USP25

gene
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Also known as USP21

Summary

USP25 (ubiquitin specific peptidase 25, HGNC:12624) is a protein-coding gene on chromosome 21q21.1, encoding Ubiquitin carboxyl-terminal hydrolase 25 (Q9UHP3). Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates and thus, functions in various biological processes including inflammation and immune response.

Ubiquitin (MIM 191339) is a highly conserved 76-amino acid protein involved in regulation of intracellular protein breakdown, cell cycle regulation, and stress response. Ubiquitin is released from degraded proteins by disassembly of the polyubiquitin chains, which is mediated by ubiquitin-specific proteases (USPs), such as USP25 (Valero et al., 1999 [PubMed 10644437]).

Source: NCBI Gene 29761 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): epilepsy, idiopathic generalized, susceptibility to, 19 (Moderate, GenCC) — +1 more curated relationship
  • GWAS associations: 9
  • Clinical variants (ClinVar): 245 total
  • Druggable target: yes
  • MANE Select transcript: NM_001283041

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12624
Approved symbolUSP25
Nameubiquitin specific peptidase 25
Location21q21.1
Locus typegene with protein product
StatusApproved
AliasesUSP21
Ensembl geneENSG00000155313
Ensembl biotypeprotein_coding
OMIM604736
Entrez29761

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 18 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000285679, ENST00000285681, ENST00000351097, ENST00000400183, ENST00000449491, ENST00000453553, ENST00000464435, ENST00000478932, ENST00000547201, ENST00000549362, ENST00000926090, ENST00000926091, ENST00000926092, ENST00000926093, ENST00000941966, ENST00000941967, ENST00000941968, ENST00000941969, ENST00000941970, ENST00000941971, ENST00000941972, ENST00000941973

RefSeq mRNA: 9 — MANE Select: NM_001283041 NM_001283041, NM_001283042, NM_001352560, NM_001352561, NM_001388299, NM_001388300, NM_001388301, NM_001388302, NM_013396

CCDS: CCDS33515, CCDS63336, CCDS63337

Canonical transcript exons

ENST00000400183 — 26 exons

ExonStartEnd
ENSE000010202631587779615877991
ENSE000010202661584239815842540
ENSE000010202791581869815818846
ENSE000010202841586626615866344
ENSE000010203051576599715766141
ENSE000010203101582403915824166
ENSE000010203141583140115831629
ENSE000010203181584977715849872
ENSE000010203231586426815864446
ENSE000010203261583053115830601
ENSE000010203311587440315874526
ENSE000010203321587006815870147
ENSE000010203341582496615825061
ENSE000010203351583334815833548
ENSE000011830631582620415826365
ENSE000011830921582697715827203
ENSE000013825091576289115762968
ENSE000017361821584766315847776
ENSE000034711731579975715799843
ENSE000035138011577790415778027
ENSE000035639041580512115805258
ENSE000036127821579150215791664
ENSE000036151861580880915808885
ENSE000036547311581113715811210
ENSE000037452041587830315880064
ENSE000039210141572998215730438

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 99.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.2039 / max 212.9012, expressed in 1807 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
18850711.19081772
1885086.85721699
1885110.155953

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001999.91gold quality
male germ cellCL:000001598.36gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451197.71gold quality
gluteal muscleUBERON:000200097.09gold quality
amniotic fluidUBERON:000017396.95gold quality
hindlimb stylopod muscleUBERON:000425296.46gold quality
biceps brachiiUBERON:000150796.44gold quality
calcaneal tendonUBERON:000370196.33gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450296.18gold quality
muscle of legUBERON:000138396.17gold quality
gastrocnemiusUBERON:000138896.17gold quality
skeletal muscle tissueUBERON:000113496.16gold quality
vastus lateralisUBERON:000137996.16gold quality
muscle organUBERON:000163096.16gold quality
deltoidUBERON:000147696.07gold quality
quadriceps femorisUBERON:000137796.04gold quality
diaphragmUBERON:000110395.08gold quality
tibialis anteriorUBERON:000138595.06gold quality
endothelial cellCL:000011594.68gold quality
triceps brachiiUBERON:000150994.24gold quality
adrenal tissueUBERON:001830393.85gold quality
secondary oocyteCL:000065593.39gold quality
cauda epididymisUBERON:000436093.09gold quality
left testisUBERON:000453392.83gold quality
colonic epitheliumUBERON:000039792.70gold quality
muscle tissueUBERON:000238592.69gold quality
right testisUBERON:000453492.58gold quality
monocyteCL:000057692.50gold quality
mononuclear cellCL:000084292.47gold quality
leukocyteCL:000073892.38gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.76

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F4

miRNA regulators (miRDB)

213 targeting USP25, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-3163100.0077.238605
HSA-MIR-3924100.0072.092394
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-196A-5P100.0068.16684
HSA-MIR-196B-5P100.0068.16681
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-186-5P99.9970.833707
HSA-MIR-511-3P99.9968.851467
HSA-MIR-318599.9968.121959
HSA-MIR-548AW99.9972.573559
HSA-MIR-569699.9872.364487
HSA-MIR-1213699.9872.815713
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593

Literature-anchored findings (GeneRIF, showing 35)

