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.

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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) 70% of variants lie beyond the ±8 splice regions
- RNA or functional confirmation performed for 16/20 variants
- 9/20 variants predicted to cause pseudoexon inclusion
- Odds ratio for enrichment of candidate splice variants in FTAAD cohort: OR = 84 (p = 9.7e-14)
- Diagnostic yield estimated at ~3% among unsolved FTAAD families

QC result: Pass.