Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0032183 SUMO binding	IBA GO_REF:0000033	ACCEPT	Summary: USP25 binds SUMO via an N-terminal SUMO-interaction domain/SIM and is sumoylated paralog-specifically; SUMO binding is experimentally documented and also inferred phylogenetically. Reason: SUMO binding is directly supported by experimental interaction with SUMO2/SUMO3 (PMID:18538659) and is consistent with the phylogenetic inference. It is a real regulatory molecular function (sumoylation impairs ubiquitin binding/hydrolysis), though it is auxiliary to the core deubiquitinase activity. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Interacts with SUMO3; the interaction sumoylates efficiently USP25.
GO:0004843 cysteine-type deubiquitinase activity	IEA GO_REF:0000120	ACCEPT	Summary: Electronic (InterPro/EC) annotation of cysteine-type deubiquitinase activity, the core catalytic function of USP25, fully corroborated by experimental evidence. Reason: USP25 is a peptidase C19 family cysteine protease (EC 3.4.19.12) with active-site Cys-178; this IEA agrees with EXP/IDA catalytic-activity evidence and is the core molecular function. Supporting Evidence: file:human/USP25/USP25-uniprot.txt EC=3.4.19.12
GO:0005634 nucleus	IEA GO_REF:0000044	MARK AS OVER ANNOTATED	Summary: Electronic localization to the nucleus from a UniProt subcellular-location keyword. USP25 is principally cytoplasmic; nuclear localization is only weakly supported (transient punctate nuclear signal of the USP25m isoform in myotubes). Reason: The strong experimental evidence places USP25 in the cytoplasm/cytosol; nuclear localization rests on an IEA keyword and an inferred-by-similarity note limited to transient USP25m signal in differentiating myotubes, so it is not a robust general localization. Supporting Evidence: file:human/USP25/USP25-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: Electronic cytoplasmic localization, consistent with strong experimental evidence for cytoplasmic USP25. Reason: Multiple EXP/IDA studies localize USP25 to the cytoplasm; this IEA agrees with the experimentally supported compartment. Supporting Evidence: file:human/USP25/USP25-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0016579 protein deubiquitination	IEA GO_REF:0000002	ACCEPT	Summary: Electronic annotation of protein deubiquitination, the biological process executed by USP25's catalytic activity; well supported. Reason: Protein deubiquitination is the direct process outcome of USP25's cysteine-type deubiquitinase activity and is corroborated by multiple experimental studies. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
GO:0005515 protein binding	IPI PMID:21516116 Next-generation sequencing to generate interactome datasets.	KEEP AS NON CORE	Summary: IntAct interaction with SYK (P43405), a validated USP25 partner (SYK phosphorylates USP25 and regulates its levels). The bare protein binding term is uninformative. Reason: Records a real interaction (SYK), but per curation guidelines bare protein binding is uninformative and not a core function; the SYK relationship is captured in regulation rather than as a molecular function. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; P43405: SYK
GO:0005515 protein binding	IPI PMID:22153077 Structural basis and sequence rules for substrate recognitio...	KEEP AS NON CORE	Summary: IntAct interaction with TNKS2 (Q9H2K2), a validated USP25 substrate (USP25 deubiquitinates and stabilizes tankyrases). The bare protein binding term is uninformative; the biologically meaningful relationship is enzyme-substrate. Reason: Real and functionally relevant interaction (TNKS2), but bare protein binding is uninformative as a molecular function; the substrate relationship informs the Wnt-regulation role rather than constituting a core MF. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; Q9H2K2: TNKS2
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	KEEP AS NON CORE	Summary: High-throughput yeast two-hybrid interactome capturing USP25 interactions with MAGEB4, SYK, RAD23A, SUMO2 and ZNF426. The bare protein binding term is uninformative. Reason: Records real high-throughput interactions but bare protein binding is uninformative and not core; SUMO2 binding and SYK are captured elsewhere. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; O15481: MAGEB4
GO:0005515 protein binding	IPI PMID:28514442 Architecture of the human interactome defines protein commun...	KEEP AS NON CORE	Summary: IntAct interactions with the proteasome-shuttle UBA-domain proteins RAD23A/RAD23B (P54725/P54727). The bare protein binding term is uninformative. Reason: Records recurrent interactions with RAD23A/B but bare protein binding is uninformative and not a core molecular function. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; P54725: RAD23A
GO:0005515 protein binding	IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari...	KEEP AS NON CORE	Summary: IntAct interaction with RAD23A (P54725). The bare protein binding term is uninformative. Reason: Records a real interaction but bare protein binding is uninformative and not core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; P54725: RAD23A
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	KEEP AS NON CORE	Summary: Multi-partner IntAct screen (RAD23A/B, PUS10, TMEM43, MID2 and others). The bare protein binding term is uninformative. Reason: Records real high-throughput interactions but bare protein binding is uninformative and not core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; Q3MIT2: PUS10
GO:0005515 protein binding	IPI PMID:32707033 Kinase Interaction Network Expands Functional and Disease Ro...	KEEP AS NON CORE	Summary: IntAct interaction with SYK (P43405), a validated partner. The bare protein binding term is uninformative. Reason: Records a real interaction (SYK) but bare protein binding is uninformative and not core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; P43405: SYK
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	KEEP AS NON CORE	Summary: Neurodegeneration interactome screen capturing interactions with PRKACA, TGFBR2 and RAD23A. The bare protein binding term is uninformative. Reason: Records high-throughput interactions but bare protein binding is uninformative and not core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; P17612: PRKACA
GO:0005515 protein binding	IPI PMID:33060197 Comparative host-coronavirus protein interaction networks re...	KEEP AS NON CORE	Summary: IntAct interaction with the SARS-CoV-2 replicase polyprotein (P0DTD1) from a viral-host interactome screen. The bare protein binding term is uninformative. Reason: Records a viral-interactome interaction but bare protein binding is uninformative and not a core function of USP25. Supporting Evidence: file:human/USP25/USP25-uniprot.txt PRO_0000449633 [P0DTD1]: rep
GO:0005515 protein binding	IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling...	KEEP AS NON CORE	Summary: BioPlex affinity-purification interactome capturing interactions with GDI1 and RAD23B. The bare protein binding term is uninformative. Reason: Records high-throughput interactions but bare protein binding is uninformative and not core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; P31150: GDI1
GO:0005515 protein binding	IPI PMID:34232536 Interactomes of SARS-CoV-2 and human coronaviruses reveal ho...	KEEP AS NON CORE	Summary: IntAct interaction with the SARS-CoV-2 replicase polyprotein (P0DTD1) from a viral-host interactome study. The bare protein binding term is uninformative. Reason: Records a viral-interactome interaction but bare protein binding is uninformative and not core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt PRO_0000449633 [P0DTD1]: rep
GO:0005515 protein binding	IPI PMID:35914814 Chr21 protein-protein interactions: enrichment in proteins i...	KEEP AS NON CORE	Summary: IntAct screen capturing interactions with GDI1, RAD23B and TNKS2. The bare protein binding term is uninformative; the TNKS2 interaction is a validated substrate relationship. Reason: Records real interactions including the TNKS2 substrate, but bare protein binding is uninformative and not a core molecular function. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; Q9H2K2: TNKS2
GO:0005515 protein binding	IPI PMID:36217029 A proteome-scale map of the SARS-CoV-2-human contactome.	KEEP AS NON CORE	Summary: IntAct interaction with the SARS-CoV-2 replicase polyprotein (P0DTD1). The bare protein binding term is uninformative. Reason: Records a viral-interactome interaction but bare protein binding is uninformative and not core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt PRO_0000449633 [P0DTD1]: rep
GO:0005515 protein binding	IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func...	KEEP AS NON CORE	Summary: Multimodal cell-maps interactome capturing interactions with RAD23A/RAD23B. The bare protein binding term is uninformative. Reason: Records high-throughput interactions but bare protein binding is uninformative and not core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Q9UHP3; P54727: RAD23B
GO:0006955 immune response	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Electronic (Ensembl ortholog) annotation of immune response. USP25 has documented roles in innate immunity and inflammation (IL-17 signaling, antiviral TRAF3/ERLIN1-2), so the broad process is plausible but non-specific. Reason: USP25 participates in immune signaling but the bare "immune response" term is broad and inherited by ortholog transfer; more specific BP terms (e.g. negative regulation of IL-17 signaling) better capture the role. Supporting Evidence: file:human/USP25/USP25-uniprot.txt functions in various biological processes including inflammation and immune response
GO:0006979 response to oxidative stress	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Electronic (ortholog) annotation of response to oxidative stress. USP25 regulates the KEAP1-NRF2 anti-oxidation axis, making the process plausible, though its specific role is negative regulation (stabilizing KEAP1, promoting NRF2 degradation). Reason: Supported in spirit by the KEAP1-NRF2 role, but the IDA term "negative regulation of response to oxidative stress" is the more precise annotation; this broad ortholog-transferred term is non-core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Regulates KEAP1- NRF2 axis in the defense against oxidative assaults by deubiquitinating
GO:0016071 mRNA metabolic process	IEA GO_REF:0000107	REMOVE	Summary: Electronic (ortholog) annotation of mRNA metabolic process. There is no direct experimental evidence in the human record linking USP25 to mRNA metabolism. Reason: No experimental or curated support ties USP25 to mRNA metabolism in the UniProt record or literature reviewed; this appears to be an over-broad ortholog-transferred annotation. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
GO:0031098 stress-activated protein kinase signaling cascade	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Electronic (ortholog) annotation of SAPK signaling. USP25 influences JNK/p38 phosphorylation via TRAF3 stabilization, so a connection exists but is indirect. Reason: USP25 modulates JNK/p38 (SAPK) levels through TRAF3 stabilization, so the term is plausible but indirect and ortholog-transferred; non-core. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Prevents the ubiquitination and degradation of TRAF3 to reduce the phosphorylation levels of JNK and P38
GO:0065003 protein-containing complex assembly	IEA GO_REF:0000107	REMOVE	Summary: Electronic (ortholog) annotation of protein-containing complex assembly. There is no direct evidence that USP25 functions in complex assembly as a biological role. Reason: No experimental support links USP25 to a complex-assembly process; this is an over-broad ortholog-transferred annotation. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
GO:0097400 interleukin-17-mediated signaling pathway	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Electronic (ortholog) annotation placing USP25 in the IL-17 signaling pathway, strongly corroborated experimentally (USP25 removes K63-Ub from TRAF5/TRAF6). The validated role is negative regulation of this pathway. Reason: USP25's involvement in IL-17 signaling is well established experimentally; the more precise IDA term "negative regulation of interleukin-17-mediated signaling pathway" captures the directionality, so this broad term is retained as non-core. Supporting Evidence: PMID:23042150 USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
GO:0016579 protein deubiquitination	TAS Reactome:R-HSA-5688426	ACCEPT	Summary: Reactome curated annotation of protein deubiquitination, the core process of USP25. Reason: Protein deubiquitination is the direct biological process of USP25's catalytic activity and is well supported across experimental and curated sources. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
GO:0004843 cysteine-type deubiquitinase activity	TAS Reactome:R-HSA-5696564	ACCEPT	Summary: Reactome curated annotation of cysteine-type deubiquitinase activity, the core catalytic molecular function of USP25. Reason: This is the central, experimentally validated molecular function of USP25 (active-site Cys-178; EC 3.4.19.12). Supporting Evidence: file:human/USP25/USP25-uniprot.txt EC=3.4.19.12
GO:0005829 cytosol	IDA GO_REF:0000052	ACCEPT	Summary: Direct immunofluorescence (HPA) cytosolic localization, consistent with the experimentally established cytoplasmic localization of USP25. Reason: IDA-supported cytosolic localization agrees with multiple experimental cytoplasm annotations and the gene's documented site of action. Supporting Evidence: file:human/USP25/USP25-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0004843 cysteine-type deubiquitinase activity	EXP PMID:23042150 Negative regulation of IL-17-mediated signaling and inflamma...	ACCEPT	Summary: Experimental demonstration of deubiquitinase catalytic activity in the context of removing K63-linked ubiquitin from TRAF5/TRAF6 during IL-17 signaling. Reason: Direct experimental evidence for cysteine-type deubiquitinase activity; this is the core molecular function of USP25. Supporting Evidence: PMID:23042150 USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
GO:0004843 cysteine-type deubiquitinase activity	EXP PMID:37339955 USP25 regulates KEAP1-NRF2 anti-oxidation axis and its inact...	ACCEPT	Summary: Experimental demonstration of deubiquitinase activity through deubiquitination and stabilization of KEAP1 (catalytic-dead C178S abolishes activity). Reason: Direct experimental support for the core cysteine-type deubiquitinase activity; C178S mutagenesis confirms catalytic dependence. Supporting Evidence: PMID:37339955 Here we report that USP25 deubiquitinates KEAP1 and prevents it from excessive ubiquitination and degradation.