  • characterization of alternatively spliced products and tissue-specific isoforms (PMID:11597335)
  • downregulation of USP25 gene in human lung cancer (PMID:18523997)
  • Seven amino acids in the SIM of USP25 are sufficient for SUMO2/3-specific binding and conjugation (PMID:18538659)
  • Data show that USP25m is regulated through alternative conjugation of ubiquitin (activating) or SUMO (inhibiting) to the same lysine residue (K99), which may promote the interaction with distinct intramolecular regulatory domains. (PMID:19440361)
  • the second SH2 domain of SYK physically interacts with a tyrosine-rich, C-terminal region of USP25 independently of tyrosine phosphorylation (PMID:19909739)
  • Studies indicate that DUBs recycle ubiquitin by processing polyubiquitin chains to generate free ubiquitin, and can be regulated by ubiquitination or phosphorylation. (PMID:21480003)
  • a model where USP25 counteracts ubiquitination of ERAD substrates by the ubiquitin ligase HRD1, rescuing them from degradation by the proteasome. (PMID:22590560)
  • USP25 is a novel deubiquitinating enzyme negatively regulating virus-induced interferon-beta production. (PMID:24260525)
  • These findings indicate that miR-200c exerts tumor-suppressive effects for NSCLC through the suppression of USP25 expression and suggests a new therapeutic application of miR-200c in the treatment of NSCLC. (PMID:24997798)
  • Findings suggest that ubiquitin-specific protease 25 (USP25) as a VRK2 substrate that acts on TRiC deubiquitination. (PMID:25755282)
  • REM Sleep Behavior Disorder patients with homozygous USP25 rs2823357 progressed to synucleinopathies faster than others. (PMID:25929833)
  • We detected SNPs at USP25 with associations of genome-wide significance for Inflammatory Bowel Disease. (PMID:27693347)
  • Results suggest inhibition of Usp25’s catalytic activity upon the non-covalent binding of SUMO2 to the Usp25 SUMO-interacting motif, and found that SUMO2 can competitively block the interaction between the Usp25 ubiquitin-binding region and its ubiquitin substrates. (PMID:28538147)
  • USP25 directly interacted with tankyrases to promote their deubiquitination and stabilization and demonstrated that USP25 deficiency could promote the degradation of tankyrases and consequent stabilization of Axin to antagonize Wnt signaling (PMID:28619731)
  • Smurf1 overexpression decreases USP25 protein turnover, and the E3 ligase enzymatic activity of Smurf1 is required for USP25 degradation. (PMID:29518389)
  • Polymorphism of SREBF1 gene rs11868035 may increase susceptibility to Parkinson’s disease in the northeastern Chinese population, while variant of USP25 gene rs2823357 may have no association with susceptibility to Parkinson’s disease in northeastern Chinese. (PMID:30231795)
  • the high stabilization of tankyrases in cultured cells by ectopic expression of a constitutive dimer of USP25 supports a biological relevance of this tetramerization/inhibition mechanism. (PMID:30478318)
  • These findings indicate that USP25 promotes stability of HBO1 in bacterial infection thereby enhances HBO1-mediated inflammatory gene transcription. (PMID:30745998)
  • We confirm oligomeric states of USP25 and USP28 in cells and show that modulating oligomerization affects substrate stabilization in accordance with in vitro activity data (PMID:30926242)
  • Our work led to the identification of significant differences between USP25 and USP28 and provided the molecular basis for the development of new and highly specific anti-cancer drugs (PMID:30926243)
  • USP25 downregulation by miR-27a-3p contributes to the epithelial-to-mesenchymal transition process, thereby inhibiting the migration and invasion of trophoblast cells, and these findings might provide potential biomarkers for recurrent miscarriage. (PMID:30953360)
  • Deubiquitylase USP25 prevents degradation of BCR-ABL protein and ensures proliferation of Ph-positive leukemia cells. (PMID:32203161)
  • USP28 and USP25 are downregulated by Vismodegib in vitro and in colorectal cancer cell lines. (PMID:32578360)
  • USP25 Regulates EGFR Fate by Modulating EGF-Induced Ubiquitylation Dynamics. (PMID:33202887)
  • The deubiquitinase USP25 supports colonic inflammation and bacterial infection and promotes colorectal cancer. (PMID:35122046)
  • Deubiquitination of TNKS1 Regulates Wnt/beta-Catenin to Affect the Expression of USP25 to Promote the Progression of Glioma. (PMID:35450028)
  • USP25 UPREGULATION BOOSTS GSDMD -MEDIATED PYROPTOSIS OF ACINAR CELLS IN ACUTE PANCREATITIS. (PMID:36155610)
  • Downregulation of deubiquitinating enzyme USP25 promotes the development of allergic rhinitis by enhancing TSLP signaling in the nasal epithelium. (PMID:36177892)
  • Regulation of USP25 by SP1 Associates with Amyloidogenesis. (PMID:36938736)
  • USP25 inhibits renal fibrosis by regulating TGFbeta-SMAD signaling pathway in Ang II-induced hypertensive mice. (PMID:37059312)
  • USP25 contributes to defective neurogenesis and cognitive impairments. (PMID:37171286)
  • USP25 promotes hepatocellular carcinoma progression by interacting with TRIM21 via the Wnt/beta-catenin signaling pathway. (PMID:37439386)
  • Usp25-Erlin1/2 activity limits cholesterol flux to restrict virus infection. (PMID:37683630)
  • Expression of USP25 associates with fibrosis, inflammation and metabolism changes in IgG4-related disease. (PMID:38521787)
  • Heterozygous variants in USP25 cause genetic generalized epilepsy. (PMID:38875478)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriousp25ENSDARG00000012314
mus_musculusUsp25ENSMUSG00000022867
rattus_norvegicusUsp25ENSRNOG00000001573

