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
LOC649330	649330	broad.mit.edu	37	1	12907356	12907356	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:12907356C>T	uc009vno.2	-	1	882	c.787G>A	c.(787-789)GGG>AGG	p.G263R	HNRNPCL1_uc010obf.1_Missense_Mutation_p.G263R	NM_001146181	NP_001139653	B7ZW38	B7ZW38_HUMAN	heterogeneous nuclear ribonucleoprotein C-like	263							nucleic acid binding|nucleotide binding				0						TGGTCATCCCCCTGATCTTCA	0.502													46	197	---	---	---	---	PASS
MST1P9	11223	broad.mit.edu	37	1	17084503	17084503	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17084503C>A	uc010ock.1	-	12	1595	c.1595G>T	c.(1594-1596)CGG>CTG	p.R532L	CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_Missense_Mutation_p.R132L	NR_002729				SubName: Full=Hepatocyte growth factor-like protein homolog;												0						TACTGGGACCCGCTGTAGGCC	0.592													4	123	---	---	---	---	PASS
TMCO4	255104	broad.mit.edu	37	1	20009748	20009748	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20009748C>G	uc001bcn.2	-	16	1932	c.1690G>C	c.(1690-1692)GGT>CGT	p.G564R	TMCO4_uc001bcm.2_Missense_Mutation_p.G395R|TMCO4_uc001bco.1_Intron|TMCO4_uc001bcp.1_Intron	NM_181719	NP_859070	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	564						integral to membrane					0		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		GATATGGGACCCTGGGTTTGC	0.667													80	128	---	---	---	---	PASS
ARID1A	8289	broad.mit.edu	37	1	27099852	27099852	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27099852C>A	uc001bmv.1	+	15	4104	c.3731C>A	c.(3730-3732)CCC>CAC	p.P1244H	ARID1A_uc001bmt.1_Missense_Mutation_p.P1243H|ARID1A_uc001bmu.1_Missense_Mutation_p.P1244H|ARID1A_uc001bmw.1_Missense_Mutation_p.P861H|ARID1A_uc001bmx.1_Missense_Mutation_p.P90H|ARID1A_uc009vsm.1_5'UTR|ARID1A_uc009vsn.1_5'Flank	NM_006015	NP_006006	O14497	ARI1A_HUMAN	AT rich interactive domain 1A isoform a	1244					androgen receptor signaling pathway|chromatin-mediated maintenance of transcription|estrogen receptor signaling pathway|glucocorticoid receptor signaling pathway|nervous system development|nucleosome mobilization|transcription, DNA-dependent	nBAF complex|npBAF complex|SWI/SNF complex	DNA binding|protein binding			ovary(124)|pancreas(5)|central_nervous_system(3)|endometrium(3)|kidney(3)|skin(2)|upper_aerodigestive_tract(1)|lung(1)	142		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GGGAGTGATCCCTTCATGTCC	0.592			Mis|N|F|S|D		clear cell ovarian carcinoma|RCC								51	80	---	---	---	---	PASS
IPO13	9670	broad.mit.edu	37	1	44425962	44425962	+	Silent	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44425962G>A	uc001ckx.2	+	12	2865	c.2070G>A	c.(2068-2070)AAG>AAA	p.K690K		NM_014652	NP_055467	O94829	IPO13_HUMAN	importin 13	690	HEAT 12.				protein import into nucleus	cytoplasm|nucleus	protein binding|protein transporter activity			central_nervous_system(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				TTATCCAGAAGGTGCTGAGCA	0.562													38	337	---	---	---	---	PASS
TTC22	55001	broad.mit.edu	37	1	55251692	55251692	+	Silent	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:55251692T>C	uc009vzt.1	-	5	1089	c.984A>G	c.(982-984)CCA>CCG	p.P328P	TTC22_uc001cxz.3_Silent_p.P328P	NM_001114108	NP_001107580	Q5TAA0	TTC22_HUMAN	tetratricopeptide repeat domain 22 isoform 1	328	TPR 5.						binding				0						AGTTGAGTTCTGGATCTCGTA	0.552													19	34	---	---	---	---	PASS
C1orf168	199920	broad.mit.edu	37	1	57258476	57258476	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:57258476C>A	uc001cym.3	-	2	416	c.10G>T	c.(10-12)GAA>TAA	p.E4*	C1orf168_uc009vzu.1_RNA|C1orf168_uc009vzv.1_Nonsense_Mutation_p.E4*	NM_001004303	NP_001004303	Q5VWT5	CA168_HUMAN	hypothetical protein LOC199920	4										ovary(3)|skin(2)	5						CTTACCCCTTCCTAAGGCAAA	0.308													26	249	---	---	---	---	PASS
LRRC7	57554	broad.mit.edu	37	1	70144085	70144085	+	Silent	SNP	A	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:70144085A>G	uc001deo.1	+	2	1479	c.24A>G	c.(22-24)GGA>GGG	p.G8G				Q96NW7	LRRC7_HUMAN	SubName: Full=Leucine rich repeat containing 7; SubName: Full=cDNA FLJ54846, highly similar to Leucine-rich repeat-containing protein 7;	Error:Variant_position_missing_in_Q96NW7_after_alignment						centrosome|focal adhesion|nucleolus	protein binding			ovary(9)|breast(2)|central_nervous_system(2)|liver(1)	14						TAATAAGGGGAAGGAATCCCC	0.383													6	7	---	---	---	---	PASS
WDR47	22911	broad.mit.edu	37	1	109554267	109554267	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:109554267T>C	uc001dwj.2	-	5	777	c.401A>G	c.(400-402)TAT>TGT	p.Y134C	WDR47_uc001dwl.2_Missense_Mutation_p.Y141C|WDR47_uc001dwi.2_Missense_Mutation_p.Y134C|WDR47_uc001dwk.2_Missense_Mutation_p.Y106C|WDR47_uc010ovf.1_Missense_Mutation_p.Y61C	NM_001142551	NP_001136023	O94967	WDR47_HUMAN	WD repeat domain 47 isoform 3	134										ovary(1)	1		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		GAGCTTACTATAGTCATCTTT	0.398													22	263	---	---	---	---	PASS
FLG	2312	broad.mit.edu	37	1	152279938	152279938	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:152279938C>G	uc001ezu.1	-	3	7460	c.7424G>C	c.(7423-7425)GGA>GCA	p.G2475A		NM_002016	NP_002007	P20930	FILA_HUMAN	filaggrin	2475	Ser-rich.				keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity			ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTAGTGGGATCCCTGCCTTCC	0.577									Ichthyosis				156	511	---	---	---	---	PASS
PGLYRP3	114771	broad.mit.edu	37	1	153274993	153274993	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:153274993A>G	uc001fbn.1	-	5	673	c.620T>C	c.(619-621)ATC>ACC	p.I207T		NM_052891	NP_443123	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3 precursor	207					defense response to Gram-positive bacterium|detection of bacterium|innate immune response|peptidoglycan catabolic process	extracellular region|intracellular|membrane	N-acetylmuramoyl-L-alanine amidase activity|peptidoglycan receptor activity|zinc ion binding			ovary(2)|pancreas(1)|skin(1)	4	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCGGTGTGGATGATGATGAC	0.483													15	124	---	---	---	---	PASS
AFTPH	54812	broad.mit.edu	37	2	64779884	64779884	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:64779884G>C	uc002sdc.2	+	1	1308	c.1276G>C	c.(1276-1278)GAT>CAT	p.D426H	AFTPH_uc002scz.2_Missense_Mutation_p.D426H|AFTPH_uc002sda.2_Missense_Mutation_p.D426H|AFTPH_uc002sdb.2_Missense_Mutation_p.D426H	NM_203437	NP_982261	Q6ULP2	AFTIN_HUMAN	aftiphilin protein isoform a	426					protein transport	AP-1 adaptor complex|cytosol|nucleus	clathrin binding			ovary(2)	2						GACTTGCAATGATATCAATGA	0.378													40	236	---	---	---	---	PASS
SLC9A4	389015	broad.mit.edu	37	2	103095413	103095413	+	Silent	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:103095413C>A	uc002tbz.3	+	2	829	c.372C>A	c.(370-372)GTC>GTA	p.V124V		NM_001011552	NP_001011552	Q6AI14	SL9A4_HUMAN	solute carrier family 9 (sodium/hydrogen	124	Extracellular (Potential).				regulation of pH	apical plasma membrane|basolateral plasma membrane|integral to membrane	sodium:hydrogen antiporter activity			skin(2)|central_nervous_system(1)	3						CGCCTCCGGTCATGGACTCCA	0.612													47	69	---	---	---	---	PASS
NFE2L2	4780	broad.mit.edu	37	2	178097099	178097099	+	Intron	SNP	A	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:178097099A>G	uc002ulh.3	-						NFE2L2_uc002ulg.3_Intron|NFE2L2_uc010zfa.1_Intron|NFE2L2_uc002uli.3_Intron|NFE2L2_uc010fra.2_3'UTR	NM_006164	NP_006155	Q16236	NF2L2_HUMAN	nuclear factor erythroid 2-like 2 isoform 1						transcription from RNA polymerase II promoter	centrosome|cytosol|nucleus|plasma membrane	protein dimerization activity|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			central_nervous_system(1)	1			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AATCTCCAGTATTACATTCTA	0.358			Mis		NSCLC|HNSCC					HNSCC(56;0.16)			9	24	---	---	---	---	PASS
TTN	7273	broad.mit.edu	37	2	179582323	179582323	+	Silent	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179582323G>A	uc010zfg.1	-	84	21770	c.21546C>T	c.(21544-21546)CAC>CAT	p.H7182H	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Silent_p.H3843H	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	8109							ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTGCCCTATGTGGCTCTGGT	0.423													11	22	---	---	---	---	PASS
COL5A2	1290	broad.mit.edu	37	2	189914113	189914113	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:189914113G>A	uc002uqk.2	-	44	3382	c.3107C>T	c.(3106-3108)CCC>CTC	p.P1036L	COL5A2_uc010frx.2_Missense_Mutation_p.P612L	NM_000393	NP_000384	P05997	CO5A2_HUMAN	alpha 2 type V collagen preproprotein	1036					axon guidance|collagen fibril organization|eye morphogenesis|skin development	collagen type V	extracellular matrix structural constituent			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GGAGCCTGGGGGCCCCACAGG	0.458													18	36	---	---	---	---	PASS
DLEC1	9940	broad.mit.edu	37	3	38163910	38163910	+	3'UTR	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:38163910G>A	uc003cho.1	+	37					DLEC1_uc003chp.1_Silent_p.P1717P|DLEC1_uc010hgv.1_3'UTR|DLEC1_uc003chr.1_3'UTR|DLEC1_uc003chs.1_Silent_p.P274P	NM_007335	NP_031361	Q9Y238	DLEC1_HUMAN	deleted in lung and esophageal cancer 1 isoform						negative regulation of cell proliferation	cytoplasm				ovary(2)|pancreas(2)|central_nervous_system(2)|skin(2)|breast(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CTGAGGCTCCGCCCCAGCCCT	0.612													42	25	---	---	---	---	PASS
PBRM1	55193	broad.mit.edu	37	3	52649373	52649373	+	Nonsense_Mutation	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:52649373T>A	uc003des.2	-	15	1930	c.1918A>T	c.(1918-1920)AAG>TAG	p.K640*	PBRM1_uc003dex.2_RNA|PBRM1_uc003deq.2_Nonsense_Mutation_p.K640*|PBRM1_uc003der.2_Nonsense_Mutation_p.K608*|PBRM1_uc003det.2_Nonsense_Mutation_p.K655*|PBRM1_uc003deu.2_Nonsense_Mutation_p.K655*|PBRM1_uc003dev.2_RNA|PBRM1_uc003dew.2_Nonsense_Mutation_p.K640*|PBRM1_uc010hmk.1_Nonsense_Mutation_p.K640*|PBRM1_uc003dey.2_Nonsense_Mutation_p.K640*|PBRM1_uc003dez.1_Nonsense_Mutation_p.K640*|PBRM1_uc003dfb.1_Nonsense_Mutation_p.K553*|PBRM1_uc003dfc.2_Nonsense_Mutation_p.K7*	NM_181042	NP_060635	Q86U86	PB1_HUMAN	polybromo 1 isoform 4	640					chromatin remodeling|mitosis|negative regulation of cell proliferation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nuclear chromosome	chromatin binding|DNA binding|protein binding			kidney(136)|breast(4)	140				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTACTCAGCTTGAGTTTGGGA	0.358			Mis|N|F|S|D|O		clear cell renal carcinoma|breast								15	47	---	---	---	---	PASS
ILDR1	286676	broad.mit.edu	37	3	121724198	121724198	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:121724198T>A	uc003ees.2	-	3	378	c.272A>T	c.(271-273)GAC>GTC	p.D91V	ILDR1_uc003eeq.2_Missense_Mutation_p.D103V|ILDR1_uc003eer.2_Missense_Mutation_p.D91V|ILDR1_uc010hrg.2_Missense_Mutation_p.D91V	NM_175924	NP_787120	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor	91	Extracellular (Potential).|Ig-like V-type.					cytosol|integral to membrane|plasma membrane	receptor activity			skin(1)	1				GBM - Glioblastoma multiforme(114;0.156)		GTCGTTGCAGTCATTGGATGG	0.577													17	68	---	---	---	---	PASS
CNBP	7555	broad.mit.edu	37	3	128890023	128890023	+	Silent	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:128890023G>A	uc003elq.3	-	4	521	c.315C>T	c.(313-315)GGC>GGT	p.G105G	CNBP_uc003elr.3_Silent_p.G98G|CNBP_uc011bku.1_Silent_p.G88G	NM_003418	NP_003409	P62633	CNBP_HUMAN	zinc finger protein 9 isoform 3	105	CCHC-type 4.				cholesterol biosynthetic process	endoplasmic reticulum	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GAGCCAGATGGCCTGGTTTGC	0.502													42	65	---	---	---	---	PASS
P2RY13	53829	broad.mit.edu	37	3	151045862	151045862	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:151045862G>T	uc003eyv.2	-	2	1003	c.982C>A	c.(982-984)CTA>ATA	p.L328I	MED12L_uc011bnz.1_Intron|MED12L_uc003eyp.2_Intron	NM_176894	NP_795713	Q9BPV8	P2Y13_HUMAN	purinergic receptor P2Y, G-protein coupled, 13	328	Cytoplasmic (Potential).					integral to membrane|plasma membrane				ovary(3)|lung(1)	4			LUSC - Lung squamous cell carcinoma(72;0.0189)|Lung(72;0.0278)			ATACATGGTAGCTTTTCTGTG	0.363													93	136	---	---	---	---	PASS
SLC33A1	9197	broad.mit.edu	37	3	155546088	155546088	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:155546088C>A	uc003fan.3	-	6	1942	c.1561G>T	c.(1561-1563)GGA>TGA	p.G521*	SLC33A1_uc003fao.1_Nonsense_Mutation_p.G521*	NM_004733	NP_004724	O00400	ACATN_HUMAN	acetyl-coenzyme A transporter	521	Helical; (Potential).				cell death|transmembrane transport	endoplasmic reticulum membrane|Golgi membrane|integral to plasma membrane|membrane fraction	acetyl-CoA transporter activity			ovary(2)|large_intestine(1)|pancreas(1)	4			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CAACCAAATCCAATGAAAACA	0.338													32	88	---	---	---	---	PASS
MCCC1	56922	broad.mit.edu	37	3	182733066	182733066	+	3'UTR	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182733066G>A	uc003fle.2	-	19					MCCC1_uc010hxi.2_RNA|MCCC1_uc011bqo.1_RNA|MCCC1_uc003flf.2_3'UTR|MCCC1_uc003flg.2_3'UTR	NM_020166	NP_064551	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)						biotin metabolic process|leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|biotin binding|biotin carboxylase activity|metal ion binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)|central_nervous_system(1)|skin(1)	3	all_cancers(143;1.84e-14)|Ovarian(172;0.0355)		all cancers(12;1.8e-44)|Epithelial(37;3.23e-38)|LUSC - Lung squamous cell carcinoma(7;5.04e-25)|Lung(8;5.03e-23)|OV - Ovarian serous cystadenocarcinoma(80;5.07e-21)		Biotin(DB00121)	GATAATTAGTGACCCAAATGC	0.328													7	32	---	---	---	---	PASS