GO:0005737 cytoplasm	EXP PMID:28619731 USP25 regulates Wnt signaling by controlling the stability o...	ACCEPT	Summary: Experimental cytoplasmic localization (from the tankyrase/Wnt study), consistent with USP25's established compartment. Reason: Experimental evidence supports cytoplasmic localization, the principal site of USP25 action. Supporting Evidence: file:human/USP25/USP25-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0005737 cytoplasm	IMP PMID:38875478 Heterozygous variants in USP25 cause genetic generalized epi...	ACCEPT	Summary: Cytoplasmic localization reported alongside characterization of epilepsy-associated USP25 variants; consistent with the established cytoplasmic compartment. Reason: Supports cytoplasmic localization, agreeing with other experimental evidence. Supporting Evidence: file:human/USP25/USP25-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0101005 deubiquitinase activity	IMP PMID:38875478 Heterozygous variants in USP25 cause genetic generalized epi...	MODIFY	Summary: Deubiquitinase activity assayed for epilepsy-associated USP25 variants; a C-terminal truncation is a gain-of-function increasing deubiquitination. This is the parent term of the more precise cysteine-type deubiquitinase activity. Reason: GO:0101005 (deubiquitinase activity) is correct but less precise than the mechanistically defined GO:0004843 (cysteine-type deubiquitinase activity) already annotated for USP25; using the specific term is preferable. Proposed replacements: cysteine-type deubiquitinase activity Supporting Evidence: file:human/USP25/USP25-uniprot.txt gain-of-function variant resulting in increased protein deubiquitination
GO:0005737 cytoplasm	IDA PMID:19440361 The UBA-UIM domains of the USP25 regulate the enzyme ubiquit...	ACCEPT	Summary: Direct evidence that USP25 is active in the cytoplasm, where its UBA-UIM domains regulate ubiquitination state and substrate recognition. Reason: The is_active_in cytoplasm annotation correctly places USP25's deubiquitinase activity in its principal compartment, with direct experimental support. Supporting Evidence: file:human/USP25/USP25-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0101005 deubiquitinase activity	IDA PMID:37339955 USP25 regulates KEAP1-NRF2 anti-oxidation axis and its inact...	MODIFY	Summary: Direct assay of deubiquitinase activity (KEAP1 deubiquitination). This is the parent of the more precise cysteine-type deubiquitinase activity term. Reason: GO:0101005 is correct but less precise; USP25 is a cysteine-type DUB (Cys-178), so GO:0004843 is the appropriate specific molecular function. Proposed replacements: cysteine-type deubiquitinase activity Supporting Evidence: PMID:37339955 Here we report that USP25 deubiquitinates KEAP1 and prevents it from excessive ubiquitination and degradation.
GO:1902883 negative regulation of response to oxidative stress	IDA PMID:37339955 USP25 regulates KEAP1-NRF2 anti-oxidation axis and its inact...	ACCEPT	Summary: USP25 negatively regulates the oxidative-stress response by deubiquitinating and stabilizing KEAP1, which promotes degradation of the antioxidant transcription factor NRF2; loss of USP25 is protective in acetaminophen liver injury. Reason: Directly supported experimentally; captures USP25's specific role in the KEAP1-NRF2 axis with correct directionality. Supporting Evidence: PMID:37339955 Here we report that USP25 deubiquitinates KEAP1 and prevents it from excessive ubiquitination and degradation.
GO:0005737 cytoplasm	IDA PMID:2304215 Problems identified by secondary review of accepted manuscri...	KEEP AS NON CORE	Summary: is_active_in cytoplasm annotation. The cited reference PMID:2304215 (a 1990 paper) predates USP25 characterization and appears to be an incorrect/legacy citation, but the cytoplasmic site of activity itself is well supported by other experimental evidence. Reason: The cytoplasmic activity location is correct and redundantly supported by stronger evidence (PMID:19440361); however the specific reference appears to be a citation error, so the annotation is retained but not relied upon. Supporting Evidence: file:human/USP25/USP25-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0101005 deubiquitinase activity	IDA PMID:23042150 Negative regulation of IL-17-mediated signaling and inflamma...	MODIFY	Summary: Direct assay of deubiquitinase activity (removal of K63-linked ubiquitin from TRAF5/TRAF6). This is the parent of the more precise cysteine-type deubiquitinase activity term. Reason: GO:0101005 is correct but less precise; USP25 is a cysteine-type DUB, so GO:0004843 is the appropriate specific molecular function. Proposed replacements: cysteine-type deubiquitinase activity Supporting Evidence: PMID:23042150 USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
GO:1903882 negative regulation of interleukin-17-mediated signaling pathway	IDA PMID:23042150 Negative regulation of IL-17-mediated signaling and inflamma...	ACCEPT	Summary: USP25 negatively regulates IL-17 signaling and inflammation by removing K63-linked ubiquitin chains from the adaptors TRAF5 and TRAF6, dampening downstream activation. Reason: Directly and specifically supported experimentally; captures USP25's role in restraining IL-17 signaling with correct directionality. Supporting Evidence: PMID:23042150 USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
GO:0032183 SUMO binding	IPI PMID:18538659 Mechanism and consequences for paralog-specific sumoylation ...	ACCEPT	Summary: Experimental interaction with SUMO (SUMO2/3 preferred) via the N-terminal SIM, mediating paralog-specific sumoylation that impairs USP25 ubiquitin binding and hydrolysis. Reason: Directly documented SUMO binding through the SUMO-interaction motif; a genuine regulatory molecular function (auxiliary to the core DUB activity). Supporting Evidence: file:human/USP25/USP25-uniprot.txt Interacts with SUMO3; the interaction sumoylates efficiently USP25.
GO:0005829 cytosol	TAS Reactome:R-HSA-5696564	ACCEPT	Summary: Reactome curated cytosolic localization, consistent with the experimentally established cytoplasmic/cytosolic localization of USP25. Reason: Agrees with IDA cytosol and multiple cytoplasm annotations. Supporting Evidence: file:human/USP25/USP25-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0019783 ubiquitin-like protein peptidase activity	NAS PMID:22590560 Ubiquitin-specific protease 25 functions in Endoplasmic Reti...	MARK AS OVER ANNOTATED	Summary: Non-author statement attributing ubiquitin-like protein peptidase activity. USP25's documented catalytic activity is deubiquitination (cysteine-type deubiquitinase); broader Ubl peptidase activity is not strongly substantiated. Reason: USP25's experimentally established activity is on ubiquitin (EC 3.4.19.12); the broader "ubiquitin-like protein peptidase activity" rests on a NAS statement and is better represented by the specific cysteine-type deubiquitinase activity. Supporting Evidence: file:human/USP25/USP25-uniprot.txt EC=3.4.19.12
GO:0005783 endoplasmic reticulum	IDA PMID:22590560 Ubiquitin-specific protease 25 functions in Endoplasmic Reti...	KEEP AS NON CORE	Summary: Direct evidence for ER association in the context of USP25's ERAD function (counteracting HRD1). A genuine but context-specific localization secondary to the predominant cytoplasmic pool. Reason: ER localization is experimentally supported in the ERAD context, but it is a specialized, partial localization relative to USP25's predominant cytoplasmic site of action. Supporting Evidence: PMID:22590560 USP25 counteracts the ubiquitin ligase function of HRD1.
GO:0016579 protein deubiquitination	IDA PMID:22590560 Ubiquitin-specific protease 25 functions in Endoplasmic Reti...	ACCEPT	Summary: Direct evidence of protein deubiquitination, here counteracting HRD1-mediated ubiquitination of ERAD substrates and rescuing them from proteasomal degradation. Reason: Protein deubiquitination is the direct, experimentally supported process of USP25's catalytic activity. Supporting Evidence: PMID:22590560 USP25 counteracts the ubiquitin ligase function of HRD1 by binding ubiquitinated species and cleaving them.
GO:0031625 ubiquitin protein ligase binding	IPI PMID:22590560 Ubiquitin-specific protease 25 functions in Endoplasmic Reti...	KEEP AS NON CORE	Summary: Interaction with the E3 ubiquitin ligase HRD1/SYVN1 (Q86TM6), consistent with USP25 counteracting HRD1 to rescue ERAD substrates. Reason: A real and functionally relevant interaction (HRD1) underlying the ERAD role; informative as a binding function but auxiliary to the core deubiquitinase activity. Supporting Evidence: PMID:22590560 USP25 counteracts the ubiquitin ligase function of HRD1.
GO:0043130 ubiquitin binding	NAS PMID:22590560 Ubiquitin-specific protease 25 functions in Endoplasmic Reti...	ACCEPT	Summary: Ubiquitin binding via the N-terminal UBA-like and tandem UIM domains, which recognize ubiquitin/ubiquitin chains and regulate substrate engagement. Reason: Ubiquitin binding through the UBA/UIM modules is well established structurally and functionally and underlies substrate recognition by USP25. Supporting Evidence: file:human/USP25/USP25-uniprot.txt The UBA-UIM domains of the USP25 regulate the enzyme ubiquitination state and modulate substrate recognition
GO:0051117 ATPase binding	IPI PMID:22590560 Ubiquitin-specific protease 25 functions in Endoplasmic Reti...	KEEP AS NON CORE	Summary: Interaction with the AAA-ATPase VCP/p97 (P55072), a central ERAD component that extracts ubiquitinated substrates from the ER membrane. Reason: A real interaction relevant to USP25's ERAD role (VCP/p97), but auxiliary to the core deubiquitinase function. Supporting Evidence: PMID:22590560 USP25 counteracts the ubiquitin ligase function of HRD1.
GO:1904293 negative regulation of ERAD pathway	IMP PMID:22590560 Ubiquitin-specific protease 25 functions in Endoplasmic Reti...	ACCEPT	Summary: USP25 negatively regulates ERAD by counteracting HRD1-mediated ubiquitination of ERAD substrates, cleaving ubiquitin from them and rescuing them from proteasomal degradation. Reason: Directly supported experimentally; captures USP25's specific ERAD-modulating role. Supporting Evidence: PMID:22590560 USP25 counteracts the ubiquitin ligase function of HRD1 by binding ubiquitinated species and cleaving them.
GO:0004843 cysteine-type deubiquitinase activity	IMP PMID:18538659 Mechanism and consequences for paralog-specific sumoylation ...	ACCEPT	Summary: Deubiquitinase activity inferred from mutational analysis in the sumoylation study; sumoylation impairs ubiquitin hydrolysis. Reason: Supports the core cysteine-type deubiquitinase activity of USP25. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Sumoylation impairs binding to and hydrolysis of ubiquitin chains.
GO:0005515 protein binding	IPI PMID:18538659 Mechanism and consequences for paralog-specific sumoylation ...	MODIFY	Summary: IntAct interaction with SUMO3 (P55854), the basis of the SUMO-binding molecular function. The bare protein binding term is uninformative; SUMO binding (GO:0032183) is the specific term. Reason: Bare protein binding is uninformative; the WITH partner is SUMO3, so SUMO binding (GO:0032183) is the appropriate specific molecular function. Proposed replacements: SUMO binding Supporting Evidence: file:human/USP25/USP25-uniprot.txt Interacts with SUMO3; the interaction sumoylates efficiently USP25.
GO:0070536 protein K63-linked deubiquitination	IMP PMID:18538659 Mechanism and consequences for paralog-specific sumoylation ...	ACCEPT	Summary: USP25 cleaves K63-linked polyubiquitin chains, consistent with its activity on TRAF5/TRAF6 K63 chains in IL-17 signaling. Reason: USP25's ability to hydrolyze K63-linked chains is experimentally supported and biologically relevant (IL-17/TRAF signaling). Supporting Evidence: PMID:23042150 USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
GO:0071108 protein K48-linked deubiquitination	IMP PMID:18538659 Mechanism and consequences for paralog-specific sumoylation ...	ACCEPT	Summary: USP25 cleaves K48-linked polyubiquitin chains, consistent with its rescue of substrates (e.g. ERAD substrates, TNKS, KEAP1) from K48-linked proteasomal degradation. Reason: USP25's activity on K48-linked chains is experimentally supported and underlies its substrate-stabilizing roles. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Sumoylation impairs binding to and hydrolysis of ubiquitin chains.
GO:0004843 cysteine-type deubiquitinase activity	TAS PMID:10644437 USP25, a novel gene encoding a deubiquitinating enzyme, is l...	ACCEPT	Summary: Original cloning paper describing USP25 as a deubiquitinating enzyme; traceable author statement of cysteine-type deubiquitinase activity. Reason: Supports the core molecular function; consistent with all later experimental evidence. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
GO:0006508 proteolysis	TAS PMID:10644437 USP25, a novel gene encoding a deubiquitinating enzyme, is l...	MARK AS OVER ANNOTATED	Summary: Broad proteolysis annotation from the original cloning paper. USP25 cleaves isopeptide/peptide bonds of ubiquitin conjugates; protein deubiquitination is the precise process. Reason: Generic "proteolysis" is imprecise for a deubiquitinase; the specific process is protein deubiquitination (already annotated). Retaining the broad term adds little. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
GO:0008233 peptidase activity	TAS PMID:10644437 USP25, a novel gene encoding a deubiquitinating enzyme, is l...	MARK AS OVER ANNOTATED	Summary: Broad peptidase activity annotation from the original cloning paper. The precise activity is cysteine-type deubiquitinase activity (peptidase C19 family). Reason: Generic "peptidase activity" is a high-level parent; the specific GO:0004843 cysteine-type deubiquitinase activity is already annotated and is far more informative. Supporting Evidence: file:human/USP25/USP25-uniprot.txt EC=3.4.19.12
GO:0036211 protein modification process	TAS PMID:10644437 USP25, a novel gene encoding a deubiquitinating enzyme, is l...	MARK AS OVER ANNOTATED	Summary: Very broad "protein modification process" annotation from the original cloning paper. The specific process (protein deubiquitination) is already annotated. Reason: This is an over-general parent term; protein deubiquitination is the precise and already-annotated process. Supporting Evidence: file:human/USP25/USP25-uniprot.txt Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates

Core Functions

Cysteine-type deubiquitinase (peptidase C19 family; active-site Cys-178, EC 3.4.19.12) that hydrolyzes K48- and K63-linked polyubiquitin from substrate proteins, recognizing ubiquitin through N-terminal UBA-like and tandem UIM domains.

Molecular Function:

cysteine-type deubiquitinase activity

Cellular Locations:

cytoplasm

Supporting Evidence:

file:human/USP25/USP25-uniprot.txt
Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
PMID:37339955
Here we report that USP25 deubiquitinates KEAP1 and prevents it from excessive ubiquitination and degradation.

Substrate stabilization through deubiquitination, rescuing specific targets from proteasomal degradation to modulate signaling pathways including Wnt/beta-catenin (tankyrases TNKS1/2), the KEAP1-NRF2 oxidative-stress axis, IL-17/innate-immune signaling (TRAF5/TRAF6/TRAF3), and ERAD (counteracting HRD1).

Molecular Function:

cysteine-type deubiquitinase activity

Cellular Locations:

cytoplasm

Supporting Evidence:

PMID:23042150
USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
PMID:22590560
USP25 counteracts the ubiquitin ligase function of HRD1 by binding ubiquitinated species and cleaving them.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:10644437

USP25, a novel gene encoding a deubiquitinating enzyme, is located in the gene-poor region 21q11.2.

USP25 was identified as a novel deubiquitinating enzyme gene in chromosome region 21q11.2 (the historical "USP on chromosome 21" basis for the USP21 alias).

PMID:18538659

Mechanism and consequences for paralog-specific sumoylation of ubiquitin-specific protease 25.

USP25 binds SUMO (SUMO2/3 preferred) via an N-terminal SUMO-interaction motif; sumoylation at Lys-99 impairs ubiquitin binding and hydrolysis.

PMID:19440361

The UBA-UIM domains of the USP25 regulate the enzyme ubiquitination state and modulate substrate recognition.

The N-terminal UBA and tandem UIM domains regulate USP25 ubiquitination state and substrate recognition; USP25 is active in the cytoplasm.

PMID:21516116

Next-generation sequencing to generate interactome datasets.

PMID:22153077

Structural basis and sequence rules for substrate recognition by Tankyrase explain the basis for cherubism disease.

PMID:22590560

Ubiquitin-specific protease 25 functions in Endoplasmic Reticulum-associated degradation.

USP25 counteracts the ubiquitin ligase function of HRD1 by binding ubiquitinated ERAD substrates and cleaving them, rescuing them from proteasomal degradation; interacts with HRD1 and VCP/p97.

PMID:2304215

Problems identified by secondary review of accepted manuscripts.

PMID:23042150

Negative regulation of IL-17-mediated signaling and inflammation by the ubiquitin-specific protease USP25.

USP25 removes K63-linked ubiquitin chains from the adaptors TRAF5 and TRAF6 to negatively regulate IL-17-mediated signaling and inflammation.

PMID:25416956

A proteome-scale map of the human interactome network.

PMID:28514442

Architecture of the human interactome defines protein communities and disease networks.

PMID:28619731

USP25 regulates Wnt signaling by controlling the stability of tankyrases.

USP25 deubiquitinates and stabilizes the tankyrases TNKS1 and TNKS2, thereby regulating Wnt/beta-catenin signaling.

PMID:31515488

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.

PMID:32296183

A reference map of the human binary protein interactome.

PMID:32707033

Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases.

PMID:32814053

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.

PMID:33060197

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

PMID:33961781

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.

PMID:34232536

Interactomes of SARS-CoV-2 and human coronaviruses reveal host factors potentially affecting pathogenesis.

PMID:35914814

Chr21 protein-protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer's disease.

PMID:36217029

A proteome-scale map of the SARS-CoV-2-human contactome.

PMID:37339955

USP25 regulates KEAP1-NRF2 anti-oxidation axis and its inactivation protects acetaminophen-induced liver injury in male mice.

USP25 deubiquitinates and stabilizes KEAP1, promoting degradation of NRF2; USP25 inactivation protects against acetaminophen-induced liver injury.

PMID:38875478

Heterozygous variants in USP25 cause genetic generalized epilepsy.

Heterozygous USP25 variants cause idiopathic generalized epilepsy (EIG19); a C-terminal truncation is a gain-of-function increasing deubiquitination and shifting the oligomeric state from inhibited tetramer toward active dimer.

PMID:40205054

Multimodal cell maps as a foundation for structural and functional genomics.

