positive regulation of cell proliferation	apical plasma membrane|basolateral plasma membrane|integral to membrane|lateral plasma membrane|tight junction	protein binding				0														0.419355	41.377223	41.551039	13	18	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	47454160	47454160	5355	2	G	A	A	40	40	EPCAM	A	1	1
ZDHHC23	254887	broad.mit.edu	36	3	115155760	115155760	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0865-01	TCGA-14-0865-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:115155760A>G	uc003eau.1	+	c.685A>G	c.(685-687)ATG>GTG	p.M229V	ZDHHC23_uc003eav.1_Missense_Mutation_p.M223V	NM_173570	NP_775841	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC domain containing 23	229						integral to membrane	acyltransferase activity|zinc ion binding			ovary(2)	2														0.528736	148.551431	148.613915	46	41	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	115155760	115155760	18202	3	A	G	G	8	8	ZDHHC23	G	4	4
HCLS1	3059	broad.mit.edu	36	3	122837289	122837289	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr3:122837289G>A	uc003eeh.2	-	c.674C>T	c.(673-675)ACG>ATG	p.T225M		NM_005335	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	225					erythrocyte differentiation|intracellular signal transduction|positive regulation of cell proliferation|positive regulation of tyrosine phosphorylation of STAT protein|regulation of transcription, DNA-dependent|response to hormone stimulus	mitochondrion|nucleus|plasma membrane	DNA binding|sequence-specific DNA binding transcription factor activity				0				GBM - Glioblastoma multiforme(114;0.0912)										0.530702	371.074472	371.261409	121	107	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	122837289	122837289	7277	3	G	A	A	40	40	HCLS1	A	1	1
OXSM	54995	broad.mit.edu	36	3	25808284	25808284	+	Missense_Mutation	SNP	A	T	T			TCGA-14-0865-01	TCGA-14-0865-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr3:25808284A>T	uc003cdn.1	+	c.769A>T	c.(769-771)AAC>TAC	p.N257Y	OXSM_uc010hfh.1_Intron	NM_017897	NP_060367	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial isoform 1	257					acyl-CoA metabolic process|medium-chain fatty acid biosynthetic process|short-chain fatty acid biosynthetic process	mitochondrion	3-oxoacyl-[acyl-carrier-protein] synthase activity			ovary(1)|breast(1)	2														0.426087	438.761415	440.406223	147	198	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	25808284	25808284	11748	3	A	T	T	1	1	OXSM	T	4	4
ANK2	287	broad.mit.edu	36	4	114336988	114336988	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:114336988C>T	uc003ibe.2	+	c.202C>T	c.(202-204)CTC>TTC	p.L68F	ANK2_uc003ibc.1_Missense_Mutation_p.L44F|ANK2_uc003ibd.2_Missense_Mutation_p.L47F|ANK2_uc003ibf.2_Missense_Mutation_p.L68F	NM_001148	NP_001139	Q01484	ANK2_HUMAN	ankyrin 2 isoform 1	68	ANK 2.				axon guidance|signal transduction	apical plasma membrane|basolateral plasma membrane|cytoskeleton|cytosol|sarcomere	protein binding|protein binding			central_nervous_system(7)|ovary(3)|large_intestine(2)|breast(1)	13		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)										0.373494	87.39679	88.565851	31	52	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	114336988	114336988	624	4	C	T	T	32	32	ANK2	T	2	2
ZFP42	132625	broad.mit.edu	36	4	189161747	189161747	+	Silent	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr4:189161747G>A	uc003izg.1	+	c.792G>A	c.(790-792)ACG>ACA	p.T264T	ZFP42_uc003izh.1_Silent_p.T264T|ZFP42_uc003izi.1_Silent_p.T264T|ZFP42_uc010isp.1_Silent_p.T264T	NM_174900	NP_777560	Q96MM3	ZFP42_HUMAN	zinc finger protein 42	264	C2H2-type 3.				female gonad development|male gonad development|meiosis|regulation of transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)										0.258427	57.483548	62.190759	23	66	GG		KEEP	---	---	---	---	capture			Silent	SNP	189161747	189161747	18238	4	G	A	A	38	38	ZFP42	A	1	1
