HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
UPF3A
UPF3A regulator of nonsense mediated mRNA decay
Chromosome 13 · 13q34
NCBI Gene: 65110Ensembl: ENSG00000169062.16HGNC: HGNC:20332UniProt: B3KUE7
56PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transporter
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
nuclear-transcribed mRNA catabolic process, nonsense-mediated decaymRNA bindingprotein bindingtelomeric repeat DNA bindinghypertensionneurodegenerative diseasecardiovascular diseaseIncreased blood pressure
✦AI Summary

UPF3A is a regulator of nonsense-mediated mRNA decay (NMD), a quality control mechanism that degrades mRNAs containing premature termination codons. UPF3A functions redundantly with its paralog UPF3B to activate NMD, contrary to earlier reports suggesting it acts as an NMD inhibitor 1. The protein associates with the exon junction complex (EJC) and recruits UPF2 to form the UPF1-UPF2-UPF3 surveillance complex that activates NMD. However, UPF3A can activate NMD independently of EJC binding, with its conserved middle domain being critical for activity 2. While single knockout of UPF3A has minimal effects on global NMD activity, co-depletion with UPF3B results in marked NMD inhibition and transcriptome-wide upregulation of NMD substrates 1. Clinically, UPF3A shows disease relevance in colorectal cancer, where high expression correlates with metastasis, poor prognosis, and serves as an independent risk factor for survival 3. Additionally, UPF3A methylation status has potential as a blood-based biomarker for early colorectal cancer detection 4. The gene also shows expression throughout spermatogenesis and may contribute to male infertility 5.

Sources cited
1
UPF3A and UPF3B function redundantly as NMD activators, with co-depletion causing marked NMD inhibition
PMID: 35451084
2
UPF3A can activate NMD independently of EJC binding, with the middle domain being critical for activity
PMID: 35451102
3
High UPF3A expression in colorectal cancer correlates with metastasis and poor prognosis
PMID: 32606924
4
UPF3A methylation has potential as a blood-based biomarker for colorectal cancer detection
PMID: 37794510
5
UPF3A is expressed throughout spermatogenesis and may contribute to male infertility
PMID: 39267058
Disease Associationsⓘ20
hypertensionOpen Targets
0.32Weak
neurodegenerative diseaseOpen Targets
0.32Weak
cardiovascular diseaseOpen Targets
0.28Weak
Increased blood pressureOpen Targets
0.26Weak
essential hypertensionOpen Targets
0.24Weak
colorectal carcinomaOpen Targets
0.09Suggestive
azoospermiaOpen Targets
0.07Suggestive
partial chromosome Y deletionOpen Targets
0.05Suggestive
spermatogenic failure 71Open Targets
0.05Suggestive
Testicular regression syndromeOpen Targets
0.05Suggestive
spermatogenic failure 57Open Targets
0.05Suggestive
spermatogenic failure 50Open Targets
0.05Suggestive
isochromosomy YpOpen Targets
0.04Suggestive
spermatogenic failure, X-linked, 2Open Targets
0.04Suggestive
spermatogenic failure 25Open Targets
0.04Suggestive
spermatogenic failure 63Open Targets
0.04Suggestive
isochromosomy YqOpen Targets
0.04Suggestive
hypogonadotropic hypogonadism 11 with or without anosmiaOpen Targets
0.04Suggestive
spinocerebellar ataxia type 32Open Targets
0.04Suggestive
ring chromosome YOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
MAGOHBProtein interaction100%DCP2Protein interaction100%NCBP2Protein interaction99%SMG7Protein interaction99%SMG1Protein interaction99%SMG6Protein interaction99%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
83%
Brain
69%
Liver
66%
Lung
55%
Heart
42%
Gene Interaction Network
Click a node to explore
UPF3AMAGOHBDCP2NCBP2SMG7SMG1SMG6
PROTEIN STRUCTURE
Preparing viewer…
PDB7QG6 · 2.95 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.20LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.90 [0.69–1.20]
RankingsWhere UPF3A stands among ~20K protein-coding genes
  • #8,151of 20,598
    Most Researched56
  • #12,589of 17,882
    Most Constrained (LOEUF)1.20
Genes detectedUPF3A
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Whole exome sequencing analysis of 167 men with primary infertility.
PMID: 39267058
BMC Med Genomics · 2024
1.00
2
Identification of the shared gene signatures and pathways between sarcopenia and type 2 diabetes mellitus.
PMID: 35271662
PLoS One · 2022
0.90
3
Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay.
PMID: 35451084
EMBO J · 2022
0.80
4
The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay.
PMID: 27040500
Cell · 2016
0.70
5
Functions and Clinical Significance of UPF3a Expression in Human Colorectal Cancer.
PMID: 32606924
Cancer Manag Res · 2020
0.60