Reactome:R-HSA-5688426

Ub-specific processing proteases (deubiquitination)

Reactome:R-HSA-5696564

Ub-specific processing proteases

Suggested Experiments

Experiment: Proteome-wide ubiquitinome (diGly) profiling comparing wild-type, catalytic-dead (C178S) and epilepsy-variant USP25 to define the global substrate landscape and test substrate-specificity hypotheses.

Experiment: Reconstitute the oligomerization switch in vitro with defined homodimer versus homotetramer assemblies and measure deubiquitination kinetics on K48- versus K63-linked chains and on physiological substrates (KEAP1, TNKS2, TRAF6).

Experiment: Neuronal models (iPSC-derived neurons) carrying EIG19 gain-of-function variants to test whether increased deubiquitination raises neuronal excitability and to identify the responsible neuronal substrates.

📚 Additional Documentation

Notes

(USP25-notes.md)

USP25 (folder labeled USP21) — review notes

IMPORTANT identity note

The folder is named USP21, but the UniProt record (USP21-uniprot.txt), GOA file, and
all existing annotations are for USP25 (UniProt Q9UHP3, UBP25_HUMAN, HGNC:12624).
The UniProt entry lists GN Name=USP25; Synonyms=USP21 — historically USP25 was briefly
called "USP21" / "USP on chromosome 21" in early papers (PubMed:10644437), which is the
likely source of the folder name. The protein here is USP25, not the distinct gene
USP21 (Q9UKM4). All review content below pertains to Q9UHP3 = USP25. The gene_symbol
field is set to USP25 to match the actual record (correct HGNC symbol for Q9UHP3).

Core identity

USP25 is a cysteine (papain-like, peptidase C19 family) deubiquitinating enzyme (DUB),
EC 3.4.19.12, with an N-terminal UBA + tandem UIM (ubiquitin-interacting motif) region,
a catalytic USP domain (active-site Cys-178), and a C-terminal region mediating
oligomerization (active homodimer vs. inhibited homotetramer).
[file:human/USP21/USP21-uniprot.txt "Belongs to the peptidase C19 family"]
[file:human/USP21/USP21-uniprot.txt "ACT_SITE 178"]

Catalytic function (well established, EXP/IDA)

Hydrolyzes ubiquitin (and SUMO/ubiquitin-like) from substrates; cleaves both K48- and
K63-linked chains.
[file:human/USP21/USP21-uniprot.txt "Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates"]
EXP catalytic activity: PMID:23042150 (IL-17/TRAF), PMID:37339955 (KEAP1-NRF2).
C178S abrogates DUB activity. [file:human/USP21/USP21-uniprot.txt "C->S: Abrogates deubiquitinating activity"]

Substrate / pathway roles (each via deubiquitination)

Wnt/beta-catenin: deubiquitinates and stabilizes tankyrases TNKS1/TNKS2
(PMID:28619731, PMID:30926243, PMID:38875478). UniProt FUNCTION + interaction with TNKS2.
KEAP1-NRF2 oxidative-stress axis: deubiquitinates/stabilizes KEAP1, promoting NRF2
degradation; USP25 loss is protective in acetaminophen liver injury (PMID:37339955).
-> GO:1902883 negative regulation of response to oxidative stress (IDA).
IL-17 signaling / inflammation: removes K63-Ub from TRAF5/TRAF6, negatively
regulating IL-17 signaling (PMID:23042150).
-> GO:1903882 negative regulation of IL-17-mediated signaling (IDA).
Innate antiviral / endotoxin tolerance: stabilizes TRAF3 (PMID:30579117); ERLIN1/2
cholesterol flux to restrict virus (PMID:37683630).
ERAD: counteracts HRD1-mediated ubiquitination of ERAD substrates, rescuing them
from degradation; interacts with HRD1/SYVN1 (Q86TM6) and VCP/p97 (P55072)
PMID:22590560
-> GO:1904293 negative regulation of ERAD pathway (IMP), GO:0031625 (HRD1 binding),
GO:0051117 ATPase binding (VCP).
Muscle: muscle-specific isoform USP25m stabilizes MYBPC1, interacts with ACTA1/FLNC
(PMID:16501887).

Regulation

SUMOylated at Lys-99 (SUMO2/3 preferred) which impairs Ub binding/hydrolysis; the N-terminal
SIM mediates paralog-specific SUMO binding (PMID:18538659). -> GO:0032183 SUMO binding.
Ubiquitinated by SMURF1 (K48) -> degradation (PMID:29518389). Phosphorylated by SYK
(PMID:19909739). Oligomerization (tetramer = inhibited; dimer = active) regulates activity
(PMID:30478318, PMID:30926243).

Localization

Cytoplasm/cytosol (multiple EXP/IDA: PMID:19440361, PMID:28619731, PMID:38875478, HPA).
ER membrane association in ERAD context (PMID:22590560, IDA). Nucleus is IEA-only (from
UniProtKB-SubCell keyword, transient nuclear punctate in myotubes for USP25m) — weak.

Disease

Heterozygous variants cause idiopathic generalized epilepsy 19 (EIG19); a C-terminal
truncation is a gain-of-function (forms active dimers, not inhibited tetramers)
(PMID:38875478).

Interactome (IPI protein binding) — WITH partners from GOA

21516116, 32707033: SYK (P43405) — validated interaction (PMID:19909739).
22153077, 35914814: TNKS2 (Q9H2K2) — substrate, validated (Wnt).
28514442, 31515488, 32296183, 40205054, 33961781, 25416956, 32814053: RAD23A/RAD23B
(P54725/P54727) — recurrent proteasome-shuttle UBA-domain proteins; plausible.
33060197, 34232536, 36217029: SARS-CoV-2 rep/nsp3 (P0DTD1) — viral interactome screens.
18538659: SUMO3 (P55854) — basis of SUMO binding MF.
Others (GDI1, MAGEB4, MID2, PRKACA, PUS10, TMEM43, TGFBR2, ZNF426, SUMO2): mostly
single high-throughput screens; uninformative as bare "protein binding".

RQC relevance

Despite the batch theme, USP25's documented roles are Wnt/tankyrase, KEAP1-NRF2, IL-17/innate
immunity, and ERAD — not collided-ribosome surveillance. No strong evidence ties USP25 to
ribosome-associated quality control. (The RQC-associated DUB framing in the task note appears
to belong to USP21, a different gene.)

Pn Notes

(USP25-pn-notes.md)

USP25 PN Consistency Notes

Generated: 2026-06-18
Project: PROTEOSTASIS
Scope: PN consistency rereview against local AIGR review and available deep-research artifacts
UniProt: Q9UHP3
AIGR review status: COMPLETE
Review batch: proteostasis-batch-2026-06-07c
Batch change status: added

Source Files Checked

AIGR review YAML: present - genes/human/USP25/USP25-ai-review.yaml
AIGR review HTML: present - genes/human/USP25/USP25-ai-review.html
Gene notes: present - genes/human/USP25/USP25-notes.md
GOA TSV: present - genes/human/USP25/USP25-goa.tsv
UniProt record: present - genes/human/USP25/USP25-uniprot.txt
PN dossier: projects/PROTEOSTASIS/reports/phase1_dossiers/USP25.md
PN consistency section: projects/PROTEOSTASIS/reports/phase1_dossiers/_sections/USP25.md
PN projection report: projects/PROTEOSTASIS/reports/pn_projection/pn_projected_gene_go_summary.tsv
PN mapping audit: projects/PROTEOSTASIS/reports/pn_mapping_audit/current_mapping_scrutiny.tsv

Deep Research Files

No *-deep-research*.md file found in this gene directory.

AIGR Review Snapshot

Description: USP25 (ubiquitin carboxyl-terminal hydrolase 25; historically called "USP on chromosome 21" / USP21) is a cytoplasmic cysteine (papain-like, peptidase C19 family) deubiquitinating enzyme. It has an N-terminal UBA-like domain and tandem ubiquitin-interacting motifs (UIM) that recognize ubiquitin, a catalytic USP domain (active-site Cys-178), and a C-terminal region that mediates oligomerization, with an inhibited homotetramer and an active homodimer state controlling catalytic output. USP25 hydrolyzes ubiquitin from substrates and can cleave both K48- and K63-linked polyubiquitin chains, thereby protecting specific substrates from proteasomal degradation and modulating signaling. Characterized substrates and pathways include stabilization of the tankyrases TNKS1/TNKS2 to modulate Wnt/beta-catenin signaling, deubiquitination and stabilization of KEAP1 within the KEAP1-NRF2 oxidative-stress axis, removal of K63-linked ubiquitin from TRAF5/TRAF6 to restrain interleukin-17 signaling and inflammation, stabilization of TRAF3 and ERLIN1/2 in innate antiviral responses, and rescue of ERAD substrates by counteracting the HRD1 ubiquitin ligase. Its activity is regulated by sumoylation at Lys-99 (which impairs ubiquitin binding), by SMURF1-mediated K48 ubiquitination targeting it for degradation, by SYK phosphorylation, and by its oligomeric state. A muscle-specific isoform (USP25m) is induced during myocyte differentiation and interacts with sarcomeric proteins (ACTA1, FLNC, MYBPC1). Heterozygous USP25 variants cause idiopathic generalized epilepsy (EIG19).
Existing/core annotation action counts: ACCEPT: 23; KEEP_AS_NON_CORE: 22; MARK_AS_OVER_ANNOTATED: 5; MODIFY: 4; REMOVE: 2

PN Consistency Summary

Consistency: Consistent BUT identity is the salient issue. The task framing ("USP25 was the synonym-resolved symbol for USP21") conflates two distinct genes. The folder/review (Q9UHP3) is genuinely USP25 (HGNC:12624), historically aliased "USP21"/"USP on chr 21" (PMID:10644437) — a separate protein from true USP21 (Q9UK80). The notes file documents this collision explicitly. PN dossier (Q9UHP3), review, and notes all agree on the USP25 identity; both PN rows are purely UPS (no TR/RQC row), matching the review's substrate biology (tankyrases/Wnt, KEAP1-NRF2, IL-17/TRAF, ERAD-HRD1). USP25 is NOT an RQC DUB — only true USP21 is.
PN story / NEW pressure: PN asserts only DUB activity (GO:0101005) and ubiquitin/UBL-reader context — all already in GOA/review (GO:0004843, GO:0043130 ubiquitin binding, GO:0032183 SUMO binding). No new-to-GOA projection. Conclude: already captured; no NEW term and no RQC pressure (correctly, since USP25 has no ribosome role).
Evidence alignment: PN row 1 cites "19734957/rev"; row 2 cites PMID:18538659 (paralog-specific sumoylation) — the latter IS in the review (GO:0032183 SUMO binding, GO:0070536/GO:0071108 K63/K48 deubiquitination), good overlap. Review is far richer (KEAP1, IL-17, ERAD, epilepsy PMIDs) than the two PN rows.
Verdict: Consistent; identity confirmed as USP25 (distinct from USP21), no RQC role. PN claims already captured; no NEW term needed.

