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Selected Publication:
Kaufmann, L.
Identification of two novel disease-causing mutations in pleiotropic genes resulting in unexpected phenotypes due to loss-of-function escape mechanisms
Doktoratsstudium der Medizinischen Wissenschaft; Humanmedizin; [ Dissertation ] Medizinische Universität Graz; 2024. pp. 108
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- Authors Med Uni Graz:
- Advisor:
- Enko Dietmar
- Wagner Klaus
- Windpassinger Christian
- Altmetrics:
- Abstract:
- The discovery of novel genotype-phenotype associations in rare diseases as well as the identification of the underlying disease mechanisms are crucial steps on the path to diagnostic success and can also serve as a starting point for the development of therapeutic interventions. A major challenge in providing a genetic diagnosis is determining whether and what effects previously unknown variants may have. Thereby, variant annotation and computer-based tools to predict possible effects of novel variants play an important role in the variant interpretation process. In this work, we successfully discovered and analyzed two previously unknown, disease-causing mutations. Both mutations share a remarkable feature: the predicted effects of the variants did not match the observed phenotype of affected individuals. The variants each affect a gene with known pleiotropy and both variants are predicted to result in a complete loss of gene function. The predicted loss-of-function (LOF) effect is circumvented by alternative gene expression mechanisms in both variants. In the first study presented, we identified the novel homozygous frameshift variant c.28_29insA, p.(Leu10Tyrfs*37) in ZMPSTE24 in affected individuals of two Pakistani families. The detected mutation is predicted to result in a complete loss-of-function of the ZMPSTE24 gene, associating the variant with lethal restrictive dermopathy (RD). However, affected individuals displayed the progeroid phenotype mandibuloacral dysplasia with type B lipodystrophy (MADB), which is associated with biallelic ZMPSTE24 mutations preserving residual enzymatic activity of the protein. Expression and localization experiments revealed utilization of two N-terminal alternative translation initiation sites to bypass complete loss-of-function, consistent with the observed phenotype in affected individuals. One of these alternative start codons is newly formed at the insertion site, which to our knowledge has not yet been described as a LOF escape mechanism in the literature. In the second study presented, we detected a previously unreported, heterozygous 22q12.1 deletion in a fetus with severe cerebral malformations. The deletion affects the MN1 gene, including the entire last exon 2 and the lncRNA gene CPMER, including the entire first exon. The expected loss-of-function of the MN1 gene is associated with mainly non-specific phenotype abnormalities, without brain anomalies, and incomplete penetrance, which also leads to a genotype-phenotype discrepancy in this case. RNA analyses indicate that the expected LOF effect is circumvented by the expression of MN1-CPMER fusion transcripts. Expression of the C-terminally truncated MN1 proteins predicted based on the RNA sequences, is associated with MN1 C-terminal truncation (MCTT) syndrome, a very rare condition characterized by distinct brain malformations. To our knowledge, a disease-causing gene fusion of a protein-coding gene and a non-coding gene in the germline leading to LOF escape has also not yet been reported. With this work, we want to raise awareness for the possibility of alternative gene expression mechanisms in the variant interpretation process and highlight the need to improve (standard) annotation pipelines in this context. Furthermore, we want to highlight the importance of additional in-depth analyses and further experiments to determine the effects of candidate variants.