CASE REPORT article
Front. Genet.
Sec. Genetics of Common and Rare Diseases
Volume 16 - 2025 | doi: 10.3389/fgene.2025.1637931
Whole-exome sequencing revealed a De novo variant in SETBP1 gene in a Chinese family with developmental delay
Provisionally accepted
- 960th Hospital of the PLA, Jinan, China
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Background: This study aims to characterize the potential genetic etiologies in children with developmental delay through whole-exome sequencing (WES) providing assistance for clinical diagnosis, genetic counseling, and reproductive guidance.. Methods: WES was performed on the proband, followed by Sanger sequencing validation of the identified variant in the parents. Results: The proband exhibits global developmental delay, including impaired motor and language development, reduced spontaneous speech, poor coordination, and attention deficits. WES revealed a heterozygous nonsense variant in SETBP1 (c.1630C>T, p.Arg544Ter), which was confirmed as de novo by Sanger sequencing. This variant was classified as pathogenic according to American College of Medical Genetics and Genomics (ACMG) guidelines. The patient was subsequently diagnosed with intellectual disability, autosomal dominant 29 (MRD29). Conclusion: The de novo SETBP1 p.Arg544Ter variant was identified as the underlying genetic cause in this case. Our findings underscore the importance of early genetic testing in children with developmental delay to enable precise diagnosis, informed genetic counseling, and evidence-based reproductive planning.
Keywords: Whole-exome sequencing, SETBP1, developmental delay, Pathogenic, case report
Received: 30 May 2025; Accepted: 20 Oct 2025.
Copyright: © 2025 Pan, Zhang, Hou, Shi, Qu, Jiang and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Haiping Liu, haipingliu960@163.com
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