Deciphering the consequence of deep intronic variants: a progeroid syndrome caused by a TAPT1 mutation is revealed by combined RNA/SI-NET sequencing

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.1237-52G>A) that segregated with the disease. Using patients’ fibroblasts, we document that TAPT1’s nascent transcription was not affected, indicating instead that this variant leads to an alteration of pre-mRNA processing. Predicted to serve as an alternative splicing branchpoint, this mutation causes 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 repercussion of non-coding variants as well as in illuminating the molecular mechanisms and underlying pathways of human diseases. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement 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.). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Parents gave their consent to participate in the present study and to have the results of this research work published. The study protocol was also approved by A*STAR IRB (A*STAR IRB reference code #2019-087, Singapore) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors