Missense substitutions in the BTB domain of ZBTB24 can lead to protein instability and cause ICF2 syndrome

ZBTB24 is a member of a protein family containing a Broad-Complex, Tramtrack, and Bric a Brac (BTB) domain, which functions in protein-protein interactions. ZBTB24, a transcription factor, binds its DNA targets through its C-terminal zinc finger (ZF) domain. Biallelic ZBTB24 pathogenic variants lead to the rare autosomal recessive Immunodeficiency, Centromeric instability and Facial anomalies type 2 (ICF2) syndrome. The majority of ICF2 patients carry biallelic loss-of-function variants in ZBTB24. The remaining patients harbor missense variants in the ZF domain that compromise the ability of ZBTB24 to transcriptionally activate CDCA7, the gene responsible for ICF subtype 3 syndrome. Although an ICF2 patient with compound heterozygous pathogenic variants, including a missense variant (p.Ser59Gly) in the BTB domain, has been reported, no ICF2 patients with biallelic missense variants in any ZBTB24 domains other than the zinc finger domain have been described. Similar to all subtypes of ICF syndrome, ZBTB24 pathogenic variants lead to significant DNA hypomethylation throughout the genome. Here we describe a patient with severe infections initiating during her first year of life, significant developmental delay and an abnormal facial shape, who carries a homozygous p.Val43Leu substitution in the BTB domain of ZBTB24. The patient's peripheral blood cells demonstrate whole genome DNA hypomethylation with patterns identical to those found in verified ICF2 patients. Both the p.Val43Leu and p.Ser59Gly variants cause significant ZBTB24 protein instability. Thus, we demonstrate that pathogenic missense variants in the BTB domain of ZBTB24 can functionally act as loss-of-function variants that result in ICF2 syndrome.