Abstract
Mutations in ADNP result in Helsmoortel–Van der Aa syndrome. Here, we describe the first de novo intronic deletion, affecting the splice-acceptor site of the first coding ADNP exon in a five-year-old girl with developmental delay and autism. Whereas exome sequencing failed to detect the non-coding deletion, genome-wide CpG methylation analysis revealed an episignature suggestive of a Helsmoortel–Van der Aa syndrome diagnosis. This diagnosis was further supported by PhenoScore, a novel facial recognition software package. Subsequent whole-genome sequencing resolved the three-base pair ADNP deletion c.[-5-1_-4del] with transcriptome sequencing showing this deletion leads to skipping of exon 4. An N-terminal truncated protein could not be detected in transfection experiments with a mutant expression vector in HEK293T cells, strongly suggesting this is a first confirmed diagnosis exclusively due to haploinsufficiency of the ADNP gene. Pathway analysis of the methylome indicated differentially methylated genes involved in brain development, the cytoskeleton, locomotion, behavior, and muscle development. Along the same line, transcriptome analysis identified most of the differentially expressed genes as upregulated, in line with the hypomethylated CpG episignature and confirmed the involvement of the cytoskeleton and muscle development pathways that are also affected in patient cell lines and animal models. In conclusion, this novel mutation for the first time demonstrates that Helsmoortel–Van der Aa syndrome can be caused by a loss-of-function mutation. Moreover, our study elegantly illustrates the use of EpiSignatures, WGS and Phenoscore as novel complementary diagnostic tools in case a of negative WES result.
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Data availability
The datasets generated during this study are available from the corresponding author upon argumented request.
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Acknowledgements
The authors would like to thank the family for participating in this study.
Funding
RFK acknowledges the support of the Research Fund of the University of Antwerp OEC-Methusalem grant “GENOMED”. This work was in part financed by grants from the ERA-NET NEURON “ADNPinMED”. This article is also based upon work from COST Action International Nucleome Consortium (INC) CA18127, supported by COST (European Cooperation in Science and Technology) ascribed to WVB.
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CPD performed the experiments, conceptualized the experimental design, performed data analysis, wrote the manuscript text, and prepared all the figures. DJA provided the bioinformatic analysis of the methylation array. EE conducted all the gene expression assays using RT-PCR under supervision of CD, JJVDS and MA performed the WES, WGS, and EpiSign at early observations of the patient, AJMD and BBADV provided analysis of the ADNP female using PhenoScore. LM provided the bioinformatic analysis of the RNA sequencing. WVB and RFK reviewed and edited the manuscript. All authors reviewed and approved the final version of manuscript.
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Written informed consent for publication of individual details and images was obtained in the context of the Helsmoortel–Van der Aa syndrome from the parents. The protocol was approved by the Ethics Committee of the Antwerp University Hospital, Antwerp, Belgium.
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D’Incal, C.P., Annear, D.J., Elinck, E. et al. Loss-of-function of activity-dependent neuroprotective protein (ADNP) by a splice-acceptor site mutation causes Helsmoortel–Van der Aa syndrome. Eur J Hum Genet (2024). https://doi.org/10.1038/s41431-024-01556-4
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DOI: https://doi.org/10.1038/s41431-024-01556-4
