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	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	filter
MST1P2	11209	broad.mit.edu	37	1	16976825	16976825	+	RNA	SNP	C	A	A	rs2761525	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:16976825C>A	uc010och.1	+	14		c.2546C>A			MST1P2_uc001azl.3_RNA|MST1P2_uc009vox.2_RNA|MST1P2_uc001azm.3_RNA	NR_027504				Homo sapiens cDNA FLJ43241 fis, clone HEART1000010, weakly  similar to Hepatocyte growth factor-like protein precursor.												0						taataaaattcatatttttac	0.164													3	16	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17085908	17085908	+	Intron	SNP	C	G	G	rs1805293	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17085908C>G	uc010ock.1	-						CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_5'UTR	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						AGCAGGCGCTCCACTCAGCCC	0.701													3	24	---	---	---	---	PASS
PADI6	353238	broad.mit.edu	37	1	17727910	17727910	+	Silent	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17727910C>T	uc001bak.1	+	17	2061	c.2061C>T	c.(2059-2061)TTC>TTT	p.F687F		NM_207421	NP_997304	Q6TGC4	PADI6_HUMAN	peptidylarginine deiminase type 6	679					peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm|nucleus	calcium ion binding|protein-arginine deiminase activity			breast(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CCTTTGCCTTCAAATGGTGGA	0.557													11	22	---	---	---	---	PASS
EPHA8	2046	broad.mit.edu	37	1	22895795	22895795	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22895795C>A	uc001bfx.1	+	2	233	c.108C>A	c.(106-108)GAC>GAA	p.D36E	EPHA8_uc001bfw.2_Missense_Mutation_p.D36E	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor	36	Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ATTTGCTGGACACGTCGACCA	0.587													42	97	---	---	---	---	PASS
EPHA8	2046	broad.mit.edu	37	1	22895796	22895796	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22895796A>C	uc001bfx.1	+	2	234	c.109A>C	c.(109-111)ACG>CCG	p.T37P	EPHA8_uc001bfw.2_Missense_Mutation_p.T37P	NM_020526	NP_065387	P29322	EPHA8_HUMAN	ephrin receptor EphA8 isoform 1 precursor	37	Extracellular (Potential).					integral to plasma membrane	ATP binding|ephrin receptor activity			central_nervous_system(5)|breast(3)|lung(2)|large_intestine(1)|stomach(1)|skin(1)	13		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.29e-27)|Colorectal(126;1.61e-07)|COAD - Colon adenocarcinoma(152;1.14e-05)|GBM - Glioblastoma multiforme(114;1.74e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000554)|KIRC - Kidney renal clear cell carcinoma(1967;0.00272)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TTTGCTGGACACGTCGACCAT	0.592													42	99	---	---	---	---	PASS
ST3GAL3	6487	broad.mit.edu	37	1	44365370	44365370	+	Silent	SNP	T	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44365370T>C	uc001ckc.2	+	9	892	c.715T>C	c.(715-717)TTG>CTG	p.L239L	ST3GAL3_uc010okj.1_RNA|ST3GAL3_uc001cjz.2_Silent_p.L254L|ST3GAL3_uc001cka.2_Intron|ST3GAL3_uc001ckb.2_Silent_p.L308L|ST3GAL3_uc001ckd.2_Silent_p.L293L|ST3GAL3_uc001cke.2_Silent_p.L223L|ST3GAL3_uc001ckf.2_Silent_p.L277L|ST3GAL3_uc001ckg.2_Silent_p.L239L|ST3GAL3_uc001ckh.2_Intron|ST3GAL3_uc001cki.2_Intron|ST3GAL3_uc009vwv.2_Silent_p.L239L|ST3GAL3_uc001ckj.2_RNA|ST3GAL3_uc009vww.2_Intron|ST3GAL3_uc001ckk.2_Silent_p.L208L|ST3GAL3_uc009vwy.2_Silent_p.L145L|ST3GAL3_uc009vwx.2_RNA|ST3GAL3_uc001ckm.2_Intron|ST3GAL3_uc001ckl.2_Intron|ST3GAL3_uc009vwz.2_Intron|ST3GAL3_uc001ckn.2_Intron|ST3GAL3_uc001ckp.2_Intron|ST3GAL3_uc001cko.2_Silent_p.L223L|ST3GAL3_uc009vxa.2_Silent_p.L26L|ST3GAL3_uc001ckq.2_Intron|ST3GAL3_uc001ckr.2_Silent_p.L192L|ST3GAL3_uc009vxb.2_Intron	NM_006279	NP_006270	Q11203	SIAT6_HUMAN	sialyltransferase 6 isoform j	239	Lumenal (Potential).				protein glycosylation	extracellular region|Golgi cisterna membrane|integral to Golgi membrane	N-acetyllactosaminide alpha-2,3-sialyltransferase activity			ovary(3)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0518)				CTTTAAGTGGTTGAAATACAT	0.587													21	33	---	---	---	---	PASS
PODN	127435	broad.mit.edu	37	1	53535790	53535790	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:53535790G>T	uc001cuv.2	+	2	414	c.407G>T	c.(406-408)CGT>CTT	p.R136L	PODN_uc001cuw.2_Missense_Mutation_p.R117L|PODN_uc010onr.1_Missense_Mutation_p.R117L|PODN_uc010ons.1_Missense_Mutation_p.R136L	NM_153703	NP_714914	Q7Z5L7	PODN_HUMAN	podocan	88	LRRNT.				negative regulation of cell migration|negative regulation of cell proliferation	cytoplasm|extracellular space|proteinaceous extracellular matrix	collagen binding			ovary(1)|pancreas(1)	2						ATTGACCTGCGTGAGTTCCCG	0.677													14	42	---	---	---	---	PASS
GPR61	83873	broad.mit.edu	37	1	110086219	110086219	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110086219C>T	uc001dxy.2	+	2	1258	c.575C>T	c.(574-576)CCC>CTC	p.P192L		NM_031936	NP_114142	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	192	Extracellular (Potential).					integral to membrane|plasma membrane	G-protein coupled receptor activity			central_nervous_system(2)	2		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		CCCAGTGTCCCCCCAGGCTGT	0.582													30	56	---	---	---	---	PASS
KCNC4	3749	broad.mit.edu	37	1	110768698	110768698	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110768698G>A	uc001dzh.2	+	3	1774	c.1717G>A	c.(1717-1719)GCC>ACC	p.A573T	KCNC4_uc009wfr.2_Missense_Mutation_p.A573T|KCNC4_uc001dzg.2_Missense_Mutation_p.A573T|KCNC4_uc001dzi.2_RNA	NM_004978	NP_004969	Q03721	KCNC4_HUMAN	Shaw-related voltage-gated potassium channel	573	Cytoplasmic (Potential).				synaptic transmission	voltage-gated potassium channel complex	voltage-gated potassium channel activity			large_intestine(1)|ovary(1)|central_nervous_system(1)	3		all_cancers(81;9.88e-06)|all_epithelial(167;3.23e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0238)|all cancers(265;0.0693)|Epithelial(280;0.0748)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGAGCGCCGGGCCCTGCGACG	0.642													23	66	---	---	---	---	PASS
PDE4DIP	9659	broad.mit.edu	37	1	144931739	144931739	+	Intron	SNP	A	C	C	rs3839010		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144931739A>C	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001emc.1_Intron|PDE4DIP_uc001emd.1_Intron|PDE4DIP_uc001emb.1_5'UTR|PDE4DIP_uc001emf.1_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AAGCTTCCCGAGGCGGCGGCG	0.652			T	PDGFRB	MPD								3	33	---	---	---	---	PASS
MTMR11	10903	broad.mit.edu	37	1	149901022	149901022	+	Nonstop_Mutation	SNP	T	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:149901022T>A	uc001etl.3	-	17	2380	c.2129A>T	c.(2128-2130)TAG>TTG	p.*710L	SF3B4_uc001etj.1_5'Flank|SF3B4_uc001etk.1_5'Flank|SF3B4_uc009wll.1_5'Flank|MTMR11_uc001etm.1_Intron	NM_001145862	NP_001139334	A4FU01	MTMRB_HUMAN	myotubularin related protein 11 isoform a	710							phosphatase activity			central_nervous_system(1)	1	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			AACCCTCCTCTACCCCAGATC	0.448													26	62	---	---	---	---	PASS
SLAMF9	89886	broad.mit.edu	37	1	159921403	159921403	+	3'UTR	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:159921403G>A	uc001fus.2	-	4					SLAMF9_uc009wtd.2_3'UTR|SLAMF9_uc001fut.2_3'UTR	NM_033438	NP_254273	Q96A28	SLAF9_HUMAN	SLAM family member 9 isoform 1							integral to membrane				ovary(1)	1	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGGATTCTCTGGGTGCTGGGA	0.547													23	48	---	---	---	---	PASS
C1orf111	284680	broad.mit.edu	37	1	162343974	162343974	+	Missense_Mutation	SNP	C	T	T	rs17853130	byFrequency	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:162343974C>T	uc001gbx.2	-	3	714	c.650G>A	c.(649-651)CGC>CAC	p.R217H		NM_182581	NP_872387	Q5T0L3	CA111_HUMAN	hypothetical protein LOC284680	217										ovary(1)	1	all_hematologic(112;0.15)		BRCA - Breast invasive adenocarcinoma(70;0.0938)			TTTGAGCTTGCGGTAGTACAC	0.607													48	103	---	---	---	---	PASS
HMCN1	83872	broad.mit.edu	37	1	186099138	186099138	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:186099138T>G	uc001grq.1	+	84	13174	c.12945T>G	c.(12943-12945)ATT>ATG	p.I4315M	HMCN1_uc001grs.1_Translation_Start_Site	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN	hemicentin 1 precursor	4315	Ig-like C2-type 42.				response to stimulus|visual perception	basement membrane	calcium ion binding			ovary(22)|skin(1)	23						AACTTGTTATTGAAAGAGTGT	0.428													29	72	---	---	---	---	PASS
KIF26B	55083	broad.mit.edu	37	1	245583033	245583033	+	Silent	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:245583033C>T	uc001ibf.1	+	4	1592	c.1152C>T	c.(1150-1152)GCC>GCT	p.A384A	KIF26B_uc010pyq.1_Silent_p.A384A	NM_018012	NP_060482	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	384					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(3)	3	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CGGTGGCCGCCTCCTTCTTTG	0.587													45	103	---	---	---	---	PASS
AHCTF1	25909	broad.mit.edu	37	1	247081660	247081660	+	Silent	SNP	T	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247081660T>G	uc001ibu.1	-	1	20	c.13A>C	c.(13-15)AGA>CGA	p.R5R	AHCTF1_uc001ibv.1_Silent_p.R14R	NM_015446	NP_056261	Q8WYP5	ELYS_HUMAN	transcription factor ELYS	5	Necessary for cytoplasmic localization (By similarity).				cytokinesis|mitotic prometaphase|mRNA transport|nuclear pore complex assembly|protein transport|transmembrane transport	condensed chromosome kinetochore|cytosol|nuclear matrix|nuclear membrane|nuclear pore|nucleoplasm	DNA binding			ovary(5)|skin(2)	7	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ACTTGAGCTCTTAAGTCTCGC	0.373													14	22	---	---	---	---	PASS
