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Updated: Jul 8, 2026
08:53
A Reporter Based Cellular Assay for Monitoring Splicing Efficiency
Published on: September 15, 2021
Utility of Urine-Derived Cells for Characterizing Aberrant Splicing Caused by a Novel Deep Intronic L1CAM Variant
Takuma Harasaki1, Sachiko Miyamoto1, Takahiro Yonekawa2
1Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
Annals of Human Genetics
|July 7, 2026
Summary
Deep intronic L1CAM variants can cause neurodevelopmental disorders. Urine-derived cell RNA testing and minigene assays effectively identified a novel deep intronic L1CAM variant impacting splicing.
Area of Science:
- Genetics
- Molecular Biology
- Neuroscience
Background:
- Pathogenic L1CAM variants at Xq28 are associated with severe neurodevelopmental disorders like MASA syndrome and agenesis of the corpus callosum.
- These disorders present with a range of clinical manifestations, including intellectual disability and congenital hydrocephalus.
Purpose of the Study:
- To identify and characterize novel pathogenic variants in the L1CAM gene.
- To investigate the molecular mechanism of a deep intronic L1CAM variant.
- To evaluate the utility of non-invasive RNA testing for variant interpretation.
Main Methods:
- Exome sequencing (ES) was performed to identify genetic variants.
- RNA studies using urine-derived cells (UDCs) were conducted to analyze transcript integrity.
- A minigene assay was employed to quantitatively assess the splicing impact of the identified variant.
Main Results:
- A deep intronic L1CAM variant (c.1124-24T>G) in Intron 10 was identified, predicted to create a cryptic splice site.
- RNA studies in UDCs revealed aberrant splicing with retention of a 23-bp intronic segment, leading to nonsense-mediated decay (NMD).
- The minigene assay confirmed the splicing defect caused by the intronic variant.
Conclusions:
- This study expands the known spectrum of intronic L1CAM variants.
- UDC-based RNA testing combined with minigene assays provides a powerful approach for interpreting deep intronic variants.
- Non-invasive RNA analysis is valuable for diagnosing L1CAM-related neurodevelopmental disorders.
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