Genetic variation to the multi-zinc finger BTB domain transcription factor ZBTB18 causes a spectrum of human neurodevelopmental disorders, but the underlying mechanisms are not well understood. Recently, we reported that pathogenic, de novo missense ZBTB18 mutations alter its DNA-binding specificity and gene regulatory functions, leading to human neurodevelopmental disease. Yet, the functional impact of general population missense ZBTB18 variants is unknown. Here, we investigated the database resources of gnomAD to discover that the ZBTB family of genes are intolerant to loss-of-function and missense mutations, but not synonymous mutations. In the case of ZBTB18, we report that general population missense variants within the zinc finger DNA-binding domain are not under-represented, as one might expect for this functional domain (aa373-501). Also, general population variants disproportionately map to non DNA-contact residues, in contrast to the majority of disease-associated variants which map to DNA-contact residues. We investigated a series of variants which map to residues with significant contribution to DNA binding (T400, K435) as well as non DNA-contact residues (L398, R403, R409, A414, S422, G425, T450, A476) to find that the majority (66.7%, 8/12 variants) influenced DNA-binding in silico and transcriptional regulation in vitro in different ways. Furthermore, several of these variants (T400M, R403C, S422L, K435R) are associated with adult-onset neurological impairment. Altogether, our findings are consistent with the functional impact of missense variation on residues within the zinc finger domain of ZBTB18, and demonstrate that general population variants influence the DNA-binding specificity and transcriptional regulatory functions of ZBTB18, with potential consequences on brain development, homeostasis and disease.