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	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	validation_status	validation_method	validation_tumor_sample	validation_alt_allele
ESPNP	284729	broad.mit.edu	37	1	17034125	17034126	+	Frame_Shift_Ins	INS	-	AGCT	AGCT	rs141324796	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:17034125_17034126insAGCT	uc001azn.1	-	3	478_479	c.364_365insAGCT	c.(364-366)TGGfs	p.W122fs	ESPNP_uc010ocj.1_Frame_Shift_Ins_p.W52fs	NR_026567				RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;												0																		---	---	---	---
COL16A1	1307	broad.mit.edu	37	1	32122425	32122426	+	Intron	DEL	AA	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:32122425_32122426delAA	uc001btk.1	-						COL16A1_uc001bti.1_Intron|COL16A1_uc001btj.1_Intron	NM_001856	NP_001847			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)														---	---	---	---
Unknown	0	broad.mit.edu	37	1	35115942	35115943	+	IGR	DEL	AA	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:35115942_35115943delAA								C1orf94 (431213 upstream) : MIR552 (19257 downstream)																																			---	---	---	---
PPT1	5538	broad.mit.edu	37	1	40557538	40557538	+	Intron	DEL	A	-	-	rs11308805		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40557538delA	uc001cfb.2	-						PPT1_uc010ojf.1_Intron|PPT1_uc010ojg.1_Intron|PPT1_uc009vwa.2_Intron	NM_000310	NP_000301			palmitoyl-protein thioesterase 1 isoform 1						brain development|cofactor metabolic process|cofactor transport|DNA fragmentation involved in apoptotic nuclear change|lysosomal lumen acidification|membrane raft organization|negative regulation of cell growth|negative regulation of neuron apoptosis|neuron development|pinocytosis|positive regulation of pinocytosis|positive regulation of receptor-mediated endocytosis|protein depalmitoylation|protein transport|receptor-mediated endocytosis|regulation of synapse structure and activity|sphingolipid catabolic process|visual perception	axon|cytosol|Golgi apparatus|lysosome|membrane fraction|membrane raft|nucleus|synaptic vesicle	palmitoyl-(protein) hydrolase activity|palmitoyl-CoA hydrolase activity			ovary(1)	1	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
Unknown	0	broad.mit.edu	37	1	41344730	41344731	+	IGR	INS	-	GAAG	GAAG	rs57314131		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:41344730_41344731insGAAG								CITED4 (16712 upstream) : CTPS (100276 downstream)																																			---	---	---	---
HIVEP3	59269	broad.mit.edu	37	1	42011235	42011237	+	Intron	DEL	CAC	-	-	rs150183501		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:42011235_42011237delCAC	uc001cgz.3	-						HIVEP3_uc001cha.3_Intron|HIVEP3_uc001cgy.2_Intron	NM_024503	NP_078779			human immunodeficiency virus type I enhancer						positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	zinc ion binding			ovary(4)|large_intestine(1)|central_nervous_system(1)	6	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)																---	---	---	---
SLC6A9	6536	broad.mit.edu	37	1	44475402	44475402	+	Intron	DEL	G	-	-	rs75103201	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:44475402delG	uc001cll.2	-						SLC6A9_uc009vxe.2_Intron|SLC6A9_uc010okm.1_Intron|SLC6A9_uc001clm.2_Intron|SLC6A9_uc009vxd.2_Intron|SLC6A9_uc010okn.1_Intron|SLC6A9_uc001cln.2_Intron|SLC6A9_uc010oko.1_Intron|SLC6A9_uc010okp.1_Intron	NM_201649	NP_964012			solute carrier family 6 member 9 isoform 2							integral to plasma membrane|membrane fraction	glycine:sodium symporter activity|neurotransmitter:sodium symporter activity				0	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			Glycine(DB00145)													---	---	---	---
USP33	23032	broad.mit.edu	37	1	78188044	78188044	+	Intron	DEL	A	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:78188044delA	uc001dht.2	-						USP33_uc001dhs.2_Intron|USP33_uc001dhu.2_Intron|USP33_uc001dhv.2_Intron|USP33_uc001dhw.2_Intron	NM_015017	NP_055832			ubiquitin specific protease 33 isoform 1						axon guidance|cell migration|endocytosis|protein K48-linked deubiquitination|protein K63-linked deubiquitination|regulation of G-protein coupled receptor protein signaling pathway|ubiquitin-dependent protein catabolic process	perinuclear region of cytoplasm|VCB complex	cysteine-type endopeptidase activity|G-protein-coupled receptor binding|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding			lung(2)|ovary(1)	3																		---	---	---	---
NBPF16	728936	broad.mit.edu	37	1	148756337	148756337	+	Intron	DEL	T	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:148756337delT	uc010pba.1	+						NBPF16_uc009wkt.1_Intron	NM_001102663	NP_001096133			hypothetical protein LOC728936												0	all_hematologic(923;0.032)																	---	---	---	---
Unknown	0	broad.mit.edu	37	1	168427175	168427176	+	IGR	INS	-	CTTTCTTT	CTTTCTTT	rs141776154	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:168427175_168427176insCTTTCTTT								MIR557 (82316 upstream) : XCL2 (82829 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	1	248844550	248844550	+	IGR	DEL	T	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248844550delT								OR2T27 (30365 upstream) : OR14I1 (120 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	6953876	6953879	+	IGR	DEL	GAGG	-	-	rs112872966		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:6953876_6953879delGAGG								LOC400940 (825512 upstream) : CMPK2 (26624 downstream)																																			---	---	---	---
SPAST	6683	broad.mit.edu	37	2	32312734	32312735	+	Intron	INS	-	TTTA	TTTA			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:32312734_32312735insTTTA	uc002roc.2	+						SPAST_uc002rod.2_Intron	NM_014946	NP_055761			spastin isoform 1						cell cycle|cell death|cell differentiation|cytokinesis, completion of separation|ER to Golgi vesicle-mediated transport|microtubule bundle formation|microtubule severing|nervous system development|protein hexamerization|protein homooligomerization	endoplasmic reticulum|endosome|integral to membrane|microtubule|microtubule organizing center|nucleus|perinuclear region of cytoplasm|spindle	alpha-tubulin binding|ATP binding|beta-tubulin binding|microtubule binding|microtubule-severing ATPase activity			breast(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)																	---	---	---	---
Unknown	0	broad.mit.edu	37	2	90475355	90475362	+	IGR	DEL	TCCTTCCT	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:90475355_90475362delTCCTTCCT								None (None upstream) : None (None downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	91764930	91764935	+	IGR	DEL	TGTGTA	-	-	rs4005278		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:91764930_91764935delTGTGTA								None (None upstream) : LOC654342 (40257 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	2	133018714	133018715	+	IGR	DEL	GT	-	-	rs141065944		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:133018714_133018715delGT								NCRNA00164 (3172 upstream) : GPR39 (155432 downstream)																																			---	---	---	---
OSBPL6	114880	broad.mit.edu	37	2	179156436	179156439	+	Intron	DEL	CCTC	-	-	rs13409754		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179156436_179156439delCCTC	uc002ulx.2	+						OSBPL6_uc002ulw.2_Intron|OSBPL6_uc002uly.2_Intron|OSBPL6_uc010zfe.1_Intron|OSBPL6_uc002ulz.2_Intron	NM_032523	NP_115912			oxysterol-binding protein-like protein 6 isoform						lipid transport		lipid binding			pancreas(1)	1			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)															---	---	---	---
USP37	57695	broad.mit.edu	37	2	219352921	219352921	+	Intron	DEL	G	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:219352921delG	uc002vie.2	-						USP37_uc010fvs.1_Intron|USP37_uc010zkf.1_Intron|USP37_uc002vif.2_Intron|USP37_uc002vig.2_Intron	NM_020935	NP_065986			ubiquitin specific peptidase 37						ubiquitin-dependent protein catabolic process	nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			skin(3)|ovary(1)|prostate(1)	5		Renal(207;0.0915)		Epithelial(149;1.08e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.00375)|Lung(261;0.00487)														---	---	---	---
PER2	8864	broad.mit.edu	37	2	239155173	239155174	+	Intron	INS	-	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:239155173_239155174insA	uc002vyc.2	-							NM_022817	NP_073728			period 2						circadian rhythm|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding|signal transducer activity			upper_aerodigestive_tract(1)|breast(1)	2		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)														---	---	---	---
FANCD2	2177	broad.mit.edu	37	3	10089935	10089936	+	Intron	DEL	TC	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10089935_10089936delTC	uc003buw.2	+						FANCD2_uc003bux.1_Intron|FANCD2_uc003buy.1_Intron|FANCD2_uc010hcw.1_5'Flank	NM_033084	NP_149075			Fanconi anemia complementation group D2 isoform						DNA repair|response to gamma radiation	nucleoplasm	protein binding|protein binding			central_nervous_system(2)|ovary(1)|skin(1)	4				OV - Ovarian serous cystadenocarcinoma(96;0.148)				D|Mis|N|F			AML|leukemia		Involved_in_tolerance_or_repair_of_DNA_crosslinks	Fanconi_Anemia				---	---	---	---
Unknown	0	broad.mit.edu	37	3	14415403	14415404	+	IGR	DEL	TC	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:14415403_14415404delTC								LSM3 (175567 upstream) : SLC6A6 (28702 downstream)																																			---	---	---	---
CELSR3	1951	broad.mit.edu	37	3	48688110	48688111	+	Intron	INS	-	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:48688110_48688111insC	uc003cul.2	-						CELSR3_uc003cuf.1_Intron|CELSR3_uc010hkg.2_Intron	NM_001407	NP_001398			cadherin EGF LAG seven-pass G-type receptor 3						homophilic cell adhesion|multicellular organismal development|neuropeptide signaling pathway	integral to membrane|plasma membrane	calcium ion binding|G-protein coupled receptor activity|protein binding			ovary(5)|upper_aerodigestive_tract(2)|central_nervous_system(2)|skin(2)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)														---	---	---	---
PLD1	5337	broad.mit.edu	37	3	171417825	171417826	+	Intron	DEL	TC	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:171417825_171417826delTC	uc003fhs.2	-						PLD1_uc003fht.2_Intron	NM_002662	NP_002653			phospholipase D1 isoform a						cell communication|chemotaxis|Ras protein signal transduction	endoplasmic reticulum membrane|Golgi membrane|late endosome membrane|perinuclear region of cytoplasm	NAPE-specific phospholipase D activity|phosphatidylinositol binding|phospholipase D activity			ovary(2)|lung(1)	3	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)													---	---	---	---
Unknown	0	broad.mit.edu	37	4	72742235	72742238	+	IGR	DEL	TCCT	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:72742235_72742238delTCCT								GC (72477 upstream) : NPFFR2 (155283 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	4	174596492	174596496	+	IGR	DEL	CTTTT	-	-	rs139835286	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:174596492_174596496delCTTTT								MORF4 (58698 upstream) : FBXO8 (561316 downstream)																																			---	---	---	---
CCT5	22948	broad.mit.edu	37	5	10250047	10250047	+	5'Flank	DEL	C	-	-	rs2607301		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10250047delC	uc003jeq.2	+						FAM173B_uc003jeo.2_5'Flank|FAM173B_uc003jep.2_5'Flank|FAM173B_uc010itr.2_5'Flank|CCT5_uc011cmq.1_5'Flank|CCT5_uc003jer.2_5'Flank|CCT5_uc010its.2_5'Flank|CCT5_uc011cmr.1_5'Flank|CCT5_uc011cms.1_5'Flank|CCT5_uc011cmt.1_5'Flank	NM_012073	NP_036205			chaperonin containing TCP1, subunit 5 (epsilon)						'de novo' posttranslational protein folding|response to virus	microtubule organizing center|nucleolus	ATP binding|unfolded protein binding			ovary(2)	2																		---	---	---	---
CDH12	1010	broad.mit.edu	37	5	21802702	21802703	+	Intron	INS	-	TTTT	TTTT	rs28497222		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:21802702_21802703insTTTT	uc010iuc.2	-						CDH12_uc011cno.1_Intron|CDH12_uc003jgk.2_Intron	NM_004061	NP_004052			cadherin 12, type 2 preproprotein						adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(2)	2															HNSCC(59;0.17)	OREG0016539	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	---	---	---	---
SPINK5	11005	broad.mit.edu	37	5	147493803	147493804	+	Intron	INS	-	A	A	rs142874955		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147493803_147493804insA	uc003lox.2	+						SPINK5_uc010jgs.1_Intron|SPINK5_uc010jgr.2_Intron|SPINK5_uc003low.2_Intron|SPINK5_uc003loy.2_Intron	NM_006846	NP_006837			serine peptidase inhibitor, Kazal type 5 isoform						anagen|epithelial cell differentiation|extracellular matrix organization|hair cell differentiation|negative regulation of angiogenesis|negative regulation of immune response|regulation of T cell differentiation	cell cortex|cytosol|endoplasmic reticulum membrane|extracellular region|lamellar body|perinuclear region of cytoplasm	serine-type endopeptidase inhibitor activity			skin(2)|ovary(1)|breast(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
ATP10B	23120	broad.mit.edu	37	5	160063990	160063991	+	Intron	INS	-	CCAC	CCAC	rs149045770		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:160063990_160063991insCCAC	uc003lym.1	-						ATP10B_uc003lyp.2_Intron|ATP10B_uc011deg.1_Intron|ATP10B_uc003lyn.2_5'Flank|ATP10B_uc003lyo.2_Intron	NM_025153	NP_079429			ATPase, class V, type 10B						ATP biosynthetic process	integral to membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			ovary(3)|central_nervous_system(1)|pancreas(1)	5	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)															---	---	---	---
Unknown	0	broad.mit.edu	37	5	166471034	166471041	+	IGR	DEL	TAAGGACA	-	-	rs2910053		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:166471034_166471041delTAAGGACA								None (None upstream) : ODZ2 (240802 downstream)																																			---	---	---	---
OR10C1	442194	broad.mit.edu	37	6	29408093	29408095	+	In_Frame_Del	DEL	TTC	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29408093_29408095delTTC	uc011dlp.1	+	1	301_303	c.301_303delTTC	c.(301-303)TTCdel	p.F103del	OR11A1_uc010jrh.1_Intron	NM_013941	NP_039229	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C,	103	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
HLA-G	3135	broad.mit.edu	37	6	29974917	29974918	+	Intron	DEL	CT	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:29974917_29974918delCT	uc011dmb.1	+						NCRNA00171_uc011dme.1_Intron|HLA-J_uc003nou.3_Intron|HLA-J_uc003rtl.3_Intron|HLA-J_uc003nov.3_Intron	NM_002127	NP_002118			major histocompatibility complex, class I, G						antigen processing and presentation of peptide antigen via MHC class I|cellular defense response|interferon-gamma-mediated signaling pathway|regulation of immune response|type I interferon-mediated signaling pathway	integral to membrane|MHC class I protein complex	MHC class I receptor activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
HLA-DRB5	3127	broad.mit.edu	37	6	32546912	32546913	+	Intron	INS	-	G	G	rs34252386		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:32546912_32546913insG	uc003obk.3	-						HLA-DRB1_uc011dqa.1_Intron|HLA-DRB6_uc003obo.1_Intron|uc010jub.1_5'Flank|HLA-DRB1_uc003obp.3_Intron|HLA-DRB1_uc011dqb.1_Intron	NM_002125	NP_002116			major histocompatibility complex, class II, DR						antigen processing and presentation of peptide or polysaccharide antigen via MHC class II|immune response	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane|late endosome membrane|lysosomal membrane|MHC class II protein complex					0																		---	---	---	---