Paralogs (71): USP2 (ENSG00000036672), USP28 (ENSG00000048028), USP36 (ENSG00000055483), USP13 (ENSG00000058056), USP33 (ENSG00000077254), USP40 (ENSG00000085982), USP48 (ENSG00000090686), USP14 (ENSG00000101557), USP11 (ENSG00000102226), USP10 (ENSG00000103194), USP31 (ENSG00000103404), USP42 (ENSG00000106346), USP5 (ENSG00000111667), USP4 (ENSG00000114316), USP9Y (ENSG00000114374), USP34 (ENSG00000115464), USP35 (ENSG00000118369), USP45 (ENSG00000123552), USP22 (ENSG00000124422), USP9X (ENSG00000124486), USP6 (ENSG00000129204), USP29 (ENSG00000131864), USP26 (ENSG00000134588), USP30 (ENSG00000135093), USP15 (ENSG00000135655), USP37 (ENSG00000135913), USP44 (ENSG00000136014), USP20 (ENSG00000136878), USP8 (ENSG00000138592), USP3 (ENSG00000140455), USP21 (ENSG00000143258), USP43 (ENSG00000154914), USP16 (ENSG00000156256), USP24 (ENSG00000162402), USP1 (ENSG00000162607), USP49 (ENSG00000164663), USP38 (ENSG00000170185), USP50 (ENSG00000170236), USP47 (ENSG00000170242), USP32 (ENSG00000170832)

Protein

Protein identifiers

Ubiquitin carboxyl-terminal hydrolase 25Q9UHP3 (reviewed: Q9UHP3)

Alternative names: Deubiquitinating enzyme 25, USP on chromosome 21, Ubiquitin thioesterase 25, Ubiquitin-specific-processing protease 25

All UniProt accessions (4): Q9UHP3, H7C1T8, H7C253, Q96B65

UniProt curated annotations — full annotation on UniProt →

Function. Deubiquitinating enzyme that hydrolyzes ubiquitin moieties conjugated to substrates and thus, functions in various biological processes including inflammation and immune response. Modulates the Wnt/beta-catenin pathway by deubiquitinating and stabilizing tankyrases TNKS1 and TNKS2. Regulates KEAP1-NRF2 axis in the defense against oxidative assaults by deubiquitinating KEAP1 and protecting it from degradation leading to degradation of the NRF2 transcription factor that is responsible for mounting an anti-oxidation gene expression program. Positively regulates RNA virus-induced innate signaling by interacting with and deubiquitinating ERLIN1 and ERLIN2. In turn, restricts virus production by regulating cholesterol biosynthetic flux. Acts as a negative regulator of interleukin-17-mediated signaling and inflammation through the removal of ‘Lys-63’-linked ubiquitination of TRAF5 and TRAF6. Prevents the ubiquitination and degradation of TRAF3 to reduce the phosphorylation levels of JNK and P38, the secretion of IL-1B and to induce endotoxin tolerance. The muscle-specific isoform (USP25m) may have a role in the regulation of muscular differentiation and function.

Subunit / interactions. Homotetramer, inhibited form. Homodimer, active form. Interacts with ACTA1 (via its C-terminus); the interaction occurs for all isoforms but is strongest for isoform USP25m in muscle differentiating cells. Interacts (isoform USP25m only) with MYBPC1; the interaction prevents proteasomal degradation of MYBPC1. Interacts (isoform USP25m only) with FLNC (via filament repeats 17-18, 20-21 and 24). Interacts with GAPDH. Interacts with SUMO3; the interaction sumoylates efficiently USP25. Interacts with SUMO2; the interaction sumoylates efficiently USP25. Interacts with SUMO1; the interaction only weakly sumoylates USP25. Interacts with SYK; phosphorylates USP25 and regulates USP25 intracellular levels.

Subcellular location. Cytoplasm Cytoplasm. Nucleus.

Tissue specificity. Isoform USP25a is found in most adult and fetal tissues; expression is moderately high in testis, pancreas, kidney, skeletal muscle, liver, lung, placenta, heart, but very low in peripheral blood, colon, small intestine, ovary, prostate, thymus and spleen. Expressed in the brain, with high levels in the cerebral cortex. Isoform USP25b is found in all tissues except heart and skeletal muscle. Isoform USP25m is heart and skeletal muscle specific.