RFC4	5984	broad.mit.edu	37	3	186522387	186522387	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:186522387G>A	uc003fqz.2	-	2	339	c.116C>T	c.(115-117)CCC>CTC	p.P39L	RFC4_uc011bsc.1_Missense_Mutation_p.P39L|RFC4_uc011bsd.1_Missense_Mutation_p.P39L	NM_002916	NP_002907	P35249	RFC4_HUMAN	replication factor C 4	39					cell cycle checkpoint|DNA strand elongation involved in DNA replication|nucleotide-excision repair, DNA gap filling|phosphatidylinositol-mediated signaling|S phase of mitotic cell cycle|telomere maintenance via recombination|telomere maintenance via semi-conservative replication|transcription-coupled nucleotide-excision repair	DNA replication factor C complex|nucleoplasm	ATP binding|DNA clamp loader activity|protein binding			breast(2)|upper_aerodigestive_tract(1)|ovary(1)|large_intestine(1)	5	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		TTCCACCCAGGGAACGGGTTT	0.398													4	182	---	---	---	---	PASS
EIF4E	1977	broad.mit.edu	37	4	99823113	99823113	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:99823113A>T	uc003hue.2	-	2	1562	c.39T>A	c.(37-39)AAT>AAA	p.N13K	EIF4E_uc011cea.1_Missense_Mutation_p.N33K|EIF4E_uc011ceb.1_Missense_Mutation_p.N13K|EIF4E_uc011cec.1_Missense_Mutation_p.N13K	NM_001968	NP_001959	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	13					G1/S transition of mitotic cell cycle|insulin receptor signaling pathway|interspecies interaction between organisms|mRNA export from nucleus|nuclear-transcribed mRNA poly(A) tail shortening|positive regulation of mitotic cell cycle|regulation of translation	cytoplasmic mRNA processing body|cytosol|eukaryotic translation initiation factor 4F complex|mRNA cap binding complex|RNA-induced silencing complex	protein binding|RNA cap binding|translation initiation factor activity			lung(1)|central_nervous_system(1)	2				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		TAGTCGGGGGATTAGGAGTAG	0.373													61	131	---	---	---	---	PASS
USP53	54532	broad.mit.edu	37	4	120214394	120214394	+	3'UTR	SNP	A	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:120214394A>G	uc003ics.3	+	18					USP53_uc003icr.3_3'UTR|USP53_uc003icu.3_3'UTR	NM_019050	NP_061923	Q70EK8	UBP53_HUMAN	ubiquitin specific protease 53						ubiquitin-dependent protein catabolic process		ubiquitin thiolesterase activity			ovary(1)|breast(1)|kidney(1)|skin(1)	4						CCTGTGTTACATAATAATCTT	0.368													8	50	---	---	---	---	PASS
MAST4	375449	broad.mit.edu	37	5	66462356	66462356	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:66462356G>A	uc003jut.1	+	28	6850	c.6782G>A	c.(6781-6783)CGA>CAA	p.R2261Q	MAST4_uc003juw.2_Missense_Mutation_p.R2189Q|MAST4_uc003jux.2_Missense_Mutation_p.R14Q	NM_015183	NP_055998	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase	2453						cytoplasm	ATP binding|magnesium ion binding|protein serine/threonine kinase activity			lung(6)|ovary(2)|kidney(2)|breast(2)|central_nervous_system(1)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGTTCTTTCCGATCCACGGCC	0.632											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	11	17	---	---	---	---	PASS
MCCC2	64087	broad.mit.edu	37	5	70952871	70952871	+	3'UTR	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:70952871T>C	uc003kbs.3	+	17					MCCC2_uc003kbt.3_RNA	NM_022132	NP_071415	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)						leucine catabolic process	mitochondrial inner membrane|mitochondrial matrix	ATP binding|methylcrotonoyl-CoA carboxylase activity			ovary(1)	1		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	TCCTTTTAAATTTTCTTAGAG	0.164													3	9	---	---	---	---	PASS
C5orf13	9315	broad.mit.edu	37	5	111071196	111071196	+	Nonsense_Mutation	SNP	G	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:111071196G>T	uc003kpl.2	-	2	491	c.12C>A	c.(10-12)TAC>TAA	p.Y4*	C5orf13_uc011cvr.1_Nonsense_Mutation_p.Y48*|C5orf13_uc011cvs.1_Nonsense_Mutation_p.Y38*|C5orf13_uc003kpk.2_RNA|C5orf13_uc003kpm.2_Nonsense_Mutation_p.Y4*|C5orf13_uc011cvk.1_Nonsense_Mutation_p.Y4*|C5orf13_uc011cvl.1_Nonsense_Mutation_p.Y4*|C5orf13_uc011cvm.1_Nonsense_Mutation_p.Y4*|C5orf13_uc011cvn.1_Nonsense_Mutation_p.Y4*|C5orf13_uc011cvo.1_Nonsense_Mutation_p.Y4*|C5orf13_uc011cvp.1_Nonsense_Mutation_p.Y4*|C5orf13_uc011cvq.1_Nonsense_Mutation_p.Y4*	NM_001142483	NP_001135955	Q16612	NP311_HUMAN	neuronal protein 3.1 isoform a	4						cytoplasm				skin(1)	1		all_cancers(142;0.00597)|all_epithelial(76;0.000144)|Prostate(80;0.0115)|Colorectal(10;0.0446)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;5.45e-09)|Epithelial(69;2e-08)|all cancers(49;1.9e-06)|COAD - Colon adenocarcinoma(37;0.0514)|Colorectal(14;0.0629)		AGAGTTCTGGGTAATAAACCT	0.403													30	117	---	---	---	---	PASS
GEMIN5	25929	broad.mit.edu	37	5	154278145	154278145	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:154278145G>A	uc003lvx.3	-	23	3283	c.3200C>T	c.(3199-3201)TCA>TTA	p.S1067L	GEMIN5_uc011ddk.1_Missense_Mutation_p.S1066L	NM_015465	NP_056280	Q8TEQ6	GEMI5_HUMAN	gemin 5	1067					ncRNA metabolic process|protein complex assembly|spliceosomal snRNP assembly	Cajal body|cytosol|spliceosomal complex	protein binding|snRNA binding			skin(2)|ovary(1)	3	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CGTTCTAAGTGATGCCGCATC	0.478													5	100	---	---	---	---	PASS
MAML1	9794	broad.mit.edu	37	5	179222879	179222879	+	3'UTR	SNP	G	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:179222879G>C	uc003mkn.1	+	5					LTC4S_uc003mko.2_Intron	NM_014757	NP_055572	Q92585	MAML1_HUMAN	mastermind-like 1						Notch signaling pathway|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nuclear speck	peptide antigen binding|protein kinase binding|transcription coactivator activity			lung(4)|ovary(2)	6	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGGCAGGGGCGCACGCGCTGG	0.711													4	34	---	---	---	---	PASS
BAT4	7918	broad.mit.edu	37	6	31632107	31632107	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:31632107T>C	uc003nvn.2	-	2	794	c.149A>G	c.(148-150)GAT>GGT	p.D50G	BAT4_uc003nvo.3_Missense_Mutation_p.D50G|BAT4_uc003nvp.3_Missense_Mutation_p.D50G|BAT4_uc003nvq.2_Missense_Mutation_p.D50G|CSNK2B_uc010jsz.1_5'Flank|CSNK2B_uc010jta.1_5'Flank|CSNK2B_uc003nvr.1_5'Flank|CSNK2B_uc003nvs.1_5'Flank	NM_033177	NP_149417	O95872	GPAN1_HUMAN	HLA-B associated transcript 4	50						intracellular	nucleic acid binding				0						GCTGCTCTCATCCCCAATCAG	0.557													44	85	---	---	---	---	PASS
UHRF1BP1	54887	broad.mit.edu	37	6	34789455	34789455	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34789455A>T	uc003oju.3	+	2	304	c.70A>T	c.(70-72)AAA>TAA	p.K24*	UHRF1BP1_uc010jvm.1_RNA|UHRF1BP1_uc010jvn.2_RNA	NM_017754	NP_060224	Q6BDS2	URFB1_HUMAN	ICBP90 binding protein 1	24										ovary(3)	3						TTCCCCAGACAAAATCAACCT	0.453													31	36	---	---	---	---	PASS
XPO5	57510	broad.mit.edu	37	6	43515440	43515440	+	Silent	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:43515440G>A	uc003ovp.2	-	19	2276	c.2065C>T	c.(2065-2067)CTG>TTG	p.L689L		NM_020750	NP_065801	Q9HAV4	XPO5_HUMAN	exportin 5	689					gene silencing by RNA	cytosol|nucleoplasm	protein binding|tRNA binding			skin(2)|breast(1)|kidney(1)	4	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			ACATCTGACAGCACTCTGAAG	0.463													19	41	---	---	---	---	PASS
SIM1	6492	broad.mit.edu	37	6	100841464	100841464	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:100841464C>A	uc003pqj.3	-	10	1676	c.1469G>T	c.(1468-1470)TGG>TTG	p.W490L	SIM1_uc010kcu.2_Missense_Mutation_p.W490L	NM_005068	NP_005059	P81133	SIM1_HUMAN	single-minded homolog 1	490	Single-minded C-terminal.				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity			ovary(4)	4		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GCGAGAGCCCCACCAGGGCTC	0.607													19	101	---	---	---	---	PASS
EGFR	1956	broad.mit.edu	37	7	55220177	55220177	+	Intron	SNP	A	G	G	rs11506105	by1000genomes	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:55220177A>G	uc003tqk.2	+						EGFR_uc003tqh.2_Intron|EGFR_uc003tqi.2_Intron|EGFR_uc003tqj.2_Intron|EGFR_uc010kzg.1_Intron|EGFR_uc011kco.1_Intron|EGFR_uc003tql.1_RNA	NM_005228	NP_005219	P00533	EGFR_HUMAN	epidermal growth factor receptor isoform a						activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity			lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)	GCTCTGCGACATCCCTGGGAA	0.463		8	A|O|Mis		glioma|NSCLC	NSCLC			Lung_Cancer_Familial_Clustering_of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			9	432	---	---	---	---	PASS
C7orf23	79161	broad.mit.edu	37	7	86848862	86848862	+	5'UTR	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:86848862C>G	uc003uio.2	-	1						NM_024315	NP_077291	Q9BU79	CG023_HUMAN	chromosome 7 open reading frame 23							integral to membrane					0	Esophageal squamous(14;0.0058)|all_lung(186;0.191)|Lung NSC(181;0.192)					AAAAGCAAGACAGCATGACCT	0.597										HNSCC(41;0.11)			17	25	---	---	---	---	PASS
TRIM4	89122	broad.mit.edu	37	7	99499621	99499621	+	Intron	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99499621C>G	uc003usd.2	-						TRIM4_uc003use.2_Intron|TRIM4_uc011kjc.1_Intron|TRIM4_uc003usf.2_3'UTR	NM_033017	NP_148977	Q9C037	TRIM4_HUMAN	tripartite motif protein TRIM4 isoform alpha						protein trimerization	cytoplasm|plasma membrane	zinc ion binding			ovary(1)|kidney(1)	2	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)	Ovarian(593;0.238)				cctcagttacctcagccttac	0.000													4	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	7	102004777	102004777	+	5'UTR	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:102004777C>A	uc003uzd.1	+	2					uc003uze.1_5'UTR|PRKRIP1_uc003uzf.2_5'UTR|PRKRIP1_uc003uzg.2_5'UTR	NM_001003686	NP_001003686			SubName: Full=Putative uncharacterized protein PMS2L3;																		GGTGACCTCGCGAGCAGACGC	0.716													9	12	---	---	---	---	PASS
SLC13A4	26266	broad.mit.edu	37	7	135370277	135370277	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:135370277C>T	uc003vta.2	-	14	2287	c.1598G>A	c.(1597-1599)TGC>TAC	p.C533Y	SLC13A4_uc003vtb.2_Missense_Mutation_p.C534Y|PL-5283_uc003vsz.3_Intron	NM_012450	NP_036582	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate	533						integral to plasma membrane	sodium:sulfate symporter activity				0						CACCAGGCTGCACAGGATGGG	0.612													16	162	---	---	---	---	PASS
MLL3	58508	broad.mit.edu	37	7	151945210	151945210	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:151945210A>T	uc003wla.2	-	14	2528	c.2309T>A	c.(2308-2310)TTT>TAT	p.F770Y		NM_170606	NP_733751	Q8NEZ4	MLL3_HUMAN	myeloid/lymphoid or mixed-lineage leukemia 3	770					intracellular signal transduction|regulation of transcription, DNA-dependent|transcription, DNA-dependent		DNA binding|protein binding|zinc ion binding			large_intestine(27)|pancreas(13)|ovary(9)|central_nervous_system(8)|breast(3)|upper_aerodigestive_tract(1)|urinary_tract(1)|skin(1)	63	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.0906)	OV - Ovarian serous cystadenocarcinoma(82;0.00715)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0597)|BRCA - Breast invasive adenocarcinoma(188;0.0462)		TGATGATGAAAATGATGACTC	0.423			N		medulloblastoma								7	223	---	---	---	---	PASS
AMAC1L2	83650	broad.mit.edu	37	8	11189539	11189539	+	Silent	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:11189539T>C	uc003wtp.1	+	1	1045	c.924T>C	c.(922-924)TCT>TCC	p.S308S		NM_054028	NP_473369	Q96KT7	AMCL2_HUMAN	acyl-malonyl condensing enzyme	308	DUF6 2.|Helical; (Potential).					integral to membrane					0			STAD - Stomach adenocarcinoma(15;0.00676)	COAD - Colon adenocarcinoma(149;0.0563)		TGGCACTTTCTGACATCATGG	0.562													3	99	---	---	---	---	PASS
ATP6V0D2	245972	broad.mit.edu	37	8	87163705	87163705	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:87163705C>T	uc003ydp.1	+	7	896	c.827C>T	c.(826-828)CCT>CTT	p.P276L		NM_152565	NP_689778	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0	276					ATP hydrolysis coupled proton transport|cellular iron ion homeostasis|insulin receptor signaling pathway|transferrin transport	apical plasma membrane|endosome membrane|proton-transporting V-type ATPase, V0 domain|vacuolar proton-transporting V-type ATPase complex	hydrogen ion transmembrane transporter activity|protein binding				0						GTATACAAACCTTTATTTGAA	0.294													3	52	---	---	---	---	PASS
TM7SF4	81501	broad.mit.edu	37	8	105367350	105367350	+	Silent	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:105367350T>A	uc003ylx.1	+	3	1324	c.1275T>A	c.(1273-1275)CTT>CTA	p.L425L		NM_030788	NP_110415	Q9H295	TM7S4_HUMAN	dendritic cell-specific transmembrane protein	425	Cytoplasmic.				osteoclast differentiation	cell surface|integral to membrane|plasma membrane				pancreas(2)|large_intestine(1)|ovary(1)	4			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			CAAAGCTGCTTAAAAAAAGAT	0.458													7	90	---	---	---	---	PASS
PTK2	5747	broad.mit.edu	37	8	141727751	141727751	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:141727751T>A	uc003yvu.2	-	23	2318	c.2088A>T	c.(2086-2088)AGA>AGT	p.R696S	PTK2_uc011ljp.1_Missense_Mutation_p.R4S|PTK2_uc003yvo.2_Missense_Mutation_p.R324S|PTK2_uc011ljq.1_Missense_Mutation_p.R391S|PTK2_uc003yvp.2_Missense_Mutation_p.R364S|PTK2_uc003yvq.2_Missense_Mutation_p.R222S|PTK2_uc003yvr.2_Missense_Mutation_p.R636S|PTK2_uc003yvs.2_Missense_Mutation_p.R696S|PTK2_uc003yvt.2_Missense_Mutation_p.R718S|PTK2_uc003yvv.2_Missense_Mutation_p.R596S|PTK2_uc011ljr.1_Missense_Mutation_p.R696S	NM_153831	NP_722560	Q05397	FAK1_HUMAN	PTK2 protein tyrosine kinase 2 isoform a	696					axon guidance|blood coagulation|cellular component disassembly involved in apoptosis|ephrin receptor signaling pathway|growth hormone receptor signaling pathway|integrin-mediated signaling pathway|peptidyl-tyrosine phosphorylation|protein autophosphorylation|regulation of cell adhesion mediated by integrin|signal complex assembly	cytoskeleton|cytosol|focal adhesion	ATP binding|JUN kinase binding|non-membrane spanning protein tyrosine kinase activity|SH2 domain binding|signal transducer activity			ovary(2)|lung(2)|central_nervous_system(1)|skin(1)	6	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TGGCCTGTCTTCTGGACTCCA	0.537													83	123	---	---	---	---	PASS