Full Consistency Review

UniProt: Q9UHP3 · batch: proteostasis-batch-2026-06-07c · review status: COMPLETE
PN placement: UPS DUBs and UBL demodifiers|USP|other|UBA, UIM and UPS Ubiquitin and UBL binding|DUB|USP / with UBD|UIM, UBA-like, SIM ; PN-node mapping: DUB-family group→GO:0101005 deubiquitinase activity (mapped, already_in_goa_exact); UBL-binding group→GO:0101005 (context_only, too_broad); UBL-binding class→GO:0140036 ubiquitin-modified protein reader activity (context_only); type/subtype/branch = no_mapping.
Consistency: Consistent BUT identity is the salient issue. The task framing ("USP25 was the synonym-resolved symbol for USP21") conflates two distinct genes. The folder/review (Q9UHP3) is genuinely USP25 (HGNC:12624), historically aliased "USP21"/"USP on chr 21" (PMID:10644437) — a separate protein from true USP21 (Q9UK80). The notes file documents this collision explicitly. PN dossier (Q9UHP3), review, and notes all agree on the USP25 identity; both PN rows are purely UPS (no TR/RQC row), matching the review's substrate biology (tankyrases/Wnt, KEAP1-NRF2, IL-17/TRAF, ERAD-HRD1). USP25 is NOT an RQC DUB — only true USP21 is.
PN story / NEW pressure: PN asserts only DUB activity (GO:0101005) and ubiquitin/UBL-reader context — all already in GOA/review (GO:0004843, GO:0043130 ubiquitin binding, GO:0032183 SUMO binding). No new-to-GOA projection. Conclude: already captured; no NEW term and no RQC pressure (correctly, since USP25 has no ribosome role).
Mapping strategy: USP25 does not change either node. DUB-family group→GO:0101005 is already_in_goa_exact (GOA has GO:0101005 IMP/IDA rows). UBL-binding class→GO:0140036 reader activity is correctly held as context_only/too_broad (USP25's UBA/UIM/SIM read ubiquitin and SUMO, but the class mixes modifiers). Scope/status all appropriate.
Evidence alignment: PN row 1 cites "19734957/rev"; row 2 cites PMID:18538659 (paralog-specific sumoylation) — the latter IS in the review (GO:0032183 SUMO binding, GO:0070536/GO:0071108 K63/K48 deubiquitination), good overlap. Review is far richer (KEAP1, IL-17, ERAD, epilepsy PMIDs) than the two PN rows.
Verdict: Consistent; identity confirmed as USP25 (distinct from USP21), no RQC role. PN claims already captured; no NEW term needed.

PN Dossier Context

review_batch: proteostasis-batch-2026-06-07c
review_yaml: genes/human/USP25/USP25-ai-review.yaml
PN workbook rows: 2

PN row 1: Ubiquitin Proteasome System | DUBs and UBL demodifiers | USP | other | UBA, UIM

UniProt: Q9UHP3
In branches: UPS
Signature domains: IPR028889
Auxiliary domains: IPR009060, IPR003903
PN references (titles):
- 19734957 / rev
PN-node mapping records (path + ancestors):
- [subtype] Ubiquitin Proteasome System|DUBs and UBL demodifiers|USP|other|UBA, UIM
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a narrower active DUB family/domain subdivision already covered by the curated parent DUB-family mapping. No additional direct GO mapping is needed at this node.
- [type] Ubiquitin Proteasome System|DUBs and UBL demodifiers|USP|other
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a narrower active DUB family/domain subdivision already covered by the curated parent DUB-family mapping. No additional direct GO mapping is needed at this node.
- [group] Ubiquitin Proteasome System|DUBs and UBL demodifiers|USP
  status=mapped scope=ok_for_propagation_to_go GO=[GO:0101005 deubiquitinase activity]
  rationale: This PN group is an active deubiquitinase family bucket. The shared molecular-function assertion is deubiquitinase activity.
- [class] Ubiquitin Proteasome System|DUBs and UBL demodifiers
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a UPS taxonomy container. Its descendants mix catalytic roles, complex membership, binding domains, regulators, adaptors, and substrate-context labels, so a single propagating GO assertion would overstate the shared biology.
- [branch] Ubiquitin Proteasome System
  status=no_mapping scope= GO=[]
  rationale: Reviewed as the top-level UPS branch. It is a project taxonomy umbrella rather than a direct GO assertion; UPS propagation must come from manually curated child nodes.

PN row 2: Ubiquitin Proteasome System | Ubiquitin and UBL binding | DUB | USP / with UBD | UIM, UBA-like, SIM

UniProt: Q9UHP3
In branches: UPS
Signature domains: IPR003903, IPR054109, PMID: 18538659
Auxiliary domains: IPR028889
PN references (titles):
- 18538659
PN-node mapping records (path + ancestors):
- [subtype] Ubiquitin Proteasome System|Ubiquitin and UBL binding|DUB|USP / with UBD|UIM, UBA-like, SIM
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a narrower UBL-binding DUB-domain subdivision. Because this subtree includes noncatalytic or pseudo-DUB cases, active DUB propagation is handled by the DUB-family branch rather than this binding-domain node.
- [type] Ubiquitin Proteasome System|Ubiquitin and UBL binding|DUB|USP / with UBD
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a narrower UBL-binding DUB-domain subdivision. Because this subtree includes noncatalytic or pseudo-DUB cases, active DUB propagation is handled by the DUB-family branch rather than this binding-domain node.
- [group] Ubiquitin Proteasome System|Ubiquitin and UBL binding|DUB
  status=context_only scope=too_broad_to_propagate GO=[GO:0101005 deubiquitinase activity]
  rationale: This UBL-binding group is DUB-related context, but it includes noncatalytic or pseudo-DUB domain cases such as NPLOC4/USP39-like entries. Active DUB propagation is handled from the DUB-family branch.
- [class] Ubiquitin Proteasome System|Ubiquitin and UBL binding
  status=context_only scope=too_broad_to_propagate GO=[GO:0140036 ubiquitin-modified protein reader activity]
  rationale: This class records ubiquitin/UBL-reader context, but the subtree mixes ubiquitin, SUMO, UBL-domain, domain-architecture, catalytic, signaling, trafficking, and nucleic-acid process buckets. It is useful context, not a safe direct propagation.
- [branch] Ubiquitin Proteasome System
  status=no_mapping scope= GO=[]
  rationale: Reviewed as the top-level UPS branch. It is a project taxonomy umbrella rather than a direct GO assertion; UPS propagation must come from manually curated child nodes.

Projected GO annotations (1)

GO:0101005 deubiquitinase activity | scope=ok_for_propagation_to_go | goa_status=already_in_goa_exact | from=Ubiquitin Proteasome System|DUBs and UBL demodifiers|USP

Note

This file is generated from the current PROTEOSTASIS phase-1 dossier and local gene-review artifacts. Edit the source review, PN mapping, or dossier rather than this generated note when correcting the underlying curation.