MEMO1	51072	broad.mit.edu	37	2	32093458	32093458	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32093458T>A	uc002rnx.2	-	9	1248	c.866A>T	c.(865-867)TAT>TTT	p.Y289F	MEMO1_uc010ymu.1_Missense_Mutation_p.Y266F|MEMO1_uc010ezq.2_Missense_Mutation_p.Y289F|MEMO1_uc002rny.2_RNA|MEMO1_uc002rnz.2_RNA	NM_015955	NP_057039	Q9Y316	MEMO1_HUMAN	mediator of cell motility 1 isoform 1	289					regulation of microtubule-based process	cytosol|nucleus				ovary(1)|skin(1)	2	Acute lymphoblastic leukemia(172;0.155)					TCCAGCTGCATAACTCACTGA	0.488													4	15	---	---	---	---	PASS
POLR1B	84172	broad.mit.edu	37	2	113308515	113308515	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:113308515C>A	uc002thw.2	+	5	1278	c.698C>A	c.(697-699)ACT>AAT	p.T233N	POLR1B_uc010fkn.2_Missense_Mutation_p.T177N|POLR1B_uc002thx.2_Missense_Mutation_p.T94N|POLR1B_uc010fko.2_Missense_Mutation_p.T233N|POLR1B_uc010fkp.2_Intron|POLR1B_uc010yxn.1_Missense_Mutation_p.T271N|POLR1B_uc002thy.2_Missense_Mutation_p.T94N|POLR1B_uc010yxo.1_Missense_Mutation_p.T10N	NM_019014	NP_061887	Q9H9Y6	RPA2_HUMAN	RNA polymerase I polypeptide B isoform 1	233					termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription initiation from RNA polymerase I promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|protein binding|ribonucleoside binding			ovary(1)	1						GAAAATGGCACTGTTATGTTG	0.358													37	151	---	---	---	---	PASS
MYO7B	4648	broad.mit.edu	37	2	128317279	128317279	+	5'UTR	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:128317279G>T	uc002top.2	+	2						NM_001080527	NP_001073996	Q6PIF6	MYO7B_HUMAN	myosin VIIB							apical plasma membrane|myosin complex	actin binding|ATP binding|motor activity			ovary(1)|pancreas(1)	2	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		ATACAGGCTTGTGGAACTGCT	0.338													7	106	---	---	---	---	PASS
ORC2L	4999	broad.mit.edu	37	2	201775984	201775984	+	3'UTR	SNP	T	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:201775984T>G	uc002uwr.2	-	18						NM_006190	NP_006181	Q13416	ORC2_HUMAN	origin recognition complex, subunit 2						cell cycle checkpoint|DNA-dependent DNA replication initiation|G1/S transition of mitotic cell cycle|M/G1 transition of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|S phase of mitotic cell cycle	nuclear origin of replication recognition complex|nucleoplasm	DNA replication origin binding|protein binding				0						GCAGCTGGGGTACAACCCTTC	0.398													6	23	---	---	---	---	PASS
ENTPD3	956	broad.mit.edu	37	3	40433669	40433669	+	Intron	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:40433669G>T	uc003ckd.3	+						ENTPD3_uc010hhy.2_Intron|uc003cke.3_RNA	NM_001248	NP_001239	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase							integral to membrane	ATP binding|hydrolase activity			ovary(1)	1				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		GGCAACAAAGGGAAGAAATGA	0.458													22	23	---	---	---	---	PASS
BAP1	8314	broad.mit.edu	37	3	52439311	52439311	+	Splice_Site	SNP	C	A	A	rs9848343		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52439311C>A	uc003ddx.2	-	11	1047	c.932_splice	c.e11-1	p.D311_splice	BAP1_uc003ddw.2_5'Flank|BAP1_uc010hmg.2_5'Flank|BAP1_uc010hmh.2_5'Flank	NM_004656	NP_004647	Q92560	BAP1_HUMAN	BRCA1 associated protein-1						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)		TCTGCACCATCTGAGACAGGG	0.582			N|Mis|F|S|O		uveal melanoma|breast|NSCLC								39	61	---	---	---	---	PASS
TMF1	7110	broad.mit.edu	37	3	69073260	69073260	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:69073260A>C	uc003dnn.2	-	16	3331	c.3084T>G	c.(3082-3084)AAT>AAG	p.N1028K	TMF1_uc011bfx.1_Missense_Mutation_p.N1031K	NM_007114	NP_009045	P82094	TMF1_HUMAN	TATA element modulatory factor 1	1028	Potential.				regulation of transcription, DNA-dependent|transcription from RNA polymerase II promoter	Golgi membrane|nucleus	DNA binding|protein binding|transcription cofactor activity				0		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		CAAGTTCATCATTTTGATTTG	0.323													34	43	---	---	---	---	PASS
SDHAP2	727956	broad.mit.edu	37	3	195400728	195400728	+	Silent	SNP	A	G	G	rs12107841	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195400728A>G	uc003fuw.2	+	9	1218	c.24A>G	c.(22-24)CCA>CCG	p.P8P	SDHAP2_uc011btb.1_Missense_Mutation_p.S156G|SDHAP2_uc011btc.1_RNA|SDHAP2_uc003fuv.2_RNA					SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);												0						GATTGTGCCCAGCCTGTACGC	0.587													3	26	---	---	---	---	PASS
MUC4	4585	broad.mit.edu	37	3	195511144	195511144	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:195511144G>T	uc011bto.1	-	2	7767	c.7307C>A	c.(7306-7308)ACC>AAC	p.T2436N	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)		GGAAACGTTGGTGACAGGAAG	0.597													3	2	---	---	---	---	PASS
ATP8A1	10396	broad.mit.edu	37	4	42581897	42581897	+	Silent	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:42581897G>T	uc003gwr.2	-	11	1165	c.933C>A	c.(931-933)GTC>GTA	p.V311V	ATP8A1_uc003gws.2_Silent_p.V311V|ATP8A1_uc011byz.1_Silent_p.V311V	NM_006095	NP_006086	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT),	311	Helical; (Potential).				ATP biosynthetic process	chromaffin granule membrane|integral to membrane|plasma membrane	aminophospholipid transporter activity|ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|cation-transporting ATPase activity|magnesium ion binding|phospholipid-translocating ATPase activity			skin(2)|central_nervous_system(1)	3					Phosphatidylserine(DB00144)	CCACAGAACAGACAAGAGACA	0.363													22	35	---	---	---	---	PASS
EMCN	51705	broad.mit.edu	37	4	101331487	101331487	+	Silent	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:101331487G>T	uc003hvr.2	-	11	956	c.777C>A	c.(775-777)ACC>ACA	p.T259T	EMCN_uc011cel.1_Silent_p.T246T|EMCN_uc011cem.1_Silent_p.T176T	NM_016242	NP_057326	Q9ULC0	MUCEN_HUMAN	endomucin isoform 1	259	Cytoplasmic (Potential).					extracellular region|integral to membrane|plasma membrane					0				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		GTCAGTTCTTGGTTTTTCCTT	0.373													44	96	---	---	---	---	PASS
BDH2	56898	broad.mit.edu	37	4	104016427	104016427	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:104016427T>A	uc003hwz.2	-	3	189	c.84A>T	c.(82-84)AGA>AGT	p.R28S	BDH2_uc003hxa.2_RNA	NM_020139	NP_064524	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2	28	NAD.				fatty acid beta-oxidation|heme metabolic process|iron ion homeostasis|siderophore biosynthetic process	cytoplasm	3-hydroxybutyrate dehydrogenase activity|NAD binding|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor				0		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		TGGCACCTTCTCTTGCAAAAG	0.393													30	72	---	---	---	---	PASS
TLL1	7092	broad.mit.edu	37	4	166929189	166929189	+	Silent	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166929189C>T	uc003irh.1	+	7	1553	c.906C>T	c.(904-906)AAC>AAT	p.N302N	TLL1_uc011cjn.1_Silent_p.N302N|TLL1_uc011cjo.1_Silent_p.N126N	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	302	Metalloprotease (By similarity).				cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		ATGCCAGGAACACCTTCTCAA	0.408													22	97	---	---	---	---	PASS
FAM92A3	403315	broad.mit.edu	37	4	183959968	183959968	+	RNA	SNP	T	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:183959968T>G	uc003ivi.3	+	1		c.1151T>G				NR_003612				Homo sapiens family with sequence similarity 92, member A3, mRNA (cDNA clone IMAGE:4822144).												0						AAGACTATATTTTCCAAATTT	0.348													5	12	---	---	---	---	PASS
NIPBL	25836	broad.mit.edu	37	5	37044460	37044460	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:37044460T>A	uc003jkl.3	+	35	6619	c.6120T>A	c.(6118-6120)GAT>GAA	p.D2040E	NIPBL_uc003jkk.3_Missense_Mutation_p.D2040E	NM_133433	NP_597677	Q6KC79	NIPBL_HUMAN	delangin isoform A	2040					brain development|cellular protein localization|cellular response to X-ray|cognition|developmental growth|ear morphogenesis|embryonic arm morphogenesis|embryonic digestive tract morphogenesis|external genitalia morphogenesis|eye morphogenesis|face morphogenesis|gall bladder development|maintenance of mitotic sister chromatid cohesion|metanephros development|negative regulation of transcription from RNA polymerase II promoter|outflow tract morphogenesis|positive regulation of histone deacetylation|regulation of developmental growth|regulation of embryonic development|regulation of hair cycle|response to DNA damage stimulus|sensory perception of sound|uterus morphogenesis	SMC loading complex	chromo shadow domain binding|histone deacetylase binding|protein C-terminus binding|protein N-terminus binding			ovary(4)|lung(2)|large_intestine(1)|breast(1)|kidney(1)	9	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CGCAAAATGATTTCATGGTTA	0.353													11	44	---	---	---	---	PASS
AGGF1	55109	broad.mit.edu	37	5	76342255	76342255	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:76342255G>T	uc003ket.2	+	6	1314	c.954G>T	c.(952-954)AAG>AAT	p.K318N		NM_018046	NP_060516	Q8N302	AGGF1_HUMAN	angiogenic factor VG5Q	318					angiogenesis|cell adhesion|positive regulation of angiogenesis|positive regulation of endothelial cell proliferation|RNA processing|vasculogenesis	extracellular region|perinuclear region of cytoplasm	eukaryotic cell surface binding|nucleic acid binding|protein binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		ATATGAAAAAGAAGGCCAAAA	0.393													59	144	---	---	---	---	PASS
DCP2	167227	broad.mit.edu	37	5	112349325	112349325	+	3'UTR	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:112349325G>T	uc003kqh.2	+	11					DCP2_uc011cwa.1_3'UTR|DCP2_uc010jcc.2_3'UTR	NM_152624	NP_689837	Q8IU60	DCP2_HUMAN	DCP2 decapping enzyme						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay|histone mRNA catabolic process|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	cytoplasmic mRNA processing body|cytosol|nucleus|RNA-induced silencing complex	exoribonuclease activity, producing 5'-phosphomonoesters|manganese ion binding|protein binding|protein binding|RNA binding				0		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		TTATAAGAGAGTAGAAAGAAA	0.363													5	14	---	---	---	---	PASS
