##gff-version 3 Q92560 UniProtKB Chain 1 729 . . . ID=PRO_0000211069;Note=Ubiquitin carboxyl-terminal hydrolase BAP1 Q92560 UniProtKB Region 301 351 . . . Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite Q92560 UniProtKB Region 372 435 . . . Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite Q92560 UniProtKB Region 464 524 . . . Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite Q92560 UniProtKB Region 575 623 . . . Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite Q92560 UniProtKB Region 596 721 . . . Note=Interaction with BRCA1 Q92560 UniProtKB Region 703 729 . . . Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite Q92560 UniProtKB Coiled coil 630 661 . . . Ontology_term=ECO:0000255;evidence=ECO:0000255 Q92560 UniProtKB Motif 363 366 . . . Note=HBM-like motif;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:19188440,ECO:0000269|PubMed:19815555,ECO:0000269|PubMed:25451922;Dbxref=PMID:19188440,PMID:19815555,PMID:25451922 Q92560 UniProtKB Motif 717 722 . . . Note=Nuclear localization signal;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18757409,ECO:0000269|PubMed:24703950;Dbxref=PMID:18757409,PMID:24703950 Q92560 UniProtKB Compositional bias 583 602 . . . Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite Q92560 UniProtKB Compositional bias 704 729 . . . Note=Basic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite Q92560 UniProtKB Active site 91 91 . . . Note=Nucleophile;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18757409,ECO:0000269|PubMed:19117993,ECO:0000269|PubMed:19188440,ECO:0000269|PubMed:19815555,ECO:0000269|PubMed:25451922,ECO:0000269|PubMed:9528852;Dbxref=PMID:18757409,PMID:19117993,PMID:19188440,PMID:19815555,PMID:25451922,PMID:9528852 Q92560 UniProtKB Active site 169 169 . . . Note=Proton donor;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P09936 Q92560 UniProtKB Site 184 184 . . . Note=Important for enzyme activity;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P09936 Q92560 UniProtKB Modified residue 292 292 . . . Note=Phosphoserine;Ontology_term=ECO:0007744;evidence=ECO:0007744|PubMed:23186163;Dbxref=PMID:23186163 Q92560 UniProtKB Modified residue 369 369 . . . Note=Phosphoserine;Ontology_term=ECO:0007744;evidence=ECO:0007744|PubMed:23186163;Dbxref=PMID:23186163 Q92560 UniProtKB Modified residue 395 395 . . . Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99PU7 Q92560 UniProtKB Modified residue 493 493 . . . Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25451922;Dbxref=PMID:25451922 Q92560 UniProtKB Modified residue 521 521 . . . Note=Phosphoserine;Ontology_term=ECO:0007744;evidence=ECO:0007744|PubMed:23186163;Dbxref=PMID:23186163 Q92560 UniProtKB Modified residue 537 537 . . . Note=Phosphoserine;Ontology_term=ECO:0007744;evidence=ECO:0007744|PubMed:23186163;Dbxref=PMID:23186163 Q92560 UniProtKB Modified residue 585 585 . . . Note=Phosphoserine;Ontology_term=ECO:0007744;evidence=ECO:0007744|PubMed:23186163;Dbxref=PMID:23186163 Q92560 UniProtKB Modified residue 597 597 . . . Note=Phosphoserine;Ontology_term=ECO:0007744;evidence=ECO:0007744|PubMed:23186163;Dbxref=PMID:23186163 Q92560 UniProtKB Natural variant 12 12 . . . ID=VAR_086937;Note=In KURIS. P->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:35051358;Dbxref=PMID:35051358 Q92560 UniProtKB Natural variant 12 12 . . . ID=VAR_086938;Note=In KURIS%3B loss-of-function variant%3B increased steady-state levels of ubiquitinated H2A are found in patient cells%3B unable to rescue impaired H2AK119ub deubiquitination when expressed in BAP1-deficient cells%3B does not affect localization to the nucleus. P->T;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:35051358;Dbxref=PMID:35051358 Q92560 UniProtKB Natural variant 31 31 . . . ID=VAR_086939;Note=In KURIS%3B uncertain significance. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:35051358;Dbxref=PMID:35051358 Q92560 UniProtKB Natural variant 47 47 . . . ID=VAR_075251;Note=Found in a primary uveal melanoma%3B somatic mutation%3B induces cytoplasmic accumulation%3B loss of deubiquitinase activity%3B up-regulates heat shock response%3B induces formation of amyloid-beta aggregates. I->F;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:25080371,ECO:0000269|PubMed:26680512;Dbxref=PMID:25080371,PMID:26680512 Q92560 UniProtKB Natural variant 49 49 . . . ID=VAR_086940;Note=In KURIS%3B uncertain significance. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:35051358;Dbxref=PMID:35051358 Q92560 UniProtKB Natural variant 63 63 . . . ID=VAR_065976;Note=Found in a malignant pleural mesothelioma sample%3B somatic mutation. S->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21642991;Dbxref=dbSNP:rs747311942,PMID:21642991 Q92560 UniProtKB Natural variant 81 81 . . . ID=VAR_065977;Note=Found in a malignant pleural mesothelioma sample%3B somatic mutation%3B induces cytoplasmic accumulation%3B loss of deubiquitinase activity%3B up-regulates heat shock response%3B induces formation of amyloid-beta aggregates. F->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:21642991,ECO:0000269|PubMed:26680512;Dbxref=PMID:21642991,PMID:26680512 Q92560 UniProtKB Natural variant 91 91 . . . ID=VAR_086941;Note=In KURIS. C->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:35051358;Dbxref=PMID:35051358 Q92560 UniProtKB Natural variant 91 91 . . . ID=VAR_086942;Note=In KURIS%3B loss-of-function variant%3B unable to rescue impaired H2AK119ub deubiquitination when expressed in BAP1-deficient cells%3B does not affect localization to the nucleus. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:35051358;Dbxref=dbSNP:rs1705222655,PMID:35051358 Q92560 UniProtKB Natural variant 91 91 . . . ID=VAR_086943;Note=In KURIS%3B loss-of-function variant%3B increased steady-state level of ubiquitinated H2A are found in patient cells%3B unable to rescue impaired H2AK119ub deubiquitination when expressed in BAP1-deficient cells%3B abolishes deubiquitinase activity without affecting its ability to interfere with BRCA1 E3 ligase activity%3B does not affect localization to the nucleus%3B has a dominant negative effect on cell growth%3B does not affect interaction with FOXK1 and FOXK2. C->S;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:19117993,ECO:0000269|PubMed:19815555,ECO:0000269|PubMed:25451922,ECO:0000269|PubMed:35051358;Dbxref=PMID:19117993,PMID:19815555,PMID:25451922,PMID:35051358 Q92560 UniProtKB Natural variant 91 91 . . . ID=VAR_065978;Note=Found in a malignant pleural mesothelioma sample. C->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21642991;Dbxref=PMID:21642991 Q92560 UniProtKB Natural variant 93 93 . . . ID=VAR_087531;Note=In TPDS1%3B significantly increased risk for renal cell carcinoma. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23684012;Dbxref=PMID:23684012 Q92560 UniProtKB Natural variant 95 95 . . . ID=VAR_063498;Note=In a lung cancer sample%3B also found in a malignant pleural mesothelioma cell line%3B induces cytoplasmic accumulation%3B loss of deubiquitinase activity%3B up-regulates heat shock response%3B induces formation of amyloid-beta aggregates. A->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10546591,ECO:0000269|PubMed:18757409,ECO:0000269|PubMed:21642991,ECO:0000269|PubMed:26680512;Dbxref=PMID:10546591,PMID:18757409,PMID:21642991,PMID:26680512 Q92560 UniProtKB Natural variant 169 169 . . . ID=VAR_086944;Note=In KURIS%3B loss-of-function variant%3B unable to rescue impaired H2AK119ub deubiquitination when expressed in BAP1-deficient cells%3B does not affect localization to the nucleus. H->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:35051358;Dbxref=PMID:35051358 Q92560 UniProtKB Natural variant 178 178 . . . ID=VAR_063499;Note=In a lung cancer sample%3B induces cytoplasmic accumulation%3B impairs deubiquitinase activity%3B up-regulates heat shock response%3B induces formation of beta-amyloid aggregates. G->V;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10546591,ECO:0000269|PubMed:18757409,ECO:0000269|PubMed:26680512;Dbxref=PMID:10546591,PMID:18757409,PMID:26680512 Q92560 UniProtKB Natural variant 267 729 . . . ID=VAR_087532;Note=In TPDS1. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21941004;Dbxref=PMID:21941004 Q92560 UniProtKB Natural variant 315 315 . . . ID=VAR_065979;Note=Found in a malignant pleural mesothelioma sample. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21642991;Dbxref=dbSNP:rs149974450,PMID:21642991 Q92560 UniProtKB Natural variant 616 616 . . . ID=VAR_051517;Note=V->E;Dbxref=dbSNP:rs35353781 Q92560 UniProtKB Natural variant 685 685 . . . ID=VAR_065980;Note=Found in a malignant pleural mesothelioma cell line. E->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21642991;Dbxref=PMID:21642991 Q92560 UniProtKB Natural variant 718 718 . . . ID=VAR_086945;Note=In KURIS%3B uncertain significance%3B able to rescue impaired H2AK119ub deubiquitination when expressed in BAP1-deficient cells%3B does not affect localization to the nucleus. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:35051358;Dbxref=dbSNP:rs1440748203,PMID:35051358 Q92560 UniProtKB Mutagenesis 91 91 . . . Note=Abolishes enzymatic activity. Has no effect on interaction with HCFC1. C->A;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:18757409,ECO:0000269|PubMed:19188440,ECO:0000269|PubMed:9528852;Dbxref=PMID:18757409,PMID:19188440,PMID:9528852 Q92560 UniProtKB Mutagenesis 363 366 . . . Note=Abolishes interaction with HCFC1 without affecting interaction with FOXK1 and FOXK2. NHNY->AAAA;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:19188440,ECO:0000269|PubMed:19815555,ECO:0000269|PubMed:25451922;Dbxref=PMID:19188440,PMID:19815555,PMID:25451922 Q92560 UniProtKB Mutagenesis 489 489 . . . Note=Does not affect interaction with FOXK1 and FOXK2. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25451922;Dbxref=PMID:25451922 Q92560 UniProtKB Mutagenesis 492 492 . . . Note=Does not affect interaction with FOXK1 and FOXK2. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25451922;Dbxref=PMID:25451922 Q92560 UniProtKB Mutagenesis 493 493 . . . Note=Abolished interaction with FOXK1 and FOXK2. T->A%2CL;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25451922;Dbxref=PMID:25451922 Q92560 UniProtKB Mutagenesis 495 495 . . . Note=Does not affect interaction with FOXK1 and FOXK2. T->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25451922;Dbxref=PMID:25451922 Q92560 UniProtKB Mutagenesis 656 661 . . . Note=Does not affect nuclear localization. KRKKFK->AAAAAA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18757409;Dbxref=PMID:18757409 Q92560 UniProtKB Mutagenesis 691 711 . . . Note=Abolishes ubiquitination by UBE2O. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24703950;Dbxref=PMID:24703950 Q92560 UniProtKB Mutagenesis 691 691 . . . Note=Abolishes interaction with BRCA1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9528852;Dbxref=PMID:9528852 Q92560 UniProtKB Mutagenesis 717 722 . . . Note=Abolishes nuclear localization. RRKRSR->AAAAAA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18757409;Dbxref=PMID:18757409 Q92560 UniProtKB Helix 12 22 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 28 30 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 46 52 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 55 59 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 68 70 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 75 79 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 91 101 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 110 119 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 124 132 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 135 143 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 148 151 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 167 175 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 178 186 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 198 200 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 203 217 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 220 222 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 228 234 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 237 242 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 648 667 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 672 685 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Helix 688 694 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T Q92560 UniProtKB Beta strand 700 703 . . . Ontology_term=ECO:0007829;evidence=ECO:0007829|PDB:8H1T