Pseudoexon activating by a deep intronic variant and phenotype variation in a Chinese family with dystrophinopathy

Xingyu Xia; Kexin Jiao; Chaoping Hu; Nachuan Cheng; Mingshi Gao; Shiyi Xiong; Ningning Wang; Bochen Zhu; Meining Diao; Dongyue Yue; Jianying Xi; Chongbo Zhao; Chengwen Chen; Wenhua Zhu

doi:10.1038/s10038-025-01361-x

Pseudoexon activating by a deep intronic variant and phenotype variation in a Chinese family with dystrophinopathy

J Hum Genet. 2025 Jun 30. doi: 10.1038/s10038-025-01361-x. Online ahead of print.

Authors

Xingyu Xia^#^{1

2

3}, Kexin Jiao^#^{1

2

3}, Chaoping Hu⁴, Nachuan Cheng^{1

2

3}, Mingshi Gao^{2

3

5}, Shiyi Xiong⁶, Ningning Wang^{1

2

3}, Bochen Zhu^{1

2

3}, Meining Diao^{1

2

3}, Dongyue Yue⁷, Jianying Xi^{1

2

3}, Chongbo Zhao^{1

2

3}, Chengwen Chen⁸, Wenhua Zhu^{9

10

11}

Affiliations

¹ Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China.
² Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China.
³ National Center for Neurological Disorders (NCND), Shanghai, China.
⁴ Department of Neurology, Children's Hospital of Fudan University, Shanghai, China; National Children's Medical Center, Shanghai, China.
⁵ Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China.
⁶ Shanghai Key Laboratory of Maternal Fetal Medicine, Department of Fetal Medicine and Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China.
⁷ Department of Neurology, Jing'an District Center Hospital of Shanghai, Shanghai, China.
⁸ Shanghai Amplicongene Co. Ltd, Shanghai, China.
⁹ Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China. whzhu@fudan.edu.cn.
¹⁰ Huashan Rare Disease Center, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China. whzhu@fudan.edu.cn.
¹¹ National Center for Neurological Disorders (NCND), Shanghai, China. whzhu@fudan.edu.cn.

^# Contributed equally.

PMID: 40583054
DOI: 10.1038/s10038-025-01361-x

Abstract

Aberrant inclusion of pseudoexons (PE) in mature mRNA is a rare splicing defect contributing to Duchenne muscular dystrophy (DMD) pathogenesis. In this study, we described two affected males from a Chinese family who presented with progressive muscle weakness, elevated creatine kinase (CK) levels, and dystrophic changes on muscle pathology. Whole-genome sequencing followed by linkage-based filtering identified a shared deep intronic variant in intron 47 of DMD gene (c.6913-4037T>G), which activated a cryptic splice site and resulted in the inclusion of a 72 bp PE between exons 47 and 48. Patient induced pluripotent stem cells (iPSCs)-derived myotubes from the patient confirmed the presence of this PE, with a significant reduction in dystrophin expression compared to controls. Quantitative PCR revealed that aberrant transcripts comprised ~89% of total DMD transcripts in myotubes and ~97% in muscle, correlating with near-complete loss of dystrophin. Functional assays further showed impaired myotube fusion and altered calcium signaling. This study underscores the diagnostic complexity of intronic DMD variants and provides evidence supporting the pathogenicity of c.6913-4037T>G.

Grants and funding

82171398/National Natural Science Foundation of China (National Science Foundation of China)