HSPA9	3313	broad.mit.edu	37	5	137903401	137903401	+	Silent	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:137903401C>T	uc003ldf.2	-	6	654	c.546G>A	c.(544-546)TTG>TTA	p.L182L	HSPA9_uc011cyw.1_Silent_p.L113L	NM_004134	NP_004125	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 precursor	182					anti-apoptosis|protein folding	cell surface|mitochondrial nucleoid	ATP binding|unfolded protein binding				0			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTGTGTGCCCCAAGTAATTTT	0.383													13	28	---	---	---	---	PASS
PCDHA10	56139	broad.mit.edu	37	5	140237390	140237390	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140237390C>T	uc003lhx.2	+	1	1757	c.1757C>T	c.(1756-1758)GCG>GTG	p.A586V	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA3_uc003lhf.2_Intron|PCDHA4_uc003lhi.2_Intron|PCDHA4_uc003lhh.1_Intron|PCDHA5_uc003lhk.1_Intron|PCDHA5_uc003lhl.2_Intron|PCDHA6_uc003lhn.2_Intron|PCDHA6_uc003lho.2_Intron|PCDHA7_uc003lhq.2_Intron|PCDHA8_uc003lhs.2_Intron|PCDHA9_uc003lhu.2_Intron|PCDHA10_uc003lhw.2_Intron|PCDHA10_uc011dad.1_Missense_Mutation_p.A586V	NM_018901	NP_061724	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10 isoform 1 precursor	586	Extracellular (Potential).				homophilic cell adhesion|nervous system development	extracellular region|integral to plasma membrane	calcium ion binding|protein binding			ovary(2)|skin(2)|breast(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCGGTGGTTGCGGGTCACGTG	0.657													4	57	---	---	---	---	PASS
CD83	9308	broad.mit.edu	37	6	14118278	14118278	+	Nonsense_Mutation	SNP	C	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:14118278C>A	uc003nbi.2	+	2	313	c.135C>A	c.(133-135)TAC>TAA	p.Y45*	CD83_uc003nbh.2_Nonsense_Mutation_p.Y45*	NM_004233	NP_004224	Q01151	CD83_HUMAN	CD83 antigen isoform a	45	Extracellular (Potential).|Ig-like V-type.				defense response|humoral immune response|signal transduction	integral to plasma membrane					0	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				AGGTTCCCTACACGGTCTCCT	0.637													3	23	---	---	---	---	PASS
SDK1	221935	broad.mit.edu	37	7	4169711	4169711	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:4169711G>C	uc003smx.2	+	27	4250	c.4111G>C	c.(4111-4113)GAG>CAG	p.E1371Q	SDK1_uc010kso.2_Missense_Mutation_p.E647Q|SDK1_uc003smy.2_5'UTR	NM_152744	NP_689957	Q7Z5N4	SDK1_HUMAN	sidekick 1 precursor	1371	Fibronectin type-III 7.				cell adhesion	integral to membrane				large_intestine(3)|ovary(2)|skin(1)	6		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CCTCATCCTGGAGCGCACCAA	0.627													19	38	---	---	---	---	PASS
DPY19L2P1	554236	broad.mit.edu	37	7	35131521	35131521	+	Silent	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:35131521G>A	uc003teq.1	-	20	2172	c.1065C>T	c.(1063-1065)AGC>AGT	p.S355S	DPY19L2P1_uc003tep.1_RNA|DPY19L2P1_uc010kwz.1_RNA					RecName: Full=Protein dpy-19 homolog 2-like 2; AltName: Full=Dpy-19-like protein 2 pseudogene 2;												0						ACAGCTTGACGCTTGCCATTG	0.398													6	70	---	---	---	---	PASS
PCLO	27445	broad.mit.edu	37	7	82785211	82785211	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82785211G>T	uc003uhx.2	-	2	1035	c.746C>A	c.(745-747)TCA>TAA	p.S249*	PCLO_uc003uhv.2_Nonsense_Mutation_p.S249*	NM_033026	NP_149015	Q9Y6V0	PCLO_HUMAN	piccolo isoform 1	249	Gln-rich.|Pro-rich.				cytoskeleton organization|synaptic vesicle exocytosis	cell junction|cytoskeleton|synaptic vesicle	calcium ion binding|calcium-dependent phospholipid binding|profilin binding|transporter activity			ovary(7)	7						TGGAGGTTGTGATTTAATTTT	0.493													24	44	---	---	---	---	PASS
MLL5	55904	broad.mit.edu	37	7	104752397	104752397	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:104752397G>T	uc003vcm.2	+	27	4728	c.4194G>T	c.(4192-4194)GAG>GAT	p.E1398D	MLL5_uc010ljc.2_Missense_Mutation_p.E1398D|MLL5_uc010ljf.1_Intron|MLL5_uc010ljg.2_Missense_Mutation_p.E132D	NM_182931	NP_891847	Q8IZD2	MLL5_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 5	1398					cell cycle arrest|cellular response to retinoic acid|DNA methylation|erythrocyte differentiation|neutrophil activation|neutrophil mediated immunity|positive regulation of granulocyte differentiation|positive regulation of transcription, DNA-dependent|retinoic acid receptor signaling pathway|transcription, DNA-dependent	MLL5-L complex|nuclear speck	enzyme binding|histone methyltransferase activity (H3-K4 specific)|transcription coactivator activity|zinc ion binding			ovary(2)|pancreas(1)	3						TAAAAACAGAGCTCCAACAAA	0.423													32	81	---	---	---	---	PASS
LRRC19	64922	broad.mit.edu	37	9	26999658	26999658	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:26999658G>A	uc003zqh.2	-	2	146	c.35C>T	c.(34-36)CCC>CTC	p.P12L	IFT74_uc010mja.2_Intron|IFT74_uc010mjb.2_Intron|IFT74_uc003zqf.3_Intron|IFT74_uc003zqg.3_Intron	NM_022901	NP_075052	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19 precursor	12						integral to membrane					0		all_neural(11;1.81e-09)		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)		CATGGAGAGGGGCCAAAAGAG	0.308													23	28	---	---	---	---	PASS
C9orf25	203259	broad.mit.edu	37	9	34402709	34402709	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:34402709C>T	uc011lok.1	-	3	564	c.257G>A	c.(256-258)CGA>CAA	p.R86Q	C9orf25_uc003zuj.2_Missense_Mutation_p.R69Q|C9orf25_uc003zuk.2_Missense_Mutation_p.R58Q|C9orf25_uc011lol.1_Missense_Mutation_p.R75Q|C9orf25_uc003zul.2_Missense_Mutation_p.R58Q	NM_147202	NP_671735	Q8IW50	CI025_HUMAN	hypothetical protein LOC203259	86											0	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.0858)		CTACCTTGTTCGGGCCATGAC	0.622													19	33	---	---	---	---	PASS
FAM75A6	389730	broad.mit.edu	37	9	43627230	43627230	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:43627230A>C	uc011lrb.1	-	4	1486	c.1457T>G	c.(1456-1458)CTG>CGG	p.L486R		NM_001145196	NP_001138668	Q5VVP1	F75A6_HUMAN	hypothetical protein LOC389730	486						integral to membrane					0						AGGTGTGGGCAGGAATTGGGG	0.537													5	95	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	9	68728904	68728904	+	RNA	SNP	T	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:68728904T>C	uc004aez.1	+	3		c.745T>C			uc004afa.1_RNA|uc010mnp.1_RNA					Homo sapiens cDNA, FLJ18209.																		GCTTGATATGTTGGTGAGTCA	0.209													5	55	---	---	---	---	PASS
GAPVD1	26130	broad.mit.edu	37	9	128099711	128099711	+	Silent	SNP	A	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:128099711A>T	uc010mwx.2	+	17	3044	c.2718A>T	c.(2716-2718)GTA>GTT	p.V906V	GAPVD1_uc011lzs.1_Silent_p.V906V|GAPVD1_uc004bpp.2_Silent_p.V933V|GAPVD1_uc004bpq.2_Silent_p.V906V|GAPVD1_uc004bpr.2_Silent_p.V885V|GAPVD1_uc004bps.2_Silent_p.V906V|GAPVD1_uc010mwy.1_Silent_p.V739V	NM_015635	NP_056450	Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	906					endocytosis|regulation of protein transport|regulation of small GTPase mediated signal transduction|signal transduction	cytosol|endosome|membrane	GTPase activating protein binding|GTPase activator activity|guanyl-nucleotide exchange factor activity			ovary(2)|central_nervous_system(1)|skin(1)	4						CTGATATAGTATCTTCTGTCC	0.353													26	51	---	---	---	---	PASS
RBM17	84991	broad.mit.edu	37	10	6147033	6147033	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:6147033G>A	uc001ijb.2	+	4	606	c.380G>A	c.(379-381)AGA>AAA	p.R127K	RBM17_uc010qav.1_Missense_Mutation_p.R127K	NM_032905	NP_116294	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	127					mRNA processing|RNA splicing	spliceosomal complex	nucleotide binding|protein binding|RNA binding				0						GAGCTGGAAAGACAAAAGGAA	0.403													22	56	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73537549	73537549	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73537549G>T	uc001jrx.3	+	37	5335	c.4958G>T	c.(4957-4959)AGC>ATC	p.S1653I		NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	1653	Cadherin 16.|Extracellular (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						CTCAACACCAGCCTCATCACC	0.577													13	35	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73571840	73571840	+	Intron	SNP	T	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73571840T>C	uc001jrx.3	+						CDH23_uc001jsg.3_Intron|CDH23_uc001jsh.3_Intron|CDH23_uc001jsi.3_Intron|CDH23_uc001jsj.3_5'UTR|CDH23_uc010qjr.1_5'UTR	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor						calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						TGGGGAGAGCTGCAGTCTCCC	0.572											OREG0020259	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	35	---	---	---	---	PASS
CDH23	64072	broad.mit.edu	37	10	73574721	73574721	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:73574721G>A	uc001jrx.3	+	68	10128	c.9751G>A	c.(9751-9753)GAG>AAG	p.E3251K	CDH23_uc001jsg.3_Missense_Mutation_p.E1011K|CDH23_uc001jsh.3_Missense_Mutation_p.E976K|CDH23_uc001jsi.3_Missense_Mutation_p.E976K|CDH23_uc001jsj.3_Missense_Mutation_p.E148K|CDH23_uc010qjr.1_Missense_Mutation_p.E113K	NM_022124	NP_071407	Q9H251	CAD23_HUMAN	cadherin-like 23 isoform 1 precursor	3251	Cytoplasmic (Potential).				calcium ion transport|calcium-dependent cell-cell adhesion|cytosolic calcium ion homeostasis|equilibrioception|homophilic cell adhesion|photoreceptor cell maintenance|response to stimulus|sensory perception of sound	cytosol|integral to membrane|plasma membrane|stereocilium	calcium ion binding|protein binding			central_nervous_system(5)|large_intestine(4)|ovary(2)	11						GATACAGACTGAGCTGGACGA	0.652													6	16	---	---	---	---	PASS
DNTT	1791	broad.mit.edu	37	10	98064450	98064450	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:98064450G>T	uc001kmf.2	+	1	366	c.196G>T	c.(196-198)GAG>TAG	p.E66*	DNTT_uc001kmg.2_Nonsense_Mutation_p.E66*	NM_004088	NP_004079	P04053	TDT_HUMAN	terminal deoxynucleotidyltransferase isoform 1	66	BRCT.				DNA modification	nucleus	DNA binding|DNA nucleotidylexotransferase activity|DNA-directed DNA polymerase activity|metal ion binding			ovary(1)	1		Colorectal(252;0.0815)|all_hematologic(284;0.224)		Epithelial(162;7.97e-08)|all cancers(201;1.89e-06)		GGTTGAAAATGAGCTCAGGTA	0.483													12	35	---	---	---	---	PASS
STK32C	282974	broad.mit.edu	37	10	134145026	134145026	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:134145026G>A	uc010quu.1	-	1	331	c.215C>T	c.(214-216)GCT>GTT	p.A72V	STK32C_uc009ybc.1_5'UTR|STK32C_uc009ybd.1_Intron|LRRC27_uc001llf.2_5'Flank|LRRC27_uc010quv.1_5'Flank|LRRC27_uc010quw.1_5'Flank|LRRC27_uc001llg.2_5'Flank|LRRC27_uc001lli.2_5'Flank	NM_173575	NP_775846	Q86UX6	ST32C_HUMAN	serine/threonine kinase 32C	Error:Variant_position_missing_in_Q86UX6_after_alignment							ATP binding|metal ion binding|protein serine/threonine kinase activity			large_intestine(2)|lung(2)|breast(1)	5		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		tcccctggcagcaagtcctga	0.234													3	56	---	---	---	---	PASS
HIPK3	10114	broad.mit.edu	37	11	33375165	33375165	+	3'UTR	SNP	A	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:33375165A>G	uc001mul.1	+	17					HIPK3_uc001mum.1_3'UTR|HIPK3_uc009yjv.1_3'UTR	NM_005734	NP_005725	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3 isoform						anti-apoptosis|apoptosis|negative regulation of JUN kinase activity|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm	ATP binding|protein serine/threonine kinase activity			large_intestine(1)|skin(1)|stomach(1)|ovary(1)|pancreas(1)	5						ATTAAAAATAAAAACATGGTA	0.313													10	27	---	---	---	---	PASS
SPRYD5	84767	broad.mit.edu	37	11	55653110	55653110	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55653110G>A	uc010rip.1	+	2	298	c.206G>A	c.(205-207)TGT>TAT	p.C69Y	SPRYD5_uc010riq.1_5'Flank	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN	SPRY domain containing 5	69						intracellular	zinc ion binding				0		all_epithelial(135;0.226)				ACTGACATTTGTTTGAAGAAC	0.488													7	14	---	---	---	---	PASS
PLEKHB1	58473	broad.mit.edu	37	11	73372729	73372729	+	3'UTR	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73372729G>T	uc001oua.2	+	8					PLEKHB1_uc001oub.2_3'UTR|PLEKHB1_uc001ouc.2_3'UTR|PLEKHB1_uc001oud.2_3'UTR|PLEKHB1_uc009ytq.2_3'UTR	NM_021200	NP_067023	Q9UF11	PKHB1_HUMAN	pleckstrin homology domain containing, family B						multicellular organismal development|phototransduction	cytoplasm|integral to membrane	signal transducer activity			ovary(1)|lung(1)	2						TACCATCCAAGCCCTGTCCCA	0.587											OREG0021217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	9	41	---	---	---	---	PASS
MMP20	9313	broad.mit.edu	37	11	102479831	102479831	+	Splice_Site	SNP	T	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:102479831T>C	uc001phc.2	-	5	663	c.650_splice	c.e5-1	p.G217_splice		NM_004771	NP_004762	O60882	MMP20_HUMAN	matrix metalloproteinase 20 preproprotein						proteolysis|regulation of enamel mineralization	extracellular space|proteinaceous extracellular matrix	calcium ion binding|metalloendopeptidase activity|protein binding|zinc ion binding			urinary_tract(1)|skin(1)	2	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)		AATTAAAACCTAGACAATATG	0.398													3	47	---	---	---	---	PASS
DSCAML1	57453	broad.mit.edu	37	11	117309653	117309653	+	Silent	SNP	C	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117309653C>A	uc001prh.1	-	24	4373	c.4371G>T	c.(4369-4371)TCG>TCT	p.S1457S		NM_020693	NP_065744	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1397	Fibronectin type-III 5.|Extracellular (Potential).				axonogenesis|brain development|cell fate determination|dorsal/ventral pattern formation|embryonic skeletal system morphogenesis|homophilic cell adhesion	cell surface|integral to membrane|plasma membrane	protein homodimerization activity			ovary(3)|large_intestine(2)|skin(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GGGTGATGGACGAAGCTGAGG	0.617													12	14	---	---	---	---	PASS
SLC2A14	144195	broad.mit.edu	37	12	7967055	7967055	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7967055C>T	uc001qtk.2	-	16	2213	c.1420G>A	c.(1420-1422)GTC>ATC	p.V474I	SLC2A14_uc001qtl.2_Missense_Mutation_p.V451I|SLC2A14_uc001qtm.2_Missense_Mutation_p.V451I|SLC2A14_uc010sgg.1_Missense_Mutation_p.V365I|SLC2A14_uc001qtn.2_Missense_Mutation_p.V474I|SLC2A14_uc001qto.2_Missense_Mutation_p.V109I|SLC2A14_uc010sgh.1_Missense_Mutation_p.V489I	NM_153449	NP_703150	Q8TDB8	GTR14_HUMAN	glucose transporter 14	474	Cytoplasmic (Potential).				cell differentiation|multicellular organismal development|spermatogenesis	integral to membrane	glucose transmembrane transporter activity			ovary(1)	1				Kidney(36;0.0883)		GTCTCAGGGACTTTGAAGAAG	0.483													19	85	---	---	---	---	PASS
SLC2A3	6515	broad.mit.edu	37	12	8074152	8074152	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:8074152C>T	uc001qtr.2	-	10	1610	c.1348G>A	c.(1348-1350)GTC>ATC	p.V450I		NM_006931	NP_008862	P11169	GTR3_HUMAN	solute carrier family 2 (facilitated glucose	450	Cytoplasmic (Potential).				carbohydrate metabolic process|water-soluble vitamin metabolic process	integral to membrane|plasma membrane	D-glucose transmembrane transporter activity|dehydroascorbic acid transporter activity			ovary(3)|pancreas(1)	4				Kidney(36;0.0866)		GTCTCAGGGACTTTGAAGAAG	0.473													7	105	---	---	---	---	PASS
RERG	85004	broad.mit.edu	37	12	15261892	15261892	+	3'UTR	SNP	A	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:15261892A>C	uc001rcs.2	-	4					RERG_uc001rct.2_3'UTR|RERG_uc010shu.1_3'UTR	NM_032918	NP_116307	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor						negative regulation of cell growth|negative regulation of cell proliferation|response to hormone stimulus|small GTPase mediated signal transduction	cytosol|membrane|nucleus	estrogen receptor binding|GDP binding|GTP binding|GTPase activity			lung(1)	1						AAACACGCTAAAACTTCCCAA	0.358													5	6	---	---	---	---	PASS
SUCLA2	8803	broad.mit.edu	37	13	48612044	48612044	+	5'UTR	SNP	A	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:48612044A>C	uc010tgd.1	-	1					NUDT15_uc001vbv.2_Intron|NUDT15_uc001vbw.1_Intron	NM_003850	NP_003841	Q9P2R7	SUCB1_HUMAN	succinate-CoA ligase, ADP-forming, beta subunit						succinyl-CoA pathway|tricarboxylic acid cycle	mitochondrial matrix	ATP binding|metal ion 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)	AGTTCGGGTGAGCAGCCGCGG	0.652											OREG0022405	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	4	23	---	---	---	---	PASS
SLITRK6	84189	broad.mit.edu	37	13	86368849	86368849	+	Nonsense_Mutation	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:86368849G>A	uc001vll.1	-	2	2254	c.1795C>T	c.(1795-1797)CGA>TGA	p.R599*	SLITRK6_uc010afe.1_Intron	NM_032229	NP_115605	Q9H5Y7	SLIK6_HUMAN	slit and trk like 6 precursor	599	Extracellular (Potential).					integral to membrane				large_intestine(1)|ovary(1)|central_nervous_system(1)	3	all_neural(89;0.117)|Medulloblastoma(90;0.163)			GBM - Glioblastoma multiforme(99;0.0456)		GTAAGAGATCGTAAAATAGTA	0.423													41	115	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	14	22616423	22616423	+	Intron	SNP	A	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22616423A>G	uc001wbw.2	+						uc010aiv.1_Intron|uc010aja.1_Intron|uc010tmk.1_Intron|uc010tmo.1_Intron|uc001wco.2_Intron|uc010aje.1_Intron|uc001wcp.2_Intron|uc001wcr.1_Intron|uc001wcs.1_Intron|uc010ajf.1_Intron|uc010ajg.1_Intron|uc001wcx.3_Intron|uc001wdd.2_Intron|uc010ajj.1_Intron|uc001wde.1_Intron|uc001wdf.2_Missense_Mutation_p.Q55R|uc010ajk.1_Missense_Mutation_p.Q55R|uc001wdg.1_5'UTR					SubName: Full=Alpha-chain C region; Flags: Fragment;																		TGGTACAGACAGGAGCCTGGG	0.483													18	15	---	---	---	---	PASS
WHAMML1	339005	broad.mit.edu	37	15	23191911	23191911	+	RNA	SNP	C	T	T	rs147199465	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23191911C>T	uc001yvg.2	-	9		c.1726G>A			WHAMML1_uc010ayc.2_RNA|WHAMML1_uc010ayd.2_RNA	NR_003521				Homo sapiens mRNA; cDNA DKFZp313L2232 (from clone DKFZp313L2232).												0						TGATTTTCTTCGCACTGATCC	0.408													3	49	---	---	---	---	PASS
NDN	4692	broad.mit.edu	37	15	23931882	23931882	+	Silent	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:23931882G>A	uc001ywk.2	-	1	569	c.483C>T	c.(481-483)CAC>CAT	p.H161H		NM_002487	NP_002478	Q99608	NECD_HUMAN	necdin	161	MAGE.				negative regulation of cell proliferation|regulation of growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|perikaryon	DNA binding				0		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		ACTCCATGGTGTGCAGGCTGG	0.637									Prader-Willi_syndrome				11	22	---	---	---	---	PASS
ATF7IP2	80063	broad.mit.edu	37	16	10524570	10524570	+	Missense_Mutation	SNP	G	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10524570G>C	uc002czu.2	+	3	320	c.93G>C	c.(91-93)AAG>AAC	p.K31N	ATF7IP2_uc002czv.2_Missense_Mutation_p.K31N|ATF7IP2_uc010uyo.1_RNA|ATF7IP2_uc010uyp.1_Intron|ATF7IP2_uc002czw.2_Missense_Mutation_p.K31N|ATF7IP2_uc010uyq.1_RNA	NM_024997	NP_079273	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting	31					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus					0						TGCTGAATAAGTCAAGGAATG	0.403													26	46	---	---	---	---	PASS
