Loss-of-function of activity-dependent neuroprotective protein (ADNP) by a splice-acceptor site mutation causes Helsmoortel–Van der Aa syndrome

• Published in: European journal of human genetics : EJHG Vol. 32; no. 6; pp. 630 - 638
• Main Authors: D’Incal, Claudio Peter, Annear, Dale John, Elinck, Ellen, van der Smagt, Jasper J., Alders, Mariëlle, Dingemans, Alexander J. M., Mateiu, Ligia, de Vries, Bert B. A., Vanden Berghe, Wim, Kooy, R. Frank
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 01.06.2024; Springer International Publishing
• Subjects: ADNP protein; Animal models; Autism; Autism Spectrum Disorder; Autistic Disorder - genetics; Autistic Disorder - pathology; Cell culture; Cell lines; Child, Preschool; Cytoskeleton; Developmental Disabilities - genetics; Developmental Disabilities - pathology; Diagnosis; DNA Methylation; Facies; Female; Gene deletion; Genomes; Genomic analysis; Haploinsufficiency; Heart Diseases; HEK293 Cells; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; Humans; Locomotion; Loss of Function Mutation; Mutation; Nerve Tissue Proteins - genetics; Nerve Tissue Proteins - metabolism; Neurodevelopmental Disorders; Neuroprotection; Pattern recognition; RNA Splice Sites; Transcriptomes; Transfection; Whole genome sequencing
• ISSN: 1018-4813; 1476-5438; 1476-5438
• DOI: 10.1038/s41431-024-01556-4

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.