Post-translational modifications. Acetylated. Sumoylation impairs binding to and hydrolysis of ubiquitin chains. Sumoylated preferentially with SUMO2 or SUMO3. Desumoylated by SENP1. Polyubiquitinated by SMURF1 by promoting the ‘Lys-48’-linkage leading to proteasomal degradation. Preferentially monoubiquitinated but can also be polyubiquitinated. Autodeubiquitinated. Ubiquitination activates the enzymatic activity either by preventing sumoylation or by allowing novel interactions. Phosphorylation in the C-terminal by SYK regulates USP25 cellular levels.

Disease relevance. Epilepsy, idiopathic generalized 19 (EIG19) [MIM:621064] An autosomal dominant form of idiopathic generalized epilepsy, a disorder characterized by recurring generalized seizures in the absence of detectable brain lesions and/or metabolic abnormalities. Generalized seizures arise diffusely and simultaneously from both hemispheres of the brain. Seizure types include juvenile myoclonic seizures, absence seizures, and generalized tonic-clonic seizures. EIG19 is characterized by onset of variable types of seizures in the first two decades of life. Disease susceptibility is associated with variants affecting the gene represented in this entry.

Induction. The muscle-specific isoform (USP25m) is up-regulated during myocyte differentiation. Levels increase up to 100-fold towards completion of differentiation.

Similarity. Belongs to the peptidase C19 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9UHP3-2USP25ayes
Q9UHP3-1USP25b
Q9UHP3-3USP25m, Muscle-specific isoform

RefSeq proteins (9): NP_001269970, NP_001269971, NP_001339489, NP_001339490, NP_001375228, NP_001375229, NP_001375230, NP_001375231, NP_037528 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001394Peptidase_C19_UCHDomain
IPR003903UIM_domConserved_site
IPR009060UBA-like_sfHomologous_superfamily
IPR018200USP_CSConserved_site
IPR028889USPDomain
IPR038765Papain-like_cys_pep_sfHomologous_superfamily
IPR050164Peptidase_C19Family
IPR054108USP25/28_UIMConserved_site
IPR054109UBA_8Domain

Pfam: PF00443, PF21909, PF22566

UniProt features (106 total): helix 39, strand 22, turn 9, mutagenesis site 8, sequence variant 5, domain 4, active site 3, region of interest 3, compositionally biased region 2, modified residue 2, cross-link 2, splice variant 2, coiled-coil region 2, chain 1, short sequence motif 1, sequence conflict 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
5GP7X-RAY DIFFRACTION1.5
6HEMX-RAY DIFFRACTION1.72
6H4KX-RAY DIFFRACTION2.05
6HELX-RAY DIFFRACTION2.94
6H4JX-RAY DIFFRACTION3.07
5O71X-RAY DIFFRACTION3.28
2MUXSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UHP3-F178.120.38

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 178; 599; 607

Post-translational modifications (4): 85, 740, 99, 99

Mutagenesis-validated functional residues (8):

PositionPhenotype
91no interaction with sumo3; when associated with a-92.
92no interaction with sumo3; when associated with a-91.
99abolishes sumoylation. decreased enzymatic activity.
178abrogates deubiquitinating activity. no effect on homo- or oligomerization.
740no effect on interaction with syk.
878no effect on interaction with syk.
880no effect on interaction with syk.
883no effect on interaction with syk.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-5689880Ub-specific processing proteases

MSigDB gene sets: 434 (showing top): WENDT_COHESIN_TARGETS_UP, GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, MODULE_97, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_RESPONSE_TO_PEPTIDE, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, IVANOVA_HEMATOPOIESIS_MATURE_CELL, HUMMERICH_BENIGN_SKIN_TUMOR_UP, MODULE_182

GO Biological Process (13): proteolysis (GO:0006508), protein deubiquitination (GO:0016579), regulation of protein stability (GO:0031647), protein modification process (GO:0036211), protein K63-linked deubiquitination (GO:0070536), protein K48-linked deubiquitination (GO:0071108), negative regulation of response to oxidative stress (GO:1902883), negative regulation of interleukin-17-mediated signaling pathway (GO:1903882), negative regulation of ERAD pathway (GO:1904293), cellular response to oxidative stress (GO:0034599), interleukin-17A-mediated signaling pathway (GO:0038173), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), protein K48-linked ubiquitination (GO:0070936)

GO Molecular Function (11): cysteine-type deubiquitinase activity (GO:0004843), peptidase activity (GO:0008233), ubiquitin-like protein peptidase activity (GO:0019783), ubiquitin protein ligase binding (GO:0031625), SUMO binding (GO:0032183), ubiquitin binding (GO:0043130), ATPase binding (GO:0051117), deubiquitinase activity (GO:0101005), protein binding (GO:0005515), cysteine-type peptidase activity (GO:0008234), hydrolase activity (GO:0016787)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Deubiquitination1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein metabolic process2
protein deubiquitination2
response to oxidative stress2
peptidase activity2
ubiquitin-like protein binding2
intracellular membrane-bounded organelle2
cellular anatomical structure2
cytoplasm2
cysteine-type deubiquitinase activity1
protein modification by small protein removal1
regulation of biological quality1
macromolecule modification1
negative regulation of response to stimulus1
regulation of response to oxidative stress1
negative regulation of cytokine-mediated signaling pathway1
interleukin-17-mediated signaling pathway1
regulation of interleukin-17-mediated signaling pathway1
ERAD pathway1
negative regulation of proteasomal protein catabolic process1
negative regulation of response to endoplasmic reticulum stress1
regulation of ERAD pathway1
cellular response to chemical stress1
cytokine-mediated signaling pathway1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
protein polyubiquitination1
cysteine-type peptidase activity1
deubiquitinase activity1
hydrolase activity1
catalytic activity, acting on a protein1
ubiquitin-like protein ligase binding1
enzyme binding1
ubiquitin-like protein peptidase activity1
binding1
catalytic activity1
intracellular anatomical structure1
endomembrane system1