GTF3C1	2975	broad.mit.edu	37	16	27504025	27504025	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:27504025A>C	uc002dov.1	-	18	2926	c.2886T>G	c.(2884-2886)ATT>ATG	p.I962M	GTF3C1_uc002dou.2_Missense_Mutation_p.I962M	NM_001520	NP_001511	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide	962						transcription factor TFIIIC complex	DNA binding|protein binding			ovary(2)|pancreas(1)|breast(1)|skin(1)	5						CCACCGAAAAAATGTAACGCC	0.552													29	79	---	---	---	---	PASS
C16orf53	79447	broad.mit.edu	37	16	29831005	29831005	+	Missense_Mutation	SNP	A	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29831005A>C	uc002dug.3	+	3	1014	c.695A>C	c.(694-696)GAC>GCC	p.D232A	uc002dtf.2_Intron|BOLA2_uc010bzb.1_Intron|uc002duh.1_Intron|MVP_uc010bzh.1_5'Flank|MVP_uc010vdz.1_5'Flank|MVP_uc002dui.2_5'Flank|MVP_uc002duj.2_5'Flank	NM_024516	NP_078792	Q9BTK6	PA1_HUMAN	PTIP-associated 1 protein	232											0						GACTCGGAGGACCCCAGCCCC	0.627													8	87	---	---	---	---	PASS
PDXDC2	283970	broad.mit.edu	37	16	70012167	70012167	+	Silent	SNP	C	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70012167C>G	uc010vlq.1	-	5	646	c.468G>C	c.(466-468)GCG>GCC	p.A156A	CLEC18C_uc002exy.2_Intron|PDXDC2_uc002eyb.2_RNA|PDXDC2_uc002eyc.2_Intron					SubName: Full=Putative uncharacterized protein;												0						GCAACTCTTGCGCACGTTGAA	0.453													55	213	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	16	70268080	70268080	+	RNA	SNP	T	C	C	rs149244259	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70268080T>C	uc010cfp.1	-	3		c.335A>G								Homo sapiens cDNA, FLJ98908.																		GTCTTACTGTTGGCTAAAAGG	0.373													3	11	---	---	---	---	PASS
SPG7	6687	broad.mit.edu	37	16	89595969	89595969	+	Missense_Mutation	SNP	A	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89595969A>T	uc002fnj.2	+	6	864	c.843A>T	c.(841-843)GAA>GAT	p.E281D	SPG7_uc002fni.2_Missense_Mutation_p.E281D	NM_003119	NP_003110	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 isoform 1	281	Mitochondrial matrix (Potential).				cell death|nervous system development|protein catabolic process|proteolysis	integral to membrane|mitochondrial membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CTGGAAGGGAAGGTGGATTCA	0.488													10	23	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8051537	8051537	+	Silent	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8051537C>T	uc002gkd.2	-	9	1327	c.1089G>A	c.(1087-1089)CGG>CGA	p.R363R	PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Silent_p.R347R	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1	363	PAS 2.				circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						TGGGTGTGTGCCGCGTAGTGA	0.597			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					4	112	---	---	---	---	PASS
PER1	5187	broad.mit.edu	37	17	8054097	8054097	+	5'UTR	SNP	T	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:8054097T>C	uc002gkd.2	-	2					PER1_uc010vuq.1_RNA|PER1_uc010vur.1_Intron|PER1_uc010vus.1_5'UTR	NM_002616	NP_002607	O15534	PER1_HUMAN	period 1						circadian rhythm|entrainment of circadian clock|negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	signal transducer activity			lung(2)|breast(2)|skin(2)|large_intestine(1)|ovary(1)|kidney(1)	9						GCCTGGAGGCTTGGCTGAGGG	0.592			T	ETV6	AML|CMML			Other_conserved_DNA_damage_response_genes					6	15	---	---	---	---	PASS
KRTAP4-11	653240	broad.mit.edu	37	17	39274206	39274206	+	Missense_Mutation	SNP	C	T	T	rs79388709		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:39274206C>T	uc002hvz.2	-	1	401	c.362G>A	c.(361-363)AGA>AAA	p.R121K		NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	121	20.|27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament					0		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcactggggtctgcagcagct	0.100													4	33	---	---	---	---	PASS
HGS	9146	broad.mit.edu	37	17	79657214	79657214	+	Missense_Mutation	SNP	C	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79657214C>A	uc002kbg.2	+	6	495	c.418C>A	c.(418-420)CAC>AAC	p.H140N	HGS_uc010wus.1_Missense_Mutation_p.H140N	NM_004712	NP_004703	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine	140	VHS.				cellular membrane organization|endosome transport|epidermal growth factor receptor signaling pathway|intracellular protein transport|negative regulation of cell proliferation|negative regulation of epidermal growth factor receptor signaling pathway|negative regulation of JAK-STAT cascade|regulation of protein catabolic process	cytosol|early endosome membrane|multivesicular body membrane	metal ion binding|protein domain specific binding			ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CTCTCCAGGGCACGTCTTTCC	0.607													4	97	---	---	---	---	PASS
TNFSF14	8740	broad.mit.edu	37	19	6669873	6669873	+	Missense_Mutation	SNP	T	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:6669873T>G	uc002mfk.1	-	2	590	c.208A>C	c.(208-210)ACC>CCC	p.T70P	TNFSF14_uc002mfj.1_Intron	NM_003807	NP_003798	O43557	TNF14_HUMAN	tumor necrosis factor ligand superfamily, member	70	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			skin(1)	1						GGCAGGCGGGTGACCATCTCT	0.602													8	47	---	---	---	---	PASS
C19orf57	79173	broad.mit.edu	37	19	14000172	14000172	+	Silent	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:14000172C>T	uc002mxl.1	-	6	1556	c.1497G>A	c.(1495-1497)CAG>CAA	p.Q499Q	C19orf57_uc002mxk.1_Silent_p.Q381Q|C19orf57_uc002mxm.1_Intron	NM_024323	NP_077299	Q0VDD7	CS057_HUMAN	hypothetical protein LOC79173	499					multicellular organismal development		protein binding			ovary(2)|upper_aerodigestive_tract(1)	3			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			GAATGCCCTGCTGAGCCCCGG	0.612													33	82	---	---	---	---	PASS
AKAP8L	26993	broad.mit.edu	37	19	15511221	15511221	+	Intron	SNP	A	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:15511221A>T	uc002naw.1	-						AKAP8L_uc002nax.1_Intron|AKAP8L_uc010xoh.1_Intron|AKAP8L_uc002nay.1_Intron|AKAP8L_uc002naz.2_3'UTR	NM_014371	NP_055186	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like							cytoplasm|nuclear matrix	DEAD/H-box RNA helicase binding|DNA binding|zinc ion binding			ovary(1)	1						TTTTTTTTTtaaaagaaacca	0.189													3	28	---	---	---	---	PASS
KIAA0892	23383	broad.mit.edu	37	19	19453474	19453474	+	Missense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:19453474G>T	uc002nmk.3	+	8	905	c.866G>T	c.(865-867)TGT>TTT	p.C289F	KIAA0892_uc002nml.3_5'Flank|KIAA0892_uc010ecd.2_5'Flank	NM_015329	NP_056144	Q9Y6X3	SCC4_HUMAN	hypothetical protein LOC23383 precursor	289					cell division|maintenance of mitotic sister chromatid cohesion	chromatin|nucleoplasm|SMC loading complex	protein N-terminus binding				0						GAGCACATGTGTGTGCTTGTC	0.657											OREG0025380	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	69	116	---	---	---	---	PASS
SPTBN4	57731	broad.mit.edu	37	19	41040294	41040294	+	Intron	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:41040294G>A	uc002ony.2	+						SPTBN4_uc002onx.2_Intron|SPTBN4_uc002onz.2_Intron|SPTBN4_uc010egx.2_Intron|SPTBN4_uc010egy.1_Intron|SPTBN4_uc002ooa.2_Intron|SPTBN4_uc010egz.1_3'UTR	NM_020971	NP_066022	Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4 isoform						actin filament capping|axon guidance|cytoskeletal anchoring at plasma membrane|vesicle-mediated transport	cytosol|nuclear matrix|PML body|spectrin	actin binding|ankyrin binding|structural constituent of cytoskeleton			ovary(3)|central_nervous_system(1)|skin(1)	5			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			ATGCCACATGGGGGCCAGgtc	0.328													5	25	---	---	---	---	PASS
OPA3	80207	broad.mit.edu	37	19	46088086	46088086	+	5'UTR	SNP	T	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46088086T>C	uc002pck.3	-	1					OPA3_uc002pcj.3_5'UTR|OPA3_uc010xxk.1_Intron	NM_025136	NP_079412	Q9H6K4	OPA3_HUMAN	OPA3 protein isoform b						response to stimulus|visual perception	mitochondrion					0		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00778)|GBM - Glioblastoma multiforme(486;0.0976)|Epithelial(262;0.242)		ACCTCTTCACTCCTCCCCCGC	0.637													11	18	---	---	---	---	PASS
SLC8A2	6543	broad.mit.edu	37	19	47969450	47969450	+	Silent	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47969450G>T	uc002pgx.2	-	2	489	c.211C>A	c.(211-213)CGG>AGG	p.R71R	SLC8A2_uc010xyq.1_Intron|SLC8A2_uc010xyr.1_Intron|SLC8A2_uc010ele.2_Silent_p.R71R	NM_015063	NP_055878	Q9UPR5	NAC2_HUMAN	solute carrier family 8 member 2 precursor	71	Helical; (Potential).				cell communication|platelet activation	integral to membrane|plasma membrane	calcium:sodium antiporter activity|calmodulin binding			skin(3)|ovary(1)	4		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		ACCACTGCCCGTGCCGCCTTG	0.642													17	33	---	---	---	---	PASS
HRC	3270	broad.mit.edu	37	19	49658118	49658118	+	Missense_Mutation	SNP	T	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49658118T>C	uc002pmv.2	-	1	564	c.377A>G	c.(376-378)GAG>GGG	p.E126G	TRPM4_uc002pmw.2_5'Flank|TRPM4_uc010emu.2_5'Flank|TRPM4_uc010yak.1_5'Flank|TRPM4_uc002pmx.2_5'Flank|TRPM4_uc010emv.2_5'Flank|TRPM4_uc010yal.1_5'Flank	NM_002152	NP_002143	P23327	SRCH_HUMAN	histidine rich calcium binding protein	126	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				muscle contraction	sarcoplasmic reticulum lumen	calcium ion binding			ovary(1)	1		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		CCCACCATGCTCTGCAAAGAC	0.607													27	63	---	---	---	---	PASS
ZNF615	284370	broad.mit.edu	37	19	52497620	52497620	+	Missense_Mutation	SNP	A	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:52497620A>G	uc002pye.1	-	6	1001	c.709T>C	c.(709-711)TGT>CGT	p.C237R	ZNF615_uc002pyf.1_Missense_Mutation_p.C248R|ZNF615_uc002pyg.1_Missense_Mutation_p.C129R|ZNF615_uc002pyh.1_Missense_Mutation_p.C248R|ZNF615_uc010epi.1_Missense_Mutation_p.C244R|ZNF615_uc010ydg.1_Missense_Mutation_p.C242R	NM_198480	NP_940882	Q8N8J6	ZN615_HUMAN	zinc finger protein 615	237	C2H2-type 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(4)|skin(1)	5		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GCTTTCCCACACATACTGCAT	0.408													79	139	---	---	---	---	PASS
