ABSTRACT: ZBTB24 is a member of a protein family that includes a Broad-Complex, Tramtrack, and Bric a Brac (BTB) domain, which functions in protein-protein interactions. ZBTB24, a transcription factor, binds its targets through its C-terminus zinc finger (ZF) domain. Biallelic ZBTB24 mutations lead to the rare autosomal recessive Immunodeficiency, Centromeric instability and Facial anomalies subtype 2 (ICF2) syndrome. The majority of the ICF2 patients have biallelic loss of function alleles. The remaining patients have missense variants in their ZF domain. As a consequence, one of ZBTB24’s targets, CDCA7, the gene responsible for ICF3, is not expressed in ICF2 patient cells. Similar to all subtypes of ICF syndrome, ZBTB24 pathogenic mutations lead to significant DNA hypomethylation throughout the genome. Here we describe a patient with a homozygous variant with unknown significance (VUS), p.Val43Leu, in the BTB domain of ZBTB24. To examine the pathogenicity of this change, we determined DNA methylation levels and patterns in patient blood and lymphoblastoid cells (LCLs). We found significant hypomethylation throughout the patient’s genome, with a methylation pattern identical to that of other ICF2 patients, albeit with less severe hypomethylation. Importantly, the satellite repeats were significantly hypomethylated, a hallmark of ICF syndrome. We found that the p.Val43Leu change significantly reduces the protein’s stability, resulting in very low levels of CDCA7 expression in the patient-derived LCLs. Additionally ,the nuclear pattern of localization of ZBTB24 was disrupted due to this amino acid change. Thus, we demonstrate for the first time that biallelic missense variants in the BTB domain of ZBTB24, can disrupt the normal functionality of the protein and lead to ICF2 syndrome.
