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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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UPF3B
UPF3B regulator of nonsense mediated mRNA decay
Chromosome X Β· Xq24
NCBI Gene: 65109Ensembl: ENSG00000125351.15HGNC: HGNC:20439UniProt: Q9BZI7
142PubMed Papers
21Diseases
0Drugs
36Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub GeneTransporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
RNA bindingexon-exon junction complexmRNA bindingprotein bindingX-linked intellectual disability with marfanoid habitusgenetic disordernon-syndromic X-linked intellectual disabilityX-linked non-syndromic intellectual disability
✦AI Summary

UPF3B is a core component of the nonsense-mediated mRNA decay (NMD) pathway that protects cells from potentially harmful transcripts containing premature termination codons 1. As an X-linked gene, UPF3B functions by associating with the nuclear exon junction complex (EJC) and recruiting UPF2 to form a surveillance complex with UPF1 that activates NMD of aberrant mRNAs 2. However, UPF3B operates with functional redundancy alongside its paralog UPF3A; depletion of both proteins substantially inhibits NMD, while either protein alone maintains partial activity 2. Notably, NMD activation by UPF3B is largely independent of EJC binding, instead depending on conserved mid-domain interactions with other NMD factors 3. Hemizygous variants in UPF3B cause X-linked neurodevelopmental disorder (XL-NDD) presenting with intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, and schizophrenia 1. Clinical features include cognitive impairment, central hypotonia, microcephaly, and brain malformations 1. Beyond developmental disorders, aberrant UPF3B splicing contributes to hepatocellular carcinoma metastasis and gastric cancer progression through altered mRNA regulation 45. These findings establish UPF3B as both a critical guardian against genomic instability and a gene whose dysregulation contributes to neuropsychiatric and malignant disease.

Sources cited
1
UPF3A and UPF3B show functional redundancy in NMD; co-depletion causes marked NMD inhibition and transcriptome-wide upregulation of NMD substrates
PMID: 35451084
2
Hemizygous UPF3B variants cause intellectual disability, autism spectrum disorder, ADHD, schizophrenia, and features including microcephaly and brain malformations
PMID: 38318947
3
UPF3B activates NMD largely independently of EJC binding; conserved mid-domain is consequential for NMD activity
PMID: 35451102
4
UPF3B-S splice variant promotes hepatocellular carcinoma metastasis by enhancing CDH1 mRNA degradation and modulating Hippo signaling
PMID: 38402949
5
UPF3B interacts with RBM8A to promote gastric cancer progression by degrading the pro-apoptotic gene BBC3 mRNA
PMID: 40613240
Disease Associationsβ“˜21
X-linked intellectual disability with marfanoid habitusOpen Targets
0.72Strong
genetic disorderOpen Targets
0.49Moderate
non-syndromic X-linked intellectual disabilityOpen Targets
0.37Weak
X-linked complex neurodevelopmental disorderOpen Targets
0.37Weak
X-linked non-syndromic intellectual disabilityOpen Targets
0.37Weak
Neurodevelopmental disorderOpen Targets
0.31Weak
neurodegenerative diseaseOpen Targets
0.31Weak
Intellectual disabilityOpen Targets
0.30Weak
microcephalyOpen Targets
0.12Weak
cataractOpen Targets
0.12Weak
Severe global developmental delayOpen Targets
0.12Weak
hepatocellular carcinomaOpen Targets
0.10Weak
neoplasmOpen Targets
0.10Suggestive
cancerOpen Targets
0.09Suggestive
Monoamine oxidase A deficiencyOpen Targets
0.06Suggestive
schizophrenia 19Open Targets
0.06Suggestive
colorectal carcinomaOpen Targets
0.04Suggestive
short-limb skeletal dysplasia with severe combined immunodeficiencyOpen Targets
0.03Suggestive
severe combined immunodeficiency due to CORO1A deficiencyOpen Targets
0.03Suggestive
Duchenne muscular dystrophyOpen Targets
0.02Suggestive
Intellectual developmental disorder, X-linked, syndromic 14UniProt
Pathogenic Variants36
NM_080632.3(UPF3B):c.674_677del (p.Arg225fs)Pathogenic