CPSF1	29894	broad.mit.edu	37	8	145623927	145623927	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145623927T>A	uc003zcj.2	-	18	1815	c.1740A>T	c.(1738-1740)GAA>GAT	p.E580D		NM_013291	NP_037423	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1,	580					mRNA cleavage|mRNA export from nucleus|mRNA polyadenylation|nuclear mRNA splicing, via spliceosome|termination of RNA polymerase II transcription	mRNA cleavage and polyadenylation specificity factor complex	mRNA 3'-UTR binding|protein binding			skin(1)	1	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TGGTGGAGTCTTCCCGGCTCA	0.682													26	214	---	---	---	---	PASS
CYHR1	50626	broad.mit.edu	37	8	145689375	145689375	+	Intron	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:145689375C>A	uc003zcv.2	-						CYHR1_uc003zcw.2_3'UTR|CYHR1_uc003zcx.2_3'UTR|CYHR1_uc003zcy.2_3'UTR|KIFC2_uc003zcz.2_5'Flank	NM_138496	NP_612505	Q6ZMK1	CYHR1_HUMAN	cysteine/histidine-rich 1 isoform 1							perinuclear region of cytoplasm	zinc ion binding				0	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			AGACTCTGCCCCTGACCAGTC	0.582											OREG0019056	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	12	55	---	---	---	---	PASS
ATP8B5P	158381	broad.mit.edu	37	9	35449946	35449946	+	RNA	SNP	G	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:35449946G>C	uc010mkn.1	+	10		c.2796G>C			ATP8B5P_uc010mko.2_RNA|ATP8B5P_uc010mkp.2_RNA|ATP8B5P_uc003zwu.2_Intron					Homo sapiens cDNA, FLJ17320.												0						CAGTGTCCCAGAAGCCCAGTC	0.403													27	56	---	---	---	---	PASS
PCSK5	5125	broad.mit.edu	37	9	78790187	78790187	+	Intron	SNP	G	C	C	rs10118321		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:78790187G>C	uc004ajz.2	+						PCSK5_uc004ajy.2_Missense_Mutation_p.W681S|PCSK5_uc004aka.2_Intron	NM_006200	NP_006191	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						anterior/posterior pattern formation|cell-cell signaling|cytokine biosynthetic process|embryo implantation|embryonic digestive tract development|embryonic skeletal system development|heart development|kidney development|limb morphogenesis|nerve growth factor processing|nerve growth factor receptor signaling pathway|peptide biosynthetic process|renin secretion into blood stream|respiratory tube development|signal peptide processing|viral assembly, maturation, egress, and release	extracellular space|Golgi lumen|stored secretory granule	peptide binding|serine-type endopeptidase activity			ovary(2)|skin(1)	3						ggaatggaatggaatcgaatc	0.119													3	13	---	---	---	---	PASS
C9orf3	84909	broad.mit.edu	37	9	97522998	97522998	+	Intron	SNP	A	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:97522998A>G	uc004ava.2	+						C9orf3_uc011lui.1_RNA|C9orf3_uc004aux.1_Intron|C9orf3_uc004auy.2_Intron|C9orf3_uc004auz.1_Intron	NM_032823	NP_116212	Q8N6M6	AMPO_HUMAN	aminopeptidase O						leukotriene biosynthetic process|proteolysis	cytoplasm	aminopeptidase activity|metallopeptidase activity|zinc ion binding			ovary(1)	1				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		TCAAATCCTTAGACCTACAGT	0.448													4	5	---	---	---	---	PASS
KIAA0368	23392	broad.mit.edu	37	9	114134741	114134741	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:114134741A>T	uc004bfe.1	-	43	5030	c.5030T>A	c.(5029-5031)TTA>TAA	p.L1677*		NM_001080398	NP_001073867			KIAA0368 protein												0						TTCGGTCCATAAATTACATTC	0.398													42	89	---	---	---	---	PASS
LHX2	9355	broad.mit.edu	37	9	126783560	126783560	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:126783560G>T	uc004boe.1	+	4	1649	c.910G>T	c.(910-912)GGC>TGC	p.G304C	LHX2_uc010mwi.1_Missense_Mutation_p.G312C	NM_004789	NP_004780	P50458	LHX2_HUMAN	LIM homeobox protein 2	304	Homeobox.					nucleus	sequence-specific DNA binding transcription factor activity|zinc ion binding				0						GCAAAAGACGGGCCTCACCAA	0.632													26	44	---	---	---	---	PASS
BAT2L1	84726	broad.mit.edu	37	9	134351423	134351423	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:134351423C>T	uc004can.3	+	15	3962	c.3907C>T	c.(3907-3909)CGC>TGC	p.R1303C	BAT2L1_uc010mzj.1_Missense_Mutation_p.R886C|BAT2L1_uc004cao.3_Missense_Mutation_p.R661C	NM_013318	NP_037450	Q5JSZ5	PRC2B_HUMAN	HLA-B associated transcript 2-like	1303							protein binding				0						CAGGAGAAGGCGCCCCCCACG	0.642											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	152	---	---	---	---	PASS
SEC16A	9919	broad.mit.edu	37	9	139369264	139369264	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139369264T>C	uc004chx.2	-	3	3113	c.2804A>G	c.(2803-2805)GAG>GGG	p.E935G	SEC16A_uc004chv.3_Intron|SEC16A_uc004chw.2_Missense_Mutation_p.E935G|SEC16A_uc010nbn.2_Missense_Mutation_p.E935G|SEC16A_uc010nbo.1_Missense_Mutation_p.E935G	NM_014866	NP_055681	O15027	SC16A_HUMAN	SEC16 homolog A	757					protein transport|vesicle-mediated transport	endoplasmic reticulum membrane|Golgi membrane					0		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		AACCAAGTTCTCTGGAACTGG	0.473													32	53	---	---	---	---	PASS
PTGDS	5730	broad.mit.edu	37	9	139873535	139873535	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:139873535G>A	uc004cke.2	+	2	280	c.205G>A	c.(205-207)GTG>ATG	p.V69M	PTGDS_uc004ckd.2_RNA|PTGDS_uc004ckf.2_RNA	NM_000954	NP_000945	P41222	PTGDS_HUMAN	prostaglandin D2 synthase, brain	69					prostaglandin biosynthetic process|regulation of circadian sleep/wake cycle, sleep	Golgi apparatus|nuclear membrane|perinuclear region of cytoplasm|rough endoplasmic reticulum	fatty acid binding|prostaglandin-D synthase activity|retinoid binding|transporter activity			ovary(1)	1	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CAAGTCTGTGGTGGCCCCTGC	0.672													30	80	---	---	---	---	PASS
FAM166A	401565	broad.mit.edu	37	9	140139965	140139965	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:140139965G>A	uc004cmi.1	-	3	371	c.316C>T	c.(316-318)CCC>TCC	p.P106S		NM_001001710	NP_001001710	Q6J272	F166A_HUMAN	hypothetical protein LOC401565	106										ovary(1)	1						ACCTCCAAGGGTGGGAGCTGG	0.637													18	157	---	---	---	---	PASS
MYOF	26509	broad.mit.edu	37	10	95093560	95093560	+	Silent	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:95093560G>A	uc001kin.2	-	42	4797	c.4674C>T	c.(4672-4674)TAC>TAT	p.Y1558Y	MYOF_uc001kio.2_Silent_p.Y1545Y|MYOF_uc009xue.2_RNA	NM_013451	NP_038479	Q9NZM1	MYOF_HUMAN	myoferlin isoform a	1558	Cytoplasmic (Potential).|C2 5.				blood circulation|muscle contraction|plasma membrane repair	caveola|cytoplasmic vesicle membrane|integral to membrane|nuclear membrane	phospholipid binding|protein binding			ovary(3)|breast(1)	4						CTCGAACAATGTAAATCCTAA	0.547													8	78	---	---	---	---	PASS
PGAM1	5223	broad.mit.edu	37	10	99186086	99186086	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:99186086C>G	uc001knh.2	+	1	60	c.22C>G	c.(22-24)CTG>GTG	p.L8V	uc001kng.1_5'Flank|PGAM1_uc009xvo.2_Missense_Mutation_p.L8V|PGAM1_uc010qov.1_5'Flank	NM_002629	NP_002620	P18669	PGAM1_HUMAN	phosphoglycerate mutase 1	8					gluconeogenesis|glycolysis|regulation of glycolysis|regulation of pentose-phosphate shunt|respiratory burst	cytosol	2,3-bisphospho-D-glycerate 2-phosphohydrolase activity|bisphosphoglycerate mutase activity|phosphoglycerate mutase activity|protein kinase binding				0		Colorectal(252;0.162)		Epithelial(162;8.36e-10)|all cancers(201;5.62e-08)		CAAACTGGTGCTGATCCGGCA	0.711													15	37	---	---	---	---	PASS
UBQLNL	143630	broad.mit.edu	37	11	5536862	5536862	+	Silent	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5536862C>T	uc001maz.3	-	1	1095	c.810G>A	c.(808-810)CTG>CTA	p.L270L	HBG2_uc001mak.1_Intron	NM_145053	NP_659490	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	270										large_intestine(2)|skin(1)	3		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		AGTTCTGACCCAGGGCATTAT	0.463													6	137	---	---	---	---	PASS
OR52N2	390077	broad.mit.edu	37	11	5841740	5841740	+	Silent	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5841740C>A	uc010qzp.1	+	1	175	c.175C>A	c.(175-177)CGG>AGG	p.R59R	TRIM5_uc001mbq.1_Intron	NM_001005174	NP_001005174	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N,	59	Helical; Name=2; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.H53_F64del(1)		ovary(1)|skin(1)	2		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.49e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCCCTGCACCGGCCCATGTA	0.522													61	93	---	---	---	---	PASS
ST5	6764	broad.mit.edu	37	11	8752093	8752093	+	Silent	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:8752093A>T	uc001mgt.2	-	3	930	c.744T>A	c.(742-744)CCT>CCA	p.P248P	ST5_uc009yfr.2_Intron|ST5_uc001mgu.2_Intron|ST5_uc001mgv.2_Silent_p.P248P|ST5_uc010rbq.1_Intron|ST5_uc001mgw.1_Silent_p.P248P	NM_213618	NP_998783	P78524	ST5_HUMAN	suppression of tumorigenicity 5 isoform 1	248					positive regulation of ERK1 and ERK2 cascade		protein binding			upper_aerodigestive_tract(1)	1				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		AGTCCCGGACAGGGAGCGCCT	0.617													5	125	---	---	---	---	PASS
NR1H3	10062	broad.mit.edu	37	11	47289515	47289515	+	Missense_Mutation	SNP	A	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:47289515A>C	uc009ylm.2	+	8	1261	c.1040A>C	c.(1039-1041)AAT>ACT	p.N347T	MADD_uc001neq.2_5'Flank|MADD_uc001ner.1_5'Flank|MADD_uc001nev.1_5'Flank|MADD_uc001nes.1_5'Flank|MADD_uc001net.1_5'Flank|MADD_uc009yln.1_5'Flank|MADD_uc001neu.1_5'Flank|MADD_uc001nex.2_5'Flank|MADD_uc001nez.2_5'Flank|MADD_uc001new.2_5'Flank|NR1H3_uc010rhk.1_Missense_Mutation_p.N353T|NR1H3_uc001nek.2_Missense_Mutation_p.N302T|NR1H3_uc001nej.2_Missense_Mutation_p.N287T|NR1H3_uc001nel.2_Missense_Mutation_p.N366T|NR1H3_uc001nen.3_Missense_Mutation_p.N287T|NR1H3_uc001nem.2_Missense_Mutation_p.N347T|NR1H3_uc001nep.2_Missense_Mutation_p.N196T	NM_005693	NP_005684	Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	347	Ligand-binding (Potential).				apoptotic cell clearance|cellular response to lipopolysaccharide|cholesterol homeostasis|negative regulation of cholesterol storage|negative regulation of inflammatory response|negative regulation of interferon-gamma-mediated signaling pathway|negative regulation of lipid transport|negative regulation of macrophage activation|negative regulation of pancreatic juice secretion|negative regulation of pinocytosis|negative regulation of secretion of lysosomal enzymes|negative regulation of transcription from RNA polymerase II promoter|positive regulation of cellular protein metabolic process|positive regulation of cholesterol efflux|positive regulation of cholesterol homeostasis|positive regulation of fatty acid biosynthetic process|positive regulation of lipoprotein lipase activity|positive regulation of receptor biosynthetic process|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of transcription from RNA polymerase II promoter|positive regulation of triglyceride biosynthetic process|regulation of circadian rhythm|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to progesterone stimulus|triglyceride homeostasis	nuclear chromatin|nucleoplasm	cholesterol binding|steroid hormone receptor activity|sterol response element binding|transcription coactivator activity|zinc ion binding			ovary(2)|lung(1)	3						AGGGCCATGAATGAGCTGCAA	0.537													20	50	---	---	---	---	PASS
TMEM132A	54972	broad.mit.edu	37	11	60701064	60701064	+	Silent	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:60701064C>A	uc001nqj.2	+	8	1600	c.1407C>A	c.(1405-1407)GGC>GGA	p.G469G	TMEM132A_uc001nqi.2_Silent_p.G470G|TMEM132A_uc001nqk.2_Silent_p.G482G|TMEM132A_uc001nql.1_3'UTR|TMEM132A_uc001nqm.2_5'Flank	NM_178031	NP_821174	Q24JP5	T132A_HUMAN	transmembrane protein 132A isoform b	469	Extracellular (Potential).					endoplasmic reticulum membrane|Golgi membrane|integral to membrane				skin(1)	1						AGAGCCGGGGCGCCCGGGGGG	0.692													14	35	---	---	---	---	PASS
RCOR2	283248	broad.mit.edu	37	11	63679957	63679957	+	Silent	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:63679957C>T	uc001nyc.2	-	11	1465	c.1077G>A	c.(1075-1077)GGG>GGA	p.G359G		NM_173587	NP_775858	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	359	SANT 2.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding			ovary(1)|skin(1)	2						GAGTCTTGTTCCCAATCACCT	0.542													17	124	---	---	---	---	PASS
PPFIA1	8500	broad.mit.edu	37	11	70184559	70184559	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:70184559G>A	uc001opo.2	+	13	1769	c.1571G>A	c.(1570-1572)GGC>GAC	p.G524D	PPFIA1_uc001opn.1_Missense_Mutation_p.G524D|PPFIA1_uc001opp.2_Intron|PPFIA1_uc001opq.1_RNA	NM_003626	NP_003617	Q13136	LIPA1_HUMAN	PTPRF interacting protein alpha 1 isoform b	524					cell-matrix adhesion	cytoplasm	protein binding|signal transducer activity			lung(2)|ovary(1)	3			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CTTCATCATGGGTATGGTATT	0.478													14	30	---	---	---	---	PASS
TAF1D	79101	broad.mit.edu	37	11	93465666	93465666	+	Intron	SNP	A	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:93465666A>C	uc001pdz.2	-						SNORA8_uc001pec.2_RNA|SNORA25_uc001pdy.3_5'Flank|SNORA32_uc009ywc.1_5'Flank|TAF1D_uc001pea.1_Intron|SNORD6_uc001peb.2_5'Flank|SNORA1_uc009ywd.1_5'Flank|SNORA8_uc009ywe.2_5'Flank	NM_024116		Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding				0						ATGCAGTGCAATTATGACTGA	0.388													23	45	---	---	---	---	PASS
CEP164	22897	broad.mit.edu	37	11	117280582	117280582	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:117280582C>A	uc001prc.2	+	30	4144	c.3997C>A	c.(3997-3999)CAA>AAA	p.Q1333K	CEP164_uc001prb.2_Missense_Mutation_p.Q1328K|CEP164_uc001prf.2_RNA|CEP164_uc009yzp.1_RNA|CEP164_uc001prg.1_Missense_Mutation_p.Q758K	NM_014956	NP_055771	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1333					cell division|DNA repair|G2/M transition of mitotic cell cycle|mitosis	centriole|cytosol|nucleus				ovary(1)|central_nervous_system(1)	2	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		CACGTCCACCCAATGGGCCTG	0.617													103	163	---	---	---	---	PASS