TRIML1	339976	broad.mit.edu	36	4	189305411	189305411	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:189305411C>T	uc003izm.1	+	c.1298C>T	c.(1297-1299)CCG>CTG	p.P433L	TRIML1_uc003izn.1_Missense_Mutation_p.P157L	NM_178556	NP_848651	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	433	B30.2/SPRY.				multicellular organismal development		ligase activity|zinc ion binding			ovary(1)|breast(1)|pancreas(1)	3		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		Melanoma(31;213 1036 16579 23968 32372)								0.435185	149.616827	150.010518	47	61	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	189305411	189305411	17100	4	C	T	T	23	23	TRIML1	T	1	1
PDGFRA	5156	broad.mit.edu	36	4	54834499	54834499	+	Missense_Mutation	SNP	A	G	G			TCGA-14-0865-01	TCGA-14-0865-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chr4:54834499A>G	uc003han.2	+	c.1403A>G	c.(1402-1404)AAT>AGT	p.N468S	PDGFRA_uc003haa.1_Intron|PDGFRA_uc010igq.1_Missense_Mutation_p.N362S|PDGFRA_uc003ham.2_Non-coding_Transcript	NM_006206	NP_006197	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor alpha	468	Ig-like C2-type 5.|Extracellular (Potential).				cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity			soft_tissue(532)|small_intestine(40)|stomach(16)|central_nervous_system(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|ovary(3)|skin(2)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|bone(1)	625	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)	Pancreas(151;208 1913 7310 23853 37092)				1045	TSP Lung(21;0.16)			0.885312	1542.520173	1615.243006	440	57	AA		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	54834499	54834499	12082	4	A	G	G	4	4	PDGFRA	G	4	4
TBC1D14	57533	broad.mit.edu	36	4	6976516	6976516	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0865-01	TCGA-14-0865-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr4:6976516T>C	uc003gjs.2	+	c.499T>C	c.(499-501)TCC>CCC	p.S167P	TBC1D14_uc010idg.1_Missense_Mutation_p.S152P	NM_020773	NP_065824	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14 isoform a	167						intracellular	Rab GTPase activator activity			ovary(1)|pancreas(1)	2														0.375	6.721387	6.831658	3	5	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	6976516	6976516	16125	4	T	C	C	58	58	TBC1D14	C	4	4
AMBN	258	broad.mit.edu	36	4	71504214	71504214	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr4:71504214C>T	uc003hfl.1	+	c.785C>T	c.(784-786)TCA>TTA	p.S262L		NM_016519	NP_057603	Q9NP70	AMBN_HUMAN	ameloblastin precursor	262					bone mineralization|cell adhesion|cell proliferation|odontogenesis of dentine-containing tooth	proteinaceous extracellular matrix	growth factor activity|structural constituent of tooth enamel			ovary(3)	3			Lung(101;0.235)											0.427273	147.506653	148.014411	47	63	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	71504214	71504214	566	4	C	T	T	29	29	AMBN	T	2	2
SLCO4C1	353189	broad.mit.edu	36	5	101623835	101623835	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0865-01	TCGA-14-0865-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr5:101623835T>C	uc003knm.1	-	c.1109A>G	c.(1108-1110)GAT>GGT	p.D370G		NM_180991	NP_851322	Q6ZQN7	SO4C1_HUMAN	solute carrier organic anion transporter family,	370	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|sodium-independent organic anion transport|spermatogenesis	basolateral plasma membrane|integral to membrane	sodium-independent organic anion transmembrane transporter activity			ovary(1)|central_nervous_system(1)|pancreas(1)	3		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)										0.333333	9.422253	9.643532	3	6	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	101623835	101623835	15227	5	T	C	C	50	50	SLCO4C1	C	4	4