STK4	6789	broad.mit.edu	37	20	43629183	43629183	+	Intron	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:43629183G>A	uc002xnb.2	+						STK4_uc010ggx.2_Intron|STK4_uc010ggy.2_Intron|STK4_uc010ggw.1_Missense_Mutation_p.G328R	NM_006282	NP_006273	Q13043	STK4_HUMAN	serine/threonine kinase 4						apoptosis|cell morphogenesis|hippo signaling cascade|intracellular protein kinase cascade|negative regulation of canonical Wnt receptor signaling pathway|peptidyl-serine phosphorylation|positive regulation of apoptosis|protein autophosphorylation	cytoplasm|nucleus	ATP binding|magnesium ion binding|protein homodimerization activity|protein serine/threonine kinase activator activity|protein serine/threonine kinase activity|transcription factor binding			ovary(1)|skin(1)	2		Myeloproliferative disorder(115;0.0122)				CCGTTGCTGTGGGCCTCAGAC	0.478													8	19	---	---	---	---	PASS
PREX1	57580	broad.mit.edu	37	20	47266686	47266686	+	Missense_Mutation	SNP	G	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47266686G>A	uc002xtw.1	-	24	2899	c.2876C>T	c.(2875-2877)CCC>CTC	p.P959L	PREX1_uc002xtv.1_Missense_Mutation_p.P256L	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,	959					actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity			lung(3)|ovary(2)|pancreas(1)	6			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CAGCGGGTGGGGCTCCAGGGG	0.602													53	109	---	---	---	---	PASS
TMPRSS15	5651	broad.mit.edu	37	21	19716370	19716370	+	Nonsense_Mutation	SNP	G	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:19716370G>T	uc002ykw.2	-	11	1210	c.1179C>A	c.(1177-1179)TAC>TAA	p.Y393*		NM_002772	NP_002763	P98073	ENTK_HUMAN	enterokinase precursor	393	Extracellular (Potential).|MAM.				proteolysis	brush border|integral to membrane	scavenger receptor activity|serine-type endopeptidase activity			ovary(5)|upper_aerodigestive_tract(1)|breast(1)|skin(1)	8						GGGTAGAAATGTAAAATCCTG	0.383													30	106	---	---	---	---	PASS
DEPDC5	9681	broad.mit.edu	37	22	32198825	32198825	+	Splice_Site	SNP	G	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:32198825G>C	uc003als.2	+	15	1223	c.1081_splice	c.e15+1	p.G361_splice	DEPDC5_uc011als.1_Splice_Site_p.G361_splice|DEPDC5_uc011alu.1_Splice_Site_p.G361_splice|DEPDC5_uc011alv.1_Splice_Site|DEPDC5_uc003alt.2_Splice_Site_p.G361_splice|DEPDC5_uc003alr.1_Splice_Site_p.G361_splice|DEPDC5_uc011alt.1_Splice_Site_p.G333_splice	NM_014662	NP_055477	O75140	DEPD5_HUMAN	DEP domain containing 5 isoform 1						intracellular signal transduction					ovary(4)|central_nervous_system(3)|pancreas(1)	8						ATAGATAATGGTAATGCTCTC	0.517													37	81	---	---	---	---	PASS
TOM1	10043	broad.mit.edu	37	22	35730353	35730353	+	Missense_Mutation	SNP	C	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:35730353C>G	uc003ann.2	+	11	1185	c.1060C>G	c.(1060-1062)CAG>GAG	p.Q354E	TOM1_uc011ami.1_Missense_Mutation_p.Q321E|TOM1_uc011amj.1_Missense_Mutation_p.Q197E|TOM1_uc003ans.2_Missense_Mutation_p.Q197E|TOM1_uc011amk.1_Missense_Mutation_p.Q316E|TOM1_uc003anp.2_Missense_Mutation_p.Q354E|TOM1_uc011aml.1_Missense_Mutation_p.Q309E|TOM1_uc003ano.2_RNA|TOM1_uc003anq.2_Missense_Mutation_p.Q348E|TOM1_uc003anr.2_Missense_Mutation_p.Q197E	NM_005488	NP_005479	O60784	TOM1_HUMAN	target of myb1 isoform 1	354					endocytosis|endosome transport|intracellular protein transport	cytosol|early endosome|membrane	protein binding			ovary(1)	1						AGCTGGCCTGCAGTCTCTGGA	0.582													3	70	---	---	---	---	PASS
HUWE1	10075	broad.mit.edu	37	X	53615356	53615356	+	Missense_Mutation	SNP	T	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:53615356T>A	uc004dsp.2	-	37	5002	c.4600A>T	c.(4600-4602)ACG>TCG	p.T1534S	HUWE1_uc004dsn.2_Missense_Mutation_p.T359S	NM_031407	NP_113584	Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1	1534					base-excision repair|cell differentiation|histone ubiquitination|protein monoubiquitination|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	cytoplasm|nucleus	DNA binding|protein binding|ubiquitin-protein ligase activity			ovary(8)|large_intestine(4)|breast(4)|kidney(1)	17						AAAAGTAGCGTTAAAAGCAAG	0.323													11	6	---	---	---	---	PASS
ARHGEF6	9459	broad.mit.edu	37	X	135829736	135829736	+	Missense_Mutation	SNP	C	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135829736C>T	uc004fab.2	-	3	727	c.265G>A	c.(265-267)GAC>AAC	p.D89N	ARHGEF6_uc011mwd.1_5'UTR|ARHGEF6_uc011mwe.1_5'UTR	NM_004840	NP_004831	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor 6	89	CH.				apoptosis|cell junction assembly|induction of apoptosis by extracellular signals|JNK cascade|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|Rho guanyl-nucleotide exchange factor activity				0	Acute lymphoblastic leukemia(192;0.000127)					GAATAAAGGTCATCAGGATCA	0.393													25	17	---	---	---	---	PASS
NOC2L	26155	broad.mit.edu	37	1	880360	880361	+	Intron	INS	-	C	C			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:880360_880361insC	uc001abz.3	-						NOC2L_uc001aby.3_Intron|NOC2L_uc009vjq.2_Intron	NM_015658	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog							nucleolus	protein binding			ovary(1)|skin(1)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-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)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		AGAGCCCCACGCCCCCCGCCCA	0.599													20	11	---	---	---	---	
HECTD3	79654	broad.mit.edu	37	1	45471978	45471980	+	Intron	DEL	CTA	-	-	rs113059779		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:45471978_45471980delCTA	uc009vxk.2	-						HECTD3_uc001cmx.3_5'Flank|HECTD3_uc001cmy.3_Intron|HECTD3_uc010olh.1_Intron	NM_024602	NP_078878	Q5T447	HECD3_HUMAN	HECT domain containing 3						proteasomal ubiquitin-dependent protein catabolic process|protein ubiquitination involved in ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm	ubiquitin-protein ligase activity				0	Acute lymphoblastic leukemia(166;0.155)					TGCCCTAtttctatttttttttt	0.256													3	3	---	---	---	---	
PDE4DIP	9659	broad.mit.edu	37	1	144858936	144858937	+	Intron	INS	-	GAGAA	GAGAA	rs71264659		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:144858936_144858937insGAGAA	uc001elw.3	-						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Intron|PDE4DIP_uc001elv.3_Intron	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein isoform						cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding			ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TAGAGGATATTGAGAAGGGGGA	0.450			T	PDGFRB	MPD								4	2	---	---	---	---	
NBPF10	100132406	broad.mit.edu	37	1	145325870	145325871	+	Intron	INS	-	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:145325870_145325871insA	uc001end.3	+						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron|NBPF10_uc001enc.2_Intron|NBPF10_uc010oym.1_Intron|NBPF10_uc010oyn.1_Intron|NBPF10_uc010oyo.1_Intron|NBPF10_uc010oyp.1_Intron	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN	hypothetical protein LOC100132406												0	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AACTCTTCCTTACGTTAGCCAT	0.431													4	2	---	---	---	---	
LAMB3	3914	broad.mit.edu	37	1	209806666	209806667	+	Intron	DEL	GT	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:209806666_209806667delGT	uc001hhg.2	-						LAMB3_uc009xco.2_Intron|LAMB3_uc001hhh.2_Intron|LAMB3_uc010psl.1_Intron|LAMB3_uc009xcp.1_Intron	NM_001017402	NP_001017402	Q13751	LAMB3_HUMAN	laminin, beta 3 precursor						cell adhesion|epidermis development|hemidesmosome assembly		structural molecule activity			central_nervous_system(2)|skin(2)|large_intestine(1)|ovary(1)	6				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GGCCCTAAACGTGTGTGTGTGT	0.460													4	2	---	---	---	---	
MATN3	4148	broad.mit.edu	37	2	20205423	20205424	+	Intron	INS	-	AAAG	AAAG	rs140894448	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:20205423_20205424insAAAG	uc002rdl.2	-						MATN3_uc010exu.1_Intron	NM_002381	NP_002372	O15232	MATN3_HUMAN	matrilin 3 precursor						skeletal system development	proteinaceous extracellular matrix	extracellular matrix structural constituent|protein binding				0	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCACCAAAAAAGAATAATACT	0.267													3	3	---	---	---	---	
REL	5966	broad.mit.edu	37	2	61128286	61128286	+	Intron	DEL	T	-	-	rs10565258		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61128286delT	uc002sam.1	+						REL_uc002san.1_Intron	NM_002908	NP_002899	Q04864	REL_HUMAN	v-rel reticuloendotheliosis viral oncogene						positive regulation of I-kappaB kinase/NF-kappaB cascade	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(2)|breast(1)	3	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			TTTCtttctcttttttttttt	0.134			A		Hodgkin Lymphoma								15	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	2	92076693	92076694	+	IGR	INS	-	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:92076693_92076694insT								GGT8P (106540 upstream) : FKSG73 (52465 downstream)																							TCTCCCTCACCttttttttttc	0.134													5	4	---	---	---	---	
RANBP2	5903	broad.mit.edu	37	2	109374753	109374753	+	Intron	DEL	A	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:109374753delA	uc002tem.3	+							NM_006267	NP_006258	P49792	RBP2_HUMAN	RAN binding protein 2						carbohydrate metabolic process|glucose transport|mitotic prometaphase|mRNA transport|protein folding|protein import into nucleus|regulation of glucose transport|transmembrane transport|viral reproduction	cytosol|nuclear pore	peptidyl-prolyl cis-trans isomerase activity|Ran GTPase binding|zinc ion binding		RANBP2/ALK(16)	soft_tissue(16)|lung(1)|pancreas(1)	18						acaccatctcaaaaaaaaaaa	0.085													4	4	---	---	---	---	
