Homozygous variants in ZSWIM6 cause severe short stature and intellectual disability

The novel homozygous ZSWIM6 variant c.3119G>A, p.Arg1040His found in two siblings by next-generation sequencing (confirmed by Sanger sequencing) and the two previously reported heterozygous variants were prepared in vitro by site-directed mutagenesis. Protein expression was confirmed in HEK293 cells via Western blot. Transcriptional activity was assessed using a dual-luciferase reporter assay with HECW2 and ZIC2 promoters, previously hypothesized to possess functional links to ZSWIM6. The siblings shared partial overlap with prior ZSWIM6-associated phenotypes (Acromelic frontonasal dysostosis, neurodevelopmental disorder without acromelic frontonasal dysostosis) but also exhibited a distinct clinical presentation. A dual-luciferase assay revealed that ZSWIM6 is a transcriptional regulator of the HECW2 and ZIC2 promoters. The three variants showed different effects on transcriptional regulation of neurodevelopment and growth.