Unknown	0	broad.mit.edu	37	6	36377716	36377717	+	IGR	INS	-	AGAAAGAAAG	AGAAAGAAAG			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:36377716_36377717insAGAAAGAAAG								PXT1 (9405 upstream) : KCTD20 (32827 downstream)																																			---	---	---	---
ROS1	6098	broad.mit.edu	37	6	117640871	117640872	+	Intron	INS	-	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:117640871_117640872insT	uc003pxp.1	-						ROS1_uc011ebi.1_Intron|GOPC_uc003pxq.1_Intron	NM_002944	NP_002935			proto-oncogene c-ros-1 protein precursor						transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity			lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)				T	GOPC|ROS1	glioblastoma|NSCLC								---	---	---	---
Unknown	0	broad.mit.edu	37	6	130207919	130207919	+	IGR	DEL	A	-	-	rs151286140	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:130207919delA								C6orf191 (25503 upstream) : L3MBTL3 (131815 downstream)																																			---	---	---	---
IRF5	3663	broad.mit.edu	37	7	128582510	128582510	+	Intron	DEL	T	-	-	rs5887397		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:128582510delT	uc003vog.2	+						IRF5_uc010llr.1_Intron|IRF5_uc011kot.1_Intron|IRF5_uc011kou.1_Intron|IRF5_uc010lls.1_Intron|IRF5_uc003voh.2_Intron|IRF5_uc010llt.2_Intron|IRF5_uc003voi.2_Intron|IRF5_uc010llu.1_Intron|IRF5_uc003vok.2_Intron|IRF5_uc003voj.3_Intron|IRF5_uc010llv.1_Intron|IRF5_uc010llw.1_Intron	NM_002200	NP_002191			interferon regulatory factor 5 isoform a						interferon-gamma-mediated signaling pathway|type I interferon-mediated signaling pathway	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity				0																		---	---	---	---
Unknown	0	broad.mit.edu	37	8	93538490	93538491	+	IGR	INS	-	AC	AC	rs145598749	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:93538490_93538491insAC								RUNX1T1 (430784 upstream) : C8orf83 (357374 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	8	94201477	94201480	+	IGR	DEL	GGAG	-	-	rs2449608		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:94201477_94201480delGGAG								C8orf83 (171576 upstream) : FAM92A1 (511293 downstream)																																			---	---	---	---
TMEM38B	55151	broad.mit.edu	37	9	108468184	108468184	+	Intron	DEL	T	-	-	rs75898442		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:108468184delT	uc004bcu.1	+						TMEM38B_uc010mtn.1_Intron	NM_018112	NP_060582			transmembrane protein 38B							integral to membrane|nuclear membrane|sarcoplasmic reticulum membrane	potassium channel activity			ovary(1)|skin(1)	2																		---	---	---	---
OBP2A	29991	broad.mit.edu	37	9	138441218	138441218	+	Intron	DEL	C	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:138441218delC	uc004cgb.2	+						OBP2A_uc004cgc.2_Intron|OBP2A_uc010nau.2_Intron|OBP2A_uc010nav.2_Intron	NM_014582	NP_055397			odorant binding protein 2A precursor						response to stimulus|sensory perception of smell	extracellular region	odorant binding|transporter activity				0				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)														---	---	---	---
WAPAL	23063	broad.mit.edu	37	10	88212829	88212829	+	Intron	DEL	G	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88212829delG	uc001kdo.2	-						WAPAL_uc009xsv.2_Intron|WAPAL_uc001kdn.2_Intron|WAPAL_uc009xsw.2_Intron	NM_015045	NP_055860			wings apart-like homolog						cell division|interspecies interaction between organisms|mitosis|negative regulation of chromatin binding|negative regulation of DNA replication|negative regulation of sister chromatid cohesion|protein localization to chromatin|regulation of cohesin localization to chromatin	chromatin|cohesin complex|cytoplasm	protein binding			ovary(1)	1																		---	---	---	---
BTRC	8945	broad.mit.edu	37	10	103292507	103292508	+	Intron	INS	-	TGTGTG	TGTGTG			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:103292507_103292508insTGTGTG	uc001kta.2	+						BTRC_uc001ktb.2_Intron|BTRC_uc001ktc.2_Intron	NM_033637	NP_378663			beta-transducin repeat containing protein						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process|interspecies interaction between organisms|negative regulation of transcription, DNA-dependent|positive regulation of proteolysis|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle|protein destabilization|viral reproduction|Wnt receptor signaling pathway	cytosol|nucleus|SCF ubiquitin ligase complex				ovary(1)	1		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)														---	---	---	---
DLG2	1740	broad.mit.edu	37	11	83585289	83585290	+	Intron	INS	-	GGAAGGAAGGAAGGAGAGAGGGAA	GGAAGGAAGGAAGGAGAGAGGGAA	rs144508115	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:83585289_83585290insGGAAGGAAGGAAGGAGAGAGGGAA	uc001paj.2	-						DLG2_uc001pai.2_Intron|DLG2_uc010rsy.1_Intron|DLG2_uc010rsz.1_Intron|DLG2_uc010rta.1_Intron|DLG2_uc001pak.2_Intron|DLG2_uc010rtb.1_Intron|DLG2_uc001pal.1_Intron|DLG2_uc001pam.1_Intron	NM_001364	NP_001355			chapsyn-110 isoform 2							cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding|protein binding			ovary(3)|pancreas(2)|skin(1)	6		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)																---	---	---	---
CNTN5	53942	broad.mit.edu	37	11	99072082	99072083	+	Intron	INS	-	TCC	TCC	rs151051937	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:99072082_99072083insTCC	uc001pga.2	+						CNTN5_uc009ywv.1_Intron|CNTN5_uc001pfz.2_Intron|CNTN5_uc001pgb.2_Intron	NM_014361	NP_055176			contactin 5 isoform long						cell adhesion	anchored to membrane|plasma membrane	protein binding			skin(3)|ovary(2)|pancreas(2)|breast(1)	8		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)														---	---	---	---
CPNE8	144402	broad.mit.edu	37	12	39242472	39242473	+	Intron	INS	-	AG	AG			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:39242472_39242473insAG	uc001rls.1	-							NM_153634	NP_705898			copine VIII											pancreas(1)	1	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)																---	---	---	---
Unknown	0	broad.mit.edu	37	14	22192892	22192926	+	IGR	DEL	CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT	-	-	rs60407029		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:22192892_22192926delCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT								OR4E2 (58656 upstream) : DAD1 (840881 downstream)																																			---	---	---	---
Unknown	0	broad.mit.edu	37	14	101656176	101656177	+	IGR	INS	-	GGAA	GGAA			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:101656176_101656177insGGAA								MIR656 (123038 upstream) : DIO3OS (362383 downstream)																																			---	---	---	---
KIAA0125	9834	broad.mit.edu	37	14	106385208	106385217	+	Intron	DEL	TTCAGTGGGG	-	-	rs71406526		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:106385208_106385217delTTCAGTGGGG	uc001ysq.2	+						ADAM6_uc010tyt.1_Intron|KIAA0125_uc001ysr.2_Intron|KIAA0125_uc001yss.2_Intron|KIAA0125_uc001yst.2_Intron					SubName: Full=HCG2029388, isoform CRA_d; SubName: Full=FAM30A protein;												0																		---	---	---	---
TJP1	7082	broad.mit.edu	37	15	30020390	30020390	+	Intron	DEL	T	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:30020390delT	uc001zcr.2	-						TJP1_uc010azl.2_Intron|TJP1_uc001zcq.2_Intron|TJP1_uc001zcs.2_Intron	NM_003257	NP_003248			tight junction protein 1 isoform a						cell-cell junction assembly|cellular component disassembly involved in apoptosis	basolateral plasma membrane|cell-cell adherens junction|Golgi apparatus|tight junction				ovary(4)|central_nervous_system(1)|pancreas(1)	6		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)														---	---	---	---
Unknown	0	broad.mit.edu	37	15	37474381	37474382	+	IGR	INS	-	TTCC	TTCC	rs67966909		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:37474381_37474382insTTCC								MEIS2 (80881 upstream) : TMCO5A (752445 downstream)																																			---	---	---	---
PPIB	5479	broad.mit.edu	37	15	64448017	64448018	+	3'UTR	INS	-	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:64448017_64448018insT	uc002and.2	-	5					SNX22_uc002anc.1_3'UTR	NM_000942	NP_000933			peptidylprolyl isomerase B precursor						protein folding	endoplasmic reticulum lumen|melanosome	peptide binding|peptidyl-prolyl cis-trans isomerase activity|unfolded protein binding				0					L-Proline(DB00172)													---	---	---	---
Unknown	0	broad.mit.edu	37	15	79477728	79477731	+	IGR	DEL	CTTG	-	-	rs146430112		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:79477728_79477731delCTTG								RASGRF1 (94513 upstream) : MIR184 (24399 downstream)																																			---	---	---	---
TEKT5	146279	broad.mit.edu	37	16	10783379	10783381	+	Intron	DEL	TTT	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:10783379_10783381delTTT	uc002czz.1	-							NM_144674	NP_653275			tektin 5						microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule				ovary(2)	2																		---	---	---	---
AQP8	343	broad.mit.edu	37	16	25239588	25239588	+	Intron	DEL	A	-	-	rs73551053	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:25239588delA	uc002doc.2	+							NM_001169	NP_001160			aquaporin 8						cellular response to cAMP	integral to plasma membrane	water channel activity			upper_aerodigestive_tract(1)|breast(1)|pancreas(1)	3				GBM - Glioblastoma multiforme(48;0.044)														---	---	---	---
SULT1A3	6818	broad.mit.edu	37	16	29472616	29472616	+	Intron	DEL	A	-	-	rs149925755		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:29472616delA	uc002dsu.2	+						LOC440354_uc002dsp.3_Intron|SULT1A3_uc002dsw.2_Intron|SULT1A3_uc002dsz.2_Intron|SULT1A3_uc002dta.2_Intron|SULT1A3_uc010vdp.1_Intron|SULT1A3_uc002dtb.2_Intron|SULT1A3_uc010byw.2_5'Flank	NM_177552	NP_808220			sulfotransferase family, cytosolic, 1A,						3'-phosphoadenosine 5'-phosphosulfate metabolic process|catecholamine metabolic process|flavonoid metabolic process|steroid metabolic process|sulfation|xenobiotic metabolic process	cytosol	aryl sulfotransferase activity				0																		---	---	---	---
NME1-NME2	654364	broad.mit.edu	37	17	49245465	49245466	+	Intron	DEL	TA	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:49245465_49245466delTA	uc002itk.2	+						NME1-NME2_uc002itj.2_Intron|NME2_uc002itl.2_Intron|NME2_uc002itm.2_Intron|NME2_uc002itn.2_Intron|NME2_uc002ito.2_Intron	NM_002512	NP_002503			nucleoside diphosphate kinase B						cell adhesion|CTP biosynthetic process|GTP biosynthetic process|negative regulation of apoptosis|nucleobase, nucleoside and nucleotide interconversion|positive regulation of epithelial cell proliferation|positive regulation of keratinocyte differentiation|UTP biosynthetic process	cytosol|lamellipodium|nucleus|ruffle	ATP binding|DNA binding|metal ion binding|nucleoside diphosphate kinase activity|protein binding|protein histidine kinase activity|sequence-specific DNA binding transcription factor activity				0			BRCA - Breast invasive adenocarcinoma(22;1.54e-08)															---	---	---	---
TTYH2	94015	broad.mit.edu	37	17	72218928	72218928	+	Intron	DEL	T	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:72218928delT	uc002jkc.2	+						TTYH2_uc010wqw.1_Intron	NM_032646	NP_116035			tweety 2 isoform 1							chloride channel complex|plasma membrane	chloride channel activity|protein binding			ovary(3)|large_intestine(1)	4																		---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42291491	42291491	+	Intron	DEL	T	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42291491delT	uc010dni.2	+						SETBP1_uc002lay.2_Intron	NM_015559	NP_056374			SET binding protein 1 isoform a							nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
DCC	1630	broad.mit.edu	37	18	50554196	50554196	+	Intron	DEL	T	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:50554196delT	uc002lfe.1	+						DCC_uc010xdr.1_Intron|DCC_uc010dpf.1_Intron	NM_005215	NP_005206			netrin receptor DCC precursor						apoptosis|induction of apoptosis|negative regulation of collateral sprouting|negative regulation of dendrite development	cytosol|integral to membrane				skin(8)|ovary(6)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	17		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)														---	---	---	---
Unknown	0	broad.mit.edu	37	19	7427254	7427254	+	IGR	DEL	G	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:7427254delG								INSR (133243 upstream) : ARHGEF18 (20466 downstream)																																			---	---	---	---
HIF3A	64344	broad.mit.edu	37	19	46811249	46811264	+	Intron	DEL	AGACAGACAGATAGAT	-	-	rs59977344	by1000genomes;by1000genomes;by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46811249_46811264delAGACAGACAGATAGAT	uc002peh.2	+						HIF3A_uc002pef.1_Intron|HIF3A_uc002peg.3_Intron|HIF3A_uc010xxx.1_Intron|HIF3A_uc002pei.3_Intron|HIF3A_uc002pej.1_Intron|HIF3A_uc002pek.2_Intron|HIF3A_uc010xxy.1_Intron|HIF3A_uc002pel.2_Intron|HIF3A_uc010xxz.1_Intron	NM_152795	NP_690008			hypoxia inducible factor 3, alpha subunit						regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			upper_aerodigestive_tract(1)|central_nervous_system(1)|skin(1)	3		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)														---	---	---	---
Unknown	0	broad.mit.edu	37	20	19831704	19831705	+	IGR	INS	-	A	A	rs145309073	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19831704_19831705insA								SLC24A3 (128164 upstream) : RIN2 (38505 downstream)																																			---	---	---	---
ZNF341	84905	broad.mit.edu	37	20	32339915	32339915	+	Intron	DEL	C	-	-	rs11477069		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:32339915delC	uc002wzy.2	+						ZNF341_uc002wzx.2_Intron|ZNF341_uc010geq.2_Intron|ZNF341_uc010ger.2_Intron	NM_032819	NP_116208			zinc finger protein 341						regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding			ovary(2)	2																		---	---	---	---
RPRD1B	58490	broad.mit.edu	37	20	36668649	36668650	+	Intron	INS	-	T	T	rs72441703		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:36668649_36668650insT	uc002xho.3	+							NM_021215	NP_067038			Regulation of nuclear pre-mRNA domain containing											pancreas(1)	1																		---	---	---	---
DMD	1756	broad.mit.edu	37	X	31676296	31676297	+	Intron	INS	-	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:31676296_31676297insT	uc004dda.1	-						DMD_uc004dcr.1_Intron|DMD_uc004dcs.1_Intron|DMD_uc004dct.1_Intron|DMD_uc004dcu.1_Intron|DMD_uc004dcv.1_Intron|DMD_uc004dcw.2_Intron|DMD_uc004dcx.2_Intron|DMD_uc004dcz.2_Intron|DMD_uc004dcy.1_Intron|DMD_uc004ddb.1_Intron	NM_004006	NP_003997			dystrophin Dp427m isoform						muscle filament sliding|peptide biosynthetic process	cell surface|costamere|cytoskeleton|cytosol|dystrophin-associated glycoprotein complex|sarcolemma	actin binding|dystroglycan binding|nitric-oxide synthase binding|protein binding|structural constituent of cytoskeleton|structural constituent of muscle|zinc ion binding			ovary(3)|pancreas(2)|large_intestine(1)	6		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)																---	---	---	---
SPANXC	64663	broad.mit.edu	37	X	140355351	140355351	+	Intron	DEL	A	-	-			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:140355351delA	uc004fbl.2	-											Homo sapiens nuclear-associated protein SPAN-Xa (SPANX) mRNA, complete cds.							cytoplasm|nucleus					0	Acute lymphoblastic leukemia(192;7.65e-05)																	---	---	---	---