SORL1	6653	broad.mit.edu	37	11	121437700	121437700	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:121437700C>A	uc001pxx.2	+	22	3181	c.3101C>A	c.(3100-3102)GCC>GAC	p.A1034D		NM_003105	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor containing LDLR class	1034	Extracellular (Potential).|EGF-like.				cholesterol metabolic process|lipid transport|receptor-mediated endocytosis	integral to plasma membrane|low-density lipoprotein particle	low-density lipoprotein particle binding|transmembrane receptor activity			ovary(5)|breast(4)|large_intestine(2)|skin(2)|central_nervous_system(1)|pancreas(1)	15		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CTGCCCAAGGCCAACAACAGT	0.567													9	45	---	---	---	---	PASS
CLEC7A	64581	broad.mit.edu	37	12	10277799	10277799	+	Intron	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10277799G>A	uc001qxg.2	-						CLEC7A_uc001qxe.3_Intron|CLEC7A_uc001qxf.2_Intron|CLEC7A_uc001qxh.2_Intron|CLEC7A_uc001qxi.2_Intron|CLEC7A_uc001qxj.2_Intron|CLEC7A_uc009zhg.1_Intron|CLEC7A_uc001qxk.1_Intron|CLEC7A_uc001qxl.1_Intron|CLEC7A_uc010sgy.1_3'UTR|CLEC7A_uc001qxm.1_3'UTR	NM_197947	NP_922938	Q9BXN2	CLC7A_HUMAN	dendritic cell-associated C-type lectin 1						carbohydrate mediated signaling|defense response to protozoan|inflammatory response|innate immune response|phagocytosis, recognition|T cell activation	cytoplasm|integral to membrane	metal ion binding|MHC protein binding|sugar binding			central_nervous_system(1)	1						aaaaaaaaaaGACTTCATTTT	0.184													5	15	---	---	---	---	PASS
CHPT1	56994	broad.mit.edu	37	12	102107933	102107933	+	Silent	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:102107933T>A	uc001tin.2	+	2	562	c.339T>A	c.(337-339)ATT>ATA	p.I113I	CHPT1_uc001tio.2_RNA|CHPT1_uc001tip.1_Silent_p.I113I	NM_020244	NP_064629	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	113	Helical; (Potential).				platelet activating factor biosynthetic process|regulation of cell growth	Golgi membrane|integral to membrane|microsome	diacylglycerol binding|diacylglycerol cholinephosphotransferase activity|metal ion binding				0						TGGATGCTATTGATGGGAAAC	0.383													97	189	---	---	---	---	PASS
TPTE2	93492	broad.mit.edu	37	13	19999143	19999143	+	Nonsense_Mutation	SNP	G	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:19999143G>C	uc001umd.2	-	20	1621	c.1410C>G	c.(1408-1410)TAC>TAG	p.Y470*	TPTE2_uc009zzk.2_RNA|TPTE2_uc009zzl.2_Nonsense_Mutation_p.Y359*|TPTE2_uc001ume.2_Nonsense_Mutation_p.Y393*|TPTE2_uc009zzm.2_Nonsense_Mutation_p.Y141*|TPTE2_uc010tcm.1_RNA|TPTE2_uc010tcl.1_Nonsense_Mutation_p.Y141*	NM_199254	NP_954863	Q6XPS3	TPTE2_HUMAN	TPTE and PTEN homologous inositol lipid	470	C2 tensin-type.					endoplasmic reticulum membrane|integral to membrane	ion channel activity|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity				0		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		AATTGTCATAGTATTTAGGAA	0.279													5	34	---	---	---	---	PASS
METT11D1	64745	broad.mit.edu	37	14	21461234	21461234	+	Intron	SNP	A	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21461234A>C	uc001vyn.2	+						METT11D1_uc010tlk.1_3'UTR|METT11D1_uc001vym.2_Intron|METT11D1_uc001vyo.2_Intron|METT11D1_uc001vyp.2_Intron|METT11D1_uc001vyq.2_Intron	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform						translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)		GTCCTAAATAAGTATCTAATT	0.388													41	58	---	---	---	---	PASS
SLC7A8	23428	broad.mit.edu	37	14	23597394	23597394	+	Silent	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:23597394C>G	uc001wiz.2	-	10	2001	c.1275G>C	c.(1273-1275)CTG>CTC	p.L425L	SLC7A8_uc001wiw.2_Silent_p.L42L|SLC7A8_uc001wix.2_Silent_p.L222L|SLC7A8_uc010tnk.1_Silent_p.L201L|SLC7A8_uc010tnl.1_Silent_p.L320L|SLC7A8_uc001wiy.2_RNA|SLC7A8_uc010akj.2_Intron	NM_012244	NP_036376	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (cationic amino acid	425	Helical; (Potential).				blood coagulation|cellular amino acid metabolic process|leukocyte migration|metal ion homeostasis|response to toxin	basolateral plasma membrane|cytoplasm|integral to plasma membrane	neutral amino acid transmembrane transporter activity|organic cation transmembrane transporter activity|peptide antigen binding|protein binding|toxin transporter activity			ovary(1)	1	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	TGATGGGGAACAGCAGGTTGA	0.582													11	30	---	---	---	---	PASS
IRF9	10379	broad.mit.edu	37	14	24632285	24632285	+	Silent	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24632285T>A	uc001wmq.2	+	3	418	c.291T>A	c.(289-291)GTT>GTA	p.V97V	RNF31_uc001wmp.2_RNA|IRF9_uc010alj.2_5'UTR	NM_006084	NP_006075	Q00978	IRF9_HUMAN	interferon-stimulated transcription factor 3,	97	IRF tryptophan pentad repeat.				interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|nucleoplasm	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1				GBM - Glioblastoma multiforme(265;0.00853)		TTAAGGAGGTTCCTGAGAGGG	0.527													7	118	---	---	---	---	PASS
ADAM21	8747	broad.mit.edu	37	14	70925009	70925009	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:70925009A>T	uc001xmd.2	+	1	793	c.793A>T	c.(793-795)AAT>TAT	p.N265Y		NM_003813	NP_003804	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21 preproprotein	265	Peptidase M12B.|Extracellular (Potential).				proteolysis|single fertilization	integral to membrane	metalloendopeptidase activity|zinc ion binding			pancreas(1)|skin(1)	2				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GAATCAAGGAAATGTTTTCCC	0.368													61	63	---	---	---	---	PASS
FLRT2	23768	broad.mit.edu	37	14	86089641	86089641	+	Nonsense_Mutation	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:86089641A>T	uc001xvr.2	+	2	2550	c.1783A>T	c.(1783-1785)AAG>TAG	p.K595*	FLRT2_uc010atd.2_Nonsense_Mutation_p.K595*	NM_013231	NP_037363	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	595	Cytoplasmic (Potential).				cell adhesion	integral to plasma membrane|proteinaceous extracellular matrix	protein binding, bridging|receptor signaling protein activity			ovary(3)|haematopoietic_and_lymphoid_tissue(1)	4				BRCA - Breast invasive adenocarcinoma(234;0.0319)		AGGCACCAAGAAGGACAACTC	0.478													82	129	---	---	---	---	PASS
FMN1	342184	broad.mit.edu	37	15	33358779	33358779	+	Missense_Mutation	SNP	T	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:33358779T>G	uc001zhf.3	-	1	1307	c.1307A>C	c.(1306-1308)GAG>GCG	p.E436A	FMN1_uc001zhg.2_Missense_Mutation_p.E436A	NM_001103184	NP_001096654	Q68DA7	FMN1_HUMAN	formin 1	186	Microtubule-binding (By similarity).				actin cytoskeleton organization	actin cytoskeleton|adherens junction|cytoplasm|nucleus	actin binding			ovary(1)	1		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TCTTAGCGACTCCTTCTCATG	0.488													17	56	---	---	---	---	PASS
TTBK2	146057	broad.mit.edu	37	15	43093327	43093327	+	Intron	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:43093327C>A	uc001zqo.2	-						TTBK2_uc010bcy.2_Intron|TTBK2_uc001zqp.2_Intron|TTBK2_uc010bcz.1_Intron	NM_173500	NP_775771	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2						cell death		ATP binding|protein serine/threonine kinase activity			ovary(2)|lung(2)|stomach(1)|pancreas(1)|skin(1)	7		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		GCTTGTGAGGCCCCCATAGGC	0.622													42	44	---	---	---	---	PASS
GCNT3	9245	broad.mit.edu	37	15	59910566	59910566	+	Silent	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:59910566G>A	uc002age.2	+	3	578	c.129G>A	c.(127-129)GAG>GAA	p.E43E	GCNT3_uc002agd.2_Silent_p.E43E	NM_004751	NP_004742	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin	43	Lumenal (Potential).				protein O-linked glycosylation	Golgi membrane|integral to membrane|membrane fraction	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity			ovary(1)|central_nervous_system(1)	2						TGGGTCTGGAGTCCAGGGAAT	0.488													74	135	---	---	---	---	PASS
HERC1	8925	broad.mit.edu	37	15	63915942	63915942	+	Silent	SNP	G	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:63915942G>T	uc002amp.2	-	73	13741	c.13593C>A	c.(13591-13593)ACC>ACA	p.T4531T		NM_003922	NP_003913	Q15751	HERC1_HUMAN	hect domain and RCC1-like domain 1	4531	HECT.				protein modification process|transport	cytosol|Golgi apparatus|membrane	acid-amino acid ligase activity|ARF guanyl-nucleotide exchange factor activity			ovary(6)|breast(6)|lung(5)|central_nervous_system(2)	19						TCTCTGTGATGGTGTCATCAA	0.522													47	95	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	15	82620366	82620366	+	RNA	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:82620366C>T	uc010bls.1	+	1		c.459C>T								Homo sapiens mRNA for FLJ00317 protein.																		CTCGGGCACACGCCTGAGCCT	0.652													4	32	---	---	---	---	PASS
SOLH	6650	broad.mit.edu	37	16	596909	596909	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:596909C>A	uc002chi.2	+	4	434	c.71C>A	c.(70-72)TCC>TAC	p.S24Y	SOLH_uc002chh.1_Missense_Mutation_p.S24Y	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes	24	RanBP2-type 1.				proteolysis	intracellular	calcium-dependent cysteine-type endopeptidase activity|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|breast(1)	2		Hepatocellular(780;0.00335)				CGCCAGTGCTCCATCTGCGAG	0.682													22	31	---	---	---	---	PASS
WDR90	197335	broad.mit.edu	37	16	700616	700616	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:700616C>G	uc002cii.1	+	5	520	c.466C>G	c.(466-468)CTG>GTG	p.L156V	WDR90_uc002cig.1_Missense_Mutation_p.L156V|WDR90_uc002cih.1_Missense_Mutation_p.L156V|WDR90_uc002cij.1_RNA	NM_145294	NP_660337	Q96KV7	WDR90_HUMAN	WD repeat domain 90	156										ovary(1)	1		Hepatocellular(780;0.0218)				CCTGGTCTACCTGAACCGGTG	0.627													34	91	---	---	---	---	PASS
CLUAP1	23059	broad.mit.edu	37	16	3586140	3586140	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:3586140G>C	uc002cvk.1	+	12	1216	c.1111G>C	c.(1111-1113)GAA>CAA	p.E371Q	CLUAP1_uc002cvj.1_3'UTR|CLUAP1_uc002cvl.1_Missense_Mutation_p.E390Q|CLUAP1_uc002cvm.1_Missense_Mutation_p.E205Q|uc002cvn.1_5'Flank	NM_015041	NP_055856	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1 isoform 1	371	Asp-rich.					nucleus	protein binding			ovary(1)|breast(1)|pancreas(1)	3						GGAGGAGAGTGAAATTGACAT	0.488													3	86	---	---	---	---	PASS
CLEC18C	283971	broad.mit.edu	37	16	70010432	70010432	+	Intron	SNP	G	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:70010432G>T	uc002exy.2	+						PDXDC2_uc002eyb.2_RNA|PDXDC2_uc002eyc.2_RNA	NM_182619	NP_872425	Q8NCF0	CL18C_HUMAN	secretory protein LOC348174 precursor							extracellular region	sugar binding				0						TATCATCCACGGAGGGTGGAA	0.299													3	14	---	---	---	---	PASS
BCAR1	9564	broad.mit.edu	37	16	75276901	75276901	+	Nonsense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75276901C>A	uc002fdv.2	-	2	223	c.100G>T	c.(100-102)GAG>TAG	p.E34*	BCAR1_uc010cgu.2_Nonsense_Mutation_p.E5*|BCAR1_uc010vna.1_Nonsense_Mutation_p.E32*|BCAR1_uc010vnb.1_Nonsense_Mutation_p.E80*|BCAR1_uc002fdw.2_Nonsense_Mutation_p.E34*|BCAR1_uc010vnc.1_Nonsense_Mutation_p.E34*|BCAR1_uc010vnd.1_Nonsense_Mutation_p.E52*|BCAR1_uc002fdx.2_Nonsense_Mutation_p.E52*	NM_014567	NP_055382	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	34	SH3.				actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway	cytosol|focal adhesion|membrane fraction|ruffle	protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity			central_nervous_system(5)|breast(2)|prostate(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.169)		GTGTCCTGCTCCAGCACCGTC	0.632													17	55	---	---	---	---	PASS
BCAR1	9564	broad.mit.edu	37	16	75276902	75276902	+	Silent	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:75276902C>A	uc002fdv.2	-	2	222	c.99G>T	c.(97-99)CTG>CTT	p.L33L	BCAR1_uc010cgu.2_Silent_p.L4L|BCAR1_uc010vna.1_Silent_p.L31L|BCAR1_uc010vnb.1_Silent_p.L79L|BCAR1_uc002fdw.2_Silent_p.L33L|BCAR1_uc010vnc.1_Silent_p.L33L|BCAR1_uc010vnd.1_Silent_p.L51L|BCAR1_uc002fdx.2_Silent_p.L51L	NM_014567	NP_055382	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	33	SH3.				actin filament organization|B cell receptor signaling pathway|blood coagulation|cell adhesion|cell division|cell migration|cell proliferation|epidermal growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|integrin-mediated signaling pathway|nerve growth factor receptor signaling pathway|platelet-derived growth factor receptor signaling pathway|positive regulation of cell migration|regulation of apoptosis|regulation of cell growth|T cell receptor signaling pathway	cytosol|focal adhesion|membrane fraction|ruffle	protein kinase binding|protein phosphatase binding|SH3 domain binding|signal transducer activity			central_nervous_system(5)|breast(2)|prostate(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.169)		TGTCCTGCTCCAGCACCGTCA	0.632													18	53	---	---	---	---	PASS
SPIRE2	84501	broad.mit.edu	37	16	89929985	89929985	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:89929985C>A	uc002foz.1	+	11	1729	c.1677C>A	c.(1675-1677)AAC>AAA	p.N559K	SPIRE2_uc010ciw.1_Missense_Mutation_p.N559K|SPIRE2_uc002fpa.1_Missense_Mutation_p.N511K|SPIRE2_uc010cix.1_Missense_Mutation_p.N426K	NM_032451	NP_115827	Q8WWL2	SPIR2_HUMAN	spire homolog 2	559					transport	cytoplasm|cytoskeleton	actin binding			central_nervous_system(1)	1		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		TTTTGCAGAACAAGGAGCTCT	0.617													37	63	---	---	---	---	PASS
FAM18B2	201158	broad.mit.edu	37	17	15449215	15449215	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:15449215T>A	uc002goq.2	-	5	529	c.346A>T	c.(346-348)AAT>TAT	p.N116Y	CDRT4_uc010vvw.1_Missense_Mutation_p.N30Y|FAM18B2_uc010vvx.1_Missense_Mutation_p.N116Y|FAM18B2_uc010cor.2_Missense_Mutation_p.N116Y	NM_145301	NP_660344	Q96ET8	F18B2_HUMAN	hypothetical protein LOC201158 isoform 1	116						integral to membrane					0				UCEC - Uterine corpus endometrioid carcinoma (92;0.0872)|BRCA - Breast invasive adenocarcinoma(8;0.0581)|READ - Rectum adenocarcinoma(1115;0.0967)		ACAGTTTTATTCTCTTGAGAG	0.323													21	80	---	---	---	---	PASS
