65: Hidden splice variants in FBN1 — genome sequencing finds Marfan diagnoses

Walker S et al., Genetics in Medicine - This episode reviews a systematic analysis of ultra-rare FBN1 variants in the 100,000 Genomes Project using SpliceAI, RNA assays and minigene tests. The study identified 20 non-canonical splice variants across 23 families, confirmed splicing defects for 16 variants, and estimates these variants account for ~3% of undiagnosed FTAAD/Marfan families. The work highlights the value of intronic analysis and confirmatory RNA testing in clinical genomics. Key terms: Marfan syndrome, FBN1, splicing, pseudoexon, genome sequencing. Study Highlights:The authors screened 78,195 genomes from the 100,000 Genomes Project and identified 20 unique non-canonical FBN1 splice variants in 23 families, with significant enrichment among participants recruited for Familial Thoracic Aortic Aneurysm Disease (OR=84, p=9.7x10-14). Experimental validation (RT-PCR, RNAseq, minigene assays) confirmed aberrant splicing in 16 of 20 variants and revealed pseudoexonization as a common mechanism. Most actionable variants lay beyond the ±8 bp windows used in routine testing, and the study estimates a diagnostic yield of ~3% from these non-canonical splice events in undiagnosed FTAAD families. Conclusion:Genome sequencing combined with expanded splice prediction and confirmatory RNA testing uncovers non-canonical FBN1 splice variants that meaningfully increase molecular diagnoses for Marfan/FTAAD and should be integrated into testing pipelines with appropriate RNA-capacity. Music:Enjoy the music based on this article at the end of the episode. Article title:Utility of genome sequencing and group-enrichment to support splice variant interpretation in Marfan syndrome First author:Walker S Journal:Genetics in Medicine DOI:10.1016/j.gim.2025.101477 Reference:Walker S, Bunyan DJ, Thomas HB, et al. Utility of genome sequencing and group-enrichment to support splice variant interpretation in Marfan syndrome. Genetics in Medicine (2025). doi: https://doi.org/10.1016/j.gim.2025.101477 License:© 2025 Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you'll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/fibrillin1-noncanonical-splice-marfan-100kgp QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2025-07-04. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Substantive audit focused on the deep intronic FBN1 splice-variant discovery, computational prediction with expanded windows, laboratory validation (RNA, minigene), enrichment statistics, diagnostic yield, and ACMG interpretation; also notes limitations and replication in UK Biobank.- transcript topics: Non-canonical FBN1 splice variants in 100kGP; SpliceAI prediction and 500bp window expansion; RNA validation: RT-PCR and RNAseq; Minigene assays and functional testing; Enrichment in FTAAD and odds ratio (OR); Diagnostic yield and cascade testing implications QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 6- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- 20 unique cryptic FBN1 splice variants identified across 23 families (32 affected individuals)- 7:14 split? (clarify not needed)...