Syndromic X-linked intellectual disability 14|not provided|UPF3B-associated intellectual disability|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 225
NM_080632.3(UPF3B):c.684_685del (p.Glu230fs)Pathogenic
not provided|Inborn genetic diseases|Syndromic X-linked intellectual disability 14
β˜…β˜…β˜†β˜†2024β†’ Residue 230
NM_080632.3(UPF3B):c.1060C>T (p.Arg354Ter)Likely pathogenic
Intellectual disability|Syndromic X-linked intellectual disability 14
β˜…β˜…β˜†β˜†2023β†’ Residue 354
NM_080632.3(UPF3B):c.697_698del (p.Arg233fs)Pathogenic
not provided|Syndromic X-linked intellectual disability 14
β˜…β˜…β˜†β˜†2019β†’ Residue 233
NM_080632.3(UPF3B):c.624+2T>GLikely pathogenic
Syndromic X-linked intellectual disability 14
β˜…β˜†β˜†β˜†2025
NM_080632.3(UPF3B):c.1265_1266del (p.Lys422fs)Likely pathogenic
Syndromic X-linked intellectual disability 14
β˜…β˜†β˜†β˜†2025β†’ Residue 422
NM_080632.3(UPF3B):c.617_620del (p.Asn206fs)Pathogenic
UPF3B-related neurodevelopmental disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 206
NM_080632.3(UPF3B):c.1270dup (p.Glu424fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 424
NM_080632.3(UPF3B):c.1149_1150del (p.Lys384fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 384
NM_080632.3(UPF3B):c.724C>T (p.Arg242Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 242
NM_080632.3(UPF3B):c.670G>T (p.Glu224Ter)Pathogenic
Syndromic X-linked intellectual disability 14
β˜…β˜†β˜†β˜†2024β†’ Residue 224
NM_080632.3(UPF3B):c.442_443del (p.Asp148fs)Pathogenic
Syndromic X-linked intellectual disability 14
β˜…β˜†β˜†β˜†2024β†’ Residue 148
NM_080632.3(UPF3B):c.263+2_263+3insTAAAAAAAALikely pathogenic
Syndromic X-linked intellectual disability 14
β˜…β˜†β˜†β˜†2024
NM_080632.3(UPF3B):c.37C>T (p.Arg13Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 13
NM_080632.3(UPF3B):c.16G>T (p.Glu6Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 6
NM_080632.3(UPF3B):c.240del (p.Phe80fs)Likely pathogenic
Syndromic X-linked intellectual disability 14
β˜…β˜†β˜†β˜†2023β†’ Residue 80
NM_080632.3(UPF3B):c.1288C>T (p.Arg430Ter)Pathogenic
Syndromic X-linked intellectual disability 14|not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 430
NM_080632.3(UPF3B):c.159_160delinsTAC (p.Val54fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 54
NM_080632.3(UPF3B):c.1147G>T (p.Glu383Ter)Likely pathogenic
Syndromic X-linked intellectual disability 14
β˜…β˜†β˜†β˜†2022β†’ Residue 383
NM_080632.3(UPF3B):c.270T>G (p.Tyr90Ter)Likely pathogenic
Syndromic X-linked intellectual disability 14
β˜…β˜†β˜†β˜†2022β†’ Residue 90
View on ClinVar β†—
Related Genes
MAGOHBProtein interaction100%DHX8Protein interaction100%PRKRIP1Protein interaction96%SDE2Protein interaction96%STAU1Protein interaction91%DDX5Protein interaction91%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
86%
Liver
75%
Brain
68%
Lung
57%
Heart
49%
Gene Interaction Network
Click a node to explore
UPF3BMAGOHBDHX8PRKRIP1SDE2STAU1DDX5
PROTEIN STRUCTURE
Preparing viewer…
PDB1UW4 Β· 1.95 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.33Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.17 [0.10–0.33]
RankingsWhere UPF3B stands among ~20K protein-coding genes
  • #3,240of 20,598
    Most Researched142 Β· top quartile
  • #1,645of 5,498
    Most Pathogenic Variants36
  • #1,350of 17,882
    Most Constrained (LOEUF)0.33 Β· top 10%
Genes detectedUPF3B
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Human UPF3A and UPF3B enable fault-tolerant activation of nonsense-mediated mRNA decay.
PMID: 35451084
EMBO J Β· 2022
1.00
2
Expanding the phenotype of UPF3B-related disorder: Case reports and literature review.
PMID: 38318947
Am J Med Genet A Β· 2024
0.90
3
The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay.
PMID: 27040500
Cell Β· 2016
0.80
4
Molecular consequences of PQBP1 deficiency, involved in the X-linked Renpenning syndrome.
PMID: 38030819
Mol Psychiatry Β· 2024
0.70
5
HnRNPR-mediated UPF3B mRNA splicing drives hepatocellular carcinoma metastasis.
PMID: 38402949
J Adv Res Β· 2025
0.60