📄 View Raw YAML

id: Q9UHP3
gene_symbol: USP25
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: USP25 (ubiquitin carboxyl-terminal hydrolase 25; historically called "USP on chromosome 21" / USP21) is a cytoplasmic cysteine (papain-like, peptidase C19 family) deubiquitinating enzyme. It has an N-terminal UBA-like domain and tandem ubiquitin-interacting motifs (UIM) that recognize ubiquitin, a catalytic USP domain (active-site Cys-178), and a C-terminal region that mediates oligomerization, with an inhibited homotetramer and an active homodimer state controlling catalytic output. USP25 hydrolyzes ubiquitin from substrates and can cleave both K48- and K63-linked polyubiquitin chains, thereby protecting specific substrates from proteasomal degradation and modulating signaling. Characterized substrates and pathways include stabilization of the tankyrases TNKS1/TNKS2 to modulate Wnt/beta-catenin signaling, deubiquitination and stabilization of KEAP1 within the KEAP1-NRF2 oxidative-stress axis, removal of K63-linked ubiquitin from TRAF5/TRAF6 to restrain interleukin-17 signaling and inflammation, stabilization of TRAF3 and ERLIN1/2 in innate antiviral responses, and rescue of ERAD substrates by counteracting the HRD1 ubiquitin ligase. Its activity is regulated by sumoylation at Lys-99 (which impairs ubiquitin binding), by SMURF1-mediated K48 ubiquitination targeting it for degradation, by SYK phosphorylation, and by its oligomeric state. A muscle-specific isoform (USP25m) is induced during myocyte differentiation and interacts with sarcomeric proteins (ACTA1, FLNC, MYBPC1). Heterozygous USP25 variants cause idiopathic generalized epilepsy (EIG19).
alternative_products:
- name: USP25a
  id: Q9UHP3-2
- name: USP25b
  id: Q9UHP3-1
  sequence_note: VSP_039632
- name: USP25m (Muscle-specific isoform)
  id: Q9UHP3-3
  sequence_note: VSP_039631
existing_annotations:
- term:
    id: GO:0032183
    label: SUMO binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: USP25 binds SUMO via an N-terminal SUMO-interaction domain/SIM and is sumoylated paralog-specifically; SUMO binding is experimentally documented and also inferred phylogenetically.
    action: ACCEPT
    reason: SUMO binding is directly supported by experimental interaction with SUMO2/SUMO3 (PMID:18538659) and is consistent with the phylogenetic inference. It is a real regulatory molecular function (sumoylation impairs ubiquitin binding/hydrolysis), though it is auxiliary to the core deubiquitinase activity.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Interacts with SUMO3; the interaction sumoylates efficiently USP25.
- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: Electronic (InterPro/EC) annotation of cysteine-type deubiquitinase activity, the core catalytic function of USP25, fully corroborated by experimental evidence.
    action: ACCEPT
    reason: USP25 is a peptidase C19 family cysteine protease (EC 3.4.19.12) with active-site Cys-178; this IEA agrees with EXP/IDA catalytic-activity evidence and is the core molecular function.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: EC=3.4.19.12
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Electronic localization to the nucleus from a UniProt subcellular-location keyword. USP25 is principally cytoplasmic; nuclear localization is only weakly supported (transient punctate nuclear signal of the USP25m isoform in myotubes).
    action: MARK_AS_OVER_ANNOTATED
    reason: The strong experimental evidence places USP25 in the cytoplasm/cytosol; nuclear localization rests on an IEA keyword and an inferred-by-similarity note limited to transient USP25m signal in differentiating myotubes, so it is not a robust general localization.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Electronic cytoplasmic localization, consistent with strong experimental evidence for cytoplasmic USP25.
    action: ACCEPT
    reason: Multiple EXP/IDA studies localize USP25 to the cytoplasm; this IEA agrees with the experimentally supported compartment.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- term:
    id: GO:0016579
    label: protein deubiquitination
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: Electronic annotation of protein deubiquitination, the biological process executed by USP25's catalytic activity; well supported.
    action: ACCEPT
    reason: Protein deubiquitination is the direct process outcome of USP25's cysteine-type deubiquitinase activity and is corroborated by multiple experimental studies.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21516116
  qualifier: enables
  review:
    summary: IntAct interaction with SYK (P43405), a validated USP25 partner (SYK phosphorylates USP25 and regulates its levels). The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records a real interaction (SYK), but per curation guidelines bare protein binding is uninformative and not a core function; the SYK relationship is captured in regulation rather than as a molecular function.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; P43405: SYK'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22153077
  qualifier: enables
  review:
    summary: IntAct interaction with TNKS2 (Q9H2K2), a validated USP25 substrate (USP25 deubiquitinates and stabilizes tankyrases). The bare protein binding term is uninformative; the biologically meaningful relationship is enzyme-substrate.
    action: KEEP_AS_NON_CORE
    reason: Real and functionally relevant interaction (TNKS2), but bare protein binding is uninformative as a molecular function; the substrate relationship informs the Wnt-regulation role rather than constituting a core MF.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; Q9H2K2: TNKS2'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  qualifier: enables
  review:
    summary: High-throughput yeast two-hybrid interactome capturing USP25 interactions with MAGEB4, SYK, RAD23A, SUMO2 and ZNF426. The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records real high-throughput interactions but bare protein binding is uninformative and not core; SUMO2 binding and SYK are captured elsewhere.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; O15481: MAGEB4'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28514442
  qualifier: enables
  review:
    summary: IntAct interactions with the proteasome-shuttle UBA-domain proteins RAD23A/RAD23B (P54725/P54727). The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records recurrent interactions with RAD23A/B but bare protein binding is uninformative and not a core molecular function.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; P54725: RAD23A'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31515488
  qualifier: enables
  review:
    summary: IntAct interaction with RAD23A (P54725). The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records a real interaction but bare protein binding is uninformative and not core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; P54725: RAD23A'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: Multi-partner IntAct screen (RAD23A/B, PUS10, TMEM43, MID2 and others). The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records real high-throughput interactions but bare protein binding is uninformative and not core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; Q3MIT2: PUS10'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32707033
  qualifier: enables
  review:
    summary: IntAct interaction with SYK (P43405), a validated partner. The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records a real interaction (SYK) but bare protein binding is uninformative and not core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; P43405: SYK'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32814053
  qualifier: enables
  review:
    summary: Neurodegeneration interactome screen capturing interactions with PRKACA, TGFBR2 and RAD23A. The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records high-throughput interactions but bare protein binding is uninformative and not core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; P17612: PRKACA'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33060197
  qualifier: enables
  review:
    summary: IntAct interaction with the SARS-CoV-2 replicase polyprotein (P0DTD1) from a viral-host interactome screen. The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records a viral-interactome interaction but bare protein binding is uninformative and not a core function of USP25.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'PRO_0000449633 [P0DTD1]: rep'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  qualifier: enables
  review:
    summary: BioPlex affinity-purification interactome capturing interactions with GDI1 and RAD23B. The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records high-throughput interactions but bare protein binding is uninformative and not core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; P31150: GDI1'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:34232536
  qualifier: enables
  review:
    summary: IntAct interaction with the SARS-CoV-2 replicase polyprotein (P0DTD1) from a viral-host interactome study. The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records a viral-interactome interaction but bare protein binding is uninformative and not core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'PRO_0000449633 [P0DTD1]: rep'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:35914814
  qualifier: enables
  review:
    summary: IntAct screen capturing interactions with GDI1, RAD23B and TNKS2. The bare protein binding term is uninformative; the TNKS2 interaction is a validated substrate relationship.
    action: KEEP_AS_NON_CORE
    reason: Records real interactions including the TNKS2 substrate, but bare protein binding is uninformative and not a core molecular function.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; Q9H2K2: TNKS2'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:36217029
  qualifier: enables
  review:
    summary: IntAct interaction with the SARS-CoV-2 replicase polyprotein (P0DTD1). The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records a viral-interactome interaction but bare protein binding is uninformative and not core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'PRO_0000449633 [P0DTD1]: rep'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  qualifier: enables
  review:
    summary: Multimodal cell-maps interactome capturing interactions with RAD23A/RAD23B. The bare protein binding term is uninformative.
    action: KEEP_AS_NON_CORE
    reason: Records high-throughput interactions but bare protein binding is uninformative and not core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'Q9UHP3; P54727: RAD23B'
- term:
    id: GO:0006955
    label: immune response
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: Electronic (Ensembl ortholog) annotation of immune response. USP25 has documented roles in innate immunity and inflammation (IL-17 signaling, antiviral TRAF3/ERLIN1-2), so the broad process is plausible but non-specific.
    action: KEEP_AS_NON_CORE
    reason: USP25 participates in immune signaling but the bare "immune response" term is broad and inherited by ortholog transfer; more specific BP terms (e.g. negative regulation of IL-17 signaling) better capture the role.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: functions in various biological processes including inflammation and immune response
- term:
    id: GO:0006979
    label: response to oxidative stress
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: Electronic (ortholog) annotation of response to oxidative stress. USP25 regulates the KEAP1-NRF2 anti-oxidation axis, making the process plausible, though its specific role is negative regulation (stabilizing KEAP1, promoting NRF2 degradation).
    action: KEEP_AS_NON_CORE
    reason: Supported in spirit by the KEAP1-NRF2 role, but the IDA term "negative regulation of response to oxidative stress" is the more precise annotation; this broad ortholog-transferred term is non-core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Regulates KEAP1- NRF2 axis in the defense against oxidative assaults by deubiquitinating
- term:
    id: GO:0016071
    label: mRNA metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: Electronic (ortholog) annotation of mRNA metabolic process. There is no direct experimental evidence in the human record linking USP25 to mRNA metabolism.
    action: REMOVE
    reason: No experimental or curated support ties USP25 to mRNA metabolism in the UniProt record or literature reviewed; this appears to be an over-broad ortholog-transferred annotation.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
- term:
    id: GO:0031098
    label: stress-activated protein kinase signaling cascade
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: Electronic (ortholog) annotation of SAPK signaling. USP25 influences JNK/p38 phosphorylation via TRAF3 stabilization, so a connection exists but is indirect.
    action: KEEP_AS_NON_CORE
    reason: USP25 modulates JNK/p38 (SAPK) levels through TRAF3 stabilization, so the term is plausible but indirect and ortholog-transferred; non-core.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Prevents the ubiquitination and degradation of TRAF3 to reduce the phosphorylation levels of JNK and P38
- term:
    id: GO:0065003
    label: protein-containing complex assembly
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: Electronic (ortholog) annotation of protein-containing complex assembly. There is no direct evidence that USP25 functions in complex assembly as a biological role.