RERE	473	broad.mit.edu	37	1	8418644	8418644	+	Silent	SNP	C	A	A	rs11121172	byFrequency;by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:8418644C>A	uc001ape.2	-	21	4761	c.3951G>T	c.(3949-3951)CGG>CGT	p.R1317R	RERE_uc001apf.2_Silent_p.R1317R|RERE_uc001apd.2_Silent_p.R763R	NM_012102	NP_036234	Q9P2R6	RERE_HUMAN	atrophin-1 like protein isoform a	1317	Arg/Glu-rich (mixed charge).				multicellular organismal development|NLS-bearing substrate import into nucleus	mitochondrion	poly-glutamine tract binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(1)|central_nervous_system(1)	2	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)														---	---	---	---
OTUD3	23252	broad.mit.edu	37	1	20230842	20230842	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:20230842A>G	uc001bcs.3	+	5	808	c.689A>G	c.(688-690)GAT>GGT	p.D230G		NM_015207	NP_056022	Q5T2D3	OTUD3_HUMAN	OTU domain containing 3	230											0		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)														---	---	---	---
USP48	84196	broad.mit.edu	37	1	22079101	22079101	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:22079101T>C	uc001bfb.2	-	5	822	c.584A>G	c.(583-585)GAT>GGT	p.D195G	USP48_uc010odq.1_Missense_Mutation_p.D195G|USP48_uc009vqc.2_Missense_Mutation_p.D195G|USP48_uc001bfc.2_Missense_Mutation_p.D195G|USP48_uc001bfe.1_Missense_Mutation_p.D195G|USP48_uc001bff.2_Missense_Mutation_p.D195G	NM_032236	NP_115612	Q86UV5	UBP48_HUMAN	ubiquitin specific protease 48 isoform a	195					ubiquitin-dependent protein catabolic process	mitochondrion|nucleus	cysteine-type peptidase activity|ubiquitin thiolesterase activity			ovary(1)|lung(1)	2		Colorectal(325;3.46e-05)|all_lung(284;4.29e-05)|Lung NSC(340;4.66e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|OV - Ovarian serous cystadenocarcinoma(117;4.74e-26)|COAD - Colon adenocarcinoma(152;1.3e-05)|GBM - Glioblastoma multiforme(114;1.86e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000614)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(1967;0.00711)|Lung(427;0.0327)|READ - Rectum adenocarcinoma(331;0.0657)|LUSC - Lung squamous cell carcinoma(448;0.0753)														---	---	---	---
NR0B2	8431	broad.mit.edu	37	1	27238398	27238398	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:27238398G>A	uc001bnf.2	-	2	848	c.712C>T	c.(712-714)CGC>TGC	p.R238C		NM_021969	NP_068804	Q15466	NR0B2_HUMAN	short heterodimer partner	238					cholesterol metabolic process|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	DNA binding|protein domain specific binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|steroid hormone receptor activity|transcription corepressor activity				0		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.01e-51)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)														---	---	---	---
GNL2	29889	broad.mit.edu	37	1	38040061	38040061	+	Intron	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:38040061A>G	uc001cbk.2	-							NM_013285	NP_037417			guanine nucleotide binding protein-like 2						ribosome biogenesis	nucleolus	GTP binding|GTPase activity|protein binding			ovary(1)|central_nervous_system(1)	2		Myeloproliferative disorder(586;0.0393)																---	---	---	---
MACF1	23499	broad.mit.edu	37	1	39913486	39913486	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:39913486C>T	uc010oiu.1	+	47	15344	c.15213C>T	c.(15211-15213)AGC>AGT	p.S5071S	MACF1_uc010ois.1_Silent_p.S4569S	NM_033044	NP_149033	Q9UPN3	MACF1_HUMAN	microfilament and actin filament cross-linker	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell cycle arrest|Golgi to plasma membrane protein transport|positive regulation of Wnt receptor signaling pathway|regulation of epithelial cell migration|regulation of focal adhesion assembly|regulation of microtubule-based process|Wnt receptor signaling pathway|wound healing	Golgi apparatus|microtubule|ruffle membrane	actin filament binding|ATPase activity|calcium ion binding|microtubule binding			ovary(8)|breast(3)|central_nervous_system(3)|skin(2)	16	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)															---	---	---	---
PABPC4	8761	broad.mit.edu	37	1	40030173	40030173	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:40030173G>A	uc010oiv.1	-	10	2273	c.1375C>T	c.(1375-1377)CGT>TGT	p.R459C	PABPC4_uc001cdl.2_Missense_Mutation_p.R459C|PABPC4_uc001cdm.2_Missense_Mutation_p.R459C	NM_003819	NP_003810	Q13310	PABP4_HUMAN	poly A binding protein, cytoplasmic 4 isoform 2	459					blood coagulation|RNA catabolic process|RNA processing|translation	cytoplasm|ribonucleoprotein complex	nucleotide binding|poly(A) RNA binding|poly(U) RNA binding|protein binding				0	Lung NSC(20;1.55e-06)|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;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)															---	---	---	---
CCDC30	728621	broad.mit.edu	37	1	43119577	43119577	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:43119577T>C	uc009vwk.1	+	16	2340	c.2230T>C	c.(2230-2232)TCC>CCC	p.S744P	CCDC30_uc001chm.2_Missense_Mutation_p.S442P|CCDC30_uc001chn.2_Missense_Mutation_p.S533P	NM_001080850	NP_001074319	Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	744											0																		---	---	---	---
TNNI3K	51086	broad.mit.edu	37	1	74834760	74834760	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:74834760A>C	uc001dgf.1	+	14	1427	c.1376A>C	c.(1375-1377)CAG>CCG	p.Q459P	TNNI3K_uc001dgc.1_Missense_Mutation_p.Q560P|TNNI3K_uc001dgd.2_Missense_Mutation_p.Q560P|TNNI3K_uc001dge.1_Missense_Mutation_p.Q560P	NM_015978	NP_057062	Q59H18	TNI3K_HUMAN	TNNI3 interacting kinase isoform b	459						cytoplasm|nucleus	ATP binding|metal ion binding|protein C-terminus binding|protein serine/threonine kinase activity|troponin I binding			large_intestine(4)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	10																		---	---	---	---
AGL	178	broad.mit.edu	37	1	100350177	100350177	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:100350177C>A	uc001dsi.1	+	20	2999	c.2599C>A	c.(2599-2601)CTG>ATG	p.L867M	AGL_uc001dsj.1_Missense_Mutation_p.L867M|AGL_uc001dsk.1_Missense_Mutation_p.L867M|AGL_uc001dsl.1_Missense_Mutation_p.L867M|AGL_uc001dsm.1_Missense_Mutation_p.L851M|AGL_uc001dsn.1_Missense_Mutation_p.L850M	NM_000642	NP_000633	P35573	GDE_HUMAN	amylo-1,6-glucosidase,	867	4-alpha-glucanotransferase.				glucose metabolic process|glycogen biosynthetic process|glycogen catabolic process	cytosol|isoamylase complex|nucleus	4-alpha-glucanotransferase activity|amylo-alpha-1,6-glucosidase activity|cation binding			ovary(1)|central_nervous_system(1)|skin(1)	3		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)														---	---	---	---
ZNF687	57592	broad.mit.edu	37	1	151261965	151261965	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:151261965G>A	uc001exq.2	+	5	2681	c.2583G>A	c.(2581-2583)CCG>CCA	p.P861P	ZNF687_uc009wmo.2_Silent_p.P861P|ZNF687_uc009wmp.2_Silent_p.P861P	NM_020832	NP_065883	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	861	C2H2-type 6.				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleolus	DNA binding|zinc ion binding			central_nervous_system(3)|ovary(1)	4	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)															---	---	---	---
SPTA1	6708	broad.mit.edu	37	1	158639545	158639545	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:158639545C>G	uc001fst.1	-	13	1830	c.1631G>C	c.(1630-1632)GGT>GCT	p.G544A		NM_003126	NP_003117	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	544	Spectrin 6.				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|breast(1)	8	all_hematologic(112;0.0378)																	---	---	---	---
ASTN1	460	broad.mit.edu	37	1	176983923	176983923	+	Intron	SNP	T	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:176983923T>G	uc001glc.2	-						ASTN1_uc001glb.1_Intron|ASTN1_uc001gld.1_Intron|ASTN1_uc009wwx.1_Intron|ASTN1_uc001gle.3_Intron	NM_004319	NP_004310			astrotactin isoform 1						cell migration|neuron cell-cell adhesion	integral to membrane				ovary(6)|skin(5)|central_nervous_system(2)|large_intestine(1)|lung(1)	15																		---	---	---	---
NVL	4931	broad.mit.edu	37	1	224468870	224468870	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:224468870G>A	uc001hok.2	-	16	1960	c.1917C>T	c.(1915-1917)TCC>TCT	p.S639S	NVL_uc001hol.2_Silent_p.S533S|NVL_uc010pvd.1_Silent_p.S548S|NVL_uc010pve.1_Silent_p.S450S|NVL_uc010pvf.1_RNA	NM_002533	NP_002524	O15381	NVL_HUMAN	nuclear VCP-like isoform 1	639						aggresome|cytoplasm|nucleolus	ATP binding|nucleoside-triphosphatase activity			skin(2)	2				GBM - Glioblastoma multiforme(131;0.00501)														---	---	---	---
PGBD5	79605	broad.mit.edu	37	1	230513257	230513257	+	Silent	SNP	G	A	A	rs145478744	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:230513257G>A	uc010pwb.1	-	1	111	c.111C>T	c.(109-111)AGC>AGT	p.S37S	PGBD5_uc001htv.2_Silent_p.S37S	NM_024554	NP_078830	Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	37						integral to membrane				ovary(2)|central_nervous_system(1)|skin(1)	4	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)														---	---	---	---
OR14A16	284532	broad.mit.edu	37	1	247978336	247978336	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:247978336C>A	uc001idm.1	-	1	696	c.696G>T	c.(694-696)CAG>CAT	p.Q232H		NM_001001966	NP_001001966	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A,	232	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0																		---	---	---	---
OR2L3	391192	broad.mit.edu	37	1	248224321	248224321	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr1:248224321T>G	uc001idx.1	+	1	338	c.338T>G	c.(337-339)CTT>CGT	p.L113R	OR2L13_uc001ids.2_Intron	NM_001004687	NP_001004687	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L,	113	Helical; Name=3; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity				0	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)															---	---	---	---
MYT1L	23040	broad.mit.edu	37	2	1812915	1812915	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:1812915C>T	uc002qxe.2	-	22	3932	c.3105G>A	c.(3103-3105)ACG>ACA	p.T1035T	MYT1L_uc002qxd.2_Silent_p.T1033T|MYT1L_uc010ewk.2_Silent_p.T31T	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1035					cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			ovary(5)|central_nervous_system(1)	6	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)														---	---	---	---
NCOA1	8648	broad.mit.edu	37	2	24930723	24930723	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:24930723C>T	uc002rfk.2	+	11	2642	c.2384C>T	c.(2383-2385)ACT>ATT	p.T795I	NCOA1_uc010eye.2_Missense_Mutation_p.T795I|NCOA1_uc002rfi.2_Missense_Mutation_p.T644I|NCOA1_uc002rfj.2_Missense_Mutation_p.T795I|NCOA1_uc002rfl.2_Missense_Mutation_p.T795I	NM_003743	NP_003734	Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1 isoform 1	795	Interaction with CREBBP.								PAX3/NCOA1(8)	soft_tissue(8)|ovary(1)|lung(1)|skin(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)							T	PAX3	alveolar rhadomyosarcoma								---	---	---	---
KIAA1841	84542	broad.mit.edu	37	2	61344681	61344681	+	Intron	SNP	T	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:61344681T>C	uc002saw.3	+						KIAA1841_uc002sax.3_Intron|KIAA1841_uc002say.2_Intron	NM_001129993	NP_001123465			KIAA1841 protein isoform a												0			Epithelial(17;0.193)															---	---	---	---
SPRED2	200734	broad.mit.edu	37	2	65541135	65541135	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:65541135G>T	uc002sdr.3	-	6	1292	c.757C>A	c.(757-759)CGC>AGC	p.R253S	SPRED2_uc010fcw.2_Missense_Mutation_p.R250S	NM_181784	NP_861449	Q7Z698	SPRE2_HUMAN	sprouty-related protein with EVH-1 domain 2	253	KBD.				inactivation of MAPK activity|multicellular organismal development	transport vesicle membrane	stem cell factor receptor binding			ovary(1)|lung(1)|central_nervous_system(1)	3																		---	---	---	---
C2orf7	84279	broad.mit.edu	37	2	73456657	73456657	+	Silent	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:73456657A>G	uc002siy.2	-	3	278	c.210T>C	c.(208-210)CCT>CCC	p.P70P		NM_032319	NP_115695	Q9BSG0	PADC1_HUMAN	chromosome 2 open reading frame 7 precursor	70						extracellular region					0																		---	---	---	---
WDR54	84058	broad.mit.edu	37	2	74649375	74649375	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:74649375C>T	uc002slb.2	+	2	155	c.95C>T	c.(94-96)ACG>ATG	p.T32M		NM_032118	NP_115494	Q9H977	WDR54_HUMAN	WD repeat domain 54	32											0																		---	---	---	---
VAMP5	10791	broad.mit.edu	37	2	85820200	85820200	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:85820200G>A	uc002spu.1	+	3	354	c.271G>A	c.(271-273)GTC>ATC	p.V91I	RNF181_uc002spv.1_5'Flank	NM_006634	NP_006625	O95183	VAMP5_HUMAN	vesicle-associated membrane protein 5	91	Helical; Anchor for type IV membrane protein; (Potential).				cell differentiation|vesicle-mediated transport	endomembrane system					0																		---	---	---	---
TTN	7273	broad.mit.edu	37	2	179593362	179593362	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:179593362A>C	uc010zfg.1	-	63	15783	c.15559T>G	c.(15559-15561)TTT>GTT	p.F5187V	TTN_uc010zfh.1_Intron|TTN_uc010zfi.1_Intron|TTN_uc010zfj.1_Intron|TTN_uc002umz.1_Missense_Mutation_p.F1848V	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	titin isoform N2-A	6114							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)															---	---	---	---
PGAP1	80055	broad.mit.edu	37	2	197708716	197708716	+	Silent	SNP	G	A	A	rs145600035		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:197708716G>A	uc002utw.2	-	25	2535	c.2421C>T	c.(2419-2421)AAC>AAT	p.N807N	PGAP1_uc002utx.2_Silent_p.N633N|PGAP1_uc010fsi.2_Silent_p.N81N	NM_024989	NP_079265	Q75T13	PGAP1_HUMAN	GPI deacylase	807	Cytoplasmic (Potential).				attachment of GPI anchor to protein|C-terminal protein lipidation|intracellular protein transport|myo-inositol transport	integral to membrane|intrinsic to endoplasmic reticulum membrane	nuclease activity|phosphoric ester hydrolase activity			ovary(3)|central_nervous_system(1)	4																		---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220342112	220342112	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:220342112C>T	uc010fwg.2	+	20	4674	c.4674C>T	c.(4672-4674)ACC>ACT	p.T1558T		NM_005876	NP_005867	Q15772	SPEG_HUMAN	SPEG complex locus	1558	Ig-like 8.				muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity			stomach(9)|ovary(4)|central_nervous_system(1)	14		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)														---	---	---	---
COL6A3	1293	broad.mit.edu	37	2	238243382	238243382	+	Missense_Mutation	SNP	G	A	A	rs116655315	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr2:238243382G>A	uc002vwl.2	-	41	9401	c.9116C>T	c.(9115-9117)ACG>ATG	p.T3039M	COL6A3_uc002vwo.2_Missense_Mutation_p.T2833M|COL6A3_uc010znj.1_Missense_Mutation_p.T2432M|COL6A3_uc002vwj.2_Missense_Mutation_p.T420M	NM_004369	NP_004360	P12111	CO6A3_HUMAN	alpha 3 type VI collagen isoform 1 precursor	3039	Fibronectin type-III.|Nonhelical region.				axon guidance|cell adhesion|muscle organ development	collagen type VI|extracellular space	serine-type endopeptidase inhibitor activity			ovary(8)|central_nervous_system(6)|skin(2)|upper_aerodigestive_tract(1)|pancreas(1)	18		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)														---	---	---	---
TMEM111	55831	broad.mit.edu	37	3	10019088	10019088	+	Silent	SNP	T	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:10019088T>C	uc003bun.2	-	2	377	c.198A>G	c.(196-198)AAA>AAG	p.K66K	CIDEC_uc003bto.2_Intron|TMEM111_uc003buo.2_Silent_p.K66K	NM_018447	NP_060917	Q9P0I2	TM111_HUMAN	transmembrane protein 111	66						integral to membrane					0																		---	---	---	---