Protein interactions and networks

STRING

1864 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
USP25USP13Q92995775
USP25SUMO1P55856728
USP25USP5P45974722
USP25USP2O75604686
USP25USP8P40818682
USP25YOD1Q5VVQ6681
USP25ZUP1Q96AP4677
USP25USP1O94782671
USP25USP7Q93009668
USP25ATXN3P54252665
USP25USP14P54578647
USP25SUMO2P55855639
USP25USP39Q53GS9632
USP25USP15Q9Y4E8626
USP25USP4Q13107624

IntAct

112 interactions, top by confidence:

ABTypeScore
RAD23AUSP25psi-mi:“MI:0915”(physical association)0.890
USP25RAD23Apsi-mi:“MI:0915”(physical association)0.890
RAD23BUSP25psi-mi:“MI:0915”(physical association)0.850
SYKUSP25psi-mi:“MI:0915”(physical association)0.830
USP25SYKpsi-mi:“MI:0915”(physical association)0.830
GDI1RAB4Apsi-mi:“MI:0914”(association)0.820
repUSP25psi-mi:“MI:0915”(physical association)0.760
repUSP25psi-mi:“MI:2364”(proximity)0.760
USP25SUMO2psi-mi:“MI:0915”(physical association)0.720
SUMO2USP25psi-mi:“MI:0915”(physical association)0.720
DYNLL2BLTP3Bpsi-mi:“MI:0914”(association)0.640
TNKS2USP25psi-mi:“MI:0407”(direct interaction)0.590
MAGEB4USP25psi-mi:“MI:0915”(physical association)0.560
USP25ZNF426psi-mi:“MI:0915”(physical association)0.560

BioGRID (227): USP25 (Reconstituted Complex), USP25 (Biochemical Activity), UBC (Biochemical Activity), UBC (Reconstituted Complex), USP25 (Two-hybrid), USP25 (Two-hybrid), USP25 (Two-hybrid), USP25 (Two-hybrid), ZNF426 (Two-hybrid), USP25 (Affinity Capture-MS), APP (Affinity Capture-Western), SYK (Two-hybrid), USP25 (Affinity Capture-MS), KCTD13 (Affinity Capture-MS), TNFAIP1 (Affinity Capture-MS)

ESM2 similar proteins: A1CHL6, A1CIL1, A1CW53, A1CX69, A2Q9N1, A2QIL5, A6RYB8, A6S9E2, A7EWF5, A7F0W2, A7KAL2, B0Y4P5, B8NSV5, C4B4E5, G2X3G1, I1RNG8, I1S8Q3, J4W0G2, M2T5U2, O14019, P0CAQ1, P0CO28, P0CO29, P0CQ10, P0CQ11, P43638, P57080, Q0CLX3, Q0CT11, Q0UY20, Q1DN93, Q2H6X2, Q2H9Y1, Q2UGZ7, Q2UUG8, Q3ZDQ4, Q4PBL3, Q4WHB7, Q4WPF2, Q4WQI1

Diamond homologs: A2BGT0, A4QNN3, D3ZPG5, Q3UN04, Q70CQ3, Q7JKC3, Q9UHP3, A0JM59, A5PMR2, B1AY13, B1WBD7, F8VPZ3, P57080, P70398, Q5ZM45, Q84WU2, Q8BW70, Q8NFA0, Q93008, Q9FPT1, Q9UPU5, Q9UTT1, A0A0R4IB93, A6QNM7, D3ZJ96, Q28CN3, Q5I043, Q5REG5, Q5ZID5, Q86UV5, Q8BWR4, Q8NB14, Q8R5K2, Q8TEY7, Q96RU2, Q9P3U0, Q9WTV6, Q9P2H5, A5PN09, A7Z056

SIGNOR signaling

5 interactions.

AEffectBMechanism
VRK2“down-regulates activity”USP25phosphorylation
USP25“up-regulates quantity by stabilization”TRiCdeubiquitination
SYK“down-regulates quantity”USP25phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 80 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Formation of Incision Complex in GG-NER628.2×3e-05
Neddylation87.0×3e-03
Ub-specific processing proteases76.9×5e-03

GO biological processes:

GO termPartnersFoldFDR
protein autoubiquitination517.0×2e-03
protein polyubiquitination813.4×1e-04
proteasome-mediated ubiquitin-dependent protein catabolic process86.0×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

245 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance190
Likely benign9
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

5457 predictions. Top by Δscore:

VariantEffectΔscore
21:15730436:AAGGT:Adonor_loss1.0000
21:15730437:AGGT:Adonor_loss1.0000
21:15730438:GGTG:Gdonor_loss1.0000
21:15762886:TCTA:Tacceptor_loss1.0000
21:15762887:CTA:Cacceptor_loss1.0000
21:15762888:TA:Tacceptor_loss1.0000
21:15762889:A:AGacceptor_gain1.0000
21:15762889:AG:Aacceptor_loss1.0000
21:15762890:G:GTacceptor_gain1.0000
21:15762890:GC:Gacceptor_gain1.0000
21:15762890:GCA:Gacceptor_gain1.0000
21:15762890:GCACC:Gacceptor_gain1.0000
21:15762964:TGAAG:Tdonor_loss1.0000
21:15762965:GAAGG:Gdonor_loss1.0000
21:15762967:AGGT:Adonor_loss1.0000
21:15762970:T:Gdonor_loss1.0000
21:15765985:T:TAacceptor_gain1.0000
21:15765989:A:AGacceptor_gain1.0000
21:15765989:ATTT:Aacceptor_gain1.0000
21:15765992:T:TAacceptor_gain1.0000
21:15765992:TGAA:Tacceptor_loss1.0000
21:15765993:GAA:Gacceptor_loss1.0000
21:15765995:A:AGacceptor_gain1.0000
21:15765995:A:Tacceptor_loss1.0000
21:15765996:G:GCacceptor_gain1.0000
21:15765996:GGATA:Gacceptor_gain1.0000
21:15766137:TACAA:Tdonor_gain1.0000
21:15766138:ACAA:Adonor_gain1.0000
21:15766139:CAA:Cdonor_gain1.0000
21:15766140:AA:Adonor_gain1.0000

AlphaMissense

7441 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
21:15777952:T:AI106N1.000
21:15777952:T:GI106S1.000
21:15791628:T:AN173K1.000
21:15791628:T:GN173K1.000
21:15791641:T:CC178R1.000
21:15791642:G:AC178Y1.000
21:15791643:T:GC178W1.000
21:15791644:T:AW179R1.000
21:15791644:T:CW179R1.000
21:15791646:G:CW179C1.000
21:15791646:G:TW179C1.000
21:15791647:T:CF180L1.000
21:15791648:T:CF180S1.000
21:15791649:T:AF180L1.000
21:15791649:T:GF180L1.000
21:15791650:A:CS181R1.000
21:15791652:T:AS181R1.000
21:15791652:T:GS181R1.000
21:15791654:C:AA182D1.000
21:15799779:T:CF193S1.000
21:15799791:T:AV197D1.000
21:15805152:T:CL225P1.000
21:15805203:C:AP242Q1.000
21:15805224:T:CL249P1.000
21:15808812:G:CD262H1.000
21:15808813:A:CD262A1.000
21:15808813:A:TD262V1.000
21:15808818:A:CS264R1.000
21:15808820:T:AS264R1.000
21:15808820:T:GS264R1.000

dbSNP variants (sampled 300 via entrez): RS1000019297 (21:15739723 C>A), RS1000032276 (21:15867192 T>G), RS1000042006 (21:15825718 T>C), RS1000046758 (21:15784496 C>T), RS1000057539 (21:15866945 T>C), RS1000073859 (21:15787846 A>G), RS1000076181 (21:15750122 A>T), RS1000083671 (21:15744478 A>C,G), RS1000088094 (21:15809291 G>A), RS1000090532 (21:15873336 G>T), RS1000100946 (21:15831485 G>A), RS1000121605 (21:15873594 C>G,T), RS1000122395 (21:15729864 G>A), RS1000139754 (21:15858547 ACT>A), RS1000158678 (21:15766826 T>C)

Disease associations

OMIM: gene MIM:604736 | disease phenotypes: MIM:621064, MIM:600669

GenCC curated gene-disease

DiseaseClassificationInheritance
epilepsy, idiopathic generalized, susceptibility to, 19ModerateAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
epilepsyDisputedAD

Mondo (2): epilepsy, idiopathic generalized, susceptibility to, 19 (MONDO:0976128), idiopathic generalized epilepsy (MONDO:0005579)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

StudyTraitp-value
GCST000320_11Panic disorder9.000000e-06
GCST001126_11Parkinson’s disease6.000000e-07
GCST003872_17QRS complex (12-leadsum)4.000000e-09
GCST006291_42Spherical equivalent or myopia (age of diagnosis)5.000000e-12
GCST008485_6Crohn’s disease2.000000e-07
GCST009066_31Mosaic loss of chromosome Y (Y chromosome dosage)1.000000e-08
GCST009391_2007Metabolite levels8.000000e-06
GCST90011900_14Serum alkaline phosphatase levels5.000000e-09
GCST90026412_2Severe autoimmune type 2 diabetes1.000000e-06

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0005054QRS complex
EFO:0007742QRS amplitude
EFO:0004847age at onset
EFO:0007783mosaic loss of chromosome Y measurement
EFO:0010347cholesteryl ester 20:3 measurement
EFO:0004533alkaline phosphatase measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C562694Epilepsy, Idiopathic Generalized (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4295975 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