    action: REMOVE
    reason: No experimental support links USP25 to a complex-assembly process; this is an over-broad ortholog-transferred annotation.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
- term:
    id: GO:0097400
    label: interleukin-17-mediated signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: Electronic (ortholog) annotation placing USP25 in the IL-17 signaling pathway, strongly corroborated experimentally (USP25 removes K63-Ub from TRAF5/TRAF6). The validated role is negative regulation of this pathway.
    action: KEEP_AS_NON_CORE
    reason: USP25's involvement in IL-17 signaling is well established experimentally; the more precise IDA term "negative regulation of interleukin-17-mediated signaling pathway" captures the directionality, so this broad term is retained as non-core.
    supported_by:
    - reference_id: PMID:23042150
      supporting_text: USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
- term:
    id: GO:0016579
    label: protein deubiquitination
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5688426
  qualifier: involved_in
  review:
    summary: Reactome curated annotation of protein deubiquitination, the core process of USP25.
    action: ACCEPT
    reason: Protein deubiquitination is the direct biological process of USP25's catalytic activity and is well supported across experimental and curated sources.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5696564
  qualifier: enables
  review:
    summary: Reactome curated annotation of cysteine-type deubiquitinase activity, the core catalytic molecular function of USP25.
    action: ACCEPT
    reason: This is the central, experimentally validated molecular function of USP25 (active-site Cys-178; EC 3.4.19.12).
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: EC=3.4.19.12
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: Direct immunofluorescence (HPA) cytosolic localization, consistent with the experimentally established cytoplasmic localization of USP25.
    action: ACCEPT
    reason: IDA-supported cytosolic localization agrees with multiple experimental cytoplasm annotations and the gene's documented site of action.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: EXP
  original_reference_id: PMID:23042150
  qualifier: enables
  review:
    summary: Experimental demonstration of deubiquitinase catalytic activity in the context of removing K63-linked ubiquitin from TRAF5/TRAF6 during IL-17 signaling.
    action: ACCEPT
    reason: Direct experimental evidence for cysteine-type deubiquitinase activity; this is the core molecular function of USP25.
    supported_by:
    - reference_id: PMID:23042150
      supporting_text: USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: EXP
  original_reference_id: PMID:37339955
  qualifier: enables
  review:
    summary: Experimental demonstration of deubiquitinase activity through deubiquitination and stabilization of KEAP1 (catalytic-dead C178S abolishes activity).
    action: ACCEPT
    reason: Direct experimental support for the core cysteine-type deubiquitinase activity; C178S mutagenesis confirms catalytic dependence.
    supported_by:
    - reference_id: PMID:37339955
      supporting_text: Here we report that USP25 deubiquitinates KEAP1 and prevents it from excessive ubiquitination and degradation.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: EXP
  original_reference_id: PMID:28619731
  qualifier: located_in
  review:
    summary: Experimental cytoplasmic localization (from the tankyrase/Wnt study), consistent with USP25's established compartment.
    action: ACCEPT
    reason: Experimental evidence supports cytoplasmic localization, the principal site of USP25 action.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IMP
  original_reference_id: PMID:38875478
  qualifier: located_in
  review:
    summary: Cytoplasmic localization reported alongside characterization of epilepsy-associated USP25 variants; consistent with the established cytoplasmic compartment.
    action: ACCEPT
    reason: Supports cytoplasmic localization, agreeing with other experimental evidence.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- term:
    id: GO:0101005
    label: deubiquitinase activity
  evidence_type: IMP
  original_reference_id: PMID:38875478
  qualifier: enables
  review:
    summary: Deubiquitinase activity assayed for epilepsy-associated USP25 variants; a C-terminal truncation is a gain-of-function increasing deubiquitination. This is the parent term of the more precise cysteine-type deubiquitinase activity.
    action: MODIFY
    reason: GO:0101005 (deubiquitinase activity) is correct but less precise than the mechanistically defined GO:0004843 (cysteine-type deubiquitinase activity) already annotated for USP25; using the specific term is preferable.
    proposed_replacement_terms:
    - id: GO:0004843
      label: cysteine-type deubiquitinase activity
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: gain-of-function variant resulting in increased protein deubiquitination
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:19440361
  qualifier: is_active_in
  review:
    summary: Direct evidence that USP25 is active in the cytoplasm, where its UBA-UIM domains regulate ubiquitination state and substrate recognition.
    action: ACCEPT
    reason: The is_active_in cytoplasm annotation correctly places USP25's deubiquitinase activity in its principal compartment, with direct experimental support.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- term:
    id: GO:0101005
    label: deubiquitinase activity
  evidence_type: IDA
  original_reference_id: PMID:37339955
  qualifier: enables
  review:
    summary: Direct assay of deubiquitinase activity (KEAP1 deubiquitination). This is the parent of the more precise cysteine-type deubiquitinase activity term.
    action: MODIFY
    reason: GO:0101005 is correct but less precise; USP25 is a cysteine-type DUB (Cys-178), so GO:0004843 is the appropriate specific molecular function.
    proposed_replacement_terms:
    - id: GO:0004843
      label: cysteine-type deubiquitinase activity
    supported_by:
    - reference_id: PMID:37339955
      supporting_text: Here we report that USP25 deubiquitinates KEAP1 and prevents it from excessive ubiquitination and degradation.
- term:
    id: GO:1902883
    label: negative regulation of response to oxidative stress
  evidence_type: IDA
  original_reference_id: PMID:37339955
  qualifier: involved_in
  review:
    summary: USP25 negatively regulates the oxidative-stress response by deubiquitinating and stabilizing KEAP1, which promotes degradation of the antioxidant transcription factor NRF2; loss of USP25 is protective in acetaminophen liver injury.
    action: ACCEPT
    reason: Directly supported experimentally; captures USP25's specific role in the KEAP1-NRF2 axis with correct directionality.
    supported_by:
    - reference_id: PMID:37339955
      supporting_text: Here we report that USP25 deubiquitinates KEAP1 and prevents it from excessive ubiquitination and degradation.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:2304215
  qualifier: is_active_in
  review:
    summary: is_active_in cytoplasm annotation. The cited reference PMID:2304215 (a 1990 paper) predates USP25 characterization and appears to be an incorrect/legacy citation, but the cytoplasmic site of activity itself is well supported by other experimental evidence.
    action: KEEP_AS_NON_CORE
    reason: The cytoplasmic activity location is correct and redundantly supported by stronger evidence (PMID:19440361); however the specific reference appears to be a citation error, so the annotation is retained but not relied upon.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- term:
    id: GO:0101005
    label: deubiquitinase activity
  evidence_type: IDA
  original_reference_id: PMID:23042150
  qualifier: enables
  review:
    summary: Direct assay of deubiquitinase activity (removal of K63-linked ubiquitin from TRAF5/TRAF6). This is the parent of the more precise cysteine-type deubiquitinase activity term.
    action: MODIFY
    reason: GO:0101005 is correct but less precise; USP25 is a cysteine-type DUB, so GO:0004843 is the appropriate specific molecular function.
    proposed_replacement_terms:
    - id: GO:0004843
      label: cysteine-type deubiquitinase activity
    supported_by:
    - reference_id: PMID:23042150
      supporting_text: USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
- term:
    id: GO:1903882
    label: negative regulation of interleukin-17-mediated signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:23042150
  qualifier: involved_in
  review:
    summary: USP25 negatively regulates IL-17 signaling and inflammation by removing K63-linked ubiquitin chains from the adaptors TRAF5 and TRAF6, dampening downstream activation.
    action: ACCEPT
    reason: Directly and specifically supported experimentally; captures USP25's role in restraining IL-17 signaling with correct directionality.
    supported_by:
    - reference_id: PMID:23042150
      supporting_text: USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
- term:
    id: GO:0032183
    label: SUMO binding
  evidence_type: IPI
  original_reference_id: PMID:18538659
  qualifier: enables
  review:
    summary: Experimental interaction with SUMO (SUMO2/3 preferred) via the N-terminal SIM, mediating paralog-specific sumoylation that impairs USP25 ubiquitin binding and hydrolysis.
    action: ACCEPT
    reason: Directly documented SUMO binding through the SUMO-interaction motif; a genuine regulatory molecular function (auxiliary to the core DUB activity).
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Interacts with SUMO3; the interaction sumoylates efficiently USP25.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5696564
  qualifier: located_in
  review:
    summary: Reactome curated cytosolic localization, consistent with the experimentally established cytoplasmic/cytosolic localization of USP25.
    action: ACCEPT
    reason: Agrees with IDA cytosol and multiple cytoplasm annotations.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Cytoplasm'
- term:
    id: GO:0019783
    label: ubiquitin-like protein peptidase activity
  evidence_type: NAS
  original_reference_id: PMID:22590560
  qualifier: enables
  review:
    summary: Non-author statement attributing ubiquitin-like protein peptidase activity. USP25's documented catalytic activity is deubiquitination (cysteine-type deubiquitinase); broader Ubl peptidase activity is not strongly substantiated.
    action: MARK_AS_OVER_ANNOTATED
    reason: USP25's experimentally established activity is on ubiquitin (EC 3.4.19.12); the broader "ubiquitin-like protein peptidase activity" rests on a NAS statement and is better represented by the specific cysteine-type deubiquitinase activity.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: EC=3.4.19.12
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:22590560
  qualifier: located_in
  review:
    summary: Direct evidence for ER association in the context of USP25's ERAD function (counteracting HRD1). A genuine but context-specific localization secondary to the predominant cytoplasmic pool.
    action: KEEP_AS_NON_CORE
    reason: ER localization is experimentally supported in the ERAD context, but it is a specialized, partial localization relative to USP25's predominant cytoplasmic site of action.
    supported_by:
    - reference_id: PMID:22590560
      supporting_text: USP25 counteracts the ubiquitin ligase function of HRD1.
- term:
    id: GO:0016579
    label: protein deubiquitination
  evidence_type: IDA
  original_reference_id: PMID:22590560
  qualifier: involved_in
  review:
    summary: Direct evidence of protein deubiquitination, here counteracting HRD1-mediated ubiquitination of ERAD substrates and rescuing them from proteasomal degradation.
    action: ACCEPT
    reason: Protein deubiquitination is the direct, experimentally supported process of USP25's catalytic activity.
    supported_by:
    - reference_id: PMID:22590560
      supporting_text: USP25 counteracts the ubiquitin ligase function of HRD1 by binding ubiquitinated species and cleaving them.
- term:
    id: GO:0031625
    label: ubiquitin protein ligase binding
  evidence_type: IPI
  original_reference_id: PMID:22590560
  qualifier: enables
  review:
    summary: Interaction with the E3 ubiquitin ligase HRD1/SYVN1 (Q86TM6), consistent with USP25 counteracting HRD1 to rescue ERAD substrates.
    action: KEEP_AS_NON_CORE
    reason: A real and functionally relevant interaction (HRD1) underlying the ERAD role; informative as a binding function but auxiliary to the core deubiquitinase activity.
    supported_by:
    - reference_id: PMID:22590560
      supporting_text: USP25 counteracts the ubiquitin ligase function of HRD1.
- term:
    id: GO:0043130
    label: ubiquitin binding
  evidence_type: NAS
  original_reference_id: PMID:22590560
  qualifier: enables
  review:
    summary: Ubiquitin binding via the N-terminal UBA-like and tandem UIM domains, which recognize ubiquitin/ubiquitin chains and regulate substrate engagement.
    action: ACCEPT
    reason: Ubiquitin binding through the UBA/UIM modules is well established structurally and functionally and underlies substrate recognition by USP25.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: The UBA-UIM domains of the USP25 regulate the enzyme ubiquitination state and modulate substrate recognition
- term:
    id: GO:0051117
    label: ATPase binding
  evidence_type: IPI
  original_reference_id: PMID:22590560