GLB1	2720	broad.mit.edu	37	3	33087686	33087686	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:33087686C>T	uc003cfi.1	-	10	1111	c.994G>A	c.(994-996)GAC>AAC	p.D332N	GLB1_uc003cfh.1_Missense_Mutation_p.D302N|GLB1_uc003cfj.1_Missense_Mutation_p.D201N|GLB1_uc011axk.1_Missense_Mutation_p.D380N	NM_000404	NP_000395	P16278	BGAL_HUMAN	galactosidase, beta 1 isoform a preproprotein	332			D -> E (in GM1G1; 2.3% of wild-type enzyme activity).|D -> N (in GM1G1).		carbohydrate metabolic process	lysosome|perinuclear region of cytoplasm	beta-galactosidase activity|cation binding|protein binding			large_intestine(1)	1		Melanoma(143;0.104)																---	---	---	---
ROBO1	6091	broad.mit.edu	37	3	78987851	78987851	+	Silent	SNP	T	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:78987851T>C	uc003dqe.2	-	4	607	c.399A>G	c.(397-399)GTA>GTG	p.V133V	ROBO1_uc003dqb.2_Silent_p.V94V|ROBO1_uc003dqc.2_Silent_p.V94V|ROBO1_uc003dqd.2_Silent_p.V94V	NM_002941	NP_002932	Q9Y6N7	ROBO1_HUMAN	roundabout 1 isoform a	133	Extracellular (Potential).|Ig-like C2-type 1.				activation of caspase activity|axon midline choice point recognition|cell migration involved in sprouting angiogenesis|chemorepulsion involved in postnatal olfactory bulb interneuron migration|homophilic cell adhesion|negative regulation of chemokine-mediated signaling pathway|negative regulation of mammary gland epithelial cell proliferation|negative regulation of negative chemotaxis|positive regulation of axonogenesis|Roundabout signaling pathway	cell surface|cytoplasm|integral to plasma membrane	axon guidance receptor activity|identical protein binding|LRR domain binding			large_intestine(2)	2		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)														---	---	---	---
GRK7	131890	broad.mit.edu	37	3	141499460	141499460	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:141499460G>A	uc011bnd.1	+	2	941	c.857G>A	c.(856-858)CGT>CAT	p.R286H		NM_139209	NP_631948	Q8WTQ7	GRK7_HUMAN	G-protein-coupled receptor kinase 7 precursor	286	Protein kinase.				visual perception	membrane	ATP binding|G-protein coupled receptor kinase activity|signal transducer activity			lung(2)|stomach(1)|ovary(1)|skin(1)	5																		---	---	---	---
SI	6476	broad.mit.edu	37	3	164760900	164760900	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:164760900G>A	uc003fei.2	-	17	2013	c.1951C>T	c.(1951-1953)CAA>TAA	p.Q651*		NM_001041	NP_001032	P14410	SUIS_HUMAN	sucrase-isomaltase	651	Lumenal.|Isomaltase.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity			ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)										HNSCC(35;0.089)			---	---	---	---
MCF2L2	23101	broad.mit.edu	37	3	182910885	182910885	+	Splice_Site	SNP	C	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:182910885C>A	uc003fli.1	-	27	3009	c.2919_splice	c.e27-1	p.S973_splice		NM_015078	NP_055893			Rho family guanine-nucleotide exchange factor						regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity			ovary(2)|large_intestine(2)|breast(1)	5	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)															---	---	---	---
EIF4G1	1981	broad.mit.edu	37	3	184049774	184049774	+	Silent	SNP	G	A	A	rs11559217		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr3:184049774G>A	uc003fnp.2	+	32	4716	c.4518G>A	c.(4516-4518)GCG>GCA	p.A1506A	EIF4G1_uc003fnt.2_Silent_p.A1217A|EIF4G1_uc003fnq.2_Silent_p.A1419A|EIF4G1_uc003fnr.2_Silent_p.A1342A|EIF4G1_uc010hxx.2_Silent_p.A1513A|EIF4G1_uc003fns.2_Silent_p.A1466A|EIF4G1_uc010hxy.2_Silent_p.A1513A|EIF4G1_uc003fnv.3_Silent_p.A1507A|EIF4G1_uc003fnu.3_Silent_p.A1506A|EIF4G1_uc003fnw.2_Silent_p.A1513A|EIF4G1_uc003fnx.2_Silent_p.A1311A|EIF4G1_uc003fny.3_Silent_p.A1310A|EIF4G1_uc003foa.2_Silent_p.A178A	NM_198241	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4	1506	W2.|EIF4A-binding.				insulin receptor signaling pathway|interspecies interaction between organisms|nuclear-transcribed mRNA poly(A) tail shortening|regulation of translational initiation	cytosol|eukaryotic translation initiation factor 4F complex	protein binding|translation initiation factor activity			lung(2)|ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)	7	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)															---	---	---	---
ARAP2	116984	broad.mit.edu	37	4	36168603	36168603	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:36168603G>A	uc003gsq.1	-	10	2262	c.1924C>T	c.(1924-1926)CGA>TGA	p.R642*	ARAP2_uc003gsr.1_Nonsense_Mutation_p.R642*	NM_015230	NP_056045	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH	642	PH 2.				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding			ovary(1)|pancreas(1)|skin(1)	3																		---	---	---	---
KLB	152831	broad.mit.edu	37	4	39447954	39447954	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:39447954C>T	uc003gua.2	+	4	1705	c.1608C>T	c.(1606-1608)CCC>CCT	p.P536P	KLB_uc011byj.1_Intron	NM_175737	NP_783864	Q86Z14	KLOTB_HUMAN	klotho beta	536	Extracellular (Potential).|Glycosyl hydrolase-1 2.				carbohydrate metabolic process	integral to membrane|plasma membrane	cation binding|fibroblast growth factor binding|hydrolase activity, hydrolyzing O-glycosyl compounds			skin(1)	1																		---	---	---	---
TLL1	7092	broad.mit.edu	37	4	166915593	166915593	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr4:166915593A>G	uc003irh.1	+	4	1069	c.422A>G	c.(421-423)GAG>GGG	p.E141G	TLL1_uc011cjn.1_Missense_Mutation_p.E141G|TLL1_uc011cjo.1_5'UTR	NM_012464	NP_036596	O43897	TLL1_HUMAN	tolloid-like 1 precursor	141					cell differentiation|proteolysis|skeletal system development	extracellular region	calcium ion binding|metalloendopeptidase activity|zinc ion binding			skin(3)|ovary(2)|breast(1)|central_nervous_system(1)	7	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)														---	---	---	---
CTNND2	1501	broad.mit.edu	37	5	10992792	10992792	+	Intron	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:10992792G>A	uc003jfa.1	-						CTNND2_uc010itt.2_Intron|CTNND2_uc011cmy.1_Intron|CTNND2_uc011cmz.1_Intron|CTNND2_uc010itu.1_Intron|CTNND2_uc011cmx.1_Intron	NM_001332	NP_001323			catenin (cadherin-associated protein), delta 2						multicellular organismal development|neuron cell-cell adhesion|regulation of transcription, DNA-dependent|signal transduction|transcription, DNA-dependent	adherens junction|cytoplasm|nucleus	protein binding			large_intestine(2)|ovary(2)|skin(2)|pancreas(1)|lung(1)	8																		---	---	---	---
DNAH5	1767	broad.mit.edu	37	5	13817734	13817734	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:13817734C>T	uc003jfd.2	-	42	6953	c.6911G>A	c.(6910-6912)CGG>CAG	p.R2304Q		NM_001369	NP_001360	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2304	AAA 2 (By similarity).				microtubule-based movement	cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity			ovary(14)|skin(13)|upper_aerodigestive_tract(1)|central_nervous_system(1)|breast(1)|pancreas(1)	31	Lung NSC(4;0.00476)													Kartagener_syndrome				---	---	---	---
ADAMTS12	81792	broad.mit.edu	37	5	33615939	33615939	+	Missense_Mutation	SNP	C	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:33615939C>A	uc003jia.1	-	15	2545	c.2382G>T	c.(2380-2382)TGG>TGT	p.W794C	ADAMTS12_uc010iuq.1_Missense_Mutation_p.W709C	NM_030955	NP_112217	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1	794	Spacer 1.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|lung(1)|kidney(1)	9															HNSCC(64;0.19)			---	---	---	---
PCDHA3	56145	broad.mit.edu	37	5	140182627	140182627	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:140182627C>T	uc003lhf.2	+	1	1845	c.1845C>T	c.(1843-1845)ACC>ACT	p.T615T	PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhd.2_Intron|PCDHA2_uc011czy.1_Intron|PCDHA3_uc011czz.1_Silent_p.T615T	NM_018906	NP_061729	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3 isoform 1 precursor	615	Cadherin 6.|Extracellular (Potential).				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding			ovary(6)|skin(2)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
JAKMIP2	9832	broad.mit.edu	37	5	147024553	147024553	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr5:147024553G>A	uc003loq.1	-	6	1325	c.943C>T	c.(943-945)CGT>TGT	p.R315C	JAKMIP2_uc011dbx.1_Missense_Mutation_p.R273C|JAKMIP2_uc003lor.1_Missense_Mutation_p.R315C|uc003lop.1_Intron|JAKMIP2_uc010jgo.1_Missense_Mutation_p.R315C	NM_014790	NP_055605	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein	315	Potential.		R -> C (in a colorectal cancer sample; somatic mutation).			Golgi apparatus		p.R315C(1)		large_intestine(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)															---	---	---	---
RHAG	6005	broad.mit.edu	37	6	49582578	49582578	+	Intron	SNP	C	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:49582578C>A	uc003ozk.3	-						RHAG_uc010jzl.2_Intron|RHAG_uc010jzm.2_Intron	NM_000324	NP_000315			Rh-associated glycoprotein						carbon dioxide transport|cellular ion homeostasis	integral to plasma membrane	ammonia transmembrane transporter activity|ammonium transmembrane transporter activity|ankyrin binding			breast(1)|skin(1)	2	Lung NSC(77;0.0255)																	---	---	---	---
GRIK2	2898	broad.mit.edu	37	6	102124507	102124507	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:102124507G>A	uc003pqp.3	+	4	800	c.551G>A	c.(550-552)CGT>CAT	p.R184H	GRIK2_uc003pqn.2_Missense_Mutation_p.R184H|GRIK2_uc003pqo.3_Missense_Mutation_p.R184H|GRIK2_uc010kcw.2_Missense_Mutation_p.R184H	NM_021956	NP_068775	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	184	Extracellular (Potential).				glutamate signaling pathway|induction of programmed cell death in response to chemical stimulus|neuron apoptosis|positive regulation of synaptic transmission|regulation of short-term neuronal synaptic plasticity	cell junction|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|kainate selective glutamate receptor activity			ovary(2)|pancreas(1)|breast(1)|skin(1)	5		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	L-Glutamic Acid(DB00142)													---	---	---	---
REV3L	5980	broad.mit.edu	37	6	111672935	111672935	+	Nonsense_Mutation	SNP	A	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:111672935A>T	uc003puy.3	-	19	7567	c.7244T>A	c.(7243-7245)TTA>TAA	p.L2415*	REV3L_uc003pux.3_Nonsense_Mutation_p.L2337*|REV3L_uc003puz.3_Nonsense_Mutation_p.L2337*|REV3L_uc003pva.1_RNA	NM_002912	NP_002903	O60673	DPOLZ_HUMAN	DNA polymerase zeta	2415					DNA-dependent DNA replication|translesion synthesis	nucleus|zeta DNA polymerase complex	DNA binding|DNA-directed DNA polymerase activity|metal ion binding|nucleotide binding			large_intestine(2)|ovary(2)|skin(2)	6		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)									DNA_polymerases_(catalytic_subunits)|Direct_reversal_of_damage					---	---	---	---
ZDHHC14	79683	broad.mit.edu	37	6	157963755	157963755	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:157963755C>T	uc003qqt.2	+	2	881	c.384C>T	c.(382-384)GCC>GCT	p.A128A	ZDHHC14_uc003qqs.2_Silent_p.A128A|ZDHHC14_uc010kjm.1_Silent_p.A23A	NM_024630	NP_078906	Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14 isoform 1	128						integral to membrane	acyltransferase activity|zinc ion binding			ovary(1)|skin(1)	2		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)														---	---	---	---
FAM120B	84498	broad.mit.edu	37	6	170628010	170628010	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr6:170628010G>C	uc003qxp.2	+	2	1640	c.1532G>C	c.(1531-1533)TGT>TCT	p.C511S	FAM120B_uc003qxo.1_Missense_Mutation_p.C511S|FAM120B_uc011ehd.1_Intron	NM_032448	NP_115824	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	511					cell differentiation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding			ovary(1)	1		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)														---	---	---	---
ABCA13	154664	broad.mit.edu	37	7	48317939	48317939	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:48317939T>G	uc003toq.2	+	18	7173	c.7148T>G	c.(7147-7149)ATA>AGA	p.I2383R		NM_152701	NP_689914	Q86UQ4	ABCAD_HUMAN	ATP binding cassette, sub-family A (ABC1),	2383					transport	integral to membrane	ATP binding|ATPase activity			ovary(5)|central_nervous_system(4)|skin(1)	10																		---	---	---	---
WBSCR17	64409	broad.mit.edu	37	7	71175785	71175785	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:71175785G>A	uc003tvy.2	+	10	1540	c.1540G>A	c.(1540-1542)GCC>ACC	p.A514T	WBSCR17_uc003tvz.2_Missense_Mutation_p.A213T	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN	UDP-GalNAc:polypeptide	514	Ricin B-type lectin.|Lumenal (Potential).					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding			skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)																---	---	---	---
SEMA3E	9723	broad.mit.edu	37	7	82997175	82997175	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:82997175G>A	uc003uhy.1	-	17	2521	c.2055C>T	c.(2053-2055)GAC>GAT	p.D685D		NM_012431	NP_036563	O15041	SEM3E_HUMAN	semaphorin 3E precursor	685					axon guidance	extracellular space|membrane	receptor activity			ovary(3)	3		Medulloblastoma(109;0.109)																---	---	---	---
TRRAP	8295	broad.mit.edu	37	7	98555639	98555639	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:98555639C>G	uc003upp.2	+	43	6455	c.6246C>G	c.(6244-6246)GAC>GAG	p.D2082E	TRRAP_uc011kis.1_Missense_Mutation_p.D2064E|TRRAP_uc003upr.2_Missense_Mutation_p.D1781E	NM_003496	NP_003487	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated	2082	Interaction with TP53.				histone deubiquitination|histone H2A acetylation|histone H4 acetylation|regulation of transcription, DNA-dependent|transcription, DNA-dependent	NuA4 histone acetyltransferase complex|PCAF complex|STAGA complex|transcription factor TFTC complex	phosphotransferase activity, alcohol group as acceptor|protein binding|transcription cofactor activity			ovary(9)|large_intestine(8)|central_nervous_system(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(1)|lung(1)|liver(1)	37	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
PTCD1	26024	broad.mit.edu	37	7	99032411	99032411	+	Splice_Site	SNP	A	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:99032411A>C	uc003uqh.2	-	2	584	c.453_splice	c.e2+1	p.K151_splice	PTCD1_uc011kiw.1_Splice_Site_p.K200_splice	NM_015545	NP_056360			pentatricopeptide repeat domain 1											ovary(1)	1	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)															---	---	---	---
ZAN	7455	broad.mit.edu	37	7	100364728	100364728	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:100364728C>T	uc003uwj.2	+	25	4873	c.4708C>T	c.(4708-4710)CGG>TGG	p.R1570W	ZAN_uc003uwk.2_Missense_Mutation_p.R1570W|ZAN_uc003uwl.2_RNA|ZAN_uc010lhh.2_RNA|ZAN_uc010lhi.2_RNA|ZAN_uc011kkd.1_Missense_Mutation_p.R147W	NM_003386	NP_003377	Q9Y493	ZAN_HUMAN	zonadhesin isoform 3	1570	Extracellular (Potential).|VWFD 2.				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)															---	---	---	---