TCAP	8557	broad.mit.edu	37	17	37821618	37821618	+	Silent	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:37821618T>A	uc002hsh.2	+	1	20	c.6T>A	c.(4-6)GCT>GCA	p.A2A	PNMT_uc002hsi.1_5'Flank	NM_003673	NP_003664	O15273	TELT_HUMAN	telethonin	2					adult heart development|cardiac muscle contraction|cardiac muscle fiber development|cardiac muscle tissue morphogenesis|detection of mechanical stimulus|muscle filament sliding|response to stress|sarcomere organization|skeletal muscle contraction|skeletal muscle myosin thick filament assembly|skeletal muscle thin filament assembly	cytosol|Z disc	structural constituent of muscle|titin binding|titin Z domain binding				0	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TGATCATGGCTACCTCAGAGC	0.602													47	63	---	---	---	---	PASS
CA10	56934	broad.mit.edu	37	17	49726541	49726541	+	Splice_Site	SNP	A	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49726541A>G	uc002itw.3	-	6	1620	c.634_splice	c.e6+1	p.N212_splice	CA10_uc002itu.3_Splice_Site_p.N141_splice|CA10_uc002itv.3_Splice_Site_p.N218_splice|CA10_uc002itx.3_Splice_Site_p.N212_splice|CA10_uc002ity.3_Splice_Site_p.N212_splice|CA10_uc002itz.2_Splice_Site_p.N212_splice	NM_020178	NP_064563	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development					ovary(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)			AACCAAACTTACTTTTATATG	0.234													24	46	---	---	---	---	PASS
KIF19	124602	broad.mit.edu	37	17	72343936	72343936	+	Silent	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72343936C>T	uc002jkm.3	+	9	1083	c.945C>T	c.(943-945)AGC>AGT	p.S315S	KIF19_uc002jkj.2_Silent_p.S315S|KIF19_uc002jkk.2_Silent_p.S273S|KIF19_uc002jkl.2_Silent_p.S273S	NM_153209	NP_694941	Q2TAC6	KIF19_HUMAN	kinesin family member 19	315					microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity				0						GAGGAAACAGCCGCACAGTGA	0.612													4	8	---	---	---	---	PASS
ITGB4	3691	broad.mit.edu	37	17	73745083	73745083	+	Silent	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:73745083C>T	uc002jpg.2	+	27	3460	c.3273C>T	c.(3271-3273)CAC>CAT	p.H1091H	ITGB4_uc002jph.2_Silent_p.H1091H|ITGB4_uc002jpi.3_Silent_p.H1091H|ITGB4_uc002jpj.2_Silent_p.H1091H	NM_000213	NP_000204	P16144	ITB4_HUMAN	integrin beta 4 isoform 1 precursor	1091	Cytoplasmic (Potential).				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity			lung(4)	4	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTGGGGCCCACCTGGGCCAGC	0.642													19	13	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	17	76482488	76482488	+	IGR	SNP	G	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:76482488G>T								DNAH17 (13632 upstream) : CYTH1 (187643 downstream)																							AACCCAAAGCGCAACTTGTCC	0.582													38	71	---	---	---	---	PASS
AATK	9625	broad.mit.edu	37	17	79098648	79098648	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79098648C>T	uc010dia.2	-	9	921	c.841G>A	c.(841-843)GAG>AAG	p.E281K	AATK_uc010dhz.2_5'Flank|hsa-mir-3065|MI0014228_5'Flank	NM_001080395	NP_001073864	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	281	Protein kinase.					integral to membrane|mitochondrion|perinuclear region of cytoplasm	ATP binding|protein binding|protein serine/threonine kinase activity|protein tyrosine kinase activity			stomach(4)|ovary(2)|lung(2)|upper_aerodigestive_tract(1)	9	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AAGTAGTCCTCCTGTTGGCAC	0.667													5	22	---	---	---	---	PASS
GRIN3B	116444	broad.mit.edu	37	19	1004979	1004979	+	Silent	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:1004979C>T	uc002lqo.1	+	3	1479	c.1479C>T	c.(1477-1479)TTC>TTT	p.F493F		NM_138690	NP_619635	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic,	493	Extracellular (Potential).				ionotropic glutamate receptor signaling pathway|protein insertion into membrane|regulation of calcium ion transport	cell junction|N-methyl-D-aspartate selective glutamate receptor complex|neuronal cell body|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|glycine binding|ionotropic glutamate receptor activity|neurotransmitter receptor activity				0		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	Glycine(DB00145)|L-Glutamic Acid(DB00142)|Orphenadrine(DB01173)	ACACGCCCTTCGACTTCGAGC	0.721													12	116	---	---	---	---	PASS
PPAN-P2RY11	692312	broad.mit.edu	37	19	10225224	10225224	+	Missense_Mutation	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:10225224T>C	uc002mna.2	+	13	2195	c.2195T>C	c.(2194-2196)CTG>CCG	p.L732P	PPAN-P2RY11_uc010xla.1_3'UTR|P2RY11_uc002mnc.2_Missense_Mutation_p.L312P	NM_001040664	NP_001035754	Q9NQ55	SSF1_HUMAN	PPAN-P2RY11 protein	Error:Variant_position_missing_in_Q9NQ55_after_alignment					RNA splicing	nucleolus	protein binding			ovary(2)	2			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			CTCATGCCCCTGGCCTTCTGT	0.672													64	84	---	---	---	---	PASS
RAB3D	9545	broad.mit.edu	37	19	11436252	11436252	+	Missense_Mutation	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:11436252A>T	uc002mqy.2	-	5	720	c.482T>A	c.(481-483)TTC>TAC	p.F161Y	TSPAN16_uc002mqv.1_Intron|RAB3D_uc002mqx.2_5'Flank	NM_004283	NP_004274	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	161					exocytosis|protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity			ovary(2)	2						GGCTTCAAAGAACTCGAAACC	0.413													45	83	---	---	---	---	PASS
IER2	9592	broad.mit.edu	37	19	13263991	13263991	+	5'UTR	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:13263991T>C	uc002mwr.2	+	2						NM_004907	NP_004898	Q9BTL4	IER2_HUMAN	immediate early response 2											kidney(1)	1			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			GCTGTCGCCGTCGAGTCGCCA	0.652											OREG0025291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	6	16	---	---	---	---	PASS
ZNF714	148206	broad.mit.edu	37	19	21300402	21300402	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21300402C>A	uc002npo.3	+	6	1295	c.935C>A	c.(934-936)TCT>TAT	p.S312Y	ZNF714_uc002npl.2_Missense_Mutation_p.S157Y|ZNF714_uc010ecp.1_Missense_Mutation_p.S263Y|ZNF714_uc002npn.2_RNA	NM_182515	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	312					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0						GGAGAGAAATCTTACAAATGT	0.333													7	16	---	---	---	---	PASS
GGN	199720	broad.mit.edu	37	19	38876474	38876474	+	Silent	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:38876474C>T	uc002oij.1	-	3	1563	c.1428G>A	c.(1426-1428)CTG>CTA	p.L476L	GGN_uc002oik.1_Intron|GGN_uc010efy.1_Silent_p.L393L	NM_152657	NP_689870	Q86UU5	GGN_HUMAN	gametogenetin	476	Interaction with GGNBP1 (By similarity).|Pro-rich.				cell differentiation|multicellular organismal development|spermatogenesis						0	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			cggtgggagccagggctgACT	0.090													3	5	---	---	---	---	PASS
NPAS1	4861	broad.mit.edu	37	19	47539306	47539306	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:47539306C>A	uc002pfw.2	+	6	803	c.607C>A	c.(607-609)CCG>ACG	p.P203T	NPAS1_uc002pfx.2_Missense_Mutation_p.P27T|NPAS1_uc002pfy.2_Missense_Mutation_p.P203T|NPAS1_uc010xyj.1_Missense_Mutation_p.P27T	NM_002517	NP_002508	Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	203	PAS 1.			P -> T (in Ref. 1; AAB47248).	central nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|signal transducer activity				0		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		GCTGCGGACGCCGACGCCCGG	0.542											OREG0025586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	7	11	---	---	---	---	PASS
ZNF749	388567	broad.mit.edu	37	19	57955937	57955937	+	Missense_Mutation	SNP	A	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57955937A>G	uc002qoq.2	+	3	1675	c.1421A>G	c.(1420-1422)AAG>AGG	p.K474R	ZNF547_uc002qpm.3_Intron	NM_001023561	NP_001018855	O43361	ZN749_HUMAN	zinc finger protein 749	474					regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)		ATTCAACACAAGAGGATTGAC	0.448													54	70	---	---	---	---	PASS
RSPO4	343637	broad.mit.edu	37	20	948634	948634	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:948634C>G	uc002wej.2	-	2	324	c.227G>C	c.(226-228)GGG>GCG	p.G76A	RSPO4_uc002wek.2_Missense_Mutation_p.G76A	NM_001029871	NP_001025042	Q2I0M5	RSPO4_HUMAN	R-spondin family, member 4 isoform 1 precursor	76					Wnt receptor signaling pathway	extracellular region	heparin binding				0						GCCGAAGTACCCAGGGGGACA	0.602													51	120	---	---	---	---	PASS
XKR7	343702	broad.mit.edu	37	20	30556225	30556225	+	Missense_Mutation	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30556225C>G	uc002wxe.2	+	1	421	c.247C>G	c.(247-249)CTG>GTG	p.L83V		NM_001011718	NP_001011718	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related	83						integral to membrane				ovary(1)|breast(1)|skin(1)	3			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CTCCTACTACCTGCAGAATCA	0.587													18	29	---	---	---	---	PASS
KCNB1	3745	broad.mit.edu	37	20	47990940	47990940	+	Missense_Mutation	SNP	T	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:47990940T>A	uc002xur.1	-	2	1321	c.1157A>T	c.(1156-1158)AAG>ATG	p.K386M	KCNB1_uc002xus.1_Missense_Mutation_p.K386M	NM_004975	NP_004966	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related	386					energy reserve metabolic process|regulation of insulin secretion	voltage-gated potassium channel complex	protein binding|voltage-gated potassium channel activity			pancreas(1)|skin(1)	2			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CAGGAGAGTCTTGGGGTAGAT	0.512													4	91	---	---	---	---	PASS
BAGE2	85319	broad.mit.edu	37	21	11038952	11038952	+	3'UTR	SNP	A	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr21:11038952A>T	uc002yit.1	-	6					TPTE_uc002yis.1_RNA	NM_182482	NP_872288			B melanoma antigen family, member 2 precursor												0			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TGATAATGAAAATGATGACTC	0.423													32	448	---	---	---	---	PASS
APOL5	80831	broad.mit.edu	37	22	36122501	36122501	+	Missense_Mutation	SNP	C	T	T	rs73411940	byFrequency	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:36122501C>T	uc003aof.2	+	3	386	c.386C>T	c.(385-387)ACC>ATC	p.T129I		NM_030642	NP_085145	Q9BWW9	APOL5_HUMAN	apolipoprotein L5	129					lipid metabolic process|lipid transport|lipoprotein metabolic process	cytoplasm|extracellular region	high-density lipoprotein particle binding|lipid binding|protein binding				0						CAAGTTGACACCACTCACGAG	0.488													4	151	---	---	---	---	PASS
TST	7263	broad.mit.edu	37	22	37414210	37414210	+	Missense_Mutation	SNP	G	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:37414210G>C	uc003aqg.2	-	1	1264	c.564C>G	c.(562-564)TTC>TTG	p.F188L	TST_uc003aqh.2_Missense_Mutation_p.F188L|MPST_uc003aqi.1_5'Flank|MPST_uc003aqj.2_5'Flank|MPST_uc003aqm.2_5'Flank|MPST_uc011amu.1_5'Flank|MPST_uc003aql.2_5'Flank	NM_003312	NP_003303	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase	188	Rhodanese 2.				cyanate catabolic process|rRNA transport	mitochondrial matrix|plasma membrane	5S rRNA binding|thiosulfate sulfurtransferase activity				0						CGGTGCCCAGGAACCGCCCTT	0.592													10	24	---	---	---	---	PASS
MEI1	150365	broad.mit.edu	37	22	42180387	42180387	+	Silent	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:42180387T>C	uc003baz.1	+	25	3157	c.3132T>C	c.(3130-3132)GCT>GCC	p.A1044A	WBP2NL_uc011ape.1_Intron|LOC339674_uc003bba.1_Intron|MEI1_uc011apd.1_RNA|MEI1_uc003bbb.1_Silent_p.A430A|MEI1_uc003bbc.1_Silent_p.A412A|MEI1_uc010gym.1_Silent_p.A377A|MEI1_uc003bbd.1_Silent_p.A287A|MEI1_uc010gyn.1_RNA|MEI1_uc003bbe.1_RNA|MEI1_uc011apf.1_Silent_p.A58A|MEI1_uc010gyo.1_Silent_p.A58A|MEI1_uc003bbf.2_Silent_p.A58A|MEI1_uc003bbg.2_Silent_p.A58A	NM_152513	NP_689726	Q5TIA1	MEI1_HUMAN	meiosis defective 1	1044							binding			central_nervous_system(1)|skin(1)	2						TATTGAAGGCTCTCAGCTTTC	0.493													26	52	---	---	---	---	PASS
TLR8	51311	broad.mit.edu	37	X	12937418	12937418	+	Nonsense_Mutation	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:12937418C>T	uc004cve.2	+	2	327	c.259C>T	c.(259-261)CAA>TAA	p.Q87*	TLR8_uc004cvd.2_Nonsense_Mutation_p.Q105*	NM_138636	NP_619542	Q9NR97	TLR8_HUMAN	toll-like receptor 8 precursor	87	Extracellular (Potential).				cellular response to mechanical stimulus|defense response to virus|I-kappaB kinase/NF-kappaB cascade|immunoglobulin mediated immune response|inflammatory response|innate immune response|positive regulation of innate immune response|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process	endosome membrane	DNA binding|double-stranded RNA binding|single-stranded RNA binding|transmembrane receptor activity			ovary(4)|lung(2)|large_intestine(1)	7						TCAAGGGCTGCAAAATCTCAC	0.418													10	203	---	---	---	---	PASS
OFD1	8481	broad.mit.edu	37	X	13776512	13776512	+	Missense_Mutation	SNP	G	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:13776512G>T	uc004cvp.3	+	15	1958	c.1599G>T	c.(1597-1599)AAG>AAT	p.K533N	OFD1_uc004cvr.3_Missense_Mutation_p.K100N|OFD1_uc011mil.1_Missense_Mutation_p.K100N|OFD1_uc004cvq.3_Missense_Mutation_p.K393N|OFD1_uc010nen.2_Missense_Mutation_p.K532N|OFD1_uc004cvs.3_Intron|OFD1_uc004cvu.3_Missense_Mutation_p.K492N|OFD1_uc004cvv.3_Missense_Mutation_p.K492N	NM_003611	NP_003602	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	533	Potential.				cilium movement involved in determination of left/right asymmetry|G2/M transition of mitotic cell cycle	centriole|cilium|cytosol|microtubule basal body|nuclear membrane	alpha-tubulin binding|gamma-tubulin binding				0						CTTCTGTAAAGAGTTTAACTA	0.343													9	77	---	---	---	---	PASS
MAGEB16	139604	broad.mit.edu	37	X	35821205	35821205	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:35821205C>A	uc010ngt.1	+	2	1171	c.892C>A	c.(892-894)CAT>AAT	p.H298N		NM_001099921	NP_001093391	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	298	MAGE.									lung(3)|ovary(2)|breast(1)|skin(1)	7						GGCCAAAGTTCATGGGTCTTA	0.498													3	27	---	---	---	---	PASS