HCN1	348980	broad.mit.edu	36	5	45298224	45298224	+	Silent	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr5:45298224C>T	uc003jok.1	-	c.2229G>A	c.(2227-2229)CCG>CCA	p.P743P		NM_021072	NP_066550	O60741	HCN1_HUMAN	hyperpolarization activated cyclic	743	Gln-rich.|Cytoplasmic (Potential).					integral to membrane	cAMP binding|sodium channel activity|voltage-gated potassium channel activity			ovary(1)	1														0.615385	26.503287	26.655566	8	5	CC		KEEP	---	---	---	---	capture			Silent	SNP	45298224	45298224	7278	5	C	T	T	27	27	HCN1	T	1	1
UHRF1BP1	54887	broad.mit.edu	36	6	34934308	34934308	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr6:34934308C>T	uc003oju.2	+	c.2197C>T	c.(2197-2199)CGC>TGC	p.R733C	UHRF1BP1_uc010jvm.1_Non-coding_Transcript|UHRF1BP1_uc010jvn.1_Non-coding_Transcript|UHRF1BP1_uc010jvo.1_Non-coding_Transcript	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1	733										ovary(3)	3														0.75	49.531322	50.666508	15	5	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	34934308	34934308	17526	6	C	T	T	23	23	UHRF1BP1	T	1	1
ICK	22858	broad.mit.edu	36	6	52991196	52991196	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr6:52991196G>A	uc003pbh.2	-	c.554C>T	c.(553-555)GCG>GTG	p.A185V	ICK_uc003pbi.2_Missense_Mutation_p.A185V|ICK_uc003pbj.1_Missense_Mutation_p.A185V	NM_016513	NP_057597	Q9UPZ9	ICK_HUMAN	intestinal cell kinase	185	Protein kinase.				intracellular protein kinase cascade|multicellular organismal development|protein phosphorylation	cytosol|nucleus	ATP binding|cyclin-dependent protein kinase activity|magnesium ion binding			ovary(1)|large_intestine(1)|lung(1)|kidney(1)|central_nervous_system(1)	5	Lung NSC(77;0.103)									283				0.580175	628.245231	630.16642	199	144	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	52991196	52991196	7784	6	G	A	A	38	38	ICK	A	1	1
PIK3CG	5294	broad.mit.edu	36	7	106295668	106295668	+	Silent	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:106295668G>A	uc003vdv.2	+	c.426G>A	c.(424-426)CCG>CCA	p.P142P	PIK3CG_uc003vdu.1_Silent_p.P142P|PIK3CG_uc003vdw.1_Silent_p.P142P	NM_002649	NP_002640	P48736	PK3CG_HUMAN	phosphoinositide-3-kinase, catalytic, gamma	142					G-protein coupled receptor protein signaling pathway|phosphatidylinositol-mediated signaling|platelet activation	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity|protein binding			central_nervous_system(8)|lung(7)|pancreas(3)|ovary(2)|skin(1)	21										292				0.423077	29.016727	29.151576	11	15	GG		KEEP	---	---	---	---	capture			Silent	SNP	106295668	106295668	12340	7	G	A	A	38	38	PIK3CG	A	1	1
FLNC	2318	broad.mit.edu	36	7	128278162	128278162	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:128278162C>T	uc003vnz.2	+	c.5468C>T	c.(5467-5469)ACG>ATG	p.T1823M	FLNC_uc003voa.2_Missense_Mutation_p.T1790M	NM_001458	NP_001449	Q14315	FLNC_HUMAN	gamma filamin isoform a	1823	Filamin 16.				cell junction assembly	cytoskeleton|cytosol|plasma membrane|sarcomere	actin binding			breast(5)|large_intestine(3)|ovary(2)	10										892				0.49711	275.945806	275.947046	86	87	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	128278162	128278162	6177	7	C	T	T	19	19	FLNC	T	1	1
ZNF212	7988	broad.mit.edu	36	7	148578537	148578537	+	Missense_Mutation	SNP	C	T	T			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr7:148578537C>T	uc003wfp.1	+	c.379C>T	c.(379-381)CGG>TGG	p.R127W		NM_012256	NP_036388	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	127					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|identical protein binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)											0.53125	55.160299	55.186618	17	15	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	148578537	148578537	18359	7	C	T	T	27	27	ZNF212	T	1	1