LAMB1	3912	broad.mit.edu	37	7	107603363	107603363	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:107603363C>T	uc003vew.2	-	15	2179	c.1844G>A	c.(1843-1845)CGC>CAC	p.R615H	LAMB1_uc003vev.2_Missense_Mutation_p.R639H|LAMB1_uc003vex.2_Missense_Mutation_p.R615H|LAMB1_uc010ljn.1_Missense_Mutation_p.R701H	NM_002291	NP_002282	P07942	LAMB1_HUMAN	laminin, beta 1 precursor	615	Laminin IV type B.				axon guidance|odontogenesis|positive regulation of cell migration|positive regulation of epithelial cell proliferation|substrate adhesion-dependent cell spreading	extracellular space|laminin-1 complex|laminin-10 complex|laminin-2 complex|laminin-8 complex|perinuclear region of cytoplasm	extracellular matrix structural constituent			ovary(4)|skin(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	8					Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)													---	---	---	---
TFEC	22797	broad.mit.edu	37	7	115596830	115596830	+	Missense_Mutation	SNP	C	G	G	rs144566004		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:115596830C>G	uc003vhj.1	-	4	469	c.285G>C	c.(283-285)TTG>TTC	p.L95F	TFEC_uc003vhk.1_Missense_Mutation_p.L66F|TFEC_uc003vhl.3_Missense_Mutation_p.L66F|TFEC_uc011kmw.1_Missense_Mutation_p.L185F|TFEC_uc003vhm.1_RNA	NM_012252	NP_036384	O14948	TFEC_HUMAN	transcription factor EC isoform a	95	Necessary for transcriptional transactivation.					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription corepressor activity			large_intestine(1)	1			STAD - Stomach adenocarcinoma(10;0.00878)															---	---	---	---
RNF133	168433	broad.mit.edu	37	7	122338851	122338851	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:122338851T>C	uc003vkj.1	-	1	358	c.122A>G	c.(121-123)TAT>TGT	p.Y41C	CADPS2_uc010lkp.2_Intron|CADPS2_uc010lkq.2_Intron	NM_139175	NP_631914	Q8WVZ7	RN133_HUMAN	ring finger protein 133	41						endoplasmic reticulum membrane|integral to membrane	ligase activity|zinc ion binding			skin(1)	1																		---	---	---	---
GRM8	2918	broad.mit.edu	37	7	126746699	126746699	+	Missense_Mutation	SNP	G	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:126746699G>C	uc003vlr.2	-	2	889	c.578C>G	c.(577-579)TCT>TGT	p.S193C	GRM8_uc003vls.2_RNA|GRM8_uc011kof.1_RNA|GRM8_uc003vlt.2_Missense_Mutation_p.S193C|GRM8_uc010lkz.1_RNA|GRM8_uc003vlu.1_5'UTR	NM_000845	NP_000836	O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8 isoform a	193	Extracellular (Potential).				negative regulation of cAMP biosynthetic process|sensory perception of smell|visual perception	integral to plasma membrane				lung(15)|ovary(5)|pancreas(1)|breast(1)|skin(1)	23		Prostate(267;0.186)			L-Glutamic Acid(DB00142)										HNSCC(24;0.065)			---	---	---	---
COPG2	26958	broad.mit.edu	37	7	130352332	130352332	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:130352332A>T	uc003vqh.1	-	2	170	c.80T>A	c.(79-81)GTT>GAT	p.V27D		NM_012133	NP_036265	Q9UBF2	COPG2_HUMAN	coatomer protein complex, subunit gamma 2	27					intra-Golgi vesicle-mediated transport|intracellular protein transport|retrograde vesicle-mediated transport, Golgi to ER	COPI vesicle coat	protein binding|structural molecule activity				0	Melanoma(18;0.0435)																	---	---	---	---
PTN	5764	broad.mit.edu	37	7	136938369	136938369	+	Missense_Mutation	SNP	T	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:136938369T>A	uc003vtq.2	-	3	494	c.131A>T	c.(130-132)AAG>ATG	p.K44M	PTN_uc010lmx.2_Missense_Mutation_p.K44M|PTN_uc003vtr.1_Missense_Mutation_p.K44M	NM_002825	NP_002816	P21246	PTN_HUMAN	pleiotrophin	44					nervous system development|positive regulation of cell division|positive regulation of cell proliferation|transmembrane receptor protein tyrosine phosphatase signaling pathway	endoplasmic reticulum|extracellular space	growth factor activity|heparin binding|protein phosphatase inhibitor activity			upper_aerodigestive_tract(1)|pancreas(1)	2																		---	---	---	---
HIPK2	28996	broad.mit.edu	37	7	139257950	139257950	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:139257950G>A	uc003vvf.3	-	15	3494	c.3320C>T	c.(3319-3321)GCG>GTG	p.A1107V	HIPK2_uc003vvd.3_Missense_Mutation_p.A1080V	NM_022740	NP_073577	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2 isoform	1107	Autoinhibitory domain (AID).				apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|negative regulation of BMP signaling pathway|positive regulation of JNK cascade|positive regulation of transforming growth factor beta receptor signaling pathway|SMAD protein signal transduction|transcription, DNA-dependent|virus-host interaction	centrosome|nuclear membrane|PML body	ATP binding|protein serine/threonine kinase activity|SMAD binding|transcription corepressor activity|virion binding			ovary(3)|central_nervous_system(3)|skin(1)	7	Melanoma(164;0.205)																	---	---	---	---
OR9A4	130075	broad.mit.edu	37	7	141619378	141619378	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr7:141619378A>G	uc003vwu.1	+	1	703	c.703A>G	c.(703-705)AGG>GGG	p.R235G		NM_001001656	NP_001001656	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A,	235	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	p.R235R(1)		skin(1)	1	Melanoma(164;0.0171)																	---	---	---	---
NPBWR1	2831	broad.mit.edu	37	8	53852864	53852864	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:53852864G>A	uc011ldu.1	+	1	397	c.397G>A	c.(397-399)GAC>AAC	p.D133N		NM_005285	NP_005276	P48145	NPBW1_HUMAN	G protein-coupled receptor 7	133	Cytoplasmic (Potential).				synaptic transmission	plasma membrane	opioid receptor activity|protein binding			ovary(2)|breast(1)	3		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)																---	---	---	---
NSMAF	8439	broad.mit.edu	37	8	59515820	59515820	+	Nonsense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:59515820G>A	uc003xtt.2	-	13	1208	c.994C>T	c.(994-996)CAG>TAG	p.Q332*	NSMAF_uc011lee.1_Nonsense_Mutation_p.Q363*|NSMAF_uc003xtu.2_Nonsense_Mutation_p.Q332*	NM_003580	NP_003571	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation	332	BEACH.				ceramide metabolic process	cytoplasm|soluble fraction	protein binding|receptor signaling protein activity			ovary(1)	1		all_lung(136;0.174)|Lung NSC(129;0.2)																---	---	---	---
TRIM55	84675	broad.mit.edu	37	8	67086721	67086721	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:67086721C>T	uc003xvv.2	+	10	1766	c.1540C>T	c.(1540-1542)CCT>TCT	p.P514S	TRIM55_uc003xvu.2_3'UTR|TRIM55_uc003xvw.2_Missense_Mutation_p.P418S|TRIM55_uc003xvx.2_Missense_Mutation_p.P207S	NM_184085	NP_908973	Q9BYV6	TRI55_HUMAN	tripartite motif-containing 55 isoform 1	514						cytoplasm|microtubule|nucleus	signal transducer activity|zinc ion binding			skin(3)|ovary(1)|central_nervous_system(1)	5		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)															---	---	---	---
PREX2	80243	broad.mit.edu	37	8	68972919	68972919	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:68972919T>G	uc003xxv.1	+	11	1271	c.1244T>G	c.(1243-1245)TTT>TGT	p.F415C	PREX2_uc003xxu.1_Missense_Mutation_p.F415C|PREX2_uc011lez.1_Missense_Mutation_p.F350C	NM_024870	NP_079146	Q70Z35	PREX2_HUMAN	DEP domain containing 2 isoform a	415	DEP 1.				G-protein coupled receptor protein signaling pathway|intracellular signal transduction	intracellular	protein binding|Rac GTPase activator activity|Rac guanyl-nucleotide exchange factor activity			skin(6)|large_intestine(4)|pancreas(3)|lung(2)|ovary(1)|kidney(1)	17																		---	---	---	---
OSGIN2	734	broad.mit.edu	37	8	90937034	90937034	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:90937034G>A	uc003yeg.2	+	6	1138	c.792G>A	c.(790-792)ACG>ACA	p.T264T	OSGIN2_uc003yeh.2_Silent_p.T308T	NM_004337	NP_004328	Q9Y236	OSGI2_HUMAN	oxidative stress induced growth inhibitor family	264					germ cell development|meiosis						0			BRCA - Breast invasive adenocarcinoma(11;0.0344)															---	---	---	---
UBR5	51366	broad.mit.edu	37	8	103324360	103324360	+	Splice_Site	SNP	A	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:103324360A>T	uc003ykr.1	-	18	2296	c.2263_splice	c.e18+1	p.G755_splice	UBR5_uc003yks.1_Splice_Site_p.G755_splice	NM_015902	NP_056986			ubiquitin protein ligase E3 component n-recognin						cell proliferation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of catenin import into nucleus|positive regulation of protein import into nucleus, translocation|progesterone receptor signaling pathway|protein polyubiquitination|protein ubiquitination involved in ubiquitin-dependent protein catabolic process|response to DNA damage stimulus	nucleus|soluble fraction	protein binding|RNA binding|ubiquitin-ubiquitin ligase activity|zinc ion binding			lung(16)|ovary(4)|large_intestine(3)|breast(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)|kidney(1)	28	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000442)															---	---	---	---
SLC45A4	57210	broad.mit.edu	37	8	142222493	142222493	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142222493C>T	uc003ywd.1	-	7	2259	c.1951G>A	c.(1951-1953)GGC>AGC	p.G651S	SLC45A4_uc003ywc.1_Missense_Mutation_p.G651S|SLC45A4_uc010meq.1_Missense_Mutation_p.G649S	NM_001080431	NP_001073900	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4	702	Helical; (Potential).				transport	integral to membrane				ovary(2)	2	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)															---	---	---	---
GPR20	2843	broad.mit.edu	37	8	142367700	142367700	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr8:142367700C>T	uc003ywf.2	-	2	413	c.324G>A	c.(322-324)ACG>ACA	p.T108T		NM_005293	NP_005284	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	108	Extracellular (Potential).					integral to plasma membrane	G-protein coupled receptor activity			upper_aerodigestive_tract(1)	1	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)															---	---	---	---
FLJ46321	389763	broad.mit.edu	37	9	84608950	84608950	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:84608950A>G	uc004amn.2	+	4	3612	c.3565A>G	c.(3565-3567)ATA>GTA	p.I1189V		NM_001001670	NP_001001670	Q6ZQQ2	F75D1_HUMAN	hypothetical protein LOC389763	1189						integral to membrane					0																		---	---	---	---
RXRA	6256	broad.mit.edu	37	9	137300151	137300151	+	Intron	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr9:137300151G>A	uc004cfb.2	+						RXRA_uc004cfc.1_Intron	NM_002957	NP_002948			retinoid X receptor, alpha						cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding			upper_aerodigestive_tract(1)|ovary(1)	2				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)													---	---	---	---
NEBL	10529	broad.mit.edu	37	10	21104614	21104614	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:21104614G>A	uc001iqi.2	-	22	2578	c.2181C>T	c.(2179-2181)ACC>ACT	p.T727T	NEBL_uc001iqj.2_RNA|NEBL_uc001iqk.2_Intron|NEBL_uc001iql.1_RNA	NM_006393	NP_006384	O76041	NEBL_HUMAN	nebulette sarcomeric isoform	727	Nebulin 20.				regulation of actin filament length		actin binding|structural constituent of muscle			ovary(2)	2																		---	---	---	---
PPYR1	5540	broad.mit.edu	37	10	47087695	47087695	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:47087695C>T	uc001jee.2	+	3	1331	c.912C>T	c.(910-912)TTC>TTT	p.F304F	ANXA8_uc001jed.3_Intron|PPYR1_uc009xna.2_Silent_p.F304F	NM_005972	NP_005963	P50391	NPY4R_HUMAN	pancreatic polypeptide receptor 1	304	Helical; Name=7; (Potential).				blood circulation|digestion|feeding behavior	integral to plasma membrane				ovary(1)|skin(1)	2																		---	---	---	---
GLUD1	2746	broad.mit.edu	37	10	88811617	88811617	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:88811617C>T	uc001keh.2	-	13	1665	c.1568G>A	c.(1567-1569)CGC>CAC	p.R523H	GLUD1_uc001keg.2_Missense_Mutation_p.R356H|GLUD1_uc010qmp.1_Missense_Mutation_p.R390H	NM_005271	NP_005262	P00367	DHE3_HUMAN	glutamate dehydrogenase 1 precursor	523					glutamate biosynthetic process|glutamate catabolic process|positive regulation of insulin secretion	mitochondrial matrix	ADP binding|ATP binding|glutamate dehydrogenase|glutamate dehydrogenase activity|GTP binding|identical protein binding|leucine binding|NAD+ binding				0					L-Glutamic Acid(DB00142)|NADH(DB00157)													---	---	---	---
CASP7	840	broad.mit.edu	37	10	115485162	115485162	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:115485162A>G	uc001lan.2	+	5	592	c.418A>G	c.(418-420)ATC>GTC	p.I140V	CASP7_uc001lam.2_Missense_Mutation_p.I140V|CASP7_uc001lao.2_Missense_Mutation_p.I173V|CASP7_uc001lap.2_Missense_Mutation_p.I140V|CASP7_uc001laq.2_Missense_Mutation_p.I140V|CASP7_uc010qsa.1_Missense_Mutation_p.I225V|CASP7_uc010qsb.1_Missense_Mutation_p.I115V	NM_033339	NP_203125	P55210	CASP7_HUMAN	caspase 7 isoform alpha	140					activation of caspase activity by cytochrome c|cellular component disassembly involved in apoptosis|induction of apoptosis by intracellular signals|proteolysis	cytosol|endoplasmic reticulum membrane|mitochondrial membrane|nucleoplasm	cysteine-type endopeptidase activity|protein binding			ovary(1)	1		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)														---	---	---	---
PRLHR	2834	broad.mit.edu	37	10	120354139	120354139	+	Silent	SNP	G	A	A	rs143477537	byFrequency	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:120354139G>A	uc001ldp.1	-	2	757	c.618C>T	c.(616-618)CAC>CAT	p.H206H		NM_004248	NP_004239	P49683	PRLHR_HUMAN	G protein-coupled receptor 10	206	Extracellular (Potential).				female pregnancy	integral to plasma membrane	neuropeptide Y receptor activity				0		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)														---	---	---	---
TACC2	10579	broad.mit.edu	37	10	123847432	123847432	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:123847432C>T	uc001lfv.2	+	4	5777	c.5417C>T	c.(5416-5418)CCG>CTG	p.P1806L	TACC2_uc001lfw.2_Intron|TACC2_uc009xzx.2_Missense_Mutation_p.P1806L|TACC2_uc010qtv.1_Missense_Mutation_p.P1806L	NM_206862	NP_996744	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing	1806						microtubule organizing center|nucleus	nuclear hormone receptor binding			ovary(4)|breast(3)|skin(2)|central_nervous_system(1)	10		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)																---	---	---	---
JAKMIP3	282973	broad.mit.edu	37	10	133950778	133950778	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr10:133950778C>T	uc001lkx.3	+	7	1269	c.1269C>T	c.(1267-1269)TAC>TAT	p.Y423Y		NM_001105521	NP_001098991			Janus kinase and microtubule interacting protein											breast(1)	1		all_cancers(35;5.63e-09)|all_epithelial(44;9.25e-07)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|Colorectal(31;0.0721)|all_neural(114;0.0726)|Breast(234;0.0949)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;0.000104)|Epithelial(32;0.000142)|all cancers(32;0.000185)|BRCA - Breast invasive adenocarcinoma(275;0.224)														---	---	---	---
OR51B5	282763	broad.mit.edu	37	11	5364665	5364665	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:5364665C>G	uc001map.1	-	1	90	c.90G>C	c.(88-90)TTG>TTC	p.L30F	HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Missense_Mutation_p.L30F	NM_001005567	NP_001005567	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B,	30	Helical; Name=1; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			skin(1)	1		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)														---	---	---	---
DCDC1	341019	broad.mit.edu	37	11	31312288	31312288	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:31312288A>C	uc001msv.2	-	7	1068	c.866T>G	c.(865-867)CTT>CGT	p.L289R	DCDC1_uc001msu.1_Intron	NM_181807	NP_861523	P59894	DCDC1_HUMAN	doublecortin domain containing 1	289					intracellular signal transduction					skin(1)	1	Lung SC(675;0.225)																	---	---	---	---
HSD17B12	51144	broad.mit.edu	37	11	43775681	43775681	+	Intron	SNP	C	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:43775681C>G	uc001mxq.3	+						HSD17B12_uc001mxp.2_Intron	NM_016142	NP_057226			hydroxysteroid (17-beta) dehydrogenase 12						long-chain fatty-acyl-CoA biosynthetic process|steroid biosynthetic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	estradiol 17-beta-dehydrogenase activity|long-chain-3-hydroxyacyl-CoA dehydrogenase activity				0																		---	---	---	---