ITIH5L	347365	broad.mit.edu	37	X	54785300	54785300	+	Missense_Mutation	SNP	C	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:54785300C>T	uc004dtj.2	-	8	1237	c.1207G>A	c.(1207-1209)GGC>AGC	p.G403S		NM_198510	NP_940912	Q6UXX5	ITH5L_HUMAN	inter-alpha (globulin) inhibitor H5-like	403	VWFA.				hyaluronan metabolic process	extracellular region	serine-type endopeptidase inhibitor activity			lung(2)|skin(2)|ovary(1)|breast(1)	6						GTCGTCACGCCGGCCGTGGGC	0.597													21	36	---	---	---	---	PASS
EDA	1896	broad.mit.edu	37	X	68836609	68836609	+	Intron	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:68836609C>G	uc004dxs.2	+						EDA_uc004dxr.2_Intron|EDA_uc011mpj.1_Intron|EDA_uc004dxn.1_Intron|EDA_uc004dxm.1_Intron|EDA_uc004dxp.1_Intron|EDA_uc004dxq.1_Intron|EDA_uc004dxl.1_3'UTR	NM_001399	NP_001390	Q92838	EDA_HUMAN	ectodysplasin A isoform EDA-A1						cell differentiation|ectoderm development|immune response|positive regulation of NF-kappaB transcription factor activity|signal transduction	collagen|cytoskeleton|membrane fraction	tumor necrosis factor receptor binding			ovary(2)|large_intestine(1)	3						CGAGGGCCCTCCGCCACAGGG	0.687													20	22	---	---	---	---	PASS
PGK1	5230	broad.mit.edu	37	X	77380396	77380396	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77380396G>A	uc004ecz.3	+	9	1134	c.962G>A	c.(961-963)AGC>AAC	p.S321N	PGK1_uc010nlz.2_RNA|PGK1_uc011mqq.1_Missense_Mutation_p.S293N	NM_000291	NP_000282	P00558	PGK1_HUMAN	phosphoglycerate kinase 1	321					gluconeogenesis|glycolysis	cytosol	ATP binding|phosphoglycerate kinase activity			upper_aerodigestive_tract(1)|ovary(1)	2						CCTGAAAGCAGCAAGAAGTAT	0.502													14	120	---	---	---	---	PASS
ZCCHC5	203430	broad.mit.edu	37	X	77913051	77913051	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:77913051C>A	uc004edc.1	-	2	1163	c.867G>T	c.(865-867)TGG>TGT	p.W289C		NM_152694	NP_689907	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	289							nucleic acid binding|zinc ion binding			ovary(1)	1						GCTGGAACCACCATCCTGCCC	0.468													10	32	---	---	---	---	PASS
SYTL4	94121	broad.mit.edu	37	X	99941139	99941139	+	Missense_Mutation	SNP	G	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:99941139G>A	uc004egd.3	-	15	1653	c.1297C>T	c.(1297-1299)CCA>TCA	p.P433S	SYTL4_uc010nnb.2_Missense_Mutation_p.P105S|SYTL4_uc010nnc.2_Missense_Mutation_p.P433S|SYTL4_uc004ege.3_Missense_Mutation_p.P433S|SYTL4_uc004egf.3_Missense_Mutation_p.P433S|SYTL4_uc004egg.3_3'UTR	NM_080737	NP_542775	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	433	C2 1.				exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding			ovary(2)	2					Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)	AGAGATTCTGGGATCTCATAC	0.453													3	31	---	---	---	---	PASS
BCORL1	63035	broad.mit.edu	37	X	129148444	129148444	+	Missense_Mutation	SNP	C	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:129148444C>A	uc004evb.1	+	4	1810	c.1696C>A	c.(1696-1698)CCT>ACT	p.P566T	BCORL1_uc010nrd.1_Missense_Mutation_p.P468T	NM_021946	NP_068765	Q5H9F3	BCORL_HUMAN	BCL6 co-repressor-like 1	566	Pro-rich.				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus				ovary(4)|breast(2)|lung(1)	7						AACTCCACAGCCTCTGCTGCC	0.632													85	129	---	---	---	---	PASS
GPR50	9248	broad.mit.edu	37	X	150345160	150345160	+	5'UTR	SNP	C	G	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150345160C>G	uc010ntg.1	+	1					uc004fes.1_Intron|GPR50_uc011myc.1_5'UTR	NM_004224	NP_004215	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50						cell-cell signaling	integral to plasma membrane	melatonin receptor activity			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)					GATCCTGAGCCTGCTGGGAGA	0.572													4	162	---	---	---	---	PASS
Unknown	0	broad.mit.edu	37	M	15779	15779	+	3'UTR	SNP	T	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrM:15779T>C	uc004coy.2	+	1					uc004coz.1_5'Flank					Homo sapiens clone 35w unknown mRNA; mitochondrial.																		AACCAGTAAGCTACCCTTTTA	0.398													7	100	---	---	---	---	PASS
COL16A1	1307	broad.mit.edu	37	1	32150538	32150539	+	Intron	DEL	AC	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32150538_32150539delAC	uc001btk.1	-						COL16A1_uc001btj.1_Intron|COL16A1_uc001btl.3_Intron	NM_001856	NP_001847	Q07092	COGA1_HUMAN	alpha 1 type XVI collagen precursor						cell adhesion|female pregnancy|integrin-mediated signaling pathway	collagen type XVI	integrin binding|structural molecule activity			ovary(8)	8		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		gctggggcatacaacagtaaac	0.218													56	31	---	---	---	---	
ZNF642	339559	broad.mit.edu	37	1	40955179	40955180	+	Intron	INS	-	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40955179_40955180insT	uc001cfo.2	+						ZNF642_uc009vwb.2_Intron|ZNF642_uc010ojk.1_Intron	NM_198494	NP_940896	Q49AA0	ZN642_HUMAN	zinc finger protein 642						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding				0	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.81e-19)			CATTCACACTGTTTTTTTTACT	0.421													22	19	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	50865017	50865017	+	IGR	DEL	T	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:50865017delT								ELAVL4 (197477 upstream) : DMRTA2 (18212 downstream)																							CACTGAGCACttttttttttc	0.204													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	88061519	88061522	+	IGR	DEL	TTCT	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:88061519_88061522delTTCT								LMO4 (246916 upstream) : None (None downstream)																							cctccctttcttctttctttcttt	0.103													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	110663159	110663161	+	IGR	DEL	ACT	-	-	rs78684230		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:110663159_110663161delACT								UBL4B (6591 upstream) : SLC6A17 (29971 downstream)																							taccaccatcactaccaccacca	0.059													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	1	161261705	161261706	+	IGR	DEL	TG	-	-	rs36038426		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:161261705_161261706delTG								PCP4L1 (6466 upstream) : MPZ (12821 downstream)																							caatgACCATtgtgtgtgtgtg	0.094													4	2	---	---	---	---	
MAEL	84944	broad.mit.edu	37	1	166976825	166976836	+	Intron	DEL	TGTGTGTGTGTA	-	-	rs71073634		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:166976825_166976836delTGTGTGTGTGTA	uc001gdy.1	+						MAEL_uc001gdz.1_Intron|MAEL_uc009wvf.1_Intron	NM_032858	NP_116247	Q96JY0	MAEL_HUMAN	maelstrom homolog						cell differentiation|DNA methylation involved in gamete generation|gene silencing by RNA|multicellular organismal development|piRNA metabolic process|spermatogenesis	piP-body	DNA binding			skin(1)	1						tgtgtgtgtgtgtgtgtgtgtatgtacacaca	0.000													4	3	---	---	---	---	
LRPPRC	10128	broad.mit.edu	37	2	44209134	44209134	+	Intron	DEL	C	-	-	rs150989251		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:44209134delC	uc002rtr.2	-						LRPPRC_uc010yob.1_Intron|LRPPRC_uc010faw.1_Intron	NM_133259	NP_573566	P42704	LPPRC_HUMAN	leucine-rich PPR motif-containing protein						mitochondrion transport along microtubule|mRNA transport|regulation of transcription, DNA-dependent|transcription, DNA-dependent	condensed nuclear chromosome|cytoskeleton|mitochondrial nucleoid|nuclear inner membrane|nuclear outer membrane|nucleoplasm|perinuclear region of cytoplasm	beta-tubulin binding|microtubule binding|RNA binding			ovary(2)|skin(1)	3		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				acaacctctgcctcctgggtt	0.010													4	2	---	---	---	---	
RMND5A	64795	broad.mit.edu	37	2	87042852	87042853	+	Intron	INS	-	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:87042852_87042853insA	uc002srs.3	+						CD8B_uc002srw.2_Intron|CD8B_uc002srx.2_Intron|CD8B_uc002sry.2_Intron|CD8B_uc010fgt.2_Intron			Q9H871	RMD5A_HUMAN	SubName: Full=cDNA FLJ10361 fis, clone NT2RM2001256, highly similar to Anaphase-promoting complex subunit 1;											ovary(1)|skin(1)	2						CTTGCAAAAAGAAAAACAAGAG	0.416													203	91	---	---	---	---	
TUBA4A	7277	broad.mit.edu	37	2	220118673	220118673	+	5'Flank	DEL	G	-	-	rs3051654		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220118673delG	uc002vkt.1	-						TUBA4A_uc010zkz.1_Intron|TUBA4B_uc002vku.2_Intron|TUBA4B_uc002vkv.1_Intron	NM_006000	NP_005991	P68366	TBA4A_HUMAN	tubulin, alpha 4a						'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|platelet activation|platelet degranulation|protein polymerization	cytosol|extracellular region|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity			ovary(3)	3		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCTTATAggcggggggggggc	0.612													4	2	---	---	---	---	
STK11IP	114790	broad.mit.edu	37	2	220462805	220462806	+	Intron	INS	-	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220462805_220462806insC	uc002vml.2	+						STK11IP_uc010zlj.1_Intron|STK11IP_uc010zlk.1_Intron|STK11IP_uc010zll.1_Intron|STK11IP_uc002vmm.1_5'Flank	NM_052902	NP_443134	Q8N1F8	S11IP_HUMAN	LKB1 interacting protein						protein localization	cytoplasm	protein kinase binding			ovary(1)	1		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCTTCCTCTTTCCCCCCCCAGG	0.653													9	5	---	---	---	---	
KIF15	56992	broad.mit.edu	37	3	44893954	44893954	+	Intron	DEL	A	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:44893954delA	uc003cnx.3	+						KIF15_uc010hiq.2_Intron|KIF15_uc010hir.2_Intron	NM_020242	NP_064627	Q9NS87	KIF15_HUMAN	kinesin family member 15						blood coagulation|cell proliferation|microtubule-based movement|mitosis	centrosome|cytosol|microtubule|plus-end kinesin complex|spindle	ATP binding|DNA binding|microtubule motor activity			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		TTCCTGAATTAAAAAAAAAAA	0.294													4	3	---	---	---	---	
PRKCD	5580	broad.mit.edu	37	3	53218691	53218692	+	Intron	INS	-	A	A	rs11424887		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:53218691_53218692insA	uc003dgl.2	+						PRKCD_uc003dgm.2_Intron|PRKCD_uc010hmt.1_Intron	NM_006254	NP_006245	Q05655	KPCD_HUMAN	protein kinase C, delta						activation of phospholipase C activity|cellular component disassembly involved in apoptosis|cellular senescence|interferon-gamma-mediated signaling pathway|intracellular signal transduction|mRNA metabolic process|negative regulation of insulin receptor signaling pathway|negative regulation of MAP kinase activity|negative regulation of peptidyl-tyrosine phosphorylation|negative regulation of protein binding|nerve growth factor receptor signaling pathway|platelet activation|positive regulation of ceramide biosynthetic process|positive regulation of glucosylceramide catabolic process|positive regulation of protein dephosphorylation|positive regulation of sphingomyelin catabolic process|protein stabilization|regulation of receptor activity|termination of signal transduction	cytosol|endoplasmic reticulum|nucleoplasm	ATP binding|calcium-independent protein kinase C activity|enzyme activator activity|enzyme binding|insulin receptor substrate binding|metal ion binding|protein C-terminus binding			central_nervous_system(4)|lung(3)|stomach(1)|skin(1)	9		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)		aactccatctcaaaaaaaaaaa	0.153													4	2	---	---	---	---	
CDV3	55573	broad.mit.edu	37	3	133302824	133302829	+	Intron	DEL	ATTTAC	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:133302824_133302829delATTTAC	uc003epq.2	+						CDV3_uc003epp.3_Intron|CDV3_uc003epr.2_Intron	NM_017548	NP_060018	Q9UKY7	CDV3_HUMAN	carnitine deficiency-associated gene expressed						cell proliferation	cytoplasm					0						TCCTTAATGAATTTACATCTTTGCTT	0.393													36	16	---	---	---	---	
ATR	545	broad.mit.edu	37	3	142168328	142168328	+	Frame_Shift_Del	DEL	T	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:142168328delT	uc003eux.3	-	47	8000	c.7878delA	c.(7876-7878)GAAfs	p.E2626fs	XRN1_uc003eus.2_5'Flank|XRN1_uc003eut.2_5'Flank|XRN1_uc003euu.2_5'Flank|XRN1_uc003euw.2_5'Flank|XRN1_uc011bnh.1_5'Flank|ATR_uc003euy.1_3'UTR	NM_001184	NP_001175	Q13535	ATR_HUMAN	ataxia telangiectasia and Rad3 related protein	2626	FATC.				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity			lung(5)|skin(5)|breast(4)|ovary(3)|stomach(1)|central_nervous_system(1)|liver(1)	20						CATCAGTAGCTTCCTGTATAA	0.348								Other_conserved_DNA_damage_response_genes					75	39	---	---	---	---	
SORCS2	57537	broad.mit.edu	37	4	7726580	7726581	+	Intron	INS	-	TTA	TTA	rs147507704	by1000genomes	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:7726580_7726581insTTA	uc003gkb.3	+						SORCS2_uc011bwi.1_Intron	NM_020777	NP_065828	Q96PQ0	SORC2_HUMAN	VPS10 domain receptor protein SORCS 2 precursor							integral to membrane	neuropeptide receptor activity			ovary(1)|central_nervous_system(1)	2						gatggtggtagtggtgatggtg	0.000													4	5	---	---	---	---	
MARCH1	55016	broad.mit.edu	37	4	164467100	164467103	+	Intron	DEL	TGTG	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:164467100_164467103delTGTG	uc003iqs.1	-						MARCH1_uc003iqr.1_Intron	NM_017923	NP_060393	Q8TCQ1	MARH1_HUMAN	membrane-associated RING-CH protein I						antigen processing and presentation of peptide antigen via MHC class II|immune response	cytoplasmic vesicle membrane|early endosome membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|plasma membrane	MHC protein binding|ubiquitin-protein ligase activity|zinc ion binding			lung(2)	2	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TAAATACATAtgtgtgtgtgtgtg	0.127													3	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	5	117010994	117010995	+	IGR	DEL	AC	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:117010994_117010995delAC								None (None upstream) : None (None downstream)																							AGacacacatacacacacacac	0.302													3	3	---	---	---	---	
CYFIP2	26999	broad.mit.edu	37	5	156766466	156766468	+	Intron	DEL	TCT	-	-	rs143579103		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:156766466_156766468delTCT	uc003lwq.2	+						CYFIP2_uc011ddn.1_Intron|CYFIP2_uc011ddo.1_Intron|CYFIP2_uc003lwr.2_Intron|CYFIP2_uc003lws.2_Intron|CYFIP2_uc003lwt.2_Intron|CYFIP2_uc011ddp.1_Intron	NM_001037333	NP_001032410	Q96F07	CYFP2_HUMAN	cytoplasmic FMR1 interacting protein 2						apoptosis|cell-cell adhesion	cell junction|perinuclear region of cytoplasm|synapse|synaptosome	protein binding				0	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			aacaattaggtcttctttcattg	0.305													4	2	---	---	---	---	