  qualifier: enables
  review:
    summary: Interaction with the AAA-ATPase VCP/p97 (P55072), a central ERAD component that extracts ubiquitinated substrates from the ER membrane.
    action: KEEP_AS_NON_CORE
    reason: A real interaction relevant to USP25's ERAD role (VCP/p97), but auxiliary to the core deubiquitinase function.
    supported_by:
    - reference_id: PMID:22590560
      supporting_text: USP25 counteracts the ubiquitin ligase function of HRD1.
- term:
    id: GO:1904293
    label: negative regulation of ERAD pathway
  evidence_type: IMP
  original_reference_id: PMID:22590560
  qualifier: involved_in
  review:
    summary: USP25 negatively regulates ERAD by counteracting HRD1-mediated ubiquitination of ERAD substrates, cleaving ubiquitin from them and rescuing them from proteasomal degradation.
    action: ACCEPT
    reason: Directly supported experimentally; captures USP25's specific ERAD-modulating role.
    supported_by:
    - reference_id: PMID:22590560
      supporting_text: USP25 counteracts the ubiquitin ligase function of HRD1 by binding ubiquitinated species and cleaving them.
- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: IMP
  original_reference_id: PMID:18538659
  qualifier: enables
  review:
    summary: Deubiquitinase activity inferred from mutational analysis in the sumoylation study; sumoylation impairs ubiquitin hydrolysis.
    action: ACCEPT
    reason: Supports the core cysteine-type deubiquitinase activity of USP25.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Sumoylation impairs binding to and hydrolysis of ubiquitin chains.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:18538659
  qualifier: enables
  review:
    summary: IntAct interaction with SUMO3 (P55854), the basis of the SUMO-binding molecular function. The bare protein binding term is uninformative; SUMO binding (GO:0032183) is the specific term.
    action: MODIFY
    reason: Bare protein binding is uninformative; the WITH partner is SUMO3, so SUMO binding (GO:0032183) is the appropriate specific molecular function.
    proposed_replacement_terms:
    - id: GO:0032183
      label: SUMO binding
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Interacts with SUMO3; the interaction sumoylates efficiently USP25.
- term:
    id: GO:0070536
    label: protein K63-linked deubiquitination
  evidence_type: IMP
  original_reference_id: PMID:18538659
  qualifier: involved_in
  review:
    summary: USP25 cleaves K63-linked polyubiquitin chains, consistent with its activity on TRAF5/TRAF6 K63 chains in IL-17 signaling.
    action: ACCEPT
    reason: USP25's ability to hydrolyze K63-linked chains is experimentally supported and biologically relevant (IL-17/TRAF signaling).
    supported_by:
    - reference_id: PMID:23042150
      supporting_text: USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
- term:
    id: GO:0071108
    label: protein K48-linked deubiquitination
  evidence_type: IMP
  original_reference_id: PMID:18538659
  qualifier: involved_in
  review:
    summary: USP25 cleaves K48-linked polyubiquitin chains, consistent with its rescue of substrates (e.g. ERAD substrates, TNKS, KEAP1) from K48-linked proteasomal degradation.
    action: ACCEPT
    reason: USP25's activity on K48-linked chains is experimentally supported and underlies its substrate-stabilizing roles.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Sumoylation impairs binding to and hydrolysis of ubiquitin chains.
- term:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  evidence_type: TAS
  original_reference_id: PMID:10644437
  qualifier: enables
  review:
    summary: Original cloning paper describing USP25 as a deubiquitinating enzyme; traceable author statement of cysteine-type deubiquitinase activity.
    action: ACCEPT
    reason: Supports the core molecular function; consistent with all later experimental evidence.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
- term:
    id: GO:0006508
    label: proteolysis
  evidence_type: TAS
  original_reference_id: PMID:10644437
  qualifier: involved_in
  review:
    summary: Broad proteolysis annotation from the original cloning paper. USP25 cleaves isopeptide/peptide bonds of ubiquitin conjugates; protein deubiquitination is the precise process.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic "proteolysis" is imprecise for a deubiquitinase; the specific process is protein deubiquitination (already annotated). Retaining the broad term adds little.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
- term:
    id: GO:0008233
    label: peptidase activity
  evidence_type: TAS
  original_reference_id: PMID:10644437
  qualifier: enables
  review:
    summary: Broad peptidase activity annotation from the original cloning paper. The precise activity is cysteine-type deubiquitinase activity (peptidase C19 family).
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic "peptidase activity" is a high-level parent; the specific GO:0004843 cysteine-type deubiquitinase activity is already annotated and is far more informative.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: EC=3.4.19.12
- term:
    id: GO:0036211
    label: protein modification process
  evidence_type: TAS
  original_reference_id: PMID:10644437
  qualifier: involved_in
  review:
    summary: Very broad "protein modification process" annotation from the original cloning paper. The specific process (protein deubiquitination) is already annotated.
    action: MARK_AS_OVER_ANNOTATED
    reason: This is an over-general parent term; protein deubiquitination is the precise and already-annotated process.
    supported_by:
    - reference_id: file:human/USP25/USP25-uniprot.txt
      supporting_text: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10644437
  title: USP25, a novel gene encoding a deubiquitinating enzyme, is located in the gene-poor region 21q11.2.
  findings:
  - statement: USP25 was identified as a novel deubiquitinating enzyme gene in chromosome region 21q11.2 (the historical "USP on chromosome 21" basis for the USP21 alias).
    reference_section_type: ABSTRACT
- id: PMID:18538659
  title: Mechanism and consequences for paralog-specific sumoylation of ubiquitin-specific protease 25.
  findings:
  - statement: USP25 binds SUMO (SUMO2/3 preferred) via an N-terminal SUMO-interaction motif; sumoylation at Lys-99 impairs ubiquitin binding and hydrolysis.
    reference_section_type: ABSTRACT
- id: PMID:19440361
  title: The UBA-UIM domains of the USP25 regulate the enzyme ubiquitination state and modulate substrate recognition.
  findings:
  - statement: The N-terminal UBA and tandem UIM domains regulate USP25 ubiquitination state and substrate recognition; USP25 is active in the cytoplasm.
    reference_section_type: ABSTRACT
- id: PMID:21516116
  title: Next-generation sequencing to generate interactome datasets.
  findings: []
- id: PMID:22153077
  title: Structural basis and sequence rules for substrate recognition by Tankyrase explain the basis for cherubism disease.
  findings: []
- id: PMID:22590560
  title: Ubiquitin-specific protease 25 functions in Endoplasmic Reticulum-associated degradation.
  findings:
  - statement: USP25 counteracts the ubiquitin ligase function of HRD1 by binding ubiquitinated ERAD substrates and cleaving them, rescuing them from proteasomal degradation; interacts with HRD1 and VCP/p97.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "Cached PMID_22590560 title/body match; body confirms USP25 is the DUB counteracting HRD1 in ERAD, supporting the substrate-stabilization core function."
- id: PMID:2304215
  title: 'Problems identified by secondary review of accepted manuscripts.'
  findings: []
- id: PMID:23042150
  title: Negative regulation of IL-17-mediated signaling and inflammation by the ubiquitin-specific protease USP25.
  findings:
  - statement: USP25 removes K63-linked ubiquitin chains from the adaptors TRAF5 and TRAF6 to negatively regulate IL-17-mediated signaling and inflammation.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "Cached PMID_23042150 title/body match; establishes USP25 K63-DUB activity on TRAF5/TRAF6 in IL-17 signaling, supporting the substrate-deubiquitination core function."
- id: PMID:25416956
  title: A proteome-scale map of the human interactome network.
  findings: []
- id: PMID:28514442
  title: Architecture of the human interactome defines protein communities and disease networks.
  findings: []
- id: PMID:28619731
  title: USP25 regulates Wnt signaling by controlling the stability of tankyrases.
  findings:
  - statement: USP25 deubiquitinates and stabilizes the tankyrases TNKS1 and TNKS2, thereby regulating Wnt/beta-catenin signaling.
    reference_section_type: ABSTRACT
- id: PMID:31515488
  title: Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
  findings: []
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
- id: PMID:32707033
  title: Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases.
  findings: []
- id: PMID:32814053
  title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
  findings: []
- id: PMID:33060197
  title: Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
  findings: []
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
  findings: []
- id: PMID:34232536
  title: Interactomes of SARS-CoV-2 and human coronaviruses reveal host factors potentially affecting pathogenesis.
  findings: []
- id: PMID:35914814
  title: "Chr21 protein-protein interactions: enrichment in proteins involved in intellectual disability, autism, and late-onset Alzheimer's disease."
  findings: []
- id: PMID:36217029
  title: A proteome-scale map of the SARS-CoV-2-human contactome.
  findings: []
- id: PMID:37339955
  title: USP25 regulates KEAP1-NRF2 anti-oxidation axis and its inactivation protects acetaminophen-induced liver injury in male mice.
  findings:
  - statement: USP25 deubiquitinates and stabilizes KEAP1, promoting degradation of NRF2; USP25 inactivation protects against acetaminophen-induced liver injury.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: "Cached PMID_37339955 title/body match; supports USP25 deubiquitination/stabilization of KEAP1 in the NRF2 axis (substrate-stabilization core function); cited in core_functions supported_by."
- id: PMID:38875478
  title: Heterozygous variants in USP25 cause genetic generalized epilepsy.
  findings:
  - statement: Heterozygous USP25 variants cause idiopathic generalized epilepsy (EIG19); a C-terminal truncation is a gain-of-function increasing deubiquitination and shifting the oligomeric state from inhibited tetramer toward active dimer.
    reference_section_type: ABSTRACT
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional genomics.
  findings: []
- id: Reactome:R-HSA-5688426
  title: Ub-specific processing proteases (deubiquitination)
  findings: []
- id: Reactome:R-HSA-5696564
  title: Ub-specific processing proteases
  findings: []
core_functions:
- description: Cysteine-type deubiquitinase (peptidase C19 family; active-site Cys-178, EC 3.4.19.12) that hydrolyzes K48- and K63-linked polyubiquitin from substrate proteins, recognizing ubiquitin through N-terminal UBA-like and tandem UIM domains.
  molecular_function:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: file:human/USP25/USP25-uniprot.txt
    supporting_text: Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates
  - reference_id: PMID:37339955
    supporting_text: Here we report that USP25 deubiquitinates KEAP1 and prevents it from excessive ubiquitination and degradation.
- description: Substrate stabilization through deubiquitination, rescuing specific targets from proteasomal degradation to modulate signaling pathways including Wnt/beta-catenin (tankyrases TNKS1/2), the KEAP1-NRF2 oxidative-stress axis, IL-17/innate-immune signaling (TRAF5/TRAF6/TRAF3), and ERAD (counteracting HRD1).
  molecular_function:
    id: GO:0004843
    label: cysteine-type deubiquitinase activity
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: PMID:23042150
    supporting_text: USP25 interacted with TRAF5 and TRAF6, but not with TRAF3 in HBECs or MEFs after IL-17 stimulation
  - reference_id: PMID:22590560
    supporting_text: USP25 counteracts the ubiquitin ligase function of HRD1 by binding ubiquitinated species and cleaving them.
proposed_new_terms: []
suggested_questions:
- question: Is USP25's deubiquitinase activity directed to substrates by a shared recognition feature, or is substrate selection determined principally by context-specific scaffolds/adaptors in each pathway (Wnt, KEAP1-NRF2, IL-17, ERAD)?
- question: How does the homotetramer-to-homodimer transition (and its disruption by epilepsy-associated C-terminal truncations) couple oligomeric state to substrate-specific deubiquitination in neurons?
- question: Does the muscle-specific isoform USP25m have a distinct substrate repertoire (e.g. sarcomeric proteins MYBPC1/FLNC) compared with the ubiquitously expressed USP25a/b isoforms?
suggested_experiments:
- description: Proteome-wide ubiquitinome (diGly) profiling comparing wild-type, catalytic-dead (C178S) and epilepsy-variant USP25 to define the global substrate landscape and test substrate-specificity hypotheses.
- description: Reconstitute the oligomerization switch in vitro with defined homodimer versus homotetramer assemblies and measure deubiquitination kinetics on K48- versus K63-linked chains and on physiological substrates (KEAP1, TNKS2, TRAF6).
- description: Neuronal models (iPSC-derived neurons) carrying EIG19 gain-of-function variants to test whether increased deubiquitination raises neuronal excitability and to identify the responsible neuronal substrates.

USP25

Gene Description