ALX4	60529	broad.mit.edu	37	11	44297029	44297029	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:44297029G>A	uc001myb.2	-	2	750	c.646C>T	c.(646-648)CGG>TGG	p.R216W		NM_021926	NP_068745	Q9H161	ALX4_HUMAN	aristaless-like homeobox 4	216	Homeobox.				hair follicle development						0																		---	---	---	---
AMBRA1	55626	broad.mit.edu	37	11	46515240	46515240	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:46515240C>T	uc010rgu.1	-	11	2799	c.2439G>A	c.(2437-2439)GAG>GAA	p.E813E	AMBRA1_uc010rgt.1_Silent_p.E379E|AMBRA1_uc009ylc.1_Silent_p.E784E|AMBRA1_uc001ncu.1_Silent_p.E723E|AMBRA1_uc001ncv.2_Silent_p.E816E|AMBRA1_uc001ncw.2_Silent_p.E694E|AMBRA1_uc001ncx.2_Silent_p.E753E	NM_017749	NP_060219	Q9C0C7	AMRA1_HUMAN	activating molecule in beclin-1-regulated	813					autophagy|cell differentiation|nervous system development	autophagic vacuole|cytoplasmic vesicle				large_intestine(1)|ovary(1)|central_nervous_system(1)	3				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)														---	---	---	---
OR4C16	219428	broad.mit.edu	37	11	55340258	55340258	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:55340258T>G	uc010rih.1	+	1	655	c.655T>G	c.(655-657)TTC>GTC	p.F219V		NM_001004701	NP_001004701	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C,	219	Cytoplasmic (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		all_epithelial(135;0.0748)																---	---	---	---
PLEKHB1	58473	broad.mit.edu	37	11	73362849	73362849	+	Silent	SNP	G	A	A	rs113230147	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:73362849G>A	uc001oua.2	+	4	695	c.264G>A	c.(262-264)GAG>GAA	p.E88E	PLEKHB1_uc001oub.2_Silent_p.E88E|PLEKHB1_uc010rrh.1_Silent_p.E69E|PLEKHB1_uc001ouc.2_Silent_p.E69E|PLEKHB1_uc001oud.2_Silent_p.E69E|PLEKHB1_uc009ytq.2_Silent_p.E69E	NM_021200	NP_067023	Q9UF11	PKHB1_HUMAN	pleckstrin homology domain containing, family B	88	PH.				multicellular organismal development|phototransduction	cytoplasm|integral to membrane	signal transducer activity			ovary(1)|lung(1)	2																		---	---	---	---
FAT3	120114	broad.mit.edu	37	11	92613927	92613927	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:92613927C>T	uc001pdj.3	+	22	12175	c.12158C>T	c.(12157-12159)ACG>ATG	p.T4053M	FAT3_uc001pdi.3_Missense_Mutation_p.T493M	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN	FAT tumor suppressor homolog 3	4053	EGF-like 2.|Extracellular (Potential).				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)	5		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)													TCGA Ovarian(4;0.039)			---	---	---	---
HTR3A	3359	broad.mit.edu	37	11	113857405	113857405	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:113857405G>A	uc010rxb.1	+	7	1122	c.889G>A	c.(889-891)GTT>ATT	p.V297I	HTR3A_uc010rxa.1_Missense_Mutation_p.V297I|HTR3A_uc009yyx.2_RNA|HTR3A_uc010rxc.1_Missense_Mutation_p.V276I	NM_213621	NP_998786	P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A	291	Helical; Name=2; (Potential).				digestion|synaptic transmission	cell junction|integral to plasma membrane|postsynaptic membrane	serotonin binding|serotonin receptor activity|serotonin-activated cation-selective channel activity				0		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Dolasetron(DB00757)|Granisetron(DB00889)|Mirtazapine(DB00370)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Tubocurarine(DB01199)													---	---	---	---
OR8B3	390271	broad.mit.edu	37	11	124266484	124266484	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124266484G>A	uc010saj.1	-	1	764	c.764C>T	c.(763-765)GCG>GTG	p.A255V	OR8B2_uc001qab.3_Intron	NM_001005467	NP_001005467	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B,	255	Helical; Name=6; (Potential).				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			ovary(1)|skin(1)	2		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)														---	---	---	---
ROBO3	64221	broad.mit.edu	37	11	124738838	124738838	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr11:124738838G>A	uc001qbc.2	+	2	493	c.301G>A	c.(301-303)GGG>AGG	p.G101R		NM_022370	NP_071765	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3	101	Ig-like C2-type 1.|Extracellular (Potential).				axon midline choice point recognition	integral to membrane	receptor activity			breast(1)|central_nervous_system(1)	2	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)														---	---	---	---
PTPN6	5777	broad.mit.edu	37	12	7066907	7066907	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:7066907G>A	uc001qsb.2	+	10	1407	c.1165G>A	c.(1165-1167)GAA>AAA	p.E389K	PTPN6_uc001qsa.1_Missense_Mutation_p.E391K|PTPN6_uc010sfr.1_Missense_Mutation_p.E350K|PTPN6_uc009zfl.1_Missense_Mutation_p.E389K|PTPN6_uc010sfs.1_Missense_Mutation_p.E377K	NM_002831	NP_002822	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type	389	Tyrosine-protein phosphatase.				apoptosis|cell junction assembly|G-protein coupled receptor protein signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|negative regulation of peptidyl-tyrosine phosphorylation|platelet activation|positive regulation of cell proliferation|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of G1/S transition of mitotic cell cycle|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol|membrane|nucleus	protein binding|protein tyrosine phosphatase activity			breast(1)	1																		---	---	---	---
KLRD1	3824	broad.mit.edu	37	12	10462003	10462003	+	Silent	SNP	G	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:10462003G>T	uc001qxw.3	+	3	221	c.24G>T	c.(22-24)CTG>CTT	p.L8L	KLRD1_uc001qxx.3_Silent_p.L8L|KLRD1_uc001qxy.3_Intron|KLRD1_uc009zhh.2_Silent_p.L8L|KLRD1_uc009zhi.2_Silent_p.L8L|KLRD1_uc001qxz.3_Silent_p.L8L	NM_001114396	NP_001107868	Q13241	KLRD1_HUMAN	killer cell lectin-like receptor subfamily D,	8	Cytoplasmic (Potential).				cell surface receptor linked signaling pathway|regulation of immune response	integral to membrane|plasma membrane	sugar binding|transmembrane receptor activity				0																		---	---	---	---
SOX5	6660	broad.mit.edu	37	12	23999031	23999031	+	Missense_Mutation	SNP	A	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:23999031A>T	uc001rfw.2	-	3	469	c.367T>A	c.(367-369)TCC>ACC	p.S123T	SOX5_uc001rfx.2_Missense_Mutation_p.S110T|SOX5_uc001rfy.2_Missense_Mutation_p.S110T|SOX5_uc010siv.1_Missense_Mutation_p.S110T|SOX5_uc010siw.1_RNA|SOX5_uc001rfz.1_Missense_Mutation_p.S75T|SOX5_uc001rga.2_Missense_Mutation_p.S88T	NM_006940	NP_008871	P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5 isoform a	123					transcription from RNA polymerase II promoter	nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity			ovary(5)|lung(1)	6																		---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41585273	41585273	+	Missense_Mutation	SNP	A	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41585273A>C	uc010skn.1	+	2	133	c.65A>C	c.(64-66)AAG>ACG	p.K22T		NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2	221							ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
PDZRN4	29951	broad.mit.edu	37	12	41967300	41967300	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:41967300C>T	uc010skn.1	+	10	2190	c.2122C>T	c.(2122-2124)CGA>TGA	p.R708*	PDZRN4_uc001rmq.3_Nonsense_Mutation_p.R649*|PDZRN4_uc009zjz.2_Nonsense_Mutation_p.R647*|PDZRN4_uc001rmr.2_Nonsense_Mutation_p.R534*	NM_013377	NP_037509	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing RING finger 4 isoform 2	907							ubiquitin-protein ligase activity|zinc ion binding			lung(3)|skin(3)|ovary(2)|large_intestine(1)|kidney(1)|pancreas(1)	11	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)																---	---	---	---
KRT84	3890	broad.mit.edu	37	12	52779213	52779213	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:52779213G>A	uc001sah.1	-	1	205	c.157C>T	c.(157-159)CGG>TGG	p.R53W		NM_033045	NP_149034	Q9NSB2	KRT84_HUMAN	keratin, hair, basic, 4	53	Head.					keratin filament	structural constituent of epidermis			skin(1)	1	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)														---	---	---	---
HOXC4	3221	broad.mit.edu	37	12	54448091	54448091	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:54448091G>A	uc001seu.2	+	3	1065	c.385G>A	c.(385-387)GCC>ACC	p.A129T	HOXC4_uc001sex.2_Missense_Mutation_p.A129T	NM_014620	NP_055435	P09017	HXC4_HUMAN	homeobox C4	129						nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity			ovary(1)	1																		---	---	---	---
ACACB	32	broad.mit.edu	37	12	109671856	109671856	+	Intron	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:109671856C>T	uc001tob.2	+						ACACB_uc001toc.2_Intron|ACACB_uc010sxl.1_Intron|ACACB_uc001tod.2_Intron|ACACB_uc010sxm.1_Intron	NM_001093	NP_001084			acetyl-Coenzyme A carboxylase beta						acetyl-CoA metabolic process|carnitine shuttle|energy reserve metabolic process|fatty acid biosynthetic process|positive regulation of cellular metabolic process|protein homotetramerization|regulation of fatty acid oxidation	cytosol|endomembrane system|Golgi apparatus|membrane	acetyl-CoA carboxylase activity|ATP binding|biotin carboxylase activity|metal ion binding|protein binding			ovary(5)|upper_aerodigestive_tract(1)|pancreas(1)|skin(1)	8					Biotin(DB00121)													---	---	---	---
PXN	5829	broad.mit.edu	37	12	120657212	120657212	+	Intron	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:120657212G>A	uc001txt.2	-						PXN_uc001txu.2_5'Flank|PXN_uc001txv.2_Intron|PXN_uc001txx.2_Intron|PXN_uc001txy.2_Intron|PXN_uc001txz.2_RNA|uc001tya.2_RNA	NM_001080855	NP_001074324			paxillin isoform 1						cell junction assembly|cell-matrix adhesion|cellular response to reactive oxygen species|epidermal growth factor receptor signaling pathway|growth hormone receptor signaling pathway|muscle contraction|signal complex assembly	cytoplasm|focal adhesion|lamellipodium|microtubule associated complex	beta-catenin binding|vinculin binding|zinc ion binding			ovary(1)|breast(1)	2	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)																	---	---	---	---
HPD	3242	broad.mit.edu	37	12	122295349	122295349	+	Intron	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:122295349G>A	uc001ubj.2	-						HPD_uc001ubk.2_Intron	NM_002150	NP_002141			4-hydroxyphenylpyruvate dioxygenase						L-phenylalanine catabolic process|tyrosine catabolic process	cytosol	4-hydroxyphenylpyruvate dioxygenase activity|metal ion binding				0	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000105)|Epithelial(86;0.000352)|BRCA - Breast invasive adenocarcinoma(302;0.225)	Nitisinone(DB00348)													---	---	---	---
AACS	65985	broad.mit.edu	37	12	125612823	125612823	+	Intron	SNP	G	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr12:125612823G>T	uc001uhc.2	+						AACS_uc001uhd.2_Intron|AACS_uc009zyh.2_Intron|AACS_uc009zyi.2_Intron	NM_023928	NP_076417			acetoacetyl-CoA synthetase						fatty acid metabolic process	cytosol	acetoacetate-CoA ligase activity|ATP binding			ovary(1)|liver(1)|central_nervous_system(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)														---	---	---	---
SMAD9	4093	broad.mit.edu	37	13	37427616	37427616	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:37427616G>A	uc001uvw.2	-	6	1543	c.1200C>T	c.(1198-1200)CAC>CAT	p.H400H	SMAD9_uc001uvx.2_Silent_p.H363H|SMAD9_uc010tep.1_Silent_p.H193H	NM_001127217	NP_001120689	O15198	SMAD9_HUMAN	SMAD family member 9 isoform a	400	MH2.				BMP signaling pathway|transforming growth factor beta receptor signaling pathway	cytosol|transcription factor complex	sequence-specific DNA binding transcription factor activity|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity				0		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)														---	---	---	---
PCDH9	5101	broad.mit.edu	37	13	67802089	67802089	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr13:67802089G>T	uc001vik.2	-	2	1176	c.484C>A	c.(484-486)CCA>ACA	p.P162T	PCDH9_uc001vil.2_Missense_Mutation_p.P162T|PCDH9_uc010thl.1_Missense_Mutation_p.P162T|PCDH9_uc001vin.3_Missense_Mutation_p.P162T	NM_203487	NP_982354	Q9HC56	PCDH9_HUMAN	protocadherin 9 isoform 1 precursor	162	Extracellular (Potential).|Cadherin 2.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			ovary(4)|pancreas(1)|skin(1)	6		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)														---	---	---	---
POTEG	404785	broad.mit.edu	37	14	19553768	19553768	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:19553768G>A	uc001vuz.1	+	1	404	c.352G>A	c.(352-354)GGC>AGC	p.G118S	POTEG_uc001vva.1_RNA|POTEG_uc010ahc.1_RNA	NM_001005356	NP_001005356	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	118										ovary(1)	1																		---	---	---	---
FOXG1	2290	broad.mit.edu	37	14	29237790	29237790	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:29237790C>T	uc001wqe.2	+	1	1504	c.1305C>T	c.(1303-1305)AGC>AGT	p.S435S		NM_005249	NP_005240	P55316	FOXG1_HUMAN	forkhead box G1	435					axon midline choice point recognition|central nervous system neuron development|dorsal/ventral pattern formation|embryo development ending in birth or egg hatching|hindbrain development|inner ear morphogenesis|negative regulation of neuron differentiation|negative regulation of transcription, DNA-dependent|nonmotile primary cilium assembly|nose development|positive regulation of cell cycle|positive regulation of neuroblast proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of mitotic cell cycle|regulation of sequence-specific DNA binding transcription factor activity|tissue development	transcription factor complex	DNA bending activity|double-stranded DNA binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding			ovary(2)|lung(2)	4			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)														---	---	---	---
AKAP6	9472	broad.mit.edu	37	14	33292374	33292374	+	Silent	SNP	T	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:33292374T>C	uc001wrq.2	+	13	5525	c.5355T>C	c.(5353-5355)ATT>ATC	p.I1785I		NM_004274	NP_004265	Q13023	AKAP6_HUMAN	A-kinase anchor protein 6	1785					protein targeting	calcium channel complex|nuclear membrane|sarcoplasmic reticulum	protein kinase A binding|receptor binding			breast(6)|ovary(5)|lung(4)|skin(3)|large_intestine(2)|pancreas(1)	21	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)														---	---	---	---
SLC25A21	89874	broad.mit.edu	37	14	37283145	37283145	+	Nonsense_Mutation	SNP	G	A	A	rs148097801	byFrequency	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:37283145G>A	uc001wtz.1	-	3	491	c.181C>T	c.(181-183)CGA>TGA	p.R61*		NM_030631	NP_085134	Q9BQT8	ODC_HUMAN	solute carrier family 25 (mitochondrial	61	Solcar 1.				lysine catabolic process	integral to membrane|mitochondrial inner membrane	alpha-ketoglutarate transmembrane transporter activity|binding			skin(1)	1	Esophageal squamous(585;0.164)|Breast(36;0.179)|Hepatocellular(127;0.213)		Lung(8;2.16e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.0112)|all cancers(34;0.0274)|LUSC - Lung squamous cell carcinoma(13;0.149)	GBM - Glioblastoma multiforme(112;0.00204)														---	---	---	---
