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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	t_alt_count	t_ref_count	validation_status	validation_method	validation_tumor_sample	validation_alt_allele	pox	qox	pox_cutoff	isArtifactMode	oxoGCut
KIF1B	23095	broad.mit.edu	37	1	10342493	10342493	+	Missense_Mutation	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:10342493T>A	uc001aqx.3	+	15	1538	c.1336T>A	c.(1336-1338)TGC>AGC	p.C446S	KIF1B_uc001aqv.3_Missense_Mutation_p.C400S|KIF1B_uc001aqw.3_Missense_Mutation_p.C400S|KIF1B_uc001aqy.2_Missense_Mutation_p.C420S|KIF1B_uc001aqz.2_Missense_Mutation_p.C446S|KIF1B_uc001ara.2_Missense_Mutation_p.C406S|KIF1B_uc001arb.2_Missense_Mutation_p.C432S	NM_015074	NP_055889	O60333	KIF1B_HUMAN	kinesin family member 1B isoform b	446					anterograde axon cargo transport|apoptosis|neuromuscular synaptic transmission|neuron-neuron synaptic transmission	cytoplasmic vesicle membrane|microtubule|microtubule associated complex|mitochondrion	ATP binding|ATPase activity|kinesin binding|microtubule motor activity|protein binding			ovary(2)|upper_aerodigestive_tract(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CCCATCTTCCTGCTCACTCAG	0.483000													21	105					0	0	0.055883	0	0
SCMH1	22955	broad.mit.edu	37	1	41503104	41503104	+	Silent	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:41503104G>A	uc001cgo.2	-	13	1889	c.1578C>T	c.(1576-1578)CAC>CAT	p.H526H	SCMH1_uc010ojr.1_Silent_p.H368H|SCMH1_uc001cgp.2_Silent_p.H465H|SCMH1_uc001cgr.2_Silent_p.H465H|SCMH1_uc001cgs.2_Silent_p.H536H|SCMH1_uc001cgt.2_Silent_p.H465H|SCMH1_uc001cgq.2_Silent_p.H479H|SCMH1_uc010ojs.1_RNA	NM_001031694	NP_001026864	Q96GD3	SCMH1_HUMAN	sex comb on midleg 1 isoform 1	526					anatomical structure morphogenesis|gene silencing|multicellular organismal development|negative regulation of transcription, DNA-dependent		DNA binding|sequence-specific DNA binding transcription factor activity				0	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)|Breast(333;0.162)	Myeloproliferative disorder(586;0.0393)				GCAAGGGCCGGTGCCTTTGGG	0.557000													20	129					0	0	0.062417	0	0
PTGFR	5737	broad.mit.edu	37	1	78959187	78959187	+	Silent	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:78959187G>A	uc001din.2	+	2	1025	c.759G>A	c.(757-759)GCG>GCA	p.A253A	PTGFR_uc001dim.2_Silent_p.A253A	NM_000959	NP_000950	P43088	PF2R_HUMAN	prostaglandin F receptor isoform a precursor	253	Helical; Name=6; (Potential).				parturition	extracellular region|integral to plasma membrane	prostaglandin F receptor activity	p.A253V(1)		ovary(3)|breast(2)|skin(1)	6				Colorectal(170;0.248)	Bimatoprost(DB00905)|Latanoprost(DB00654)|Travoprost(DB00287)	AGCTCCTGGCGATAATGTGTG	0.393000													14	94					0	0	0.024245	0	0
AGL	178	broad.mit.edu	37	1	100346330	100346330	+	Missense_Mutation	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:100346330T>A	uc001dsi.1	+	14	2278	c.1878T>A	c.(1876-1878)CAT>CAA	p.H626Q	AGL_uc001dsj.1_Missense_Mutation_p.H626Q|AGL_uc001dsk.1_Missense_Mutation_p.H626Q|AGL_uc001dsl.1_Missense_Mutation_p.H626Q|AGL_uc001dsm.1_Missense_Mutation_p.H610Q|AGL_uc001dsn.1_Missense_Mutation_p.H609Q	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,	626	4-alpha-glucanotransferase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		ATATTACGCATGATAATGAGT	0.388000													3	55					0	0	0.009096	0	0
LRIG2	9860	broad.mit.edu	37	1	113657326	113657326	+	Silent	SNP	C	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:113657326C>A	uc001edf.1	+	15	2556	c.2358C>A	c.(2356-2358)TCC>TCA	p.S786S	LRIG2_uc009wgn.1_Silent_p.S683S	NM_014813	NP_055628	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like	786	Extracellular (Potential).					cytoplasm|integral to membrane|plasma membrane				ovary(3)	3	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		TCATTTCATCCCCCAATTGTG	0.468000													10	82					9.31168e-06	1.03698e-05	0.105934	1	0
RPTN	126638	broad.mit.edu	37	1	152127897	152127897	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:152127897C>T	uc001ezs.1	-	3	1743	c.1678G>A	c.(1678-1680)GGT>AGT	p.G560S		NM_001122965	NP_001116437	Q6XPR3	RPTN_HUMAN	repetin	560	Gln-rich.					proteinaceous extracellular matrix	calcium ion binding				0						TCTGTCTGACCGTAGTGGGAA	0.502000													6	266					0	0	0.021553	0	0
PEX19	5824	broad.mit.edu	37	1	160253370	160253370	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:160253370C>T	uc001fvs.2	-	2	157	c.130G>A	c.(130-132)GCC>ACC	p.A44T	DCAF8_uc010pjc.1_Intron|PEX19_uc010pje.1_RNA|PEX19_uc001fvt.2_Intron	NM_002857	NP_002848	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19 isoform a	44	Necessary for PEX19 function on peroxisome biogenesis.|Docking to the peroxisome membrane and binding to PEX3.				peroxisome membrane biogenesis|peroxisome organization|protein targeting to peroxisome|transmembrane transport	brush border membrane|cytosol|integral to membrane|nucleus|peroxisomal membrane	protein binding|protein N-terminus binding				0	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GCATCAGGGGCCGTGGTGGTA	0.562000													20	124					0	0	0.083992	0	0
RYR2	6262	broad.mit.edu	37	1	237713899	237713899	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:237713899G>A	uc001hyl.1	+	27	3242	c.3122G>A	c.(3121-3123)CGA>CAA	p.R1041Q		NM_001035	NP_001026	Q92736	RYR2_HUMAN	cardiac muscle ryanodine receptor	1041	Cytoplasmic (By similarity).|2.|B30.2/SPRY 2.|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|cytosol|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)			CTGGATGACCGAACCAAGAAA	0.522000													3	15					0	0	0.004672	0	0
EPC1	80314	broad.mit.edu	37	10	32560793	32560793	+	Silent	SNP	A	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:32560793A>G	uc001iwg.1	-	14	2397	c.2127T>C	c.(2125-2127)CAT>CAC	p.H709H	EPC1_uc001iwi.3_Silent_p.H636H|EPC1_uc001iwh.1_Silent_p.H686H	NM_025209	NP_079485	Q9H2F5	EPC1_HUMAN	enhancer of polycomb 1	709					histone H2A acetylation|histone H4 acetylation|negative regulation of gene expression, epigenetic|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of growth|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|nuclear membrane|Piccolo NuA4 histone acetyltransferase complex				ovary(3)|central_nervous_system(1)	4		Prostate(175;0.0199)				ATGGACTTGTATGTACAAGTG	0.413000													4	28					0	0	0.014758	0	0
CUEDC2	79004	broad.mit.edu	37	10	104184514	104184514	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:104184514C>T	uc001kvn.2	-	3	261	c.110G>A	c.(109-111)GGG>GAG	p.G37E	CUEDC2_uc001kvm.2_5'Flank	NM_024040	NP_076945	Q9H467	CUED2_HUMAN	CUE domain containing 2	37						cytoplasm|nucleus	protein binding				0		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		CTCCAGGACCCCAAGCACATA	0.592000													27	163					0	0	0.091800	0	0
HTRA1	5654	broad.mit.edu	37	10	124273765	124273765	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:124273765G>A	uc001lgj.2	+	9	1461	c.1333G>A	c.(1333-1335)GCC>ACC	p.A445T		NM_002775	NP_002766	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1 precursor	445	PDZ.				proteolysis|regulation of cell growth	extracellular space	insulin-like growth factor binding|serine-type endopeptidase activity				0		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				CGTGGTCTCCGCCAATGATGT	0.468000													7	319					0	0	0.058154	0	0