NOP58	51602	broad.mit.edu	37	2	203157338	203157339	+	Intron	INS	-	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:203157338_203157339insA	uc002uzb.2	+						SNORD11_uc002uzd.1_5'Flank	NM_015934	NP_057018	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein homolog						cell growth|rRNA processing|snRNP protein import into nucleus	box C/D snoRNP complex|Cajal body|cytoplasm|pre-snoRNP complex	protein binding|snoRNA binding				0						tccagcctggGAAAAAAAAAAA	0.203													6	3	---	---	---	---	
FANCD2	2177	broad.mit.edu	37	3	10076009	10076009	+	Intron	DEL	A	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10076009delA	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc003buv.2_Intron	NM_033084	NP_149075	Q9BXW9	FACD2_HUMAN	Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)		actccatctcaaaaaaaaaaa	0.124			D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				5	4	---	---	---	---	
VHL	7428	broad.mit.edu	37	3	10183858	10183859	+	Frame_Shift_Ins	INS	-	CA	CA	rs17855706		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10183858_10183859insCA	uc003bvc.2	+	1	540_541	c.327_328insCA	c.(325-330)ATCCACfs	p.I109fs	VHL_uc003bvd.2_Frame_Shift_Ins_p.I109fs	NM_000551	NP_000542	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor isoform 1	109_110	Involved in binding to CCT complex.				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.?(2)|p.I109N(2)|p.H110fs*49(1)|p.H110_S111del(1)|p.I109_R113del(1)|p.G106fs*49(1)|p.I109fs*50(1)|p.I109S(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)		GCCGCCGCATCCACAGCTACCG	0.653		1	D|Mis|N|F|S		renal|hemangioma|pheochromocytoma	renal|hemangioma|pheochromocytoma			von_Hippel-Lindau_disease|Chuvash_Polycythemia_|Pheochromocytoma_(Adrenal)_Familial				13	11	---	---	---	---	
TBC1D5	9779	broad.mit.edu	37	3	17469888	17469889	+	Intron	DEL	TG	-	-	rs35081140		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:17469888_17469889delTG	uc003cbf.2	-						TBC1D5_uc010hev.2_Intron|TBC1D5_uc003cbe.2_Intron	NM_014744	NP_055559	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5 isoform b							intracellular	protein binding|Rab GTPase activator activity			ovary(1)	1						TAATATTAtatgtgtgtgtgtg	0.228													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	4	25625027	25625027	+	IGR	DEL	T	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:25625027delT								ANAPC4 (204908 upstream) : SLC34A2 (32408 downstream)																							CCAGGAACACTTTTTGAAGTC	0.448													11	7	---	---	---	---	
MAP9	79884	broad.mit.edu	37	4	156281741	156281741	+	Intron	DEL	A	-	-	rs78652179		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:156281741delA	uc003ios.2	-						MAP9_uc011cin.1_Intron|MAP9_uc010iqa.1_Intron|MAP9_uc003iot.1_Intron	NM_001039580	NP_001034669	Q49MG5	MAP9_HUMAN	aster-associated protein						cell division|mitosis	cytoplasm|microtubule|spindle				ovary(1)|central_nervous_system(1)	2	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		AGTGATTTACAAAAAAAAATA	0.254													4	2	---	---	---	---	
IPO11	51194	broad.mit.edu	37	5	61763288	61763290	+	Intron	DEL	ATA	-	-	rs143944846		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:61763288_61763290delATA	uc003jtc.2	+						IPO11_uc011cqr.1_Intron|IPO11_uc003jtb.1_Intron	NM_016338	NP_057422	Q9UI26	IPO11_HUMAN	Ran binding protein 11 isoform 2							cytoplasm|nucleus	protein binding			lung(2)|skin(2)	4		Lung NSC(810;8.99e-06)|Prostate(74;0.0235)|Ovarian(174;0.0511)|Breast(144;0.077)		Lung(70;0.0613)		GAAAGCACATATAATAAGTTGAA	0.330													1	5	---	---	---	---	
C6orf153	88745	broad.mit.edu	37	6	42989414	42989419	+	In_Frame_Del	DEL	GCCGGG	-	-	rs3833662		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:42989414_42989419delGCCGGG	uc003otp.1	+	1	30_35	c.22_27delGCCGGG	c.(22-27)GCCGGGdel	p.AG14del		NM_033112	NP_149103	Q96EU6	RRP36_HUMAN	hypothetical protein LOC88745	14_15					ribosomal small subunit biogenesis|rRNA processing	nucleolus					0			Colorectal(64;0.00237)|all cancers(41;0.0034)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0539)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TAACTAccgcgccggggccggggccg	0.529													4	2	---	---	---	---	
FAM162B	221303	broad.mit.edu	37	6	117073894	117073895	+	Intron	INS	-	AG	AG	rs61228007		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117073894_117073895insAG	uc003pxi.2	-							NM_001085480	NP_001078949	Q5T6X4	F162B_HUMAN	hypothetical protein LOC221303							integral to membrane					0						tatatatatatatagatacacg	0.292													3	3	---	---	---	---	
ANLN	54443	broad.mit.edu	37	7	36465193	36465194	+	Intron	INS	-	TTAA	TTAA	rs144494427	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:36465193_36465194insTTAA	uc003tff.2	+						ANLN_uc011kaz.1_Intron|ANLN_uc003tfg.2_Intron|ANLN_uc010kxe.2_Intron	NM_018685	NP_061155	Q9NQW6	ANLN_HUMAN	anillin, actin binding protein						cytokinesis|mitosis|regulation of exit from mitosis|septin ring assembly	actomyosin contractile ring|nucleus	actin binding			ovary(2)|skin(1)	3						gtgagccactgctcccggcTAA	0.104													6	4	---	---	---	---	
SLC26A5	375611	broad.mit.edu	37	7	103017133	103017135	+	Intron	DEL	AGA	-	-	rs66928926	byFrequency	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:103017133_103017135delAGA	uc003vbz.2	-						SLC26A5_uc003vbt.1_Intron|SLC26A5_uc003vbu.1_Intron|SLC26A5_uc003vbv.1_Intron|SLC26A5_uc003vbw.2_Intron|SLC26A5_uc003vbx.2_Intron|SLC26A5_uc003vby.2_Intron|SLC26A5_uc010liy.2_Intron	NM_198999	NP_945350	P58743	S26A5_HUMAN	prestin isoform a						regulation of cell shape|sensory perception of sound	integral to membrane	secondary active sulfate transmembrane transporter activity			ovary(1)	1						GTGATTTTTCAGAAGAACAATTT	0.320													3	5	---	---	---	---	
ZNF786	136051	broad.mit.edu	37	7	148771739	148771740	+	Intron	INS	-	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148771739_148771740insA	uc003wfh.2	-						ZNF786_uc011kuk.1_Intron|ZNF786_uc003wfi.2_Intron	NM_152411	NP_689624	Q8N393	ZN786_HUMAN	zinc finger protein 786						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			breast(3)|skin(1)	4	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			AACAACATGTCAAAAAAAAAAA	0.376													8	4	---	---	---	---	
ZNF398	57541	broad.mit.edu	37	7	148875840	148875840	+	Frame_Shift_Del	DEL	T	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:148875840delT	uc003wfl.2	+	6	1151	c.876delT	c.(874-876)GCTfs	p.A292fs	ZNF398_uc011kul.1_Frame_Shift_Del_p.A121fs|ZNF398_uc011kum.1_Frame_Shift_Del_p.A297fs	NM_170686	NP_733787	Q8TD17	ZN398_HUMAN	zinc finger 398 isoform a	292					positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(1)	1	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			CAAAGGATGCTTTTTCAGATG	0.507													261	116	---	---	---	---	
ASPN	54829	broad.mit.edu	37	9	95227128	95227129	+	Intron	INS	-	A	A			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:95227128_95227129insA	uc004ase.1	-						CENPP_uc004arz.2_Intron|CENPP_uc010mqx.2_Intron|ASPN_uc010mqy.1_Intron	NM_017680	NP_060150	Q9BXN1	ASPN_HUMAN	asporin precursor						bone mineralization|negative regulation of tooth mineralization|negative regulation of transforming growth factor beta receptor signaling pathway	proteinaceous extracellular matrix	calcium ion binding				0						GCACAGTTTACAATATTAGATT	0.327													10	12	---	---	---	---	
HIATL1	84641	broad.mit.edu	37	9	97200570	97200580	+	Intron	DEL	TCTGTTTTGGG	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97200570_97200580delTCTGTTTTGGG	uc004aur.2	+						HIATL1_uc011luh.1_Intron	NM_032558	NP_115947	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1						transmembrane transport	integral to membrane|plasma membrane	protein binding|transporter activity			ovary(2)	2		Acute lymphoblastic leukemia(62;0.136)				AAAGTATTATTCTGTTTTGGGGGCAGTACAA	0.218													4	3	---	---	---	---	
NOLC1	9221	broad.mit.edu	37	10	103920996	103920996	+	Intron	DEL	T	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103920996delT	uc001kuo.2	+						NOLC1_uc001kup.2_Intron|NOLC1_uc001kuq.2_Intron|NOLC1_uc009xxb.1_Intron|NOLC1_uc001kur.2_Intron	NM_004741	NP_004732	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1						mitosis|rRNA processing	cytoplasm|nucleolus	ATP binding|GTP binding|protein binding			ovary(1)	1		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		ACTGGTTACCttttttttttt	0.259													3	3	---	---	---	---	
FNBP4	23360	broad.mit.edu	37	11	47768072	47768072	+	Intron	DEL	T	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47768072delT	uc009ylv.2	-						FNBP4_uc001ngj.2_Intron|FNBP4_uc001ngl.2_Intron	NM_015308	NP_056123	Q8N3X1	FNBP4_HUMAN	formin binding protein 4											ovary(1)	1						TAAAAACGACttttttttttt	0.164													4	2	---	---	---	---	
SF3B2	10992	broad.mit.edu	37	11	65825457	65825458	+	Intron	DEL	AG	-	-	rs60074596		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:65825457_65825458delAG	uc001ogy.1	+							NM_006842	NP_006833	Q13435	SF3B2_HUMAN	splicing factor 3B subunit 2						interspecies interaction between organisms	catalytic step 2 spliceosome|nucleoplasm|U12-type spliceosomal complex	nucleic acid binding|protein binding			ovary(2)|breast(1)	3						aaaaaaaaaaagaaagaaagaa	0.233													8	6	---	---	---	---	