NIN	51199	broad.mit.edu	37	14	51226729	51226729	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:51226729C>T	uc001wym.2	-	17	2436	c.2245G>A	c.(2245-2247)GCC>ACC	p.A749T	NIN_uc001wyi.2_Missense_Mutation_p.A749T|NIN_uc001wyj.2_RNA|NIN_uc001wyk.2_Missense_Mutation_p.A749T|NIN_uc010tqp.1_Missense_Mutation_p.A755T|NIN_uc001wyo.2_Missense_Mutation_p.A749T	NM_182946	NP_891991	Q8N4C6	NIN_HUMAN	ninein isoform 5	749	Potential.				centrosome localization	centrosome|microtubule	calcium ion binding|GTP binding|protein binding			skin(3)|ovary(1)|kidney(1)|central_nervous_system(1)	6	all_epithelial(31;0.00244)|Breast(41;0.127)							T	PDGFRB	MPD								---	---	---	---
C14orf37	145407	broad.mit.edu	37	14	58563449	58563449	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:58563449T>G	uc001xdc.2	-	5	2193	c.2082A>C	c.(2080-2082)CAA>CAC	p.Q694H	C14orf37_uc010tro.1_Missense_Mutation_p.Q732H|C14orf37_uc001xdd.2_Missense_Mutation_p.Q694H	NM_001001872	NP_001001872	Q86TY3	CN037_HUMAN	hypothetical protein LOC145407 precursor	694	Extracellular (Potential).					integral to membrane	binding				0																		---	---	---	---
SYNE2	23224	broad.mit.edu	37	14	64476778	64476778	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:64476778A>G	uc001xgm.2	+	32	4902	c.4672A>G	c.(4672-4674)ATC>GTC	p.I1558V	SYNE2_uc001xgl.2_Missense_Mutation_p.I1558V	NM_015180	NP_055995	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	1558	Cytoplasmic (Potential).				centrosome localization|cytoskeletal anchoring at nuclear membrane|nuclear migration along microfilament|positive regulation of cell migration	cytoskeleton|filopodium membrane|focal adhesion|integral to membrane|lamellipodium membrane|mitochondrial part|nuclear outer membrane|nucleoplasm|sarcoplasmic reticulum membrane|SUN-KASH complex|Z disc	actin binding|protein binding			ovary(8)|breast(4)|central_nervous_system(1)|pancreas(1)	14				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)														---	---	---	---
TMEM229B	161145	broad.mit.edu	37	14	67940176	67940176	+	Silent	SNP	G	A	A	rs147441533		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:67940176G>A	uc001xjk.2	-	3	875	c.465C>T	c.(463-465)GGC>GGT	p.G155G	TMEM229B_uc001xjj.1_RNA	NM_182526	NP_872332	Q8NBD8	T229B_HUMAN	transmembrane protein 229B	155	Cytoplasmic (Potential).					integral to membrane				central_nervous_system(1)	1																		---	---	---	---
TSHR	7253	broad.mit.edu	37	14	81610659	81610659	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr14:81610659G>A	uc001xvd.1	+	10	2413	c.2257G>A	c.(2257-2259)GGC>AGC	p.G753S		NM_000369	NP_000360	P16473	TSHR_HUMAN	thyroid stimulating hormone receptor isoform 1	753	Cytoplasmic (Potential).				cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity			thyroid(289)|ovary(5)|lung(3)|kidney(1)|skin(1)	299				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism 						---	---	---	---
ATP10A	57194	broad.mit.edu	37	15	25981296	25981296	+	Intron	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:25981296A>G	uc010ayu.2	-							NM_024490	NP_077816			ATPase, class V, type 10A						ATP biosynthetic process|regulation of cell shape	integral to membrane|plasma membrane	ATP binding|ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism|magnesium ion binding|phospholipid-translocating ATPase activity			pancreas(2)|ovary(1)|breast(1)|liver(1)	5		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)														---	---	---	---
IREB2	3658	broad.mit.edu	37	15	78777251	78777251	+	Missense_Mutation	SNP	T	C	C			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:78777251T>C	uc002bdr.2	+	12	1724	c.1562T>C	c.(1561-1563)ATG>ACG	p.M521T	IREB2_uc010unb.1_Missense_Mutation_p.M271T	NM_004136	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	521							4 iron, 4 sulfur cluster binding|metal ion binding|protein binding				0				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)														---	---	---	---
ADAMTSL3	57188	broad.mit.edu	37	15	84651311	84651311	+	Silent	SNP	C	T	T	rs142014884		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr15:84651311C>T	uc002bjz.3	+	21	3155	c.2931C>T	c.(2929-2931)ATC>ATT	p.I977I	ADAMTSL3_uc010bmt.1_Silent_p.I977I|ADAMTSL3_uc010bmu.1_Silent_p.I977I	NM_207517	NP_997400	P82987	ATL3_HUMAN	ADAMTS-like 3 precursor	977	Ig-like C2-type 1.					proteinaceous extracellular matrix	metallopeptidase activity|zinc ion binding			ovary(6)|central_nervous_system(5)|lung(5)|large_intestine(4)|breast(3)|skin(2)|kidney(1)|pancreas(1)	27			BRCA - Breast invasive adenocarcinoma(143;0.211)															---	---	---	---
SOLH	6650	broad.mit.edu	37	16	601551	601551	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:601551G>T	uc002chi.2	+	9	2595	c.2232G>T	c.(2230-2232)TGG>TGT	p.W744C	SOLH_uc002chj.2_5'Flank	NM_005632	NP_005623	O75808	CAN15_HUMAN	small optic lobes	744	Calpain catalytic.				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)																---	---	---	---
ROGDI	79641	broad.mit.edu	37	16	4848189	4848189	+	Intron	SNP	C	T	T	rs3747610	byFrequency	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:4848189C>T	uc002cxv.2	-						ROGDI_uc002cxu.2_Intron|ROGDI_uc010bua.2_Intron|ROGDI_uc002cxw.2_Intron	NM_024589	NP_078865			leucine zipper domain protein							intracellular				ovary(1)|skin(1)	2																		---	---	---	---
CPNE2	221184	broad.mit.edu	37	16	57180027	57180027	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:57180027G>A	uc002eks.1	+	15	1562	c.1333G>A	c.(1333-1335)GGG>AGG	p.G445R	CPNE2_uc010cct.1_Missense_Mutation_p.G471R|CPNE2_uc010ccu.1_Missense_Mutation_p.G445R|CPNE2_uc002ekt.1_Missense_Mutation_p.G141R	NM_152727	NP_689940	Q96FN4	CPNE2_HUMAN	copine II	445	VWFA.									central_nervous_system(1)|skin(1)	2		all_neural(199;0.224)																---	---	---	---
CES8	283848	broad.mit.edu	37	16	67035217	67035217	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67035217C>T	uc002eqv.2	+	5	586	c.543C>T	c.(541-543)GAC>GAT	p.D181D	CES8_uc010vix.1_Silent_p.D181D|CES8_uc002eqw.2_Silent_p.D181D|CES8_uc002eqy.2_Silent_p.D83D|CES8_uc002eqx.2_Translation_Start_Site|CES8_uc010viy.1_Silent_p.D87D|CES8_uc010viz.1_Silent_p.D83D	NM_173815	NP_776176	Q5XG92	EST4A_HUMAN	carboxylesterase 8 (putative)	181						extracellular region	carboxylesterase activity				0																		---	---	---	---
CTRL	1506	broad.mit.edu	37	16	67963906	67963906	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr16:67963906G>A	uc002euw.2	-	7	736	c.726C>T	c.(724-726)CGC>CGT	p.R242R		NM_001907	NP_001898	P40313	CTRL_HUMAN	chymotrypsin-like precursor	242	Peptidase S1.				digestion|proteolysis	extracellular space	serine-type endopeptidase activity				0		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)														---	---	---	---
SCARF1	8578	broad.mit.edu	37	17	1540133	1540133	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:1540133C>T	uc002fsz.1	-	10	1553	c.1503G>A	c.(1501-1503)CCG>CCA	p.P501P	SCARF1_uc002fsy.1_Intron|SCARF1_uc002fta.1_RNA|SCARF1_uc010cjv.1_Silent_p.P415P	NM_003693	NP_003684	Q14162	SREC_HUMAN	scavenger receptor class F, member 1 isoform 1	501	Pro/Ser-rich.|Cytoplasmic (Potential).				cell adhesion|neuron remodeling|positive regulation of axon regeneration|receptor-mediated endocytosis	integral to membrane	low-density lipoprotein particle binding|scavenger receptor activity			skin(1)	1				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)														---	---	---	---
KIAA0664	23277	broad.mit.edu	37	17	2595320	2595320	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:2595320C>T	uc002fuy.1	-	23	3601	c.3515G>A	c.(3514-3516)GGT>GAT	p.G1172D	KIAA0664_uc002fux.1_Missense_Mutation_p.G1105D|KIAA0664_uc010ckc.1_Missense_Mutation_p.G158D	NM_015229	NP_056044	O75153	K0664_HUMAN	hypothetical protein LOC23277	1172	TPR 4.						binding			breast(2)	2																		---	---	---	---
TP53	7157	broad.mit.edu	37	17	7577539	7577539	+	Missense_Mutation	SNP	G	A	A	rs121912651		TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:7577539G>A	uc002gim.2	-	7	936	c.742C>T	c.(742-744)CGG>TGG	p.R248W	TP53_uc002gig.1_Missense_Mutation_p.R248W|TP53_uc002gih.2_Missense_Mutation_p.R248W|TP53_uc010cne.1_5'Flank|TP53_uc010cnf.1_Missense_Mutation_p.R116W|TP53_uc010cng.1_Missense_Mutation_p.R116W|TP53_uc002gii.1_Missense_Mutation_p.R116W|TP53_uc010cnh.1_Missense_Mutation_p.R248W|TP53_uc010cni.1_Missense_Mutation_p.R248W|TP53_uc002gij.2_Missense_Mutation_p.R248W|TP53_uc010cnj.1_RNA|TP53_uc002gin.2_Missense_Mutation_p.R155W|TP53_uc002gio.2_Missense_Mutation_p.R116W	NM_001126112	NP_001119584	P04637	P53_HUMAN	tumor protein p53 isoform a	248	|Interaction with HIPK1 (By similarity).|Interacts with the 53BP2 SH3 domain.|Interaction with AXIN1 (By similarity).		R -> W (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> P (in sporadic cancers; somatic mutation).|R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|NR -> KW (in sporadic cancers; somatic mutation).|R -> C (in a sporadic cancer; somatic mutation).|NR -> IP (in a sporadic cancer; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.R248Q(516)|p.R248W(443)|p.R248L(63)|p.R248P(12)|p.R248G(11)|p.R248R(10)|p.0?(7)|p.N247_R248delNR(2)|p.N247_R248>KW(2)|p.M246_P250delMNRRP(2)|p.R248fs*97(2)|p.R248_P250delRRP(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R248C(1)|p.G245fs*14(1)|p.N247_R248>IP(1)		large_intestine(4656)|breast(2429)|upper_aerodigestive_tract(2212)|lung(2028)|ovary(1592)|oesophagus(1462)|haematopoietic_and_lymphoid_tissue(1228)|stomach(1136)|urinary_tract(1114)|central_nervous_system(1085)|liver(805)|skin(694)|pancreas(375)|biliary_tract(247)|soft_tissue(209)|prostate(194)|endometrium(150)|bone(102)|vulva(79)|kidney(79)|cervix(68)|thyroid(54)|salivary_gland(43)|adrenal_gland(37)|peritoneum(33)|eye(24)|thymus(21)|genital_tract(16)|autonomic_ganglia(16)|small_intestine(14)|testis(11)|penis(10)|vagina(6)|meninges(5)|pituitary(4)|pleura(3)|gastrointestinal_tract_(site_indeterminate)(1)|NS(1)|Fallopian tube(1)|placenta(1)	22245		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)		R248W(CAS1_CENTRAL_NERVOUS_SYSTEM)|R248W(COLO680N_OESOPHAGUS)|R248W(SW837_LARGE_INTESTINE)|R248W(KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(RD_SOFT_TISSUE)|R248W(VCAP_PROSTATE)|R248W(JIMT1_BREAST)|R248W(GCT_SOFT_TISSUE)|R248W(DB_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|R248W(786O_KIDNEY)|R248W(COLO320_LARGE_INTESTINE)|R248W(LXF289_LUNG)|R248W(LUDLU1_LUNG)|R248W(MIAPACA2_PANCREAS)|R248W(HCC2157_BREAST)	111	Mis|N|F		breast|colorectal|lung|sarcoma|adrenocortical|glioma|multiple other tumour types	breast|sarcoma|adrenocortical carcinoma|glioma|multiple other tumour types		Other_conserved_DNA_damage_response_genes	Hereditary_Adrenocortical_Cancer|Endometrial_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_non-BRCA1/2|Li-Fraumeni_syndrome|Osteosarcoma_Familial_Clustering_of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)			---	---	---	---
COL1A1	1277	broad.mit.edu	37	17	48268166	48268166	+	Intron	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:48268166C>T	uc002iqm.2	-							NM_000088	NP_000079			alpha 1 type I collagen preproprotein						axon guidance|blood vessel development|collagen biosynthetic process|collagen fibril organization|embryonic skeletal system development|leukocyte migration|platelet activation|positive regulation of canonical Wnt receptor signaling pathway|positive regulation of cell migration|positive regulation of epithelial to mesenchymal transition|positive regulation of transcription, DNA-dependent|protein localization to nucleus|sensory perception of sound|skin morphogenesis|tooth mineralization|visual perception	collagen type I|extracellular space|plasma membrane	identical protein binding|platelet-derived growth factor binding		COL1A1/PDGFB(372)	soft_tissue(372)|central_nervous_system(7)|skin(1)|breast(1)|pancreas(1)	382					Collagenase(DB00048)|Palifermin(DB00039)			T	PDGFB|USP6	dermatofibrosarcoma protuberans|aneurysmal bone cyst 		Osteogenesis imperfecta						---	---	---	---
ARHGDIA	396	broad.mit.edu	37	17	79827634	79827634	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr17:79827634C>T	uc002kbp.2	-	1	212	c.173G>A	c.(172-174)CGC>CAC	p.R58H	ARHGDIA_uc002kjk.1_5'Flank|ARHGDIA_uc002kbq.2_Missense_Mutation_p.R58H|ARHGDIA_uc002kbr.2_Missense_Mutation_p.R58H|ARHGDIA_uc002kbs.1_Intron|ARHGDIA_uc002kbt.1_Missense_Mutation_p.R58H|ARHGDIA_uc010dig.1_RNA	NM_004309	NP_004300	P52565	GDIR1_HUMAN	Rho GDP dissociation inhibitor (GDI) alpha	58					anti-apoptosis|cellular component movement|negative regulation of axonogenesis|negative regulation of cell adhesion|nerve growth factor receptor signaling pathway|positive regulation of axonogenesis|regulation of small GTPase mediated signal transduction|Rho protein signal transduction	cytoskeleton|cytosol	GTPase activator activity|identical protein binding|Rho GDP-dissociation inhibitor activity				0	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)															---	---	---	---
DSG1	1828	broad.mit.edu	37	18	28934721	28934721	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:28934721C>T	uc002kwp.2	+	15	2774	c.2562C>T	c.(2560-2562)CAC>CAT	p.H854H	DSG1_uc010xbp.1_Silent_p.H213H	NM_001942	NP_001933	Q02413	DSG1_HUMAN	desmoglein 1 preproprotein	854	Desmoglein repeat 2.|Cytoplasmic (Potential).				calcium-dependent cell-cell adhesion|cell-cell junction assembly|cellular component disassembly involved in apoptosis|homophilic cell adhesion|protein stabilization	cytosol|desmosome|integral to membrane|internal side of plasma membrane	calcium ion binding|gamma-catenin binding|toxin binding			skin(3)|ovary(2)|central_nervous_system(2)	7			OV - Ovarian serous cystadenocarcinoma(10;0.00559)															---	---	---	---
SETBP1	26040	broad.mit.edu	37	18	42529890	42529890	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr18:42529890G>A	uc010dni.2	+	4	881	c.585G>A	c.(583-585)ACG>ACA	p.T195T		NM_015559	NP_056374	Q9Y6X0	SETBP_HUMAN	SET binding protein 1 isoform a	195						nucleus	DNA binding			upper_aerodigestive_tract(2)|large_intestine(1)	3				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)										Schinzel-Giedion_syndrome				---	---	---	---
TBXA2R	6915	broad.mit.edu	37	19	3595783	3595783	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3595783C>T	uc002lyg.1	-	3	1149	c.935G>A	c.(934-936)CGC>CAC	p.R312H	TBXA2R_uc002lye.1_Silent_p.P182P	NM_001060	NP_001051	P21731	TA2R_HUMAN	thromboxane A2 receptor isoform alpha	312	Cytoplasmic (Potential).				platelet activation	integral to plasma membrane	guanyl-nucleotide exchange factor activity|protein binding|thromboxane A2 receptor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)													---	---	---	---
TBXA2R	6915	broad.mit.edu	37	19	3600540	3600540	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:3600540G>A	uc002lyg.1	-	2	307	c.93C>T	c.(91-93)GCC>GCT	p.A31A	TBXA2R_uc002lye.1_Silent_p.A31A	NM_001060	NP_001051	P21731	TA2R_HUMAN	thromboxane A2 receptor isoform alpha	31	Helical; Name=1; (Potential).				platelet activation	integral to plasma membrane	guanyl-nucleotide exchange factor activity|protein binding|thromboxane A2 receptor activity				0		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)													---	---	---	---
ZNF85	7639	broad.mit.edu	37	19	21131567	21131567	+	Missense_Mutation	SNP	G	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:21131567G>T	uc002npg.3	+	4	374	c.247G>T	c.(247-249)GCC>TCC	p.A83S	ZNF85_uc010ecn.2_Missense_Mutation_p.A18S|ZNF85_uc010eco.2_Missense_Mutation_p.A31S|ZNF85_uc002npi.2_Missense_Mutation_p.A24S	NM_003429	NP_003420	Q03923	ZNF85_HUMAN	zinc finger protein 85	83						nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|transcription corepressor activity|zinc ion binding			central_nervous_system(1)	1																		---	---	---	---