MUC2	4583	broad.mit.edu	37	11	1104253	1104253	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:1104253G>A	uc001lsx.1	+	52	15557	c.15530G>A	c.(15529-15531)GGG>GAG	p.G5177E		NM_002457	NP_002448	Q02817	MUC2_HUMAN	mucin 2 precursor	5177						inner mucus layer|outer mucus layer	protein binding			lung(1)|breast(1)	2		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	AGGCATCTGGGGAGCGGGTGA	0.692000													13	70					0	0	0.024245	0	0
MRGPRX3	117195	broad.mit.edu	37	11	18159638	18159638	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:18159638G>A	uc001mnu.2	+	3	1250	c.889G>A	c.(889-891)GAC>AAC	p.D297N		NM_054031	NP_473372	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	297	Cytoplasmic (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			ovary(1)|pancreas(1)	2						GGCTCTGCAGGACACGCCTGA	0.557000													8	140					0	0	0.058154	0	0
SNX15	29907	broad.mit.edu	37	11	64802325	64802325	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:64802325T>G	uc001oci.3	+	7	916	c.263T>G	c.(262-264)TTT>TGT	p.F88C	SNX15_uc009ypy.2_Missense_Mutation_p.F88C|SNX15_uc001ocj.2_Missense_Mutation_p.F88C|SNX15_uc001ock.2_Missense_Mutation_p.F88C	NM_013306	NP_037438	Q9NRS6	SNX15_HUMAN	sorting nexin 15 isoform A	88	PX.				cell communication|intracellular protein transport	cytoplasmic vesicle membrane|cytosol	phosphatidylinositol binding|protein transporter activity			ovary(1)	1						GTAGGCCGGTTTGAAGCCTCA	0.622000													21	176					0	0	0.083992	0	0
FOLH1B	219595	broad.mit.edu	37	11	89413808	89413808	+	Silent	SNP	A	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:89413808A>G	uc001pda.2	+	8	1006	c.480A>G	c.(478-480)CCA>CCG	p.P160P		NM_153696	NP_710163	Q9HBA9	FOH1B_HUMAN	folate hydrolase 1B	160					proteolysis	cytoplasm	dipeptidase activity|metal ion binding|metallopeptidase activity			ovary(3)|skin(2)|central_nervous_system(1)	6						ATTGTACACCACTGATGTACA	0.294000													4	15					0	0	0.021553	0	0
BIRC3	330	broad.mit.edu	37	11	102206814	102206814	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:102206814T>G	uc001pgx.2	+	8	1664	c.1442T>G	c.(1441-1443)GTT>GGT	p.V481G		NM_182962	NP_892007	Q13489	BIRC3_HUMAN	baculoviral IAP repeat-containing protein 3	481	CARD.				anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway	cytoplasm|nucleus	protein binding|ubiquitin-protein ligase activity|zinc ion binding			ovary(3)|skin(1)	4	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GAACATGATGTTATTAAACAG	0.353000			T	MALT1	MALT								10	45					0	0	0.080935	0	0
CASP1	834	broad.mit.edu	37	11	104903803	104903803	+	Missense_Mutation	SNP	A	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:104903803A>T	uc010rve.1	-	3	342	c.325T>A	c.(325-327)TCT>ACT	p.S109T	CASP1_uc001pig.2_Intron|CASP1_uc001pik.2_Intron|CASP1_uc010rvf.1_Intron|CASP1_uc010rvg.1_Intron|CASP1_uc010rvh.1_Intron|CASP1_uc010rvi.1_Intron|CASP1_uc001pim.3_Missense_Mutation_p.S109T|CASP1_uc009yxi.2_Intron|CASP1_uc010rvj.1_Missense_Mutation_p.S109T|CASP1_uc009yxj.2_Intron|CASP1_uc010rvk.1_Missense_Mutation_p.S70T|CASP1_uc010rvl.1_Missense_Mutation_p.S109T	NM_033292	NP_150634	P29466	CASP1_HUMAN	caspase 1 isoform alpha precursor	109					cellular response to mechanical stimulus|cellular response to organic substance|positive regulation of I-kappaB kinase/NF-kappaB cascade|proteolysis|signal transduction	cytosol	caspase activator activity|cysteine-type endopeptidase activity|protein binding			ovary(2)	2		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)|Penicillamine(DB00859)	GGAAAGGAAGAAAGTACTCCT	0.358000													3	12					0	0	0.004672	0	0
PKNOX2	63876	broad.mit.edu	37	11	125280693	125280693	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:125280693C>T	uc001qbu.2	+	9	1051	c.737C>T	c.(736-738)CCG>CTG	p.P246L	PKNOX2_uc010saz.1_Missense_Mutation_p.P217L|PKNOX2_uc010sba.1_Missense_Mutation_p.P217L|PKNOX2_uc010sbb.1_Missense_Mutation_p.P182L|PKNOX2_uc001qbv.2_5'Flank	NM_022062	NP_071345	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	246						nucleus	sequence-specific DNA binding transcription factor activity			ovary(3)	3		Breast(109;0.00234)|all_lung(97;0.0191)|Lung NSC(97;0.0196)|Medulloblastoma(222;0.0447)|all_neural(223;0.116)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.117)		TTATACCAACCGGTTACCATG	0.577000													20	97					0	0	0.069288	0	0
HSN2	378465	broad.mit.edu	37	12	978188	978188	+	Missense_Mutation	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:978188T>A	uc001qiq.2	+	1	1319	c.1193T>A	c.(1192-1194)TTC>TAC	p.F398Y	WNK1_uc001qio.3_Intron|WNK1_uc001qip.3_Intron|WNK1_uc001qir.3_Intron	NM_213655	NP_998820			hereditary sensory neuropathy, type II												0	all_cancers(10;0.0107)|all_epithelial(11;0.0151)|Ovarian(42;0.0512)|all_lung(10;0.0521)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.000967)|BRCA - Breast invasive adenocarcinoma(9;0.0178)			TCCCCACTTTTCTTCTGTTTC	0.493000													45	225					0	0	0.048971	0	0
CD27	939	broad.mit.edu	37	12	6554287	6554287	+	Missense_Mutation	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:6554287T>A	uc001qod.2	+	1	237	c.26T>A	c.(25-27)CTG>CAG	p.L9Q	LOC678655_uc001qob.2_Intron|LOC678655_uc001qoc.2_Intron|LOC678655_uc009zel.1_Intron|CD27_uc001qoe.2_5'Flank	NM_001242	NP_001233	P26842	CD27_HUMAN	tumor necrosis factor receptor superfamily,	9					anti-apoptosis|apoptosis|cell surface receptor linked signaling pathway|immunoglobulin mediated immune response|induction of apoptosis|positive regulation of B cell differentiation|positive regulation of JNK cascade|release of cytoplasmic sequestered NF-kappaB	extracellular region|integral to plasma membrane	caspase inhibitor activity|protein binding|transmembrane receptor activity				0						CCCTGGTGGCTGTGCGTTCTG	0.642000													5	32					0	0	0.021553	0	0
LOC653113	653113	broad.mit.edu	37	12	8386990	8386990	+	RNA	SNP	C	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:8386990C>G	uc010sgk.1	-	4		c.466G>C				NR_024254				Homo sapiens family with sequence similarity 86, member A pseudogene (LOC653113), non-coding RNA.												0						CCCCGACCAGCGACACGATGG	0.597000													5	79					0	0	0.038147	0	0
SOX5	6660	broad.mit.edu	37	12	24102509	24102509	+	Missense_Mutation	SNP	C	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:24102509C>G	uc001rfw.2	-	1	129	c.27G>C	c.(25-27)CAG>CAC	p.Q9H	SOX5_uc001rfx.2_Intron|SOX5_uc001rfy.2_Intron|SOX5_uc010siv.1_Intron|SOX5_uc010siw.1_Intron|SOX5_uc001rfz.1_Intron|SOX5_uc001rga.2_Missense_Mutation_p.Q9H	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	9					transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6						TTTCAAACTCCTGAGGTAAAT	0.433000													13	67					0	0	0.028581	0	0
SRGAP1	57522	broad.mit.edu	37	12	64377805	64377805	+	Missense_Mutation	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:64377805T>A	uc010ssp.1	+	2	202	c.146T>A	c.(145-147)CTG>CAG	p.L49Q	SRGAP1_uc001srt.2_Missense_Mutation_p.L49Q|SRGAP1_uc001srv.2_Missense_Mutation_p.L9Q	NM_020762	NP_065813	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	49	FCH.				axon guidance	cytosol				ovary(2)|central_nervous_system(2)	4			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CTCCAGGATCTGCAAGATTTC	0.428000													10	70					0	0	0.069234	0	0