DOCK2	1794	broad.mit.edu	37	5	169129675	169129676	+	Intron	INS	-	TGTA	TGTA			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:169129675_169129676insTGTA	uc003maf.2	+						DOCK2_uc011der.1_Intron|DOCK2_uc010jjm.2_5'Flank|DOCK2_uc010jjl.1_Intron	NM_004946	NP_004937	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2						actin cytoskeleton organization|regulation of defense response to virus by virus|viral reproduction	cytoskeleton|cytosol|endomembrane system|membrane	electron carrier activity|GTP binding|GTPase binding|heme binding|Rac guanyl-nucleotide exchange factor activity|T cell receptor binding			ovary(5)|pancreas(2)	7	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAACTTCTTCTtgtatgtatgt	0.297													4	2	---	---	---	---	
ANKS1A	23294	broad.mit.edu	37	6	34935300	34935302	+	Intron	DEL	AAA	-	-	rs10559753		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:34935300_34935302delAAA	uc003ojx.3	+						ANKS1A_uc011dss.1_Intron|ANKS1A_uc011dst.1_Intron|ANKS1A_uc010jvp.1_Intron|ANKS1A_uc010jvq.1_5'Flank	NM_015245	NP_056060	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain							cytoplasm	protein binding			ovary(3)|upper_aerodigestive_tract(1)	4						ccatctccacaaaaaaaaaaaaa	0.000													4	2	---	---	---	---	
FKBP6	8468	broad.mit.edu	37	7	72442401	72442401	+	Intron	DEL	A	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72442401delA	uc003twz.2	+						NSUN5P2_uc010lao.2_5'Flank|uc003twv.2_Intron|STAG3L3_uc011kem.1_Intron|LOC541473_uc010lap.2_Intron|LOC541473_uc003twx.3_Intron	NM_001135211	NP_001128683	O75344	FKBP6_HUMAN	FK506 binding protein 6 isoform b						protein folding	membrane	FK506 binding|peptidyl-prolyl cis-trans isomerase activity				0		Lung NSC(55;0.0908)|all_lung(88;0.198)				actccatctcaaaaaaaaaaa	0.109													4	2	---	---	---	---	
TRIM50	135892	broad.mit.edu	37	7	72729266	72729267	+	Intron	INS	-	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:72729266_72729267insA	uc010lbd.1	-						FKBP6_uc003twz.2_Intron|TRIM50_uc003txy.1_Intron|TRIM50_uc003txz.1_Intron	NM_178125	NP_835226	Q86XT4	TRI50_HUMAN	tripartite motif protein 50A							cytoplasm|intracellular membrane-bounded organelle	ligase activity|zinc ion binding			skin(1)	1						AATTTTCCTTCAAAAAAAAAAA	0.287													4	2	---	---	---	---	
ZAN	7455	broad.mit.edu	37	7	100373941	100373948	+	Intron	DEL	AGGGAGGG	-	-	rs3991185		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100373941_100373948delAGGGAGGG	uc003uwj.2	+						ZAN_uc003uwk.2_Intron|ZAN_uc003uwl.2_Intron|ZAN_uc010lhh.2_Intron|ZAN_uc010lhi.2_Intron|ZAN_uc011kke.1_Intron	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3						binding of sperm to zona pellucida|cell-cell adhesion	integral to membrane|plasma membrane				ovary(4)|large_intestine(3)|central_nervous_system(2)|pancreas(2)	11	Lung NSC(181;0.041)|all_lung(186;0.0581)		STAD - Stomach adenocarcinoma(171;0.19)			actTGAaggaagggagggagggagggag	0.125													4	5	---	---	---	---	
WNT2	7472	broad.mit.edu	37	7	116932348	116932349	+	Intron	DEL	CA	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:116932348_116932349delCA	uc003viz.2	-						WNT2_uc003vja.2_Intron	NM_003391	NP_003382	P09544	WNT2_HUMAN	wingless-type MMTV integration site family						atrial cardiac muscle tissue morphogenesis|canonical Wnt receptor signaling pathway|cardiac epithelial to mesenchymal transition|cellular response to retinoic acid|cellular response to transforming growth factor beta stimulus|dorsal/ventral axis specification|iris morphogenesis|labyrinthine layer blood vessel development|lens development in camera-type eye|lung induction|mammary gland epithelium development|neuron differentiation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cardiac muscle cell proliferation|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of fibroblast proliferation|positive regulation of mesenchymal cell proliferation|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|Wnt receptor signaling pathway, calcium modulating pathway	cytoplasm|extracellular space|proteinaceous extracellular matrix	cytokine activity|frizzled binding|frizzled-2 binding|signal transducer activity			breast(2)|central_nervous_system(2)|ovary(1)|lung(1)|skin(1)	7	all_epithelial(6;2.24e-06)|Lung NSC(10;0.000936)|all_lung(10;0.00109)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		CAACcacactcacacacacaca	0.287													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	8	6981232	6981234	+	IGR	DEL	AAC	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:6981232_6981234delAAC								DEFA5 (66973 upstream) : LOC349196 (136908 downstream)																							ACAAACAAGAAACAACAATGAAA	0.202													4	2	---	---	---	---	
C8orf34	116328	broad.mit.edu	37	8	69728373	69728374	+	Intron	INS	-	TGTG	TGTG	rs138646973	by1000genomes	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:69728373_69728374insTGTG	uc010lyz.2	+						C8orf34_uc003xyb.2_Intron	NM_052958	NP_443190	Q49A92	CH034_HUMAN	hypothetical protein LOC116328						signal transduction		cAMP-dependent protein kinase regulator activity			large_intestine(1)	1			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			gtgtgtttctctgtgtgtgtgt	0.277													12	7	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	66333430	66333430	+	IGR	DEL	A	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:66333430delA								FAM74A4 (839044 upstream) : LOC442421 (163040 downstream)																							TGAACAGGTTAAAAAAAAAAA	0.537													5	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	9	67791249	67791250	+	5'Flank	DEL	AC	-	-	rs74992488		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:67791249_67791250delAC	uc004aes.1	+											Homo sapiens cDNA FLJ36039 fis, clone TESTI2017311.																		agaatgggagacacacacacac	0.064													15	7	---	---	---	---	
LOC100133308	100133308	broad.mit.edu	37	10	45634780	45634780	+	Intron	DEL	C	-	-	rs141209668		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:45634780delC	uc001jbz.2	-						LOC100133308_uc009xmq.1_Intron					Homo sapiens cDNA FLJ32851 fis, clone TESTI2003432.												0						AAAAAAAAAACAAAATTTGTA	0.164													4	2	---	---	---	---	
WDFY4	57705	broad.mit.edu	37	10	50155036	50155037	+	Intron	INS	-	AC	AC	rs143220554	by1000genomes	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:50155036_50155037insAC	uc001jha.3	+						WDFY4_uc009xob.2_Intron|WDFY4_uc010qgn.1_Intron	NM_020945	NP_065996	Q6ZS81	WDFY4_HUMAN	WDFY family member 4							integral to membrane	binding				0						CCACTCTCTGTacacacacaca	0.465													3	3	---	---	---	---	
PCGF5	84333	broad.mit.edu	37	10	93011143	93011144	+	Frame_Shift_Del	DEL	TA	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93011143_93011144delTA	uc001khh.2	+	6	667_668	c.420_421delTA	c.(418-423)GCTATCfs	p.A140fs	PCGF5_uc010qnk.1_Frame_Shift_Del_p.A140fs|PCGF5_uc001khi.2_Frame_Shift_Del_p.A140fs	NM_032373	NP_115749	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5	140_141					regulation of transcription, DNA-dependent|transcription, DNA-dependent	centrosome|PcG protein complex	zinc ion binding			lung(1)	1						CACAAATTGCTATCTGTCTAGA	0.337													62	40	---	---	---	---	
BTAF1	9044	broad.mit.edu	37	10	93711918	93711919	+	Intron	DEL	TG	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:93711918_93711919delTG	uc001khr.2	+						BTAF1_uc009xua.1_Intron	NM_003972	NP_003963	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription						negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity			ovary(1)|central_nervous_system(1)|skin(1)	3		Colorectal(252;0.0846)				tgtgtgtgtttgtgtgtgtgtg	0.218													4	3	---	---	---	---	
TUBGCP2	10844	broad.mit.edu	37	10	135097178	135097195	+	Intron	DEL	TCCCTGCCTCTCCCGCAT	-	-	rs66529543	by1000genomes	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:135097178_135097195delTCCCTGCCTCTCCCGCAT	uc001lmg.1	-						TUBGCP2_uc001lmf.1_Intron|TUBGCP2_uc010qvc.1_Intron|TUBGCP2_uc009ybk.1_Intron|TUBGCP2_uc010qvd.1_Intron|TUBGCP2_uc001lmh.1_Intron	NM_006659	NP_006650	Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2						G2/M transition of mitotic cell cycle|microtubule nucleation|protein complex assembly	centrosome|cytoplasmic microtubule|cytosol|spindle pole	protein binding				0		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		ctccctgcactccctgcctctcccgcattccctgcctc	0.193													10	5	---	---	---	---	
TNKS1BP1	85456	broad.mit.edu	37	11	57077336	57077336	+	Frame_Shift_Del	DEL	T	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:57077336delT	uc001njr.2	-	5	3161	c.2849delA	c.(2848-2850)CAGfs	p.Q950fs	TNKS1BP1_uc001njs.2_Frame_Shift_Del_p.Q950fs|TNKS1BP1_uc009ymd.1_Frame_Shift_Del_p.Q401fs	NM_033396	NP_203754	Q9C0C2	TB182_HUMAN	tankyrase 1-binding protein 1	950	Acidic.				nuclear-transcribed mRNA poly(A) tail shortening|telomere maintenance via telomerase	cytoskeleton|cytosol|nuclear telomeric heterochromatin	ankyrin binding|enzyme binding			skin(1)	1		all_epithelial(135;0.21)				CCCAAACTCCTGTTCCTGTGG	0.592													158	80	---	---	---	---	
Unknown	0	broad.mit.edu	37	11	112490619	112490626	+	IGR	DEL	GTGTGTGT	-	-	rs35701216		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:112490619_112490626delGTGTGTGT								PTS (349942 upstream) : NCAM1 (341369 downstream)																							GGAGGTAGGGgtgtgtgtgtgtgtgtgt	0.375													4	2	---	---	---	---	
CLIP1	6249	broad.mit.edu	37	12	122794215	122794215	+	Intron	DEL	A	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122794215delA	uc001ucg.1	-						CLIP1_uc001uch.1_Intron|CLIP1_uc001uci.1_Intron|CLIP1_uc001ucj.1_Intron	NM_002956	NP_002947	P30622	CLIP1_HUMAN	restin isoform a						mitotic prometaphase|positive regulation of microtubule polymerization	centrosome|cytosol|endosome|intermediate filament|kinetochore	nucleic acid binding|protein homodimerization activity|zinc ion binding			ovary(2)|breast(1)	3	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		ACCCCACCACACTGAGCAGAC	0.527													40	28	---	---	---	---	
FZD10	11211	broad.mit.edu	37	12	130649317	130649317	+	3'UTR	DEL	T	-	-	rs112714527		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:130649317delT	uc001uii.2	+	1					uc001uih.1_5'Flank	NM_007197	NP_009128	Q9ULW2	FZD10_HUMAN	frizzled 10 precursor						brain development|canonical Wnt receptor signaling pathway|cellular response to retinoic acid|embryo development|gonad development|negative regulation of Rho GTPase activity|neuron differentiation|non-canonical Wnt receptor signaling pathway|positive regulation of JUN kinase activity|positive regulation of Rac GTPase activity|regulation of actin cytoskeleton organization|vasculature development	cell projection|cell surface|cytoplasm|integral to plasma membrane	G-protein coupled receptor activity|PDZ domain binding|Wnt receptor activity|Wnt-protein binding			lung(3)|breast(1)|central_nervous_system(1)	5	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		cttcttcttcttttttttttt	0.388													3	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	13	23253536	23253538	+	IGR	DEL	CTT	-	-	rs113089800		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:23253536_23253538delCTT								FGF9 (974896 upstream) : SGCG (501522 downstream)																							ccaccaccaccttcaccaccacc	0.059													3	3	---	---	---	---	
LCP1	3936	broad.mit.edu	37	13	46704723	46704724	+	Intron	INS	-	T	T	rs35095925		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:46704723_46704724insT	uc001vaz.3	-						LCP1_uc010ack.2_Intron|LCP1_uc001vay.3_Intron|LCP1_uc001vba.3_Intron	NM_002298	NP_002289	P13796	PLSL_HUMAN	L-plastin						regulation of intracellular protein transport|T cell activation involved in immune response	cell junction|cytosol|ruffle membrane	calcium ion binding			lung(4)|ovary(3)	7		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		TTATTGGGTTGTTTTTTTTTTT	0.337			T	BCL6	NHL 								4	3	---	---	---	---	
GPC6	10082	broad.mit.edu	37	13	94197839	94197839	+	Intron	DEL	T	-	-	rs34963201		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:94197839delT	uc001vlt.2	+						GPC6_uc010tig.1_Intron|GPC6_uc001vlu.1_Intron	NM_005708	NP_005699	Q9Y625	GPC6_HUMAN	glypican 6 precursor							anchored to membrane|extracellular space|integral to plasma membrane|proteinaceous extracellular matrix	heparan sulfate proteoglycan binding				0	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TTGACAGTAATTTTTTTTTTT	0.264													6	3	---	---	---	---	
C13orf39	196541	broad.mit.edu	37	13	103343225	103343226	+	Frame_Shift_Ins	INS	-	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:103343225_103343226insA	uc001vpj.2	-	2	225_226	c.219_220insT	c.(217-222)TTTGCAfs	p.F73fs	C13orf39_uc001vpk.2_Frame_Shift_Ins_p.F73fs	NM_001010977	NP_001010977	Q5VZV1	MT21C_HUMAN	hypothetical protein LOC196541	73_74							methyltransferase activity				0						TCCTTTCCTGCAAACCGATAAT	0.460													84	42	---	---	---	---	
METT11D1	64745	broad.mit.edu	37	14	21464039	21464039	+	Intron	DEL	T	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:21464039delT	uc001vyn.2	+						METT11D1_uc001vym.2_Intron|METT11D1_uc001vyo.2_Intron|METT11D1_uc001vyp.2_Intron|METT11D1_uc001vyq.2_Intron	NM_022734	NP_073571	Q9H7H0	MET17_HUMAN	methyltransferase 11 domain containing 1 isoform						translation	mitochondrion|ribosome	copper ion binding|methyltransferase activity				0	all_cancers(95;0.00267)		OV - Ovarian serous cystadenocarcinoma(11;1.34e-10)|Epithelial(56;1.57e-08)|all cancers(55;7.45e-08)	GBM - Glioblastoma multiforme(265;0.0191)		GCTTTATTTCTTTTATTTCCT	0.418													54	28	---	---	---	---	
