Splice site variants in the canonical donor site of exon 7 lead to intron retention in patients with syndrome.

Pathogenic variants in the gene are associated with the autosomal dominant syndrome, which is characterised by global developmental delay and cardiac malformations. We investigated two heterozygous variants located at the canonical donor splice site motif of exon 7: c.1009+1G>C and c.1009+5G>C. We report that in silico predictions suggested two possible outcomes: exon 7 skipping, resulting in loss of the phosphodegron motif essential for regulation, or activation of a cryptic donor site in intron 7, leading to intron retention. RNA analysis confirmed that both variants affected the exon 7 splice donor site, resulting in the retention of 73 bp of intron 7. This retention caused a frameshift and premature translation termination, consistent with haploinsufficiency. Our results highlight the importance of combining predictive and experimental approaches to understand the functional impact of splice site variants. These insights into the molecular consequences of variants provide a deeper understanding of the genetic basis of syndrome.