SLC35E3	55508	broad.mit.edu	37	12	69140471	69140471	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:69140471T>C	uc001suh.2	+	1	536	c.314T>C	c.(313-315)CTG>CCG	p.L105P		NM_018656	NP_061126	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E2	105						integral to membrane					0	Breast(13;2.31e-06)|Renal(347;0.0684)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00372)			ACCTATCAGCTGGCCAAGGCC	0.562000													24	362					0	0	0.030593	0	0
MYBPC1	4604	broad.mit.edu	37	12	102045044	102045044	+	Missense_Mutation	SNP	C	G	G	rs146314887	byFrequency	TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:102045044C>G	uc001tii.2	+	14	1426	c.1324C>G	c.(1324-1326)CAG>GAG	p.Q442E	MYBPC1_uc001tif.1_Missense_Mutation_p.Q455E|MYBPC1_uc001tig.2_Missense_Mutation_p.Q467E|MYBPC1_uc010svq.1_Missense_Mutation_p.Q429E|MYBPC1_uc001tih.2_Missense_Mutation_p.Q467E|MYBPC1_uc001tij.2_Missense_Mutation_p.Q442E|MYBPC1_uc010svr.1_Missense_Mutation_p.Q442E|MYBPC1_uc010svs.1_Missense_Mutation_p.Q442E|MYBPC1_uc010svt.1_Missense_Mutation_p.Q430E|MYBPC1_uc010svu.1_Missense_Mutation_p.Q423E|MYBPC1_uc001tik.2_Missense_Mutation_p.Q416E	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	442	Ig-like C2-type 4.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4						TCTGACTGATCAGACTGTAAA	0.423000													3	42					0	0	0.004672	0	0
MYBPC1	4604	broad.mit.edu	37	12	102046970	102046970	+	Nonsense_Mutation	SNP	G	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:102046970G>T	uc001tii.2	+	16	1738	c.1636G>T	c.(1636-1638)GAG>TAG	p.E546*	MYBPC1_uc001tig.2_Nonsense_Mutation_p.E571*|MYBPC1_uc010svq.1_Nonsense_Mutation_p.E533*|MYBPC1_uc001tih.2_Nonsense_Mutation_p.E571*|MYBPC1_uc001tij.2_Nonsense_Mutation_p.E546*|MYBPC1_uc010svr.1_Nonsense_Mutation_p.E546*|MYBPC1_uc010svs.1_Nonsense_Mutation_p.E546*|MYBPC1_uc010svt.1_Nonsense_Mutation_p.E534*|MYBPC1_uc010svu.1_Nonsense_Mutation_p.E527*|MYBPC1_uc001tik.2_Nonsense_Mutation_p.E520*	NM_206820	NP_996556	Q00872	MYPC1_HUMAN	myosin binding protein C, slow type isoform 3	546	Ig-like C2-type 5.				cell adhesion|muscle filament sliding	cytosol|myofibril|myosin filament	actin binding|structural constituent of muscle|titin binding			ovary(2)|liver(1)|skin(1)	4						GCTTCGTCTTGAGATCCCCAT	0.393000													3	28					6.4e-05	6.96889e-05	0.004672	1	0
METT11D1	64745	broad.mit.edu	37	14	21464718	21464719	+	Missense_Mutation	DNP	GG	TT	TT			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr14:21464718_21464719GG>TT	uc001vyn.2	+	13	1310_1311	c.1113_1114GG>TT	c.(1111-1116)ATGGTG>ATTTTG	p.371_372MV>IL	METT11D1_uc001vym.2_Missense_Mutation_p.371_372MV>IL|METT11D1_uc001vyo.2_Missense_Mutation_p.371_372MV>IL|METT11D1_uc001vyp.2_Missense_Mutation_p.213_214MV>IL|METT11D1_uc001vyq.2_Missense_Mutation_p.213_214MV>IL|SLC39A2_uc001vyr.2_5'Flank|SLC39A2_uc001vys.2_5'Flank	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform	371_372					translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)		AGTTCTCTATGGTGATCCTTGC	0.465000													23	124					0	0	0.004672	0	0
Unknown	0	broad.mit.edu	37	14	36840695	36840695	+	Missense_Mutation	SNP	A	G	G	rs3742593	by1000genomes	TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr14:36840695A>G	uc001wtp.2	+	1	326	c.77A>G	c.(76-78)GAT>GGT	p.D26G		NM_199286	NP_954980			stella																		TCCCGGGACGATTCAGGGGCC	0.478000													2	5					0	0	0.004672	0	0
NID2	22795	broad.mit.edu	37	14	52485956	52485956	+	Missense_Mutation	SNP	A	C	C			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr14:52485956A>C	uc001wzo.2	-	14	3085	c.2851T>G	c.(2851-2853)TAT>GAT	p.Y951D	NID2_uc010tqs.1_Missense_Mutation_p.Y903D|NID2_uc010tqt.1_Missense_Mutation_p.Y951D|NID2_uc001wzp.2_Missense_Mutation_p.Y951D	NM_007361	NP_031387	Q14112	NID2_HUMAN	nidogen 2 precursor	951	Thyroglobulin type-1 1.					basement membrane	calcium ion binding|collagen binding			pancreas(2)|breast(2)|ovary(1)|liver(1)|skin(1)	7	Breast(41;0.0639)|all_epithelial(31;0.123)					GGGTAGGCATACTGGGCCTGG	0.577000													20	66					0	0	0.083992	0	0
ARHGAP11B	89839	broad.mit.edu	37	15	30938483	30938483	+	RNA	SNP	T	C	C	rs145453249	by1000genomes	TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr15:30938483T>C	uc010azv.1	+	11		c.1293T>C			ARHGAP11B_uc001zeu.2_RNA			Q3KRB8	RHGBB_HUMAN	Homo sapiens cDNA, FLJ17072.						regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity				0		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		CCACCAGGCTTCTCCTTTCCC	0.463000													3	56					0	0	0.004672	0	0
C15orf23	90417	broad.mit.edu	37	15	40685795	40685795	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr15:40685795G>T	uc001zll.2	+	9	1063	c.948G>T	c.(946-948)ATG>ATT	p.M316I	C15orf23_uc010ucp.1_3'UTR|C15orf23_uc001zlo.2_3'UTR|C15orf23_uc001zlm.2_RNA|C15orf23_uc001zln.2_RNA	NM_033286	NP_150628	Q9Y448	T4AF1_HUMAN	TRAF4 associated factor 1 isoform a	316	Potential.					nucleus	protein binding			ovary(1)|skin(1)	2		all_cancers(109;2.34e-14)|all_epithelial(112;9.21e-12)|Lung NSC(122;2.95e-09)|all_lung(180;6.03e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3.39e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0798)		TATTAGAAATGTAAGAAGaag	0.194000													13	63					6.72482e-11	7.66317e-11	0.024245	1	0
RAB27A	5873	broad.mit.edu	37	15	55516128	55516128	+	Silent	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr15:55516128T>A	uc002aco.2	-	6	659	c.426A>T	c.(424-426)GTA>GTT	p.V142V	RAB27A_uc002acr.2_Silent_p.V142V|RAB27A_uc002acp.2_Silent_p.V142V|RAB27A_uc002acq.2_Silent_p.V142V	NM_183234	NP_899057	P51159	RB27A_HUMAN	Ras-related protein Rab-27A	142					small GTPase mediated signal transduction	dendrite|exocytic vesicle|late endosome|lysosome|melanosome	GTP binding|GTPase activity			ovary(1)	1				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		CCTCTTTCACTACTCTCTGGT	0.398000													11	62					0	0	0.080935	0	0
PIGQ	9091	broad.mit.edu	37	16	624651	624651	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:624651T>G	uc002cho.2	+	2	679	c.577T>G	c.(577-579)TCG>GCG	p.S193A	PIGQ_uc010bqw.2_Missense_Mutation_p.S193A|PIGQ_uc002chm.2_Missense_Mutation_p.S193A|PIGQ_uc002chn.2_Missense_Mutation_p.S193A|PIGQ_uc010uui.1_Missense_Mutation_p.S207A	NM_148920	NP_683721	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis,	193					C-terminal protein lipidation|carbohydrate metabolic process|preassembly of GPI anchor in ER membrane	endoplasmic reticulum membrane|integral to membrane	phosphatidylinositol N-acetylglucosaminyltransferase activity			central_nervous_system(1)	1		Hepatocellular(780;0.00335)				CCACTGGCAGTCGGAGGGCGT	0.682000													5	12					0	0	0.058154	0	0