369 potent at pChembl≥5 of 383 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.70IC50200nMCHEMBL4174196
6.70IC50200nMCHEMBL4300392
6.70IC50200nMCHEMBL4443504
6.70IC50200nMCHEMBL4584152
6.70IC50200nMCHEMBL4451295
6.70IC50200nMCHEMBL4462420
6.70IC50200nMCHEMBL4459980
6.70IC50200nMCHEMBL4585832
6.70IC50200nMCHEMBL4533281
6.70IC50200nMCHEMBL4593462
6.70IC50200nMCHEMBL4590597
6.70IC50200nMCHEMBL4527267
6.70IC50200nMCHEMBL4580403
6.70IC50200nMCHEMBL4556612
6.70IC50200nMCHEMBL4590745
6.70IC50200nMCHEMBL4557308
6.70IC50200nMCHEMBL4534946
6.70IC50200nMCHEMBL4541247
6.70IC50200nMCHEMBL4521756
6.70IC50200nMCHEMBL4588664
6.70IC50200nMCHEMBL4583154
6.70IC50200nMCHEMBL4553911
6.70IC50200nMCHEMBL4530046
6.70IC50200nMCHEMBL4574201
6.70IC50200nMCHEMBL4581055
6.70IC50200nMCHEMBL4548150
6.70IC50200nMCHEMBL4552439
6.70IC50200nMCHEMBL4539489
6.70IC50200nMCHEMBL4575333
6.70IC50200nMCHEMBL4548452
6.70IC50200nMCHEMBL4574312
6.70IC50200nMCHEMBL4514285
6.70IC50200nMCHEMBL4551619
6.70IC50200nMCHEMBL4542243
6.70IC50200nMCHEMBL4575704
6.70IC50200nMCHEMBL4562757
6.70IC50200nMCHEMBL4572877
6.70IC50200nMCHEMBL4483621
6.70IC50200nMCHEMBL4535435
6.70IC50200nMCHEMBL4568633
6.70IC50200nMCHEMBL4538680
6.70IC50200nMCHEMBL4519889
6.70IC50200nMCHEMBL4537585
6.70IC50200nMCHEMBL4569303
6.70IC50200nMCHEMBL4585155
6.70IC50200nMCHEMBL4539113
6.70IC50200nMCHEMBL4556121
6.70IC50200nMCHEMBL4565666
6.70IC50200nMCHEMBL4526977
6.70IC50200nMCHEMBL4539562

PubChem BioAssay actives

7 with measured affinity, of 34 total; 7 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
7-amino-N-[2-[4-(3,8-diazabicyclo[3.2.1]octan-3-yl)-2,5-difluorophenyl]ethyl]-3-methylthieno[2,3-b]pyrazine-6-carboxamide;hydrochloride1504900: Inhibition of recombinant human His6-tagged USP25 expressed in baculovirus infected Sf21 insect cells using Ub-Rh110 as substrate pretreated for 30 mins followed by substrate addition measured after 45 mins by fluorescence assayic500.2000uM
7-amino-N-[2-[4-(3,8-diazabicyclo[3.2.1]octan-3-yl)-3-fluorophenyl]ethyl]-3-methylthieno[2,3-b]pyrazine-6-carboxamide;hydrochloride1504900: Inhibition of recombinant human His6-tagged USP25 expressed in baculovirus infected Sf21 insect cells using Ub-Rh110 as substrate pretreated for 30 mins followed by substrate addition measured after 45 mins by fluorescence assayic500.2000uM
2-[[5-bromo-2-[[4-fluoro-3-(trifluoromethyl)phenyl]methoxy]phenyl]methylamino]ethanol1930832: Inhibition of USP25 (unknown origin) using Ub-Rho100 as substrate by calorimetric analysisic500.6200uM
2-[[5-bromo-2-[[3-(trifluoromethoxy)phenyl]methoxy]phenyl]methylamino]ethanol1930832: Inhibition of USP25 (unknown origin) using Ub-Rho100 as substrate by calorimetric analysisic500.8800uM
7-amino-N-[(2S)-2-[4-(3,8-diazabicyclo[3.2.1]octan-3-yl)-3-fluorophenyl]propyl]-3-methylthieno[2,3-b]pyrazine-6-carboxamide1504900: Inhibition of recombinant human His6-tagged USP25 expressed in baculovirus infected Sf21 insect cells using Ub-Rh110 as substrate pretreated for 30 mins followed by substrate addition measured after 45 mins by fluorescence assayic502.0000uM
7-amino-N-[(2R)-2-[4-(3,8-diazabicyclo[3.2.1]octan-3-yl)-3-fluorophenyl]propyl]-3-methylthieno[2,3-b]pyrazine-6-carboxamide1504900: Inhibition of recombinant human His6-tagged USP25 expressed in baculovirus infected Sf21 insect cells using Ub-Rh110 as substrate pretreated for 30 mins followed by substrate addition measured after 45 mins by fluorescence assayic502.0000uM
7-amino-N-[2-(2,5-difluoro-4-piperazin-1-ylphenyl)ethyl]-3-methylthieno[2,3-b]pyrazine-6-carboxamide1504900: Inhibition of recombinant human His6-tagged USP25 expressed in baculovirus infected Sf21 insect cells using Ub-Rh110 as substrate pretreated for 30 mins followed by substrate addition measured after 45 mins by fluorescence assayic502.0000uM

