Abstract
Autosomal dominant Kabuki syndrome (KS) is a rare multiple congenital anomalies/neurodevelopmental disorder caused by heterozygous inactivating variants or structural rearrangements of the lysine-specific methyltransferase 2D (KMT2D) gene. While it is often recognizable due to a distinctive gestalt, the disorder is clinically variable, and a phenotypic scoring system has been introduced to help clinicians to reach a clinical diagnosis. The phenotype, however, can be less pronounced in some patients, including those carrying postzygotic mutations. The full spectrum of pathogenic variation in KMT2D has not fully been characterized, which may hamper the clinical classification of a portion of these variants. DNA methylation (DNAm) profiling has successfully been used as a tool to classify variants in genes associated with several neurodevelopmental disorders, including KS. In this work, we applied a KS-specific DNAm signature in a cohort of 13 individuals with KMT2D VUS and clinical features suggestive or overlapping with KS. We succeeded in correctly classifying all the tested individuals, confirming diagnosis for three subjects and rejecting the pathogenic role of 10 VUS in the context of KS. In the latter group, exome sequencing allowed to identify the genetic cause underlying the disorder in three subjects. By testing five individuals with postzygotic pathogenic KMT2D variants, we also provide evidence that DNAm profiling has power to recognize pathogenic variants at different levels of mosaicism, identifying 15% as the minimum threshold for which DNAm profiling can be applied as an informative diagnostic tool in KS mosaics.
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Data availability
The genetic and clinical data that support the findings of this work are provided in the manuscript. Previously unreported variants and those that have been reclassified based on DNAm profiling were submitted to ClinVar (SCV004232735 to SCV004232752). The DNAm data are not publicly available due to privacy/ethical restrictions but are available on request from the corresponding author.
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Acknowledgements
We are grateful to the families who participated in this study.
Funding
This work was supported, in part, by the Italian Ministry of Health (5 × 1000_2019 and RCR-2022-23682289 to MT, and Current Research Funds to AC), and Italian Ministry of Research (FOE_2020 to MT).
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MN, AC, and MT conceived the work, interpreted the data, and wrote the manuscript. AC, MF, LP, CC, CN, MH, LC, EM, and ZT contributed to the DNAm analyses. MN, MLD, MG, CC, EP, AB, AN, SM, AS, GM, BD, and MCD collected the clinical and genetic data. MP contributed to the clinical data analyses. All co-authors contributed to the final version of the manuscript.
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The study was approved by the local Institutional Ethical Committee (ref. 1702_OPBG_2018). Clinical data, and DNA samples were collected and used after signed informed consents from the participating subjects/families were secured.
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Niceta, M., Ciolfi, A., Ferilli, M. et al. DNA methylation profiling in Kabuki syndrome: reclassification of germline KMT2D VUS and sensitivity in validating postzygotic mosaicism. Eur J Hum Genet (2024). https://doi.org/10.1038/s41431-024-01597-9
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DOI: https://doi.org/10.1038/s41431-024-01597-9