RNPS1	10921	broad.mit.edu	37	16	2313224	2313224	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:2313224T>G	uc002cpt.2	-	4	838	c.292A>C	c.(292-294)AGC>CGC	p.S98R	RNPS1_uc002cpu.2_Missense_Mutation_p.S98R|RNPS1_uc002cpv.2_5'UTR|RNPS1_uc002cpw.2_Missense_Mutation_p.S98R|RNPS1_uc002cpx.2_Missense_Mutation_p.S75R|RNPS1_uc010uwa.1_RNA	NM_080594	NP_542161	Q15287	RNPS1_HUMAN	RNA-binding protein S1, serine-rich domain	98	Necessary for interaction with SRP54, nuclear localization and exon-skipping.|Ser-rich.|Necessary for interactions with UPF2 and UPF3B and UPF2-dependent NMD.|Necessary for interaction with the cleaved p110 isoform of CDC2L1.				mRNA 3'-end processing|mRNA export from nucleus|nuclear mRNA splicing, via spliceosome|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|termination of RNA polymerase II transcription	cytosol|nuclear speck	mRNA 3'-UTR binding|nucleotide binding|protein binding			ovary(1)	1						gaggaagagctggagccactg	0.239000													6	48					0	0	0.093190	0	0
TMC7	79905	broad.mit.edu	37	16	19073098	19073098	+	Splice_Site	SNP	A	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:19073098A>T	uc002dfq.2	+	16	2237	c.2107_splice	c.e16-2	p.E703_splice	TMC7_uc010vap.1_Splice_Site_p.E593_splice	NM_024847	NP_079123	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7 isoform a							integral to membrane				skin(2)|ovary(1)	3						ATTATTTTTTAGGAAAGTCGT	0.378000													13	64					0	0	0.093190	0	0
DNAH3	55567	broad.mit.edu	37	16	21080893	21080893	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr16:21080893C>T	uc010vbe.1	-	23	3224	c.3224G>A	c.(3223-3225)CGC>CAC	p.R1075H		NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1075	Stem (By similarity).				ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		GTCTTGTATGCGAATTAGCTT	0.453000													11	73					0	0	0.093190	0	0
TMEM107	84314	broad.mit.edu	37	17	8079579	8079579	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:8079579G>T	uc002gkg.3	-	1	136	c.26C>A	c.(25-27)CCC>CAC	p.P9H	TMEM107_uc002gkh.3_Missense_Mutation_p.P9H|TMEM107_uc002gki.3_Missense_Mutation_p.P9H|TMEM107_uc002gkj.3_RNA|TMEM107_uc002gkk.2_Missense_Mutation_p.P9H	NM_183065	NP_898888	Q6UX40	TM107_HUMAN	transmembrane protein 107 isoform 2	9	Helical; (Potential).					integral to membrane					0						GAAGCGAGAGGGCACAAGCCC	0.632000													16	108					1.45105e-14	1.71329e-14	0.038395	1	0
LOC284100	284100	broad.mit.edu	37	17	36214775	36214775	+	RNA	SNP	G	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:36214775G>T	uc002hom.1	-	2		c.184C>A			LOC284100_uc002hon.1_RNA					Homo sapiens cDNA FLJ37577 fis, clone BRCOC2003513, moderately similar to 14-3-3 protein epsilon (14-3-3E).												0						CTTGCCAGTGGTAGCTGCTGG	0.353000													9	9					2.62144e-13	3.02237e-13	0.047766	1	0
PSMC3IP	29893	broad.mit.edu	37	17	40726133	40726133	+	Nonsense_Mutation	SNP	G	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:40726133G>T	uc002iai.2	-	4	364	c.321C>A	c.(319-321)TGC>TGA	p.C107*	PSMC3IP_uc002iaj.2_Nonsense_Mutation_p.C44*|PSMC3IP_uc002iak.2_Nonsense_Mutation_p.C107*|PSMC3IP_uc010wgn.1_Nonsense_Mutation_p.C28*|PSMC3IP_uc010wgo.1_Intron|PSMC3IP_uc010wgp.1_RNA	NM_016556	NP_057640	Q9P2W1	HOP2_HUMAN	PSMC3 interacting protein isoform 2	107	Potential.				DNA recombination|meiosis	nucleus	DNA binding			upper_aerodigestive_tract(1)|skin(1)	2		all_cancers(22;0.00426)|Breast(137;0.00116)|all_epithelial(22;0.0395)		BRCA - Breast invasive adenocarcinoma(366;0.13)		CCATGTAGCGGCAGCTCTGCT	0.512000													7	23					0.000219431	0.000233742	0.020292	1	0
TMEM106A	113277	broad.mit.edu	37	17	41365849	41365849	+	Silent	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:41365849C>T	uc002idn.1	+	4	451	c.214C>T	c.(214-216)CTG>TTG	p.L72L	TMEM106A_uc010why.1_Silent_p.L24L|TMEM106A_uc010cze.1_Silent_p.L72L|TMEM106A_uc010whz.1_Silent_p.L72L	NM_145041	NP_659478	Q96A25	T106A_HUMAN	transmembrane protein 106A	72						integral to membrane					0		Breast(137;0.0164)		BRCA - Breast invasive adenocarcinoma(366;0.0917)		CTCTCTAGAGCTGGAGAAGCA	0.552000													12	118					0	0	0.105934	0	0
ME2	4200	broad.mit.edu	37	18	48442562	48442562	+	Missense_Mutation	SNP	C	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr18:48442562C>G	uc002ley.2	+	5	673	c.417C>G	c.(415-417)GAC>GAG	p.D139E	ME2_uc010dpd.2_Missense_Mutation_p.D139E	NM_002396	NP_002387	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	139					malate metabolic process	mitochondrial matrix	electron carrier activity|malate dehydrogenase (decarboxylating) activity|malate dehydrogenase (oxaloacetate-decarboxylating) activity|metal ion binding|NAD binding				0		Colorectal(6;0.0273)|all_epithelial(6;0.118)		Colorectal(21;0.0313)|READ - Rectum adenocarcinoma(32;0.105)|STAD - Stomach adenocarcinoma(97;0.184)	NADH(DB00157)	CGATCTCAGACAGAGGTCATG	0.333000													3	28					0	0	0.009096	0	0
ACSBG2	81616	broad.mit.edu	37	19	6177251	6177251	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:6177251T>G	uc002mef.1	+	8	977	c.750T>G	c.(748-750)ATT>ATG	p.I250M	ACSBG2_uc002mee.1_Missense_Mutation_p.I63M|ACSBG2_uc002meg.1_Missense_Mutation_p.I250M|ACSBG2_uc002meh.1_Missense_Mutation_p.I250M|ACSBG2_uc002mei.1_Missense_Mutation_p.I200M|ACSBG2_uc010xiz.1_Missense_Mutation_p.I250M	NM_030924	NP_112186	Q5FVE4	ACBG2_HUMAN	bubblegum-related acyl-CoA synthetase 2	250					cell differentiation|fatty acid metabolic process|multicellular organismal development|spermatogenesis	membrane|microsome|mitochondrion	acyl-CoA thioesterase activity|ATP binding|long-chain fatty acid-CoA ligase activity			ovary(1)	1						TCACGTGGATTGCAGGAGCAG	0.393000													3	23					0	0	0.014758	0	0
MUC16	94025	broad.mit.edu	37	19	9067237	9067237	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:9067237T>G	uc002mkp.2	-	3	20413	c.20209A>C	c.(20209-20211)ACT>CCT	p.T6737P		NM_024690	NP_078966	Q8WXI7	MUC16_HUMAN	mucin 16	6739	Thr-rich.|Extracellular (Potential).				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding			lung(30)|ovary(15)|breast(8)|large_intestine(1)|skin(1)|prostate(1)|pancreas(1)	57						CCTGTTCGAGTGATGATGGTC	0.507000													3	61					0	0	0.004672	0	0
APLP1	333	broad.mit.edu	37	19	36362560	36362560	+	Nonsense_Mutation	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:36362560T>A	uc002oce.2	+	5	722	c.584T>A	c.(583-585)TTA>TAA	p.L195*	APLP1_uc010xsz.1_Nonsense_Mutation_p.L156*|APLP1_uc002ocf.2_Nonsense_Mutation_p.L195*|APLP1_uc002ocg.2_Nonsense_Mutation_p.L98*|APLP1_uc010xta.1_Nonsense_Mutation_p.L189*	NM_005166	NP_005157	P51693	APLP1_HUMAN	amyloid precursor-like protein 1 isoform 2	195	Extracellular (Potential).				apoptosis|cell adhesion|cellular response to norepinephrine stimulus|endocytosis|negative regulation of cAMP biosynthetic process|nervous system development|organ morphogenesis	basement membrane|integral to membrane|perinuclear region of cytoplasm|plasma membrane	alpha-2A adrenergic receptor binding|alpha-2B adrenergic receptor binding|alpha-2C adrenergic receptor binding|heparin binding|identical protein binding|metal ion binding			ovary(2)	2	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGCATGCTCTTACCCTGTGGC	0.642000													42	221					0	0	0.048971	0	0
WDR62	284403	broad.mit.edu	37	19	36582178	36582178	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:36582178C>T	uc002odc.2	+	17	2202	c.2111C>T	c.(2110-2112)TCG>TTG	p.S704L	WDR62_uc002odd.2_Missense_Mutation_p.S704L	NM_173636	NP_775907	O43379	WDR62_HUMAN	WD repeat domain 62 isoform 2	704	WD 11.				cerebral cortex development	nucleus					0	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GACTTTTACTCGGGCGAGTGC	0.582000													21	103					0	0	0.069288	0	0
