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26 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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USP39
ubiquitin specific peptidase 39
Chromosome 2 · 2p11.2
NCBI Gene: 10713Ensembl: ENSG00000168883.20HGNC: HGNC:20071UniProt: A0A087X1B2
177PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
RESEARCH IMPACT
Trending
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
cysteine-type deubiquitinase activityprotein bindingspliceosomal complex assemblymRNA splicing, via spliceosomealcohol drinkingNeonatal acute respiratory distress with surfactant metabolism deficiencysurfactant metabolism dysfunction, pulmonary, 1Moderate albuminuria
✦AI Summary

USP39 (ubiquitin specific peptidase 39) is a deubiquitinating enzyme that functions as both a component of the U4/U6-U5 tri-snRNP spliceosome complex and a regulator of protein stability through deubiquitination 1. As a spliceosome component, USP39 is essential for pre-mRNA splicing and regulates alternative splicing of numerous genes, including autophagy-related genes like HSF1 in hepatocytes and CTLA-4 in regulatory T cells 23. USP39 deficiency leads to impaired spliceosome assembly and pathogenic cryptic splicing that produces misfolded proteins, causing proteotoxic aggregates and cell death 1. Through its deubiquitinating activity, USP39 stabilizes key proteins including β-catenin by direct deubiquitination and ZEB1 in multiple myeloma cells 45. USP39 also enhances NAT10 protein stability through protein-protein interactions, promoting cancer metastasis 6. Clinically, USP39 is overexpressed in various cancers including hepatocellular carcinoma, multiple myeloma, and leukemia, where high expression correlates with poor patient survival 758. USP39's dual role in RNA splicing regulation and protein stabilization makes it a critical regulator of cellular homeostasis and a potential therapeutic target in cancer.

Sources cited
1
USP39 is essential for spliceosome assembly and its deficiency causes cryptic splicing leading to proteotoxic cell death
PMID: 39541449
2
USP39 regulates alternative splicing of autophagy-related genes like HSF1 in hepatocytes
PMID: 37923718
3
USP39 facilitates CTLA-4 expression through RNA splicing in regulatory T cells
PMID: 38417442
4
USP39 directly deubiquitinates and stabilizes β-catenin in hepatocellular carcinoma
PMID: 36707504
5
USP39 stabilizes ZEB1 in multiple myeloma and high expression correlates with poor survival
PMID: 39736693
6
USP39 enhances NAT10 protein stability through protein interactions, promoting cancer metastasis
PMID: 36882514
7
USP39 is overexpressed in hepatocellular carcinoma and promotes tumorigenesis
PMID: 37821439
8
USP39 overexpression correlates with poor survival in leukemia patients
PMID: 30898977
Disease Associationsⓘ20
alcohol drinkingOpen Targets
0.21Weak
Neonatal acute respiratory distress with surfactant metabolism deficiencyOpen Targets
0.17Weak
surfactant metabolism dysfunction, pulmonary, 1Open Targets
0.17Weak
Moderate albuminuriaOpen Targets
0.16Weak
neurodegenerative diseaseOpen Targets
0.13Weak
hepatocellular carcinomaOpen Targets
0.11Weak
neoplasmOpen Targets
0.11Weak
infectionOpen Targets
0.11Weak
gliomaOpen Targets
0.10Weak
nephritisOpen Targets
0.10Suggestive
NephropathyOpen Targets
0.10Suggestive
cancerOpen Targets
0.10Suggestive
esophageal squamous cell carcinomaOpen Targets
0.09Suggestive
gastric cancerOpen Targets
0.09Suggestive
renal cell carcinomaOpen Targets
0.08Suggestive
lung cancerOpen Targets
0.08Suggestive
ovarian cancerOpen Targets
0.08Suggestive
Miyoshi myopathyOpen Targets
0.08Suggestive
head and neck squamous cell carcinomaOpen Targets
0.08Suggestive
posterior cortical atrophyOpen Targets
0.08Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
SF3B3Protein interaction100%SNRNP200Protein interaction100%SF3B5Protein interaction100%SNRPA1Protein interaction100%EFTUD2Protein interaction100%SF3A3Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
90%
Lung
83%
Heart
71%
Ovary
59%
Liver
50%
Gene Interaction Network
Click a node to explore
USP39SF3B3SNRNP200SF3B5SNRPA1EFTUD2SF3A3
PROTEIN STRUCTURE
Preparing viewer…
PDB6QW6 · 2.92 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.74LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.57 [0.44–0.74]
RankingsWhere USP39 stands among ~20K protein-coding genes
  • #2,474of 20,598
    Most Researched177 · top quartile
  • #5,864of 17,882
    Most Constrained (LOEUF)0.74
Genes detectedUSP39
Sources retrieved26 papers
Response time—
📄 Sources
26▼
1
Lysine 2-hydroxyisobutyrylation of NAT10 promotes cancer metastasis in an ac4C-dependent manner.
PMID: 36882514
Cell Res · 2023
1.00
2
Spliceosome component Usp39 contributes to hepatic lipid homeostasis through the regulation of autophagy.
PMID: 37923718
Nat Commun · 2023
0.90
3
Lactate modulates RNA splicing to promote CTLA-4 expression in tumor-infiltrating regulatory T cells.
PMID: 38417442
Immunity · 2024
0.80
4
USP39 promotes hepatocellular carcinogenesis through regulating alternative splicing in cooperation with SRSF6/HNRNPC.
PMID: 37821439
Cell Death Dis · 2023
0.70
5
USP39 phase separates into the nucleolus and drives lung adenocarcinoma progression by promoting GLI1 expression.
PMID: 39885503
Cell Commun Signal · 2025
0.68