ADCY4	196883	broad.mit.edu	37	14	24795777	24795778	+	Intron	INS	-	TG	TG			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:24795777_24795778insTG	uc001wov.2	-						ADCY4_uc001wow.2_Intron|ADCY4_uc010toh.1_Intron|ADCY4_uc001wox.2_Intron|ADCY4_uc001woy.2_Intron	NM_139247	NP_640340	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4						activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding|protein binding			ovary(1)|lung(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(265;0.0192)		CCCAGGATCTTtgtgtgtgtgt	0.252													3	4	---	---	---	---	
GOLGA6A	342096	broad.mit.edu	37	15	74373249	74373249	+	Intron	DEL	A	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:74373249delA	uc002axa.1	-							NM_001038640	NP_001033729	Q9NYA3	GOG6A_HUMAN	golgi autoantigen, golgin subfamily a, 6												0						TATTATGGCTAAAAAAAAAAG	0.428													4	2	---	---	---	---	
Unknown	0	broad.mit.edu	37	16	9165667	9165682	+	IGR	DEL	TGCGTGTGTATGTGTG	-	-	rs13339100	by1000genomes	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:9165667_9165682delTGCGTGTGTATGTGTG								USP7 (108326 upstream) : C16orf72 (19855 downstream)																							caggaaaacctgcgtgtgtatgtgtgtgtgtgtgtg	0.000													3	3	---	---	---	---	
DNAH3	55567	broad.mit.edu	37	16	21136284	21136285	+	Intron	INS	-	TG	TG	rs145787563	by1000genomes	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:21136284_21136285insTG	uc010vbe.1	-						DNAH3_uc002die.2_Intron	NM_017539	NP_060009	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3						ciliary or flagellar motility|microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|microtubule motor activity			ovary(10)|skin(3)|large_intestine(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)	18				GBM - Glioblastoma multiforme(48;0.207)		catttaccatttgtgtgtgtgt	0.079													5	3	---	---	---	---	
PRSS53	339105	broad.mit.edu	37	16	31106653	31106653	+	5'Flank	DEL	A	-	-	rs74635928		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31106653delA	uc002ear.2	-						VKORC1_uc002eas.2_5'Flank|VKORC1_uc002eat.2_5'Flank|VKORC1_uc002eau.2_5'Flank	NM_001039503	NP_001034592	Q2L4Q9	PRS53_HUMAN	polyserase 3 precursor						proteolysis	extracellular region	serine-type endopeptidase activity				0						actctgtctcaaaaaaaaaaa	0.184													4	2	---	---	---	---	
COX6A2	1339	broad.mit.edu	37	16	31439243	31439244	+	Intron	INS	-	C	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:31439243_31439244insC	uc002ebx.1	-							NM_005205	NP_005196	Q02221	CX6A2_HUMAN	cytochrome c oxidase subunit VIa polypeptide 2						generation of precursor metabolites and energy	mitochondrial respiratory chain complex IV	cytochrome-c oxidase activity				0						cgccccgcgcgacccccccccc	0.347													4	2	---	---	---	---	
NAE1	8883	broad.mit.edu	37	16	66839540	66839541	+	Intron	INS	-	A	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:66839540_66839541insA	uc002eqf.2	-						NAE1_uc002eqe.2_Intron|NAE1_uc002eqg.2_Intron|NAE1_uc010cdv.2_Intron	NM_003905	NP_003896	Q13564	ULA1_HUMAN	NEDD8 activating enzyme E1 subunit 1 isoform a						apoptosis|cell cycle|DNA replication|mitotic cell cycle DNA replication checkpoint|protein neddylation|signal transduction	cytoplasm|insoluble fraction|plasma membrane	catalytic activity|protein heterodimerization activity			ovary(1)	1		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0914)|Epithelial(162;0.214)	Adenosine triphosphate(DB00171)	gactgcgtctcaaaaaaaaaaa	0.124													4	2	---	---	---	---	
PLA2G15	23659	broad.mit.edu	37	16	68283470	68283470	+	Intron	DEL	G	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68283470delG	uc002evr.2	+						PLA2G15_uc010vld.1_Intron|PLA2G15_uc010vle.1_Intron|PLA2G15_uc010vlf.1_Intron	NM_012320	NP_036452	Q8NCC3	PAG15_HUMAN	lysophospholipase 3 (lysosomal phospholipase A2)						fatty acid catabolic process	extracellular region|lysosome	lysophospholipase activity|phosphatidylcholine-sterol O-acyltransferase activity|phospholipid binding			ovary(1)	1						CCAGGTCCTCggtctggtctg	0.517													13	11	---	---	---	---	
PRMT7	54496	broad.mit.edu	37	16	68386205	68386205	+	Frame_Shift_Del	DEL	A	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:68386205delA	uc002evy.1	+	15	1744	c.1468delA	c.(1468-1470)AACfs	p.N490fs	PRMT7_uc002evx.1_Frame_Shift_Del_p.N416fs|PRMT7_uc010vlg.1_Frame_Shift_Del_p.N440fs|PRMT7_uc002evz.1_Frame_Shift_Del_p.N262fs|PRMT7_uc010cfd.1_5'UTR	NM_019023	NP_061896	Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	490					cell differentiation|DNA methylation involved in gamete generation|regulation of gene expression by genetic imprinting|regulation of transcription, DNA-dependent|spliceosomal snRNP assembly|transcription, DNA-dependent	cytosol|nucleus	[myelin basic protein]-arginine N-methyltransferase activity|histone methyltransferase activity (H4-R3 specific)|protein-arginine omega-N monomethyltransferase activity|protein-arginine omega-N symmetric methyltransferase activity|ribonucleoprotein binding				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		GCCGTGGCACAACCTCTACTT	0.647													130	65	---	---	---	---	
GCSH	2653	broad.mit.edu	37	16	81118317	81118317	+	Intron	DEL	T	-	-	rs111388132		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:81118317delT	uc002fgd.2	-						GCSH_uc002fge.2_Intron	NM_004483	NP_004474	P23434	GCSH_HUMAN	glycine cleavage system protein H (aminomethyl							glycine cleavage complex|mitochondrion	aminomethyltransferase activity				0					Glycine(DB00145)	TCCAAAtttcttttttttttt	0.119													4	2	---	---	---	---	
ASGR2	433	broad.mit.edu	37	17	7010880	7010881	+	Intron	DEL	AT	-	-	rs143843681		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7010880_7010881delAT	uc002gep.3	-						ASGR2_uc010vtk.1_Intron|ASGR2_uc002gem.1_Intron|ASGR2_uc002gen.1_Intron|ASGR2_uc002geo.1_Intron|ASGR2_uc002ger.3_Intron|ASGR2_uc002geq.3_Intron	NM_001181	NP_001172	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2 isoform a						cell surface receptor linked signaling pathway|endocytosis	focal adhesion|integral to membrane|nucleolus	asialoglycoprotein receptor activity|protein binding|sugar binding			ovary(1)	1					Antihemophilic Factor(DB00025)	gtacacacacatataccatacc	0.025													4	3	---	---	---	---	
Unknown	0	broad.mit.edu	37	17	43663455	43663456	+	IGR	INS	-	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:43663455_43663456insT								LRRC37A4 (67939 upstream) : LOC644172 (14035 downstream)																							TGAGCACCAGCTATCCTGCTGT	0.668													4	3	---	---	---	---	
KIAA1267	284058	broad.mit.edu	37	17	44127972	44127981	+	Frame_Shift_Del	DEL	GTGAATTTCG	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:44127972_44127981delGTGAATTTCG	uc002ikb.2	-	6	2023_2032	c.1938_1947delCGAAATTCAC	c.(1936-1947)CCCGAAATTCACfs	p.P646fs	KIAA1267_uc002ikc.2_Frame_Shift_Del_p.P646fs|KIAA1267_uc002ikd.2_Frame_Shift_Del_p.P646fs|KIAA1267_uc010dav.2_Frame_Shift_Del_p.P646fs	NM_015443	NP_056258	Q7Z3B3	K1267_HUMAN	hypothetical protein LOC284058	646_649						MLL1 complex	protein binding			skin(2)	2		Melanoma(429;0.211)				GGGCTTCATAGTGAATTTCGGGAGGCATGG	0.495													45	21	---	---	---	---	
ABCA9	10350	broad.mit.edu	37	17	67025161	67025161	+	Intron	DEL	T	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:67025161delT	uc002jhu.2	-						ABCA9_uc010dez.2_Intron	NM_080283	NP_525022	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A, member 9						transport	integral to membrane	ATP binding|ATPase activity			ovary(4)|upper_aerodigestive_tract(1)|central_nervous_system(1)	6	Breast(10;1.47e-12)					GTTTTATGGGTTTTTTTTTTA	0.274													4	2	---	---	---	---	
CD300A	11314	broad.mit.edu	37	17	72470064	72470064	+	Intron	DEL	G	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72470064delG	uc002jkv.2	+						CD300A_uc002jkw.2_Intron|CD300A_uc010dfr.2_Intron|CD300A_uc010dfs.2_Intron	NM_007261	NP_009192	Q9UGN4	CLM8_HUMAN	leukocyte membrane antigen						cell adhesion	integral to membrane|plasma membrane	receptor activity			ovary(1)|skin(1)	2						TGGAATTGTTGGGGCAGGAAT	0.572													44	20	---	---	---	---	
RNF157	114804	broad.mit.edu	37	17	74163947	74163947	+	Intron	DEL	T	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:74163947delT	uc002jqz.2	-						RNF157_uc002jra.2_Intron	NM_052916	NP_443148	Q96PX1	RN157_HUMAN	ring finger protein 157								zinc ion binding			ovary(1)	1			LUSC - Lung squamous cell carcinoma(166;0.187)			TTTAAAAAAATTAGCAATATA	0.388													32	23	---	---	---	---	
ZNF430	80264	broad.mit.edu	37	19	21239294	21239294	+	Intron	DEL	A	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21239294delA	uc002npj.2	+						ZNF430_uc002npk.2_Intron	NM_025189	NP_079465	Q9H8G1	ZN430_HUMAN	zinc finger protein 430						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			skin(2)	2						gactctgtctaaaaaaaaaaa	0.124													4	2	---	---	---	---	
PLEKHG2	64857	broad.mit.edu	37	19	39907851	39907851	+	Intron	DEL	G	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39907851delG	uc010xuz.1	+						PLEKHG2_uc010xuy.1_Intron|PLEKHG2_uc002olj.2_Intron|PLEKHG2_uc010xva.1_Intron	NM_022835	NP_073746	Q9H7P9	PKHG2_HUMAN	common-site lymphoma/leukemia guanine nucleotide						apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity			skin(2)|pancreas(1)|breast(1)	4	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			ggagtacagtggtgcgatctt	0.015													4	2	---	---	---	---	
PAFAH1B3	5050	broad.mit.edu	37	19	42801727	42801728	+	Intron	INS	-	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42801727_42801728insT	uc002otg.2	-						PAFAH1B3_uc010xwi.1_Intron|PAFAH1B3_uc010xwj.1_Intron	NM_002573	NP_002564	Q15102	PA1B3_HUMAN	platelet-activating factor acetylhydrolase,						lipid catabolic process|nervous system development	cytoplasm	1-alkyl-2-acetylglycerophosphocholine esterase activity|protein binding				0		Prostate(69;0.0704)				ctttcgttttcttttttttttt	0.223													4	2	---	---	---	---	
BCAM	4059	broad.mit.edu	37	19	45323171	45323187	+	Intron	DEL	CATCCCCAACTCATCCT	-	-	rs3842409		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45323171_45323187delCATCCCCAACTCATCCT	uc002ozu.2	+						BCAM_uc002ozt.1_3'UTR	NM_005581	NP_005572	P50895	BCAM_HUMAN	basal cell adhesion molecule isoform 1						cell-matrix adhesion	integral to plasma membrane	laminin binding|laminin receptor activity			skin(1)	1	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				AATCCACAGCCATCCCCAACTCATcctcatccccaac	0.065													4	2	---	---	---	---	
LILRA5	353514	broad.mit.edu	37	19	54824527	54824528	+	5'Flank	INS	-	T	T	rs35949168		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:54824527_54824528insT	uc002qfe.2	-						LILRA5_uc002qff.2_5'Flank|LILRA5_uc010yev.1_5'Flank|LILRA5_uc010yew.1_5'Flank|LILRA5_uc002qfh.1_5'Flank|LILRA5_uc002qfg.1_5'Flank	NM_021250	NP_067073	A6NI73	LIRA5_HUMAN	leukocyte immunoglobulin-like receptor subfamily						innate immune response	extracellular region|integral to membrane	receptor activity			upper_aerodigestive_tract(1)	1	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACTTCCCTTAAttttttttttt	0.416											OREG0003655	type=REGULATORY REGION|Gene=LILRA5|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	5	3	---	---	---	---	
ZIM3	114026	broad.mit.edu	37	19	57648045	57648046	+	Intron	INS	-	A	A	rs145532440	by1000genomes	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:57648045_57648046insA	uc002qnz.1	-							NM_052882	NP_443114	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			pancreas(1)|skin(1)	2		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		aaaaaaaaaagaaaaaaaaaaG	0.188													4	4	---	---	---	---	
GCAT	23464	broad.mit.edu	37	22	38209775	38209775	+	Intron	DEL	T	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:38209775delT	uc003atz.2	+						GCAT_uc003aua.1_Intron	NM_014291	NP_055106	O75600	KBL_HUMAN	glycine C-acetyltransferase precursor						biosynthetic process|cellular amino acid metabolic process		glycine C-acetyltransferase activity|pyridoxal phosphate binding|transferase activity, transferring nitrogenous groups				0	Melanoma(58;0.045)				Glycine(DB00145)|Pyridoxal Phosphate(DB00114)	agcattattcttttttttttt	0.000													4	2	---	---	---	---	
POLR3H	171568	broad.mit.edu	37	22	41926704	41926704	+	Frame_Shift_Del	DEL	G	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:41926704delG	uc003baf.2	-	6	608	c.548delC	c.(547-549)CCGfs	p.P183fs	POLR3H_uc003bae.2_RNA|POLR3H_uc003bag.2_Frame_Shift_Del_p.P183fs|POLR3H_uc003bai.2_Frame_Shift_Del_p.P154fs	NM_138338	NP_612211	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide	183					innate immune response|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	DNA-directed RNA polymerase III complex	DNA binding|DNA-directed RNA polymerase activity			skin(1)	1						AAGCGTGTACGGAGCCTCCTT	0.622													41	24	---	---	---	---	
SSX4	6759	broad.mit.edu	37	X	48243360	48243361	+	Intron	DEL	AC	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48243360_48243361delAC	uc004djf.1	+						SSX4_uc004djg.1_Intron	NM_005636	NP_005627	O60224	SSX4_HUMAN	synovial sarcoma, X breakpoint 4 isoform a						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding		SS18/SSX4(12)	soft_tissue(12)	12						aaaaaaaaaaactcctgggctc	0.099			T	SS18	synovial sarcoma								5	3	---	---	---	---	
FHL1	2273	broad.mit.edu	37	X	135291228	135291229	+	Intron	INS	-	T	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:135291228_135291229insT	uc004ezo.2	+						FHL1_uc010nrz.2_Intron|FHL1_uc004ezm.2_Intron|FHL1_uc004ezl.2_Intron|FHL1_uc004ezq.2_Intron|FHL1_uc011mvy.1_Intron|FHL1_uc011mvz.1_Intron|FHL1_uc004ezn.2_Intron|FHL1_uc011mwa.1_Intron|FHL1_uc011mwb.1_Intron|FHL1_uc004ezp.2_Intron|FHL1_uc004ezr.2_Intron	NM_001159702	NP_001153174	Q13642	FHL1_HUMAN	four and a half LIM domains 1 isoform 1						cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding				0	Acute lymphoblastic leukemia(192;0.000127)					GGCAGGGTTTCTTTTTTTTTTG	0.421													5	4	---	---	---	---	
Unknown	0	broad.mit.edu	37	Y	13487812	13487812	+	IGR	DEL	C	-	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrY:13487812delC								None (None upstream) : None (None downstream)																							GGCTGGCTGTCCCAGGGCTCA	0.398													5	4	---	---	---	---	