INTS1	26173	broad.mit.edu	36	7	1504912	1504912	+	Missense_Mutation	SNP	G	A	A			TCGA-14-0865-01	TCGA-14-0865-01	G	G								Phase_I	Unspecified				Illumina GAIIx	g.chr7:1504912G>A	uc003skn.2	-	c.1240C>T	c.(1240-1242)CTC>TTC	p.L414F	INTS1_uc003skq.2_Missense_Mutation_p.L414F	NM_001080453	NP_001073922	Q8N201	INT1_HUMAN	integrator complex subunit 1	414					snRNA processing	integral to membrane|integrator complex|nuclear membrane					0		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)										0.22619	50.884504	56.664217	19	65	GG		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	1504912	1504912	8076	7	G	A	A	35	35	INTS1	A	2	2
DNAH11	8701	broad.mit.edu	36	7	21756431	21756431	+	Missense_Mutation	SNP	T	C	C			TCGA-14-0865-01	TCGA-14-0865-01	T	T								Phase_I	Unspecified				Illumina GAIIx	g.chr7:21756431T>C	uc003svc.1	+	c.8885T>C	c.(8884-8886)GTT>GCT	p.V2962A		NM_003777	NP_003768	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2962	AAA 4 (By similarity).				microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15														0.385689	713.346387	719.907038	221	352	TT		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	21756431	21756431	4781	7	T	C	C	60	60	DNAH11	C	4	4
CNOT7	29883	broad.mit.edu	36	8	17134387	17134387	+	Missense_Mutation	SNP	C	G	G			TCGA-14-0865-01	TCGA-14-0865-01	C	C								Phase_I	Unspecified				Illumina GAIIx	g.chr8:17134387C>G	uc003wxf.1	-	c.649G>C	c.(649-651)GAG>CAG	p.E217Q	CNOT7_uc003wxg.1_Missense_Mutation_p.E217Q|CNOT7_uc003wxh.1_Missense_Mutation_p.E217Q	NM_013354	NP_037486	Q9UIV1	CNOT7_HUMAN	CCR4-NOT transcription complex, subunit 7	217					carbohydrate metabolic process|nuclear-transcribed mRNA poly(A) tail shortening	CCR4-NOT complex|cytoplasmic mRNA processing body|cytosol	nucleic acid binding|protein binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			central_nervous_system(1)	1				Colorectal(111;0.0523)|COAD - Colon adenocarcinoma(73;0.209)										0.433437	476.759466	478.005822	140	183	CC		KEEP	---	---	---	---	capture			Missense_Mutation	SNP	17134387	17134387	3762	8	C	G	G	32	32	CNOT7	G	3	3
ESX1	80712	broad.mit.edu	36	X	103381680	103381681	+	Missense_Mutation	DNP	CC	TG	TG			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chrX:103381680_103381681CC>TG	uc004ely.1	-	c.1105_1106GG>CA	c.(1105-1107)GGG>CAG	p.G369Q		NM_153448	NP_703149	Q8N693	ESX1_HUMAN	extraembryonic, spermatogenesis, homeobox	369	15 X 9 AA tandem repeats of P-P-x-x-P-x- P-P-x.|14.				regulation of cell cycle|regulation of transcription, DNA-dependent	cytoplasm|nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|specific transcriptional repressor activity			ovary(1)	1						Pancreas(200;1705 2227 25194 28471 45274)								0.25	12.318002	13.906401	7	21	CC		KEEP	---	---	---	---	capture			Missense_Mutation	DNP	103381680	103381681	5456	23	CC	TG	TG	22	22	ESX1	TG	2	2
IL1RAPL2	26280	broad.mit.edu	36	X	104871252	104871252	+	Silent	SNP	A	T	T			TCGA-14-0865-01	TCGA-14-0865-01	A	A								Phase_I	Unspecified				Illumina GAIIx	g.chrX:104871252A>T	uc004elz.1	+	c.960A>T	c.(958-960)TCA>TCT	p.S320S		NM_017416	NP_059112	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	320	Ig-like C2-type 3.|Extracellular (Potential).				central nervous system development|innate immune response	integral to membrane	interleukin-1, Type II, blocking receptor activity			breast(2)|ovary(1)	3														0.942598	1168.035305	1208.762115	312	19	AA		KEEP	---	---	---	---	capture			Silent	SNP	104871252	104871252	7963	23	A	T	T	7	7	IL1RAPL2	T	4	4
KDM2B	84678	broad.mit.edu	36	12	120431749	120431755	+	Splice_Site_Del	DEL	CCACCTT	-	-			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr12:120431749_120431755delCCACCTT	uc001uat.1	-	c.e11_splice_site			KDM2B_uc001uas.1_Splice_Site_Del|KDM2B_uc009zxe.1_Splice_Site_Del|KDM2B_uc001uau.1_Splice_Site_Del|KDM2B_uc009zxf.1_Splice_Site_Del|KDM2B_uc001uav.2_Splice_Site_Del|KDM2B_uc001uar.1_Splice_Site_Del	NM_032590	NP_115979			F-box and leucine-rich repeat protein 10 isoform						oxidation-reduction process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|histone demethylase activity (H3-K36 specific)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen|protein binding|rRNA binding|zinc ion binding			ovary(1)	1														0.38			8	13				---	---	---	---	capture_indel			Splice_Site_Del	DEL	120431749	120431755	8431	12	CCACCTT	-	-	22	22	KDM2B	-	5	5
SEPT12	124404	broad.mit.edu	36	16	4767851	4767852	+	Frame_Shift_Ins	INS	-	G	G			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr16:4767851_4767852insG	uc002cxq.1	-	c.1024_1025insC	c.(1024-1026)CGGfs	p.R342fs	SEPT12_uc010bty.1_Non-coding_Transcript|SEPT12_uc002cxr.1_Frame_Shift_Ins_p.R296fs	NM_144605	NP_653206	Q8IYM1	SEP12_HUMAN	septin 12	342					cell cycle|cell division	cleavage furrow|midbody|perinuclear region of cytoplasm|septin complex|spindle|stress fiber	GDP binding|GTP binding|phosphatidylinositol binding|protein homodimerization activity				0														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	4767851	4767852	14548	16	-	G	G	23	23	SEPT12	G	5	5
RHBDF2	79651	broad.mit.edu	36	17	71986530	71986530	+	Frame_Shift_Del	DEL	T	-	-			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr17:71986530_71986530delT	uc002jrq.1	-	c.712_712delA	c.(712-714)ATGfs	p.M238fs	RHBDF2_uc002jrp.1_Frame_Shift_Del_p.M209fs|RHBDF2_uc002jrr.1_Frame_Shift_Del_p.M90fs|RHBDF2_uc002jrs.1_Frame_Shift_Del_p.M233fs	NM_024599	NP_078875	Q6PJF5	RHDF2_HUMAN	rhomboid, veinlet-like 6 isoform 1	238	Cytoplasmic (Potential).				negative regulation of protein secretion	endoplasmic reticulum membrane|integral to membrane	serine-type endopeptidase activity				0														0.38			3	5				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	71986530	71986530	13795	17	T	-	-	52	52	RHBDF2	-	5	5
LILRA6	79168	broad.mit.edu	36	19	59436780	59436783	+	Frame_Shift_Del	DEL	CCTG	-	-			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:59436780_59436783delCCTG	uc002qek.1	-	c.691_694delCAGG	c.(691-696)CAGGGCfs	p.Q231fs	LILRB3_uc002qes.1_Intron|LILRB3_uc002qeg.1_Intron|LILRB3_uc002qeh.1_Intron|LILRB3_uc002qei.1_Intron|LILRB3_uc010erh.1_Intron|LILRB3_uc002qej.1_Intron|LILRA6_uc002qel.1_Frame_Shift_Del_p.Q231fs|LILRA6_uc002qem.1_Non-coding_Transcript|LILRB3_uc002qen.1_Non-coding_Transcript|LILRB3_uc002qeo.1_Frame_Shift_Del_p.Q231fs|LILRB3_uc002qep.1_Intron|LILRB3_uc002qeq.1_Frame_Shift_Del_p.Q231fs|LILRB3_uc002qer.1_Non-coding_Transcript|LILRA6_uc002qet.2_Non-coding_Transcript|LILRA6_uc002qeu.1_Frame_Shift_Del_p.Q231fs|LILRA6_uc002qev.1_Frame_Shift_Del_p.Q92fs	NM_024318	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor,	231_232	Extracellular (Potential).|Ig-like C2-type 1.					integral to membrane	receptor activity				0	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)										0.58			11	8				---	---	---	---	capture_indel			Frame_Shift_Del	DEL	59436780	59436783	9115	19	CCTG	-	-	22	22	LILRA6	-	5	5
TNFSF14	8740	broad.mit.edu	36	19	6616329	6616330	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr19:6616329_6616330insC	uc002mfk.1	-	c.330_331insG	c.(328-333)GGGCCGfs	p.G110fs	TNFSF14_uc002mfj.1_Frame_Shift_Ins_p.G74fs	NM_003807	NP_003798	O43557	TNF14_HUMAN	tumor necrosis factor ligand superfamily, member	110_111	Extracellular (Potential).				cellular response to mechanical stimulus|immune response|induction of apoptosis|release of cytoplasmic sequestered NF-kappaB|T cell homeostasis|T cell proliferation	cytoplasm|extracellular space|integral to membrane|plasma membrane	caspase inhibitor activity|cytokine activity|tumor necrosis factor receptor binding				0														0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	6616329	6616330	16848	19	-	C	C	42	42	TNFSF14	C	5	5