CTD chemical–gene interactions

43 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression7
trichostatin Aaffects cotreatment, increases expression3
sodium arsenitedecreases expression, increases abundance3
bisphenol Adecreases expression, decreases methylation2
potassium chromate(VI)decreases expression, affects cotreatment2
entinostatincreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tretinoinincreases expression2
Cyclosporineincreases expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
geldanamycinincreases expression1
methylmercuric chloridedecreases expression, increases expression1
alpha-pineneincreases oxidation, increases abundance, affects cotreatment1
arseniteaffects binding, decreases reaction1
butyraldehydedecreases expression1
methacrylaldehydeincreases abundance, affects cotreatment, increases oxidation1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinincreases expression, affects cotreatment1
jinfukangdecreases expression1
(+)-JQ1 compoundincreases expression1
Sunitinibincreases expression1
Acetaminophenincreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1

ChEMBL screening assays

19 unique, capped per target: 19 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4136598BindingInhibition of recombinant human His6-tagged USP25 expressed in baculovirus infected Sf21 insect cells using Ub-Rh110 as substrate pretreated for 30 mins followed by substrate addition measured after 45 mins by fluorescence assayUbiquitin-Specific Inhibitors for the Treatment of Cancers, Autoimmune, and Infectious Diseases. — ACS Med Chem Lett

Cellosaurus cell lines

5 cell lines: 4 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D6BFHyCyte HEK293 KO-hUSP25Transformed cell lineFemale
CVCL_D8Y0Ubigene HCT 116 USP25 KOCancer cell lineMale
CVCL_DX67HAP1 USP25 (-) USP28 (-) 1Cancer cell lineMale
CVCL_DX68HAP1 USP25 (-) USP28 (-) 2Cancer cell lineMale
CVCL_TW79HAP1 USP25 (-)Cancer cell lineMale

Clinical trials (associated diseases)

21 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT03590197PHASE4COMPLETEDEffect of Melatonin on Seizure Outcome, Neuronal Damage and Quality of Life in Patients With Generalized Epilepsy
NCT03940326PHASE4COMPLETEDLevetiracetam Versus Valproate in Idiopathic Generalized Tonic-clonic Seizures
NCT00150735PHASE3COMPLETEDMonotherapy With Levetiracetam in Newly Diagnosed Patients Suffering From Epilepsy
NCT00150748PHASE3COMPLETEDLong Term Follow up Treatment With Levetiracetam in Subjects of 4 Years and Older With Generalized Epilepsy
NCT03678753PHASE3COMPLETEDRandomized, Double-Blind Study to Evaluate Efficacy and Safety of Cenobamate Adjunctive Therapy in PGTC Seizures
NCT05147571PHASE3ACTIVE_NOT_RECRUITINGRNS System NAUTILUS Study
NCT06908356PHASE2RECRUITINGAn Open Label Trial to Evaluate the Efficacy and Safety of PRAX-628 in Adults With Focal Onset or Tonic-Clonic Seizures
NCT06425159PHASE2/PHASE3TERMINATEDA Study to Determine if BHV-7000 is Effective and Safe in Adults With Idiopathic Generalized Epilepsy With Generalized Tonic-clonic Seizures
NCT00001325Not specifiedCOMPLETEDMetabolic Abnormalities in Children With Epilepsy
NCT00916903Not specifiedTERMINATEDGenetic Disease Gene Identification
NCT01311440Not specifiedCOMPLETEDModified Atkins Diet Treatment for Adults With Drug-resistant Epilepsy
NCT01432821Not specifiedCOMPLETEDBlinking and Yawning in Epilepsy: The Role of Dopamine
NCT03368469Not specifiedWITHDRAWNTranscranial Direct Current Stimulation (tDCS) in Children and Adolescents With Epilepsy and Depression
NCT03457961Not specifiedUNKNOWNPost-market Study of AMPA Receptor Antagonists for Epilepsy Patients in Hong Kong
NCT03955432Not specifiedTERMINATEDLong-term Cardiac Monitoring in Epilepsy
NCT04252846Not specifiedCOMPLETEDA Study to Investigate Dosage, Effectiveness, and Safety of Perampanel When Used as First Add-on Therapy in Participants >=12 Years With Partial Onset Seizures With or Without Secondary Generalization or With Primary Generalized Tonic-Clonic Seizures Associated With Idiopathic Generalized Epilepsy
NCT04965571Not specifiedCOMPLETEDClinical Features and Outcome of Wilson’s Disease With Generalized Epilepsy in Chinese Patients
NCT05374928Not specifiedACTIVE_NOT_RECRUITINGHuman Epilepsy Project 3
NCT05530109Not specifiedTERMINATEDStudy of Attentional Disorders in Patients Suffering From Idiopathic Generalized Epilepsy.
NCT06388174Not specifiedRECRUITINGIdiopathic Generalized Epilepsy Syndromes
NCT06797791Not specifiedCOMPLETEDAssessment of Multifocal Continuous Theta Burst Transcranial Magnetic Stimulation (cTBS) Effects in Generalized Epilepsy Patients.