A Novel Intronic Variant in the KH3 Domain of HNRNPK Leads to a Mild Form of Au-Kline Syndrome

Despite the massive adoption of sequencing technologies, disease-specific diagnosis remains challenging, particularly for genes with highly homologous pseudogenes like HNRNPK. Pathogenic HNRNPK variants cause Au-Kline syndrome (AKS), a neurodevelopmental disorder with malformations and distinctive facial features. We validated a novel de novo HNRNPK intronic variant (c.1192-3 C>A, p.Leu398ValfsTer21) in a patient previously misdiagnosed with Kabuki Syndrome (KS). By combining sequencing, in vitro splicing assays, molecular modelling, and protein function analysis, we characterised the molecular defect. A unique DNA methylation (DNAm) signature was recently identified in AKS, with missense variants showing an intermediate DNAm pattern, suggesting an epi-genotype–phenotype correlation linked to milder clinical features. The DNAm signature is a valuable tool for variant interpretation, especially in unclear AKS cases. We demonstrate that two independent approaches—functional characterisation and DNAm evaluation—confirmed a partial loss of HNRNPK function and validated an AKS diagnosis with a mild phenotype. Our findings highlight that a multidisciplinary approach integrating genomic and epigenomic analyses with functional studies and clinical assessment significantly improves rare disease diagnosis.