A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing

Nasrinsadat Nabavizadeh, Annkatrin Bressin, Mohammad Shboul, Ricardo Moreno Traspas, Poh Hui Chia, Carine Bonnard, Emmanuelle Szenker-Ravi, Burak Sarıbaş, Emmanuel Beillard, Umut Altunoglu, Zohreh Hojati, Scott Drutman, Susanne Freier, Mohammad El-Khateeb, Rajaa Fathallah, Jean-Laurent Casanova, Wesam Soror, Alaa Arafat, Nathalie Escande-Beillard, Andreas Mayer

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Exome sequencing has introduced a paradigm shift for the identification of germline variations responsible for Mendelian diseases. However, non-coding regions, which make up 98% of the genome, cannot be captured. The lack of functional annotation for intronic and intergenic variants makes RNA-seq a powerful companion diagnostic. Here, we illustrate this point by identifying six patients with a recessive Osteogenesis Imperfecta (OI) and neonatal progeria syndrome. By integrating homozygosity mapping and RNA-seq, we delineated a deep intronic TAPT1 mutation (c.1237-52 G>A) that segregated with the disease. Using SI-NET-seq, we document that TAPT1's nascent transcription was not affected in patients' fibroblasts, indicating instead that this variant leads to an alteration of pre-mRNA processing. Predicted to serve as an alternative splicing branchpoint, this mutation enhances TAPT1 exon 12 skipping, creating a protein-null allele. Additionally, our study reveals dysregulation of pathways involved in collagen and extracellular matrix biology in disease-relevant cells. Overall, our work highlights the power of transcriptomic approaches in deciphering the repercussions of non-coding variants, as well as in illuminating the molecular mechanisms of human diseases.
Original languageEnglish (US)
JournalEMBO Molecular Medicine
StatePublished - Jan 18 2023
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2023-01-20
Acknowledgements: B.R. is a fellow of the Branco Weiss Foundation and EMBO Young Investigator. This work was also supported by a Strategic Positioning Fund on Genetic Orphan Diseases (GODAFIT) and an Use-Inspired Basic Research (UIBR) grant from Agency for Science, Technology and Research (A*STAR) in Singapore to B.R. This work was also funded by the Max Planck Society (to A.M.) and the Deutsche Forschungsgemeinschaft (DFG, grant 418415292 to A. M.). This work was also supported by a 2232 International Fellowship for Outstanding Researchers Program of TÜBİTAK (Project No: 118C318 to N.E.B). Funding for the open access charge was provided by the Max Planck Society. We are profoundly grateful to all patient family members for their participation in this study. We would like to thank all members of Reversade laboratory for their kind help and support. We would like to thank Dr. Shokouh Karimi for her help in careful clinical evaluation. We would also acknowledge Dr. Victor L. Ruiz-Perez for his generosity in providing the pSPL3 trapping vector for this study. We thank the Sequencing facility of the MPI for Molecular Genetics for sequencing.

ASJC Scopus subject areas

  • Molecular Medicine


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