ZNF585B	92285	broad.mit.edu	37	19	37678072	37678072	+	Missense_Mutation	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:37678072T>A	uc002ofq.2	-	5	621	c.367A>T	c.(367-369)ATT>TTT	p.I123F	ZNF585B_uc002ofr.1_5'UTR	NM_152279	NP_689492	Q52M93	Z585B_HUMAN	zinc finger protein 585B	123					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding|zinc ion binding			ovary(1)	1			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCAGAATAAATTTTTTGATCT	0.373000													8	73					0	0	0.038147	0	0
ZNF320	162967	broad.mit.edu	37	19	53385207	53385207	+	Silent	SNP	A	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:53385207A>G	uc002qag.2	-	4	363	c.172T>C	c.(172-174)TTG>CTG	p.L58L	ZNF320_uc010eqh.1_5'Flank|ZNF320_uc010eqi.1_Intron|ZNF320_uc002qah.2_Silent_p.L4L|ZNF320_uc002qai.2_Silent_p.L58L	NM_207333	NP_997216	A2RRD8	ZN320_HUMAN	zinc finger protein 320	58	KRAB.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				GBM - Glioblastoma multiforme(134;0.0534)		GTTGATGACAATGTATTCATC	0.358000													4	166					0	0	0.014758	0	0
WDR35	57539	broad.mit.edu	37	2	20175308	20175308	+	Missense_Mutation	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:20175308T>A	uc002rdi.2	-	6	661	c.553A>T	c.(553-555)AAT>TAT	p.N185Y	WDR35_uc002rdj.2_Missense_Mutation_p.N185Y|WDR35_uc010ext.2_RNA|WDR35_uc002rdh.2_5'UTR	NM_001006657	NP_001006658	Q9P2L0	WDR35_HUMAN	WD repeat domain 35 isoform 1	185	WD 4.									ovary(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTCCTTGATTATCGTAAATG	0.318000													4	17					0	0	0.009096	0	0
LRP2	4036	broad.mit.edu	37	2	170029726	170029726	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:170029726C>T	uc002ues.2	-	57	11236	c.11023G>A	c.(11023-11025)GCC>ACC	p.A3675T		NM_004525	NP_004516	P98164	LRP2_HUMAN	low density lipoprotein-related protein 2	3675	Extracellular (Potential).				hormone biosynthetic process|protein glycosylation|receptor-mediated endocytosis|vitamin D metabolic process	coated pit|integral to membrane|lysosome	calcium ion binding|receptor activity|SH3 domain binding			ovary(13)|skin(6)|central_nervous_system(4)|large_intestine(3)|kidney(2)|pancreas(1)	29				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	Gentamicin(DB00798)|Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)|Urokinase(DB00013)	CAGAGATGGGCAGAGCTCACT	0.468000													6	58					0	0	0.021553	0	0
SPHKAP	80309	broad.mit.edu	37	2	228882137	228882137	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:228882137C>T	uc002vpq.2	-	7	3480	c.3433G>A	c.(3433-3435)GAG>AAG	p.E1145K	SPHKAP_uc002vpp.2_Missense_Mutation_p.E1145K|SPHKAP_uc010zlx.1_Missense_Mutation_p.E1145K	NM_001142644	NP_001136116	Q2M3C7	SPKAP_HUMAN	sphingosine kinase type 1-interacting protein	1145						cytoplasm	protein binding			skin(5)|ovary(4)|lung(1)	10		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		AGCAGTAACTCAAATCCTCTC	0.527000													22	108					0	0	0.062417	0	0
PLK1S1	55857	broad.mit.edu	37	20	21143713	21143713	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:21143713C>T	uc002wsb.2	+	6	1398	c.1265C>T	c.(1264-1266)GCC>GTC	p.A422V	PLK1S1_uc010zsh.1_Missense_Mutation_p.A319V|PLK1S1_uc010zsi.1_Missense_Mutation_p.A289V|PLK1S1_uc010zsj.1_RNA|uc002wsc.2_Intron|PLK1S1_uc002wsd.2_RNA	NM_018474	NP_060944	Q2M2Z5	KIZ_HUMAN	polo-like kinase 1 substrate 1 isoform 1	422					spindle organization	centrosome	protein kinase binding				0						GAAAGAGTTGCCCTATCCACT	0.433000													4	25					0	0	0.014758	0	0
MYH7B	57644	broad.mit.edu	37	20	33577862	33577862	+	Silent	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:33577862C>T	uc002xbi.1	+	19	2031	c.1939C>T	c.(1939-1941)CTG>TTG	p.L647L	MIR499_hsa-mir-499|MI0003183_5'Flank	NM_020884	NP_065935	A7E2Y1	MYH7B_HUMAN	myosin, heavy polypeptide 7B, cardiac muscle,	605	Myosin head-like.					membrane|myosin filament	actin binding|ATP binding|motor activity			ovary(1)|breast(1)	2			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CAAGGATCCCCTGAATGAGAC	0.572000													10	354					0	0	0.069234	0	0
CSE1L	1434	broad.mit.edu	37	20	47675025	47675025	+	Missense_Mutation	SNP	C	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:47675025C>A	uc002xty.2	+	2	159	c.25C>A	c.(25-27)CAA>AAA	p.Q9K	CSE1L_uc010zyg.1_5'UTR|CSE1L_uc010ghx.2_Missense_Mutation_p.Q9K	NM_001316	NP_001307	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like protein	9					apoptosis|cell proliferation|intracellular protein transport	cytoplasm|nucleus	importin-alpha export receptor activity			large_intestine(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TGCAAATCTGCAAACACTAAC	0.333000													19	175					1.55795e-14	1.8176e-14	0.062417	1	0
ZNF512B	57473	broad.mit.edu	37	20	62598869	62598870	+	Missense_Mutation	DNP	CG	AA	AA			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr20:62598869_62598870CG>AA	uc002yhl.1	-	3	182_183	c.128_129CG>TT	c.(127-129)CCG>CTT	p.P43L		NM_020713	NP_065764	Q96KM6	Z512B_HUMAN	zinc finger protein 512B	43					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CACGGACCACCGGCATCCCTGC	0.639000													57	263					0	0	0.004672	0	0
DSCAM	1826	broad.mit.edu	37	21	41447083	41447083	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr21:41447083T>C	uc002yyq.1	-	27	5221	c.4769A>G	c.(4768-4770)AAC>AGC	p.N1590S	DSCAM_uc002yyr.1_Intron	NM_001389	NP_001380	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule isoform	1590	Extracellular (Potential).				cell adhesion|dendrite self-avoidance|negative regulation of cell adhesion|positive regulation of axon extension involved in axon guidance|positive regulation of phosphorylation	axon|extracellular region|growth cone|integral to plasma membrane|membrane fraction	protein binding			ovary(6)|skin(4)|upper_aerodigestive_tract(1)	11		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GAGCCCCTCGTTGGTCGTCAG	0.547000													5	163					0	0	0.021553	0	0
POM121L9P	29774	broad.mit.edu	37	22	24659809	24659809	+	RNA	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr22:24659809G>A	uc002zzs.3	+	7		c.3541G>A			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						CCCTATCTGCGCACCCGGAGG	0.612000													3	21					0	0	0.004672	0	0
POM121L9P	29774	broad.mit.edu	37	22	24659813	24659813	+	RNA	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr22:24659813C>T	uc002zzs.3	+	7		c.3545C>T			uc011ajp.1_5'Flank	NR_003714				Homo sapiens mRNA; cDNA DKFZp434P211 (from clone DKFZp434P211).												0						ATCTGCGCACCCGGAGGTGGG	0.607000													3	20					0	0	0.004672	0	0
OXSM	54995	broad.mit.edu	37	3	25832524	25832524	+	Missense_Mutation	SNP	C	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:25832524C>A	uc003cdn.2	+	2	120	c.13C>A	c.(13-15)CTG>ATG	p.L5M	NGLY1_uc011awo.1_5'Flank|OXSM_uc011awp.1_Translation_Start_Site|OXSM_uc010hfh.2_Missense_Mutation_p.L5M	NM_017897	NP_060367	Q9NWU1	OXSM_HUMAN	3-oxoacyl-ACP synthase, mitochondrial isoform 1	5					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						GTCCAACTGCCTGCAAAATTT	0.368000													31	135					3.90053e-15	4.66161e-15	0.050027	1	0
