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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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UBE3D
ubiquitin protein ligase E3D
Chromosome 6 · 6q14.1
NCBI Gene: 90025Ensembl: ENSG00000118420.17HGNC: HGNC:21381UniProt: D6RD24
24PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
cytosolubiquitin ligase complexcyclin bindingprotein bindingneurodegenerative diseaseCrohn's diseasebile duct disorderAbnormality of the skeletal system
✦AI Summary

UBE3D (ubiquitin protein ligase E3D) is an E3 ubiquitin ligase that catalyzes ubiquitin transfer from E2 enzymes to protein substrates, promoting their proteasomal degradation 1. Beyond its canonical ligase function, UBE3D acts as a cytoplasmic binding partner and inhibitor of CPSF3 endonuclease, blocking its active site through direct coordination of catalytic metal ions via a conserved cysteine residue 2. In this capacity, UBE3D functions as a cytoplasmic chaperone required for CPSF3's nuclear function in pre-mRNA 3' end processing 2. UBE3D also de-ubiquitinates CPSF3, maintaining its cellular levels 3. UBE3D is critical for embryonic development; knockout mice exhibit severe growth retardation, neural tube defects, and lethality (E10.5-E11.5), with disrupted expression of homeobox genes essential for forebrain and neural tube development 3. In the retina, UBE3D regulates age-related macular degeneration (AMD) pathogenesis through ubiquitin-proteasome system function; genetic variants associate with neovascular AMD in East Asian populations 45, and conditional RPE-specific knockout accelerates age-associated retinal degeneration involving oxidative stress and autophagy dysfunction 6. Additionally, UBE3D regulates 3βHSD1 homeostasis, influencing DHEA metabolism and prostate cancer aggressiveness 7.

Sources cited
1
UBE3D functions as E3 ubiquitin-protein ligase accepting ubiquitin from E2 enzymes and transferring it to substrates
PMID: 15749827
2
UBE3D is a binding partner for CPSF73/CPSF3 that inhibits its endonuclease activity by blocking the active site and coordinating metal ions
PMID: 39032490
3
UBE3D knockout mice exhibit severe embryonic abnormalities, neural tube defects, lethality at E10.5-E11.5, and downregulation of homeobox genes; UBE3D de-ubiquitinates and maintains CPSF3 levels
PMID: 40075082
4
UBE3D missense variants associate with neovascular AMD in East Asian populations; UBE3D deficiency causes abnormal retinal pigment epithelium changes and ERG abnormalities
PMID: 25872646
5
UBE3D knockdown impairs eye development, increases angiogenesis, promotes oxidative damage and inflammatory reactions in retinal cells, and negatively correlates with CyclinB1
PMID: 32200270
6
Conditional Ube3d knockout in retinal pigment epithelium accelerates age-associated retinal degeneration with defective ubiquitin-proteasome system, autophagy dysfunction, and oxidative stress
PMID: 37772657
7
UBE3D regulates 3βHSD1 homeostasis and controls DHEA utilization heterogeneity in prostate cancer
PMID: 38099500
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.50Moderate
Crohn's diseaseOpen Targets
0.29Weak
bile duct disorderOpen Targets
0.25Weak
Abnormality of the skeletal systemOpen Targets
0.16Weak
tympanic membrane perforationOpen Targets
0.15Weak
schizophreniaOpen Targets
0.11Weak
placenta praeviaOpen Targets
0.08Suggestive
retinitis pigmentosaOpen Targets
0.07Suggestive
choroidal dystrophy, central areolar, 1Open Targets
0.06Suggestive
allergic rhinitisOpen Targets
0.06Suggestive
liver diseaseOpen Targets
0.06Suggestive
retinitis pigmentosa 87 with choroidal involvementOpen Targets
0.05Suggestive
choroideremiaOpen Targets
0.04Suggestive
Leber congenital amaurosis 13Open Targets
0.04Suggestive
Familial drusenOpen Targets
0.04Suggestive
Stargardt diseaseOpen Targets
0.04Suggestive
Sorsby fundus dystrophyOpen Targets
0.04Suggestive
Sorsby's fundus dystrophyOpen Targets
0.04Suggestive
retinitis pigmentosa 86Open Targets
0.04Suggestive
central areolar choroidal dystrophyOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
UBE2CProtein interaction95%RBBP6Protein interaction85%CPSF3Protein interaction85%NHLRC3Shared pathway50%RMND5AShared pathway50%RNF220Shared pathway43%
Tissue Expression6 tissues
Brain
100%
Ovary
64%
Heart
50%
Bone Marrow
48%
Liver
48%
Lung
38%
Gene Interaction Network
Click a node to explore
UBE3DUBE2CRBBP6CPSF3NHLRC3RMND5ARNF220
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q4G0J6
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.15LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.87 [0.66–1.15]
RankingsWhere UBE3D stands among ~20K protein-coding genes
  • #13,346of 20,598
    Most Researched24
  • #12,036of 17,882
    Most Constrained (LOEUF)1.15
Genes detectedUBE3D
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Active DHEA uptake in the prostate gland correlates with aggressive prostate cancer.
PMID: 38099500
J Clin Invest · 2023
1.00
2
ube3d, a New Gene Associated with Age-Related Macular Degeneration, Induces Functional Changes in Both In Vivo and In Vitro Studies.
PMID: 32200270
Mol Ther Nucleic Acids · 2020
0.90
3
Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.
PMID: 39032490
Mol Cell · 2024
0.80
4
Deficiency of UBE3D in mice leads to severe embryonic abnormalities and disrupts the mRNA of Homeobox genes via CPSF3.
PMID: 40075082
Cell Death Discov · 2025
0.70
5
Conditional loss of Ube3d in the retinal pigment epithelium accelerates age-associated alterations in the retina of mice.
PMID: 37772657
J Pathol · 2023
0.60