Identification of an emerging heterozygous variant in KAT6A by whole exome sequencing: a case report

Background: Arboleda-Tham syndrome is an autosomal dominant disorder caused by mutations in the lysine acetyltransferase 6A (KAT6A) gene, leading to intellectual disability and a broad phenotypic spectrum. Diagnosis can be challenging due to phenotypic heterogeneity. The aim of this study was to define the genetic basis of unexplained global developmental delay in a Chinese boy and expand the KAT6A mutational spectrum. Case Description: We report a 4-year and 7-month-old Chinese boy who presented with global developmental delay, severe intellectual disability, and markedly limited expressive language. Physical examination revealed no seizures, cardiac malformations, or growth retardation. Initial chromosomal copy number variation sequencing (CNV-seq) detected no pathogenic abnormalities. To identify the underlying molecular defect, whole-exome sequencing (WES) was performed on the proband and both parents. WES revealed a novel, de novo heterozygous frameshift variant (c.4099del, p.Glu1367Argfs*40) in exon 17 of the KAT6A gene. Sanger sequencing confirmed the absence of this variant in either parent, supporting its de novo origin. The mutation is predicted to introduce a premature termination codon 40 amino acids downstream and is classified as pathogenic according to American College of Medical Genetics and Genomics (ACMG) criteria. Conclusions: This report expands the mutational spectrum of KAT6A and underscores the critical diagnostic utility of WES in children with unexplained neurodevelopmental disorders, enabling precise genetic counseling and avoiding unnecessary investigations.