ZNF167	55888	broad.mit.edu	37	3	44612491	44612491	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:44612491C>T	uc010hin.2	+	6	2277	c.1889C>T	c.(1888-1890)ACG>ATG	p.T630M	ZNF167_uc003cni.2_Intron|ZNF167_uc010hio.2_Intron|ZNF167_uc003cnj.2_Missense_Mutation_p.T630M|ZNF167_uc003cnk.2_Intron	NM_018651	NP_061121	Q9P0L1	ZN167_HUMAN	zinc finger protein 167 isoform 1	630					viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(2)	2				KIRC - Kidney renal clear cell carcinoma(197;0.0486)|Kidney(197;0.0609)		AGACTTCACACGGGTGAAAAG	0.408000													3	39					0	0	0.004672	0	0
PROS1	5627	broad.mit.edu	37	3	93624723	93624723	+	Missense_Mutation	SNP	C	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:93624723C>G	uc003drb.3	-	6	847	c.506G>C	c.(505-507)GGA>GCA	p.G169A	PROS1_uc010hoo.2_Missense_Mutation_p.G38A|PROS1_uc003dqz.3_Missense_Mutation_p.G38A	NM_000313	NP_000304	P07225	PROS_HUMAN	protein S, alpha preproprotein	169	EGF-like 2; calcium-binding (Potential).				leukocyte migration|peptidyl-glutamic acid carboxylation|platelet activation|platelet degranulation|post-translational protein modification|proteolysis	endoplasmic reticulum membrane|extracellular region|Golgi lumen|Golgi membrane|platelet alpha granule lumen	calcium ion binding|endopeptidase inhibitor activity			large_intestine(1)	1					Antihemophilic Factor(DB00025)|Drotrecogin alfa(DB00055)|Menadione(DB00170)	ACTGCAACCTCCATTTATATT	0.294000													41	215					0	0	0.111260	0	0
FBXO40	51725	broad.mit.edu	37	3	121341915	121341915	+	Missense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:121341915C>T	uc003eeg.2	+	3	1849	c.1639C>T	c.(1639-1641)CCG>TCG	p.P547S		NM_016298	NP_057382	Q9UH90	FBX40_HUMAN	F-box protein 40	547					muscle cell differentiation	centrosome|nucleus	ubiquitin-protein ligase activity|zinc ion binding			ovary(2)|lung(1)|breast(1)|central_nervous_system(1)	5				GBM - Glioblastoma multiforme(114;0.189)		TGCCATTAAGCCGGAGGTTGC	0.493000													21	97					0	0	0.062417	0	0
MUC4	4585	broad.mit.edu	37	3	195511945	195511945	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:195511945G>A	uc011bto.1	-	2	6966	c.6506C>T	c.(6505-6507)GCA>GTA	p.A2169V	MUC4_uc003fvo.2_Intron|MUC4_uc003fvp.2_Intron|MUC4_uc010hzu.1_Intron	NM_018406	NP_060876	Q99102	MUC4_HUMAN	mucin 4 isoform a	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell-matrix adhesion	integral to plasma membrane|proteinaceous extracellular matrix	ErbB-2 class receptor binding|extracellular matrix constituent, lubricant activity				0	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.572000													3	4					0	0	0.004672	0	0
Unknown	0	broad.mit.edu	37	5	17354258	17354258	+	RNA	SNP	A	C	C			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:17354258A>C	uc003jfy.2	-	1		c.471T>G			uc003jfz.2_RNA					full-length cDNA clone CS0DC022YF01 of Neuroblastoma Cot 25-normalized of Homo sapiens (human).																		TCTCCCAGTCATCACAGTCCG	0.468000													82	429					0	0	0.048971	0	0
GPBP1	65056	broad.mit.edu	37	5	56542173	56542173	+	Silent	SNP	T	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:56542173T>A	uc003jrh.3	+	7	1799	c.525T>A	c.(523-525)ATT>ATA	p.I175I	GPBP1_uc010iwg.2_Silent_p.I195I|GPBP1_uc003jri.3_Silent_p.I4I|GPBP1_uc003jrj.3_Silent_p.I182I|GPBP1_uc003jrk.3_Silent_p.I182I|GPBP1_uc003jrl.3_RNA	NM_022913	NP_075064	Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1 isoform 1	175					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding			large_intestine(1)|central_nervous_system(1)	2		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		TGCTGGTCATTAAGAAAGGTA	0.383000													9	51					0	0	0.058154	0	0
PCDHA4	56144	broad.mit.edu	37	5	140188710	140188710	+	Silent	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr5:140188710C>T	uc003lhi.2	+	1	2039	c.1938C>T	c.(1936-1938)CGC>CGT	p.R646R	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhh.1_Silent_p.R646R|PCDHA4_uc011daa.1_Silent_p.R646R	NM_018907	NP_061730	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4 isoform 1 precursor	646	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding			ovary(4)|skin(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCGCCACCGCCTACTGGTAC	0.682000													34	200					0	0	0.098360	0	0
PBX2	5089	broad.mit.edu	37	6	32156280	32156280	+	Silent	SNP	G	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr6:32156280G>T	uc003oav.1	-	3	568	c.297C>A	c.(295-297)GGC>GGA	p.G99G	PBX2_uc003oaw.2_Silent_p.G99G	NM_002586	NP_002577	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	99							transcription factor binding			ovary(1)	1						GAATGCTGAGGCCTAGCATGC	0.612000													11	100					3.86212e-05	4.25267e-05	0.069234	1	0
LAMA2	3908	broad.mit.edu	37	6	129670492	129670492	+	Missense_Mutation	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr6:129670492G>A	uc003qbn.2	+	31	4591	c.4486G>A	c.(4486-4488)GCT>ACT	p.A1496T	LAMA2_uc003qbo.2_Missense_Mutation_p.A1496T	NM_000426	NP_000417	P24043	LAMA2_HUMAN	laminin alpha 2 subunit isoform a precursor	1496	Laminin EGF-like 16.				cell adhesion|muscle organ development|regulation of cell adhesion|regulation of cell migration|regulation of embryonic development	laminin-1 complex	receptor binding|structural molecule activity			ovary(8)|breast(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CCGCTGCACGGCTTGTCCACG	0.428000													3	18					0	0	0.009096	0	0
STXBP5	134957	broad.mit.edu	37	6	147637421	147637421	+	Silent	SNP	G	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr6:147637421G>A	uc003qlz.2	+	16	1841	c.1680G>A	c.(1678-1680)GAG>GAA	p.E560E	STXBP5_uc010khz.1_Silent_p.E560E|STXBP5_uc003qlx.2_RNA|STXBP5_uc003qly.2_Silent_p.E231E	NM_001127715	NP_001121187	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn) isoform b	560	WD 9.				exocytosis|positive regulation of exocytosis|protein transport	cell junction|cytoplasmic vesicle membrane|nicotinic acetylcholine-gated receptor-channel complex|synaptic vesicle	syntaxin-1 binding				0		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		CGGAGGGTGAGCAGCCACCAC	0.458000													3	18					0	0	0.004672	0	0
NOD1	10392	broad.mit.edu	37	7	30472766	30472766	+	Missense_Mutation	SNP	A	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr7:30472766A>G	uc003tav.2	-	12	3174	c.2651T>C	c.(2650-2652)GTG>GCG	p.V884A		NM_006092	NP_006083	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain	884	LRR 7.				activation of MAPK activity|detection of bacterium|induction of apoptosis|inflammatory response|innate immune response|interleukin-8 biosynthetic process|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of dendritic cell antigen processing and presentation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of NF-kappaB transcription factor activity|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	basolateral plasma membrane|cytosol	ATP binding|CARD domain binding|caspase activator activity|peptidoglycan binding|protein homodimerization activity			ovary(1)|skin(1)	2						ACTCTCTGCCACTTCATCGTT	0.388000													8	28					0	0	0.038147	0	0