U2AF1L4	199746	broad.mit.edu	37	19	36234764	36234764	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36234764C>T	uc002obg.2	-	6	539	c.230G>A	c.(229-231)CGG>CAG	p.R77Q	TMEM149_uc002obb.2_5'Flank|TMEM149_uc002obc.2_5'Flank|TMEM149_uc002obd.3_5'Flank|TMEM149_uc010xsy.1_5'Flank|TMEM149_uc010eej.2_5'UTR|U2AF1L4_uc002obh.1_Silent_p.A34A|U2AF1L4_uc002obe.2_Missense_Mutation_p.R136Q|U2AF1L4_uc002obf.2_Missense_Mutation_p.G117S|PSENEN_uc002obi.1_5'Flank|PSENEN_uc002obj.1_5'Flank|PSENEN_uc002obk.1_5'Flank			Q8WU68	U2AF4_HUMAN	Homo sapiens cDNA FLJ35525 fis, clone SPLEN2001650.	175	C3H1-type 2.				mRNA processing|RNA splicing	nuclear speck|spliceosomal complex	nucleotide binding|RNA binding|zinc ion binding				0	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)															---	---	---	---
ARHGAP33	115703	broad.mit.edu	37	19	36278503	36278503	+	Silent	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:36278503G>A	uc002obs.1	+	21	2638	c.2553G>A	c.(2551-2553)GCG>GCA	p.A851A	ARHGAP33_uc002obt.1_Intron|ARHGAP33_uc010eel.2_Intron|ARHGAP33_uc002obv.1_Silent_p.A600A	NM_052948	NP_443180	O14559	RHG33_HUMAN	sorting nexin 26	Error:AA_residue_mismatch_between_GAF_and_UniProt_prot_seqs_after_alignment					cell communication|protein transport|signal transduction	intracellular	GTPase activator activity|phosphatidylinositol binding|protein binding			skin(2)|ovary(1)|pancreas(1)	4																		---	---	---	---
SAMD4B	55095	broad.mit.edu	37	19	39871241	39871241	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:39871241C>G	uc002olb.2	+	13	2699	c.1664C>G	c.(1663-1665)TCC>TGC	p.S555C	SAMD4B_uc002ola.2_Missense_Mutation_p.S555C	NM_018028	NP_060498	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	555							protein binding				0	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)															---	---	---	---
MEGF8	1954	broad.mit.edu	37	19	42837888	42837888	+	Nonsense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:42837888C>T	uc002otl.3	+	2	954	c.319C>T	c.(319-321)CGA>TGA	p.R107*		NM_001410	NP_001401	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	107	Extracellular (Potential).|CUB 1.					integral to membrane	calcium ion binding|structural molecule activity			ovary(1)	1		Prostate(69;0.00682)																---	---	---	---
CEACAM19	56971	broad.mit.edu	37	19	45175258	45175258	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:45175258G>A	uc002ozo.3	+	1	535	c.55G>A	c.(55-57)GCC>ACC	p.A19T	CEACAM19_uc002ozp.3_Missense_Mutation_p.A19T	NM_020219	NP_064604	Q7Z692	CEA19_HUMAN	carcinoembryonic antigen-related cell adhesion	19						integral to membrane					0	Lung NSC(12;0.00308)|all_lung(12;0.00806)	Prostate(69;0.0376)																---	---	---	---
FOXA3	3171	broad.mit.edu	37	19	46375727	46375727	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:46375727G>A	uc002pdr.2	+	2	661	c.464G>A	c.(463-465)CGG>CAG	p.R155Q		NM_004497	NP_004488	P55318	FOXA3_HUMAN	forkhead box A3	155	Fork-head.				brain development|cellular glucose homeostasis|cellular response to starvation|chromatin modification|embryo development|endocrine pancreas development|negative regulation of cell proliferation|neural plate anterior/posterior regionalization|neuron fate specification|positive regulation of hepatocyte differentiation|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity|spermatogenesis	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			breast(1)	1		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00453)|GBM - Glioblastoma multiforme(486;0.0518)|Epithelial(262;0.236)														---	---	---	---
LHB	3972	broad.mit.edu	37	19	49519499	49519499	+	Silent	SNP	G	A	A	rs138049984	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr19:49519499G>A	uc002plt.2	-	3	261	c.252C>T	c.(250-252)TTC>TTT	p.F84F		NM_000894	NP_000885	P01229	LSHB_HUMAN	luteinizing hormone beta subunit precursor	84					cell-cell signaling|cellular nitrogen compound metabolic process|male gonad development|peptide hormone processing|progesterone biosynthetic process|signal transduction	extracellular region|soluble fraction	hormone activity				0		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)	Lutropin alfa(DB00044)|Menotropins(DB00032)													---	---	---	---
PLCB1	23236	broad.mit.edu	37	20	8689336	8689336	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:8689336C>T	uc002wnb.2	+	12	1190	c.1187C>T	c.(1186-1188)GCG>GTG	p.A396V	PLCB1_uc010zrb.1_Missense_Mutation_p.A295V|PLCB1_uc002wna.2_Missense_Mutation_p.A396V|PLCB1_uc002wnc.1_Missense_Mutation_p.A295V	NM_015192	NP_056007	Q9NQ66	PLCB1_HUMAN	phosphoinositide-specific phospholipase C beta 1	396	PI-PLC X-box.				activation of meiosis involved in egg activation|CD24 biosynthetic process|cerebral cortex development|G1 phase|G2/M transition of mitotic cell cycle|glutamate signaling pathway|insulin-like growth factor receptor signaling pathway|interleukin-1-mediated signaling pathway|interleukin-12-mediated signaling pathway|interleukin-15-mediated signaling pathway|intracellular signal transduction|lipid catabolic process|memory|muscarinic acetylcholine receptor signaling pathway|negative regulation of monocyte extravasation|negative regulation of transcription, DNA-dependent|phosphatidylinositol metabolic process|positive regulation of acrosome reaction|positive regulation of developmental growth|positive regulation of embryonic development|positive regulation of interleukin-12 production|positive regulation of JNK cascade|positive regulation of myoblast differentiation|positive regulation of transcription, DNA-dependent|regulation of fertilization|regulation of G-protein coupled receptor protein signaling pathway|synaptic transmission	cytosol|nuclear chromatin|nuclear speck	calcium ion binding|calmodulin binding|enzyme binding|GTPase activator activity|phosphatidylinositol phospholipase C activity|phosphatidylinositol-4,5-bisphosphate binding|protein homodimerization activity|signal transducer activity			ovary(4)|breast(3)|upper_aerodigestive_tract(2)|skin(2)|lung(1)	12																		---	---	---	---
SLC24A3	57419	broad.mit.edu	37	20	19560723	19560723	+	Intron	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:19560723G>A	uc002wrl.2	+							NM_020689	NP_065740			solute carrier family 24							integral to membrane|plasma membrane	calcium, potassium:sodium antiporter activity|symporter activity			ovary(1)	1																		---	---	---	---
HM13	81502	broad.mit.edu	37	20	30142622	30142622	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:30142622C>T	uc002wwe.2	+	8	912	c.798C>T	c.(796-798)GTC>GTT	p.V266V	HM13_uc002wwc.2_Silent_p.V266V|HM13_uc002wwd.2_Silent_p.V266V|HM13_uc002wwf.2_Silent_p.V142V|HM13_uc010gdu.2_Silent_p.V142V	NM_030789	NP_110416	Q8TCT9	HM13_HUMAN	minor histocompatibility antigen 13 isoform 1	266	Helical; (Potential).				membrane protein proteolysis	cell surface|endoplasmic reticulum membrane|integral to membrane|plasma membrane	aspartic-type endopeptidase activity|protein binding			breast(1)	1	all_cancers(5;3.44e-05)|Lung NSC(7;4.38e-06)|all_lung(7;7.65e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		all cancers(5;0.000479)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)															---	---	---	---
DNMT3B	1789	broad.mit.edu	37	20	31376781	31376781	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:31376781G>A	uc002wyc.2	+	7	1097	c.776G>A	c.(775-777)CGG>CAG	p.R259Q	DNMT3B_uc010ztx.1_RNA|DNMT3B_uc010zty.1_RNA|DNMT3B_uc002wyd.2_Missense_Mutation_p.R259Q|DNMT3B_uc002wye.2_Missense_Mutation_p.R259Q|DNMT3B_uc010gee.2_RNA|DNMT3B_uc010gef.2_RNA|DNMT3B_uc010ztz.1_Missense_Mutation_p.R217Q|DNMT3B_uc010zua.1_Missense_Mutation_p.R183Q|DNMT3B_uc002wyf.2_Missense_Mutation_p.R271Q|DNMT3B_uc002wyg.2_5'Flank	NM_006892	NP_008823	Q9UBC3	DNM3B_HUMAN	DNA cytosine-5 methyltransferase 3 beta isoform	259	PWWP.|Interaction with DNMT1 and DNMT3A.				negative regulation of histone H3-K9 methylation|positive regulation of gene expression|positive regulation of histone H3-K4 methylation		metal ion binding|protein binding|transcription corepressor activity			lung(3)|ovary(2)	5																		---	---	---	---
VAPB	9217	broad.mit.edu	37	20	57019200	57019200	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:57019200C>T	uc002xza.2	+	6	912	c.641C>T	c.(640-642)ACT>ATT	p.T214I	VAPB_uc002xzb.2_RNA|VAPB_uc010zzo.1_Missense_Mutation_p.T91I|VAPB_uc002xzc.2_Silent_p.N93N	NM_004738	NP_004729	O95292	VAPB_HUMAN	VAMP-associated protein B/C	214	Cytoplasmic (Potential).				cell death|endoplasmic reticulum unfolded protein response|positive regulation of viral genome replication|sphingolipid metabolic process|virus-host interaction	endoplasmic reticulum membrane|Golgi apparatus|integral to membrane	beta-tubulin binding|enzyme binding|protein heterodimerization activity|protein homodimerization activity|structural molecule activity			kidney(1)	1	Lung NSC(12;0.000615)|all_lung(29;0.00186)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;3.7e-08)|all cancers(14;3.88e-07)															---	---	---	---
SYCP2	10388	broad.mit.edu	37	20	58491600	58491600	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:58491600C>T	uc002yaz.2	-	7	593	c.454G>A	c.(454-456)GTA>ATA	p.V152I	SYCP2_uc010gju.1_Missense_Mutation_p.V53I	NM_014258	NP_055073	Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	152					cell division|meiotic prophase I|synaptonemal complex assembly		DNA binding			ovary(3)|lung(2)	5	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)															---	---	---	---
CDH4	1002	broad.mit.edu	37	20	59829898	59829898	+	Missense_Mutation	SNP	T	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:59829898T>G	uc002ybn.1	+	2	88	c.74T>G	c.(73-75)CTT>CGT	p.L25R		NM_001794	NP_001785	P55283	CADH4_HUMAN	cadherin 4, type 1 preproprotein	25					adherens junction organization|cell junction assembly		calcium ion binding			lung(3)|ovary(2)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)															---	---	---	---
EEF1A2	1917	broad.mit.edu	37	20	62120393	62120393	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr20:62120393C>T	uc002yfd.1	-	6	1243	c.1142G>A	c.(1141-1143)CGG>CAG	p.R381Q	EEF1A2_uc002yfe.1_Missense_Mutation_p.R381Q|EEF1A2_uc010gkg.1_Intron	NM_001958	NP_001949	Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha	381						nucleus	GTP binding|GTPase activity|protein binding|translation elongation factor activity				0	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)															---	---	---	---
ARVCF	421	broad.mit.edu	37	22	19960456	19960456	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:19960456G>A	uc002zqz.2	-	15	2813	c.2542C>T	c.(2542-2544)CGC>TGC	p.R848C	ARVCF_uc002zqy.2_Missense_Mutation_p.R364C	NM_001670	NP_001661	O00192	ARVC_HUMAN	armadillo repeat protein	848					cell adhesion|multicellular organismal development		protein binding			liver(1)	1	Colorectal(54;0.0993)																	---	---	---	---
CRYBB2	1415	broad.mit.edu	37	22	25627687	25627687	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:25627687G>A	uc003abp.1	+	6	614	c.566G>A	c.(565-567)CGT>CAT	p.R189H		NM_000496	NP_000487	P43320	CRBB2_HUMAN	crystallin, beta B2	189	Beta/gamma crystallin 'Greek key' 4.				response to stimulus|visual perception		structural constituent of eye lens				0																		---	---	---	---
APOBEC3A	200315	broad.mit.edu	37	22	39357648	39357648	+	Missense_Mutation	SNP	G	A	A			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39357648G>A	uc003awn.2	+	3	601	c.431G>A	c.(430-432)CGG>CAG	p.R144Q	APOBEC3A_uc011aob.1_Missense_Mutation_p.R126Q|APOBEC3A_uc011aoc.1_Missense_Mutation_p.R144Q	NM_145699	NP_663745	P31941	ABC3A_HUMAN	phorbolin 1	144					cellular response to xenobiotic stimulus|defense response to virus|DNA cytosine deamination|DNA demethylation|innate immune response|negative regulation of transposition|negative regulation of viral genome replication	cytoplasm|nucleus	cytidine deaminase activity|zinc ion binding			ovary(1)	1	Melanoma(58;0.04)																	---	---	---	---
MGAT3	4248	broad.mit.edu	37	22	39884034	39884034	+	Missense_Mutation	SNP	C	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:39884034C>G	uc003axv.3	+	2	921	c.682C>G	c.(682-684)CTG>GTG	p.L228V	MGAT3_uc010gxy.2_Missense_Mutation_p.L228V	NM_002409	NP_002400	Q09327	MGAT3_HUMAN	mannosyl (beta-1,4-)-glycoprotein	228	Lumenal (Potential).				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	beta-1,4-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity				0	Melanoma(58;0.04)																	---	---	---	---
GRAMD4	23151	broad.mit.edu	37	22	47059001	47059001	+	Silent	SNP	C	T	T	rs141555305	by1000genomes	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chr22:47059001C>T	uc003bhx.2	+	5	570	c.531C>T	c.(529-531)TAC>TAT	p.Y177Y	GRAMD4_uc010had.2_Silent_p.Y116Y	NM_015124	NP_055939	Q6IC98	GRAM4_HUMAN	death-inducing-protein	177					apoptosis	integral to membrane|mitochondrial membrane				ovary(1)	1		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.166)														---	---	---	---
TFE3	7030	broad.mit.edu	37	X	48891674	48891674	+	Silent	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:48891674C>T	uc004dmb.3	-	6	1216	c.978G>A	c.(976-978)CTG>CTA	p.L326L	TFE3_uc004dmc.3_Silent_p.L221L|TFE3_uc004dme.1_RNA	NM_006521	NP_006512	P19532	TFE3_HUMAN	transcription factor E3	326					humoral immune response|positive regulation of transcription from RNA polymerase II promoter	cytoplasm|nucleus	sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding		ASPSCR1/TFE3(161)|PRCC/TFE3(25)|SFPQ/TFE3(6)|NONO/TFE3(2)|CLTC/TFE3(2)	soft_tissue(120)|kidney(76)|central_nervous_system(1)	197								T	SFPQ|ASPSCR1|PRCC|NONO|CLTC	papillary renal|alveolar soft part sarcoma|renal								---	---	---	---
CAPN6	827	broad.mit.edu	37	X	110489938	110489938	+	Missense_Mutation	SNP	A	G	G			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110489938A>G	uc004epc.1	-	13	1961	c.1793T>C	c.(1792-1794)CTG>CCG	p.L598P	CAPN6_uc011msu.1_Missense_Mutation_p.L343P	NM_014289	NP_055104	Q9Y6Q1	CAN6_HUMAN	calpain 6	598	C2.				microtubule bundle formation|proteolysis|regulation of cytoskeleton organization	perinuclear region of cytoplasm|spindle microtubule	calcium-dependent cysteine-type endopeptidase activity|microtubule binding			ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
CAPN6	827	broad.mit.edu	37	X	110494194	110494194	+	Missense_Mutation	SNP	C	T	T			TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:110494194C>T	uc004epc.1	-	8	1277	c.1109G>A	c.(1108-1110)CGC>CAC	p.R370H	CAPN6_uc011msu.1_Missense_Mutation_p.R115H	NM_014289	NP_055104	Q9Y6Q1	CAN6_HUMAN	calpain 6	370	Domain III.				microtubule bundle formation|proteolysis|regulation of cytoskeleton organization	perinuclear region of cytoplasm|spindle microtubule	calcium-dependent cysteine-type endopeptidase activity|microtubule binding			ovary(2)|upper_aerodigestive_tract(1)|large_intestine(1)|lung(1)|skin(1)	6																		---	---	---	---
PRRG3	79057	broad.mit.edu	37	X	150869273	150869273	+	Missense_Mutation	SNP	C	T	T	rs142444421	byFrequency	TCGA-BR-4367-01A-01D-1158-08	TCGA-BR-4367-11A-01D-1158-08									Somatic	Phase_I	Capture				Illumina GAIIx	g.chrX:150869273C>T	uc004few.1	+	4	854	c.464C>T	c.(463-465)CCC>CTC	p.P155L		NM_024082	NP_076987	Q9BZD7	TMG3_HUMAN	proline rich Gla (G-carboxyglutamic acid) 3	155	Cytoplasmic (Potential).					extracellular region|integral to membrane	calcium ion binding			ovary(3)|skin(1)	4	Acute lymphoblastic leukemia(192;6.56e-05)																	---	---	---	---