MSTO1	55154	broad.mit.edu	36	1	153850166	153850167	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:153850166_153850167insC	uc001fky.1	+	c.1483_1484insC	c.(1483-1485)TCCfs	p.S495fs	MSTO1_uc001fkw.2_Intron|MSTO1_uc001fkx.2_Frame_Shift_Ins_p.S495fs|MSTO1_uc001fld.2_Intron|MSTO1_uc001fkz.1_Frame_Shift_Ins_p.S426fs|MSTO1_uc009wqs.1_Frame_Shift_Ins_p.S374fs|MSTO1_uc001fla.1_Frame_Shift_Ins_p.S314fs|MSTO1_uc001flb.1_Frame_Shift_Ins_p.F376fs|MSTO1_uc001flc.2_Frame_Shift_Ins_p.S317fs	NM_018116	NP_060586	Q9BUK6	MSTO1_HUMAN	misato	495					mitochondrion distribution|protein polymerization	mitochondrial outer membrane|protein complex					0	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)													0.33			2	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	153850166	153850167	10287	1	-	C	C	62	62	MSTO1	C	5	5
HSPG2	3339	broad.mit.edu	36	1	22046504	22046505	+	Frame_Shift_Ins	INS	-	A	A			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:22046504_22046505insA	uc009vqd.1	-	c.8096_8097insT	c.(8095-8097)GCCfs	p.A2699fs	HSPG2_uc001bfj.1_Frame_Shift_Ins_p.A2698fs	NM_005529	NP_005520	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2698	Ig-like C2-type 12.				angiogenesis|cell adhesion|lipid metabolic process|lipoprotein metabolic process	basement membrane|extracellular space|plasma membrane	protein C-terminus binding			ovary(5)|large_intestine(2)|central_nervous_system(1)	8		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Becaplermin(DB00102)|Palifermin(DB00039)									0.50			4	4				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	22046504	22046505	7730	1	-	A	A	47	47	HSPG2	A	5	5
MAP7D1	55700	broad.mit.edu	36	1	36409350	36409351	+	Frame_Shift_Ins	INS	-	C	C			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr1:36409350_36409351insC	uc001bzz.1	+	c.238_239insC	c.(238-240)GCCfs	p.A80fs	MAP7D1_uc001caa.1_Frame_Shift_Ins_p.A80fs|MAP7D1_uc001cab.1_Frame_Shift_Ins_p.A80fs|MAP7D1_uc001cac.1_5'Flank	NM_018067	NP_060537	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	80	Pro-rich.					cytoplasm|spindle				ovary(3)|breast(2)	5		Myeloproliferative disorder(586;0.0393)												0.36			4	7				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	36409350	36409351	9650	1	-	C	C	34	34	MAP7D1	C	5	5
GUSB	2990	broad.mit.edu	36	7	65072687	65072703	+	Splice_Site_Del	DEL	GGGACCCCCAGGCTCAC	-	-			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr7:65072687_65072703delGGGACCCCCAGGCTCAC	uc003tun.1	-	c.e9_splice_site				NM_000181	NP_000172			glucuronidase, beta						glycosaminoglycan catabolic process	lysosome	beta-glucuronidase activity|cation binding				0														0.36			39	70				---	---	---	---	capture_indel			Splice_Site_Del	DEL	65072687	65072703	7182	7	GGGACCCCCAGGCTCAC	-	-	43	43	GUSB	-	5	5
WHSC1L1	54904	broad.mit.edu	36	8	38314130	38314131	+	Frame_Shift_Ins	INS	-	T	T			TCGA-14-0865-01	TCGA-14-0865-01										Phase_I	Unspecified				Illumina GAIIx	g.chr8:38314130_38314131insT	uc003xli.1	-	c.759_760insA	c.(757-762)ATACTAfs	p.I253fs	WHSC1L1_uc010lwe.1_Frame_Shift_Ins_p.I253fs|WHSC1L1_uc003xlj.1_Frame_Shift_Ins_p.I253fs	NM_023034	NP_075447	Q9BZ95	NSD3_HUMAN	WHSC1L1 protein isoform long	253_254					cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome|nucleus	histone-lysine N-methyltransferase activity|zinc ion binding				0	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)						p.L254L(JHOC5-Tumor)	521				0.38			96	154				---	---	---	---	capture_indel			Frame_Shift_Ins	INS	38314130	38314131	17937	8	-	T	T	36	36	WHSC1L1	T	5	5