HERPUD2	64224	broad.mit.edu	37	7	35674964	35674964	+	Missense_Mutation	SNP	G	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr7:35674964G>T	uc003tet.2	-	6	1527	c.722C>A	c.(721-723)CCA>CAA	p.P241Q	HERPUD2_uc003tes.3_Missense_Mutation_p.P241Q	NM_022373	NP_071768	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	241					response to unfolded protein	integral to membrane				ovary(3)	3						GTTTGGAGCTGGTGGGGGTTC	0.473000													16	84					2.23348e-06	2.51588e-06	0.028581	1	0
NAPEPLD	222236	broad.mit.edu	37	7	102769017	102769017	+	Nonsense_Mutation	SNP	C	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr7:102769017C>T	uc003vbc.2	-	2	535	c.207G>A	c.(205-207)TGG>TGA	p.W69*	NAPEPLD_uc003vbd.2_Nonsense_Mutation_p.W69*|NAPEPLD_uc011klj.1_Nonsense_Mutation_p.W142*|NAPEPLD_uc003vbe.2_RNA|NAPEPLD_uc003vbf.2_Nonsense_Mutation_p.W69*	NM_198990	NP_945341	Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	69					phospholipid catabolic process	membrane	metal ion binding			skin(1)	1						TCCATGTTGGCCACGGATTCA	0.403000													4	52					0	0	0.009096	0	0
FLJ10661	286042	broad.mit.edu	37	8	8092104	8092104	+	RNA	SNP	T	C	C			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr8:8092104T>C	uc011kwt.1	+	4		c.472T>C			FLJ10661_uc010lrq.2_Intron|FLJ10661_uc003wsf.3_RNA	NR_024362				Homo sapiens cDNA FLJ60033 complete cds, highly similar to Protein FAM86A.												0						GAGCTATTTGTTGGTATGAGA	0.473000													4	75					0	0	0.021553	0	0
Unknown	0	broad.mit.edu	37	9	43818062	43818062	+	RNA	SNP	T	A	A	rs78142446	by1000genomes	TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr9:43818062T>A	uc004acz.1	+	7		c.1181T>A								Homo sapiens cDNA FLJ30083 fis, clone BGGI12001097, weakly similar to Homo sapiens contactin associated protein (Caspr) mRNA.																		GGGAATTCTGTCACCCGGAAG	0.338000													4	84					0	0	0.009096	0	0
LOC442421	442421	broad.mit.edu	37	9	66499867	66499867	+	Missense_Mutation	SNP	T	C	C			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr9:66499867T>C	uc004aee.1	+	1	677	c.677T>C	c.(676-678)CTG>CCG	p.L226P	LOC442421_uc004aed.1_RNA					Homo sapiens hypothetical LOC442421, mRNA (cDNA clone IMAGE:40031134).												0						TTCACTTTGCTGGTGAGCCAG	0.567000													9	87					0	0	0.049695	0	0
COL4A6	1288	broad.mit.edu	37	X	107433650	107433650	+	Missense_Mutation	SNP	T	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chrX:107433650T>G	uc004enw.3	-	20	1504	c.1401A>C	c.(1399-1401)AAA>AAC	p.K467N	COL4A6_uc004env.3_Missense_Mutation_p.K466N|COL4A6_uc011msn.1_Missense_Mutation_p.K466N|COL4A6_uc010npk.2_Missense_Mutation_p.K466N	NM_001847	NP_001838	Q14031	CO4A6_HUMAN	type IV alpha 6 collagen isoform A precursor	467	Triple-helical region.				cell adhesion|extracellular matrix organization	collagen type IV	extracellular matrix structural constituent|protein binding			ovary(6)|urinary_tract(1)|large_intestine(1)	8						CTAGGTTTCCTTTTGGACCTT	0.443000									Alport_syndrome_with_Diffuse_Leiomyomatosis				30	53					0	0	0.064281	0	0
FCGR2A	2212	broad.mit.edu	37	1	161475799	161475804	+	Splice_Site	DEL	TGAGTA	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr1:161475799_161475804delTGAGTA	uc001gan.2	+	2	159	c.106_splice	c.e2+2	p.A36_splice	FCGR2A_uc001gam.2_Splice_Site_p.A36_splice|FCGR2A_uc001gao.2_5'Flank	NM_001136219	NP_001129691	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor							integral to membrane|plasma membrane	IgG binding|receptor activity			ovary(1)	1	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GTCAAGCTGGTGAGTATGCCCTTTGC	0.471													13	1184	---	---	---	---					
PITRM1	10531	broad.mit.edu	37	10	3199645	3199645	+	Frame_Shift_Del	DEL	A	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:3199645delA	uc010qah.1	-	11	1265	c.1233delT	c.(1231-1233)TTTfs	p.F411fs	PITRM1_uc001igr.1_Frame_Shift_Del_p.F443fs|PITRM1_uc001igt.1_Frame_Shift_Del_p.F443fs|PITRM1_uc009xhv.1_Frame_Shift_Del_p.F8fs|PITRM1_uc001igu.1_Frame_Shift_Del_p.F435fs|PITRM1_uc010qai.1_Frame_Shift_Del_p.F414fs|PITRM1_uc001igw.1_Frame_Shift_Del_p.F443fs			E7ES23	E7ES23_HUMAN	SubName: Full=cDNA FLJ54065, moderately similar to Mus musculus pitrilysin metallepetidase 1 (Pitrm1), mRNA;	411					proteolysis		metalloendopeptidase activity|zinc ion binding			pancreas(1)	1						GCATCAGCCCAAAGCTGGTAG	0.318													8	27	---	---	---	---					
TCF7L2	6934	broad.mit.edu	37	10	114925317	114925317	+	Frame_Shift_Del	DEL	A	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr10:114925317delA	uc001lae.3	+	14	1902	c.1395delA	c.(1393-1395)AGAfs	p.R465fs	TCF7L2_uc001lac.3_Frame_Shift_Del_p.R459fs|TCF7L2_uc010qrk.1_Frame_Shift_Del_p.E435fs|TCF7L2_uc010qrl.1_Frame_Shift_Del_p.R442fs|TCF7L2_uc010qrm.1_Frame_Shift_Del_p.E441fs|TCF7L2_uc010qrn.1_Frame_Shift_Del_p.E384fs|TCF7L2_uc001lad.3_Frame_Shift_Del_p.E431fs|TCF7L2_uc001lag.3_Frame_Shift_Del_p.E465fs|TCF7L2_uc001laf.3_Frame_Shift_Del_p.R442fs|TCF7L2_uc010qro.1_Frame_Shift_Del_p.E418fs|TCF7L2_uc001lah.2_3'UTR|TCF7L2_uc010qrp.1_3'UTR|TCF7L2_uc010qrq.1_3'UTR|TCF7L2_uc010qrr.1_Frame_Shift_Del_p.R397fs|TCF7L2_uc010qrs.1_Frame_Shift_Del_p.R353fs|TCF7L2_uc010qrt.1_Frame_Shift_Del_p.R353fs|TCF7L2_uc010qru.1_Frame_Shift_Del_p.E357fs|TCF7L2_uc010qrv.1_3'UTR|TCF7L2_uc010qrw.1_3'UTR|TCF7L2_uc010qrx.1_3'UTR	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 isoform 1	482	Promoter-specific activation domain.				anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding	p.R465C(1)		large_intestine(3)|ovary(1)	4		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		TTTCTAGGAGAAAAAAAAAGT	0.522													7	553	---	---	---	---					
GDPD5	81544	broad.mit.edu	37	11	75146590	75146591	+	Frame_Shift_Ins	INS	-	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr11:75146590_75146591insG	uc001owo.3	-	18	2316_2317	c.1779_1780insC	c.(1777-1782)GGCAGCfs	p.G593fs	GDPD5_uc001owp.3_Frame_Shift_Ins_p.G593fs|GDPD5_uc001own.3_Frame_Shift_Ins_p.G348fs|GDPD5_uc009yuc.2_Frame_Shift_Ins_p.G455fs|GDPD5_uc009yud.2_Frame_Shift_Ins_p.G474fs	NM_030792	NP_110419	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain	593_594	Cytoplasmic (Potential).				glycerol metabolic process|lipid metabolic process|nervous system development	endomembrane system|growth cone|integral to membrane|perinuclear region of cytoplasm	glycerophosphodiester phosphodiesterase activity			ovary(1)	1						TTGGTGTGGCTGCCACCCCCTC	0.579													7	250	---	---	---	---					
CLIP1	6249	broad.mit.edu	37	12	122812690	122812691	+	Frame_Shift_Ins	INS	-	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr12:122812690_122812691insT	uc001ucg.1	-	16	3158_3159	c.3052_3053insA	c.(3052-3054)AGCfs	p.S1018fs	CLIP1_uc001uch.1_Frame_Shift_Ins_p.S1007fs|CLIP1_uc001uci.1_Frame_Shift_Ins_p.S972fs|CLIP1_uc001ucj.1_Frame_Shift_Ins_p.S593fs	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a	1018	Potential.				mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CTGGTTGTGGCTTGTTTCCATT	0.505													8	416	---	---	---	---					