MLL	4297	broad.mit.edu	37	11	118353037	118353038	+	Intron	INS	-	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:118353037_118353038insT	uc001pta.2	+						MLL_uc001ptb.2_Intron|MLL_uc001pte.1_Intron|MLL_uc009zab.1_Intron	NM_005933	NP_005924	Q03164	MLL1_HUMAN	myeloid/lymphoid or mixed-lineage leukemia						apoptosis|embryonic hemopoiesis|histone H4-K16 acetylation|positive regulation of transcription, DNA-dependent|protein complex assembly|transcription from RNA polymerase II promoter	MLL1 complex	AT DNA binding|histone acetyl-lysine binding|histone methyltransferase activity (H3-K4 specific)|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|unmethylated CpG binding|zinc ion binding			lung(7)|ovary(5)|kidney(5)|central_nervous_system(3)|pancreas(2)|urinary_tract(1)|breast(1)|skin(1)	25	all_hematologic(175;0.046)	all_hematologic(192;1.13e-50)|all_neural(223;3.18e-06)|Breast(348;1.07e-05)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.244)		OV - Ovarian serous cystadenocarcinoma(223;2.77e-44)|BRCA - Breast invasive adenocarcinoma(274;1.2e-11)|Lung(307;3.48e-06)|LUSC - Lung squamous cell carcinoma(976;7.92e-05)|Colorectal(284;0.144)		AGTTTAAATAGTTTTTTTTTTT	0.292			T|O	MLL|MLLT1|MLLT2|MLLT3|MLLT4|MLLT7|MLLT10|MLLT6|ELL|EPS15|AF1Q|CREBBP|SH3GL1|FNBP1|PNUTL1|MSF|GPHN|GMPS|SSH3BP1|ARHGEF12|GAS7|FOXO3A|LAF4|LCX|SEPT6|LPP|CBFA2T1|GRAF|EP300|PICALM|HEAB	AML|ALL								3	3	---	---	---	---	
NCAPD3	23310	broad.mit.edu	37	11	134037240	134037241	+	Intron	INS	-	ACTT	ACTT	rs72311832		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:134037240_134037241insACTT	uc001qhd.1	-						NCAPD3_uc010scm.1_Intron|NCAPD3_uc009zda.1_Intron|NCAPD3_uc001qhc.1_Intron	NM_015261	NP_056076	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3						cell division|mitotic chromosome condensation	nuclear centromeric heterochromatin|nuclear condensin complex	methylated histone residue binding			ovary(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	5	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GGCGCACACTCGTGAGATGAGC	0.589													4	2	---	---	---	---	
PKP2	5318	broad.mit.edu	37	12	32994260	32994261	+	Intron	INS	-	G	G	rs143525894	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:32994260_32994261insG	uc001rlj.3	-						PKP2_uc001rlk.3_Intron|PKP2_uc010skj.1_Intron	NM_004572	NP_004563	Q99959	PKP2_HUMAN	plakophilin 2 isoform 2b						cell-cell adhesion	desmosome|integral to membrane|nucleus	binding			ovary(1)|pancreas(1)	2	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					TTTGGGGGGTTGGGGGGCCAGC	0.465													5	5	---	---	---	---	
SLC25A3	5250	broad.mit.edu	37	12	98992547	98992548	+	Intron	INS	-	T	T	rs71756041		TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:98992547_98992548insT	uc001tfo.2	+						SLC25A3_uc001tfm.2_Intron|SLC25A3_uc001tfn.2_Intron|SLC25A3_uc001tfp.2_Intron|SLC25A3_uc001tfq.2_Intron|SLC25A3_uc001tfr.2_Intron|SLC25A3_uc001tfs.2_Intron|SLC25A3_uc009ztn.2_Intron|SLC25A3_uc001tft.2_Intron|SNORA53_uc001tfu.1_5'Flank	NM_005888	NP_005879	Q00325	MPCP_HUMAN	solute carrier family 25 member 3 isoform a						generation of precursor metabolites and energy	integral to plasma membrane|mitochondrial inner membrane	phosphate carrier activity|symporter activity				0		Lung NSC(355;4.08e-05)|Breast(359;0.00191)|Colorectal(145;0.00205)|Myeloproliferative disorder(1001;0.0255)		GBM - Glioblastoma multiforme(134;1.36e-23)|BRCA - Breast invasive adenocarcinoma(302;0.000115)		Atttttttttgttttttttttt	0.134													9	4	---	---	---	---	
GNPTAB	79158	broad.mit.edu	37	12	102224492	102224494	+	5'UTR	DEL	GCC	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102224492_102224494delGCC	uc001tit.2	-	1					GNPTAB_uc001tiu.1_5'UTR|GNPTAB_uc001tiw.2_RNA	NM_024312	NP_077288	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase						cell differentiation	Golgi membrane|integral to membrane|nucleus	metal ion binding|transcription factor binding|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity			ovary(1)|skin(1)	2						AGGAGCCTGAgccgccgccgccg	0.596													11	5	---	---	---	---	
CALML4	91860	broad.mit.edu	37	15	68491621	68491622	+	Intron	INS	-	G	G			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:68491621_68491622insG	uc002arb.2	-						CALML4_uc002arc.2_Intron|CALML4_uc002ard.2_Intron|CALML4_uc002are.2_Intron|CALML4_uc010bhz.2_Intron	NM_033429	NP_219501	Q96GE6	CALL4_HUMAN	calmodulin-like 4 isoform 1								calcium ion binding				0						GCTGTCAGCGCGATTTTTCTCT	0.396													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9250813	9250813	+	IGR	DEL	T	-	-	rs115093816	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9250813delT								C16orf72 (37268 upstream) : GRIN2A (596454 downstream)																							cggagccctcttttttttttt	0.164													3	4	---	---	---	---	
LOC595101	595101	broad.mit.edu	37	16	30291742	30291742	+	Intron	DEL	A	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:30291742delA	uc002dxp.1	-							NR_002453				Homo sapiens cDNA FLJ39663 fis, clone SMINT2007187.												0						AACAAAATAGAAAAAAAAAAA	0.358													4	2	---	---	---	---	
ATP2C2	9914	broad.mit.edu	37	16	84456439	84456440	+	Intron	INS	-	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:84456439_84456440insT	uc002fhx.2	+						ATP2C2_uc010chj.2_Intron|ATP2C2_uc002fhy.2_Intron|ATP2C2_uc002fhz.2_Intron	NM_014861	NP_055676	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						ATP biosynthetic process	Golgi membrane|integral to membrane	ATP binding|calcium-transporting ATPase activity|metal ion binding|protein binding			breast(1)|central_nervous_system(1)	2						TAAACATTTAAttttttttttt	0.178													10	7	---	---	---	---	
FTSJ3	117246	broad.mit.edu	37	17	61900955	61900955	+	Intron	DEL	A	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:61900955delA	uc002jbz.2	-						FTSJ3_uc002jca.2_Intron	NM_017647	NP_060117	Q8IY81	RRMJ3_HUMAN	FtsJ homolog 3						RNA methylation|rRNA processing	nucleolus	methyltransferase activity|nucleic acid binding			ovary(1)	1						actccgtctcaaaaaaaaaaa	0.169													4	4	---	---	---	---	
AFG3L2	10939	broad.mit.edu	37	18	12337643	12337645	+	Intron	DEL	CAG	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:12337643_12337645delCAG	uc002kqz.1	-							NM_006796	NP_006787	Q9Y4W6	AFG32_HUMAN	AFG3 ATPase family gene 3-like 2						cell death|protein catabolic process|proteolysis	integral to membrane	ATP binding|metalloendopeptidase activity|nucleoside-triphosphatase activity|unfolded protein binding|zinc ion binding				0					Adenosine triphosphate(DB00171)	TCTGTGTAGCcagcagcagcagc	0.384													4	2	---	---	---	---	
ZNF791	163049	broad.mit.edu	37	19	12734687	12734688	+	Intron	INS	-	GGA	GGA	rs139467837	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:12734687_12734688insGGA	uc002mua.2	+						ZNF791_uc010xml.1_Intron|ZNF791_uc010dyu.1_Intron|ZNF791_uc010xmm.1_Intron	NM_153358	NP_699189	Q3KP31	ZN791_HUMAN	zinc finger protein 791						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2						ttttttttggggggggacagag	0.139													7	6	---	---	---	---	
PRIC285	85441	broad.mit.edu	37	20	62190831	62190832	+	Intron	INS	-	T	T			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62190831_62190832insT	uc002yfm.2	-						PRIC285_uc002yfl.1_Intron	NM_001037335	NP_001032412	Q9BYK8	PR285_HUMAN	PPAR-alpha interacting complex protein 285						cellular lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleoplasm	ATP binding|DNA binding|helicase activity|ribonuclease activity|RNA binding|transcription coactivator activity|zinc ion binding			central_nervous_system(2)	2	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;1.27e-08)|all cancers(9;7.32e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)			tcaggtgggaggagtcagggtc	0.139													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	21	9907174	9907175	+	IGR	DEL	CA	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:9907174_9907175delCA								None (None upstream) : TPTE (999568 downstream)																							TCCCACCGGGCACACACACACA	0.574													5	3	---	---	---	---	
C2CD2	25966	broad.mit.edu	37	21	43332591	43332592	+	Intron	INS	-	TTATTTATTTAT	TTATTTATTTAT	rs150526292	by1000genomes	TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:43332591_43332592insTTATTTATTTAT	uc002yzw.2	-						C2CD2_uc002yzu.2_Intron|C2CD2_uc002yzv.2_Intron|C2CD2_uc002yzx.1_Intron	NM_015500	NP_056315	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2 isoform							cytosol|extracellular region|nucleus				ovary(1)	1						GTTTATTtttattatttattta	0.228													4	3	---	---	---	---	
IL3RA	3563	broad.mit.edu	37	X	1467599	1467600	+	Intron	INS	-	TTTC	TTTC			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:1467599_1467600insTTTC	uc004cps.2	+						IL3RA_uc011mhd.1_Intron	NM_002183	NP_002174	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha precursor							integral to membrane|plasma membrane	interleukin-3 receptor activity			skin(2)|lung(1)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	ctttctttctgtttctgtttct	0.045													3	3	---	---	---	---	
TMEM164	84187	broad.mit.edu	37	X	109387871	109387871	+	Intron	DEL	T	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:109387871delT	uc004eom.2	+						TMEM164_uc004eol.2_Intron|TMEM164_uc010npq.2_Intron	NM_032227	NP_115603	Q5U3C3	TM164_HUMAN	transmembrane protein 164 isoform b							integral to membrane				large_intestine(1)|lung(1)|skin(1)	3						CATTTTGTTCTTTTTTTTTTC	0.323													6	4	---	---	---	---	
AFF2	2334	broad.mit.edu	37	X	147924998	147924998	+	Intron	DEL	T	-	-			TCGA-CZ-5985-01A-11D-1669-08	TCGA-CZ-5985-11A-01D-1669-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:147924998delT	uc004fcp.2	+						AFF2_uc004fco.2_Intron|AFF2_uc004fcq.2_Intron|AFF2_uc004fcr.2_Intron|AFF2_uc011mxb.1_Intron|AFF2_uc004fcs.2_Intron|AFF2_uc011mxc.1_Intron	NM_002025	NP_002016	P51816	AFF2_HUMAN	fragile X mental retardation 2						brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding			ovary(3)|pancreas(2)	5	Acute lymphoblastic leukemia(192;6.56e-05)					TTTGGGGATATTTGGCAAGGA	0.418													19	28	---	---	---	---	
