️ 31: Decoding Hidden Signals — Genome Sequencing Reveals Cryptic Splicing Variants in Marfan Syndrome

️ Episode 31: Decoding Hidden Signals — Genome Sequencing Reveals Cryptic Splicing Variants in Marfan Syndrome In this episode of Base por Base, we delve into a breakthrough study by Walker et al. (2025), published in Genetics in Medicine, which leverages whole-genome sequencing and RNA-based validation to uncover non-canonical splicing variants in the FBN1 gene, often overlooked in conventional genetic testing for Marfan Syndrome (MFS). The authors analyzed data from over 78,000 individuals in the 100,000 Genomes Project to identify ultra-rare splice-altering variants contributing to undiagnosed cases of Familial Thoracic Aortic Aneurysm Disease (FTAAD), a hallmark feature of MFS. Study Highlights:This study systematically identified FBN1 splice variants predicted by SpliceAI to alter mRNA splicing — even when located deep within introns beyond conventional ±8 bp thresholds.Among individuals with FTAAD, these variants were highly enriched compared to non-FTAAD participants (OR=84, p = 9.7×10⁻¹⁴), suggesting a significant pathogenic contribution.Experimental validation using RT-PCR, minigene assays, and RNA sequencing confirmed aberrant splicing in 16 of 20 predicted variants, many of which induced pseudoexon insertions or exon extensions that introduce premature stop codons.Nearly 70% of the identified splice variants lay outside canonical splice regions, revealing a previously underestimated mechanism behind unexplained MFS cases.The study illustrates how expanding the SpliceAI analysis window from 50 to 500 bp enhances sensitivity for variant detection and aids in designing confirmatory RNA tests.A recurrent variant (c.1589-1217G>T) was identified in multiple unrelated families across the UK, demonstrating the importance of screening for deep intronic mutations in FBN1 regardless of population background. Conclusion:This research reframes the molecular diagnosis of Marfan Syndrome by showing that non-coding FBN1 variants with splicing effects account for ~3% of undiagnosed cases. It underscores the necessity of genome sequencing and RNA validation in clinical pipelines and provides a compelling case for integrating advanced splicing prediction tools in routine diagnostics. Reference:Walker, S., Bunyan, D. J., Thomas, H. B., et al. (2025). Utility of genome sequencing and group-enrichment to support splice variant interpretation in Marfan syndrome. Genetics in Medicine. https://doi.org/10.1016/j.gim.2025.101477 License:This episode is based on an article provided as a pre-proof by Genetics in Medicine (Elsevier) and is subject to final editing. © 2025 Elsevier Inc. on behalf of the American College of Medical Genetics and Genomics.

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