PHB	5245	broad.mit.edu	37	17	47486482	47486483	+	Frame_Shift_Del	DEL	CT	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr17:47486482_47486483delCT	uc002iox.1	-	5	504_505	c.431_432delAG	c.(430-432)GAGfs	p.E144fs		NM_002634	NP_002625	P35232	PHB_HUMAN	prohibitin	144					cellular response to interleukin-6|DNA replication|glucocorticoid receptor signaling pathway|histone deacetylation|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of transcription by competitive promoter binding|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|progesterone receptor signaling pathway|regulation of apoptosis	integral to plasma membrane|mitochondrial inner membrane|nucleoplasm	histone deacetylase binding|transcription regulatory region DNA binding				0	all_cancers(4;2.62e-14)|Breast(4;4.21e-29)|all_epithelial(4;6.9e-18)		Epithelial(5;8.1e-06)|all cancers(6;7.71e-05)			TGGAGACCAGCTCTCTCTGGGT	0.554													17	122	---	---	---	---					
SLC25A42	284439	broad.mit.edu	37	19	19221630	19221630	+	Frame_Shift_Del	DEL	T	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:19221630delT	uc002nlf.1	+	8	1053	c.902delT	c.(901-903)ATCfs	p.I301fs		NM_178526	NP_848621	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	301	Helical; Name=6; (Potential).|Solcar 3.				transmembrane transport	integral to membrane|mitochondrial inner membrane	binding				0			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			GCCGTGGGCATCAGCTTCACC	0.657													24	179	---	---	---	---					
ZNF808	388558	broad.mit.edu	37	19	53067676	53067677	+	RNA	INS	-	A	A			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr19:53067676_53067677insA	uc002pzq.2	+	4		c.4188_4189insA						Q8N4W9	ZN808_HUMAN	Homo sapiens zinc finger protein 808, mRNA (cDNA clone IMAGE:3542548), complete cds.						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		CCTTTCATTTCAAAAAAAAAAT	0.287													2	4	---	---	---	---					
PEX13	5194	broad.mit.edu	37	2	61275734	61275735	+	Frame_Shift_Ins	INS	-	G	G			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr2:61275734_61275735insG	uc002sau.3	+	4	1124_1125	c.1041_1042insG	c.(1039-1044)AAAGTTfs	p.K347fs		NM_002618	NP_002609	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	347_348	Cytoplasmic (Potential).				cerebral cortex cell migration|fatty acid alpha-oxidation|locomotory behavior|microtubule-based peroxisome localization|neuron migration|protein import into peroxisome matrix, docking|suckling behavior	integral to peroxisomal membrane|membrane fraction	protein binding			skin(1)	1			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			AATCAAGTAAAGTTTCCAAGCA	0.411													8	75	---	---	---	---					
TRIOBP	11078	broad.mit.edu	37	22	38129406	38129406	+	Frame_Shift_Del	DEL	C	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr22:38129406delC	uc003atr.2	+	8	4320	c.4049delC	c.(4048-4050)GCCfs	p.A1350fs	TRIOBP_uc003atu.2_Frame_Shift_Del_p.A1178fs	NM_001039141	NP_001034230	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein isoform 6	1350					actin modification|barbed-end actin filament capping	actin cytoskeleton|cytoplasm|nucleus	actin binding|GTP-Rho binding|myosin II binding|protein binding|ubiquitin protein ligase binding			central_nervous_system(1)	1	Melanoma(58;0.0574)					TCCAGCCCTGCCCCCAGCAGG	0.697													2	4	---	---	---	---					
VHL	7428	broad.mit.edu	37	3	10188203	10188204	+	Frame_Shift_Ins	INS	-	T	T			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:10188203_10188204insT	uc003bvc.2	+	2	559_560	c.346_347insT	c.(346-348)CTTfs	p.L116fs	VHL_uc003bvd.2_Intron	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	116	Involved in binding to CCT complex.		L -> V (in VHLD).		anti-apoptosis|cell morphogenesis|negative regulation of cell proliferation|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cell differentiation|positive regulation of transcription, DNA-dependent|protein stabilization|protein ubiquitination|proteolysis	cytosol|endoplasmic reticulum|membrane|mitochondrion|nucleus	protein binding|transcription factor binding	p.?(3)|p.L116V(1)|p.W117fs*14(1)|p.W117fs*42(1)|p.L116fs*43(1)|p.H115fs*41(1)|p.H115fs*42(1)		kidney(1273)|soft_tissue(24)|adrenal_gland(15)|large_intestine(13)|pancreas(5)|endometrium(4)|thyroid(3)|upper_aerodigestive_tract(3)|central_nervous_system(2)|lung(2)|pleura(1)|paratesticular_tissues(1)	1346				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GATAGGTCACCTTTGGCTCTTC	0.347		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				81	372	---	---	---	---					
LAMB2	3913	broad.mit.edu	37	3	49167097	49167098	+	Frame_Shift_Del	DEL	GG	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:49167097_49167098delGG	uc003cwe.2	-	11	1756_1757	c.1457_1458delCC	c.(1456-1458)CCCfs	p.P486fs	LAMB2_uc003cwf.1_Frame_Shift_Del_p.P486fs	NM_002292	NP_002283	P55268	LAMB2_HUMAN	laminin, beta 2 precursor	486	Laminin EGF-like 4.				cell adhesion	laminin-11 complex|laminin-3 complex	structural molecule activity			ovary(3)	3				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATCCACTGTTGGGGTCACAAGG	0.559													12	119	---	---	---	---					
BAP1	8314	broad.mit.edu	37	3	52437889	52437889	+	Frame_Shift_Del	DEL	C	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:52437889delC	uc003ddx.2	-	13	1387	c.1272delG	c.(1270-1272)GGGfs	p.G424fs	BAP1_uc003ddw.2_RNA|BAP1_uc010hmg.2_RNA|BAP1_uc010hmh.2_RNA	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1	424					monoubiquitinated histone H2A deubiquitination|negative regulation of cell proliferation|protein K48-linked deubiquitination|regulation of cell cycle|regulation of cell growth|ubiquitin-dependent protein catabolic process	cytoplasm|nucleolus|PR-DUB complex	chromatin binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity			pleura(32)|eye(28)|lung(2)|ovary(2)|breast(1)	65				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		CCCCTGGCTTCCCTGTTCCCT	0.557			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								62	274	---	---	---	---					
ZXDC	79364	broad.mit.edu	37	3	126178522	126178522	+	Frame_Shift_Del	DEL	T	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr3:126178522delT	uc003eiv.2	-	7	2240	c.2186delA	c.(2185-2187)AAGfs	p.K729fs	ZXDC_uc010hsh.2_Intron|ZXDC_uc003eix.2_3'UTR	NM_025112	NP_079388	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C isoform 1	729					positive regulation of transcription, DNA-dependent	nucleus	C2H2 zinc finger domain binding|identical protein binding|LRR domain binding|nucleic acid binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)	1				GBM - Glioblastoma multiforme(114;0.155)		TCCTCTCTGCTTTTTTTCCTT	0.522													7	890	---	---	---	---					
KIAA1967	57805	broad.mit.edu	37	8	22474942	22474942	+	Frame_Shift_Del	DEL	G	-	-			TCGA-AL-3473-01A-01D-1252-08	TCGA-AL-3473-10A-01D-1252-08									Somatic	Phase_I	Capture				Illumina GAIIx	23f15c01-fc74-46bf-8ba5-afc140084aa1	0e794ded-be71-4cd3-932d-121f1b81ecf2	g.chr8:22474942delG	uc003xch.2	+	15	1992	c.1855delG	c.(1855-1857)GGGfs	p.G619fs	KIAA1967_uc003xci.2_Frame_Shift_Del_p.G619fs|KIAA1967_uc003xcj.1_Frame_Shift_Del_p.G288fs	NM_199205	NP_954675	Q8N163	K1967_HUMAN	p30 DBC protein	619					apoptosis|positive regulation of apoptosis	mitochondrial matrix|nucleus	enzyme binding|enzyme inhibitor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00593)|Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		GAAGGAGGATGGGCTTTTGCC	0.478													97	586	---	---	---	---					
