Chromatinopathies: clinically overlapping disorders, revealing novel variants and their DNA methylation signatures

Background: Chromatinopathies represent a genetically and clinically heterogeneous group of neurodevelopmental disorders (NDDs) caused by pathogenic variants in genes regulating chromatin structure and function. The phenotypic overlap and genetic complexity of these conditions pose significant diagnostic challenges, often resulting in unresolved variants of uncertain significance (VUS). Results: We investigated a cohort of 400 routine diagnostic individuals with NDD using whole-exome sequencing and genome-wide DNA methylation profiling via the clinically validated EpiSign assay. Episignature classification was used to aid in variant interpretation and to define molecular subtypes of chromatinopathy. Seventeen percent of individuals (67/400) harbored variants in chromatinopathy-associated genes, including 55 novel variants. DNA methylation profiling was performed in 60 individuals with 62 variants in chromatin regulator genes. Of these, 26 individuals (43%) exhibited disorder-specific episignatures consistent with the associated clinical diagnosis. Importantly, methylation profiles supported the pathogenicity of several variants previously classified as VUS and demonstrated diagnostic concordance with known disease-associated genes including ANKRD11, SETD5, KMT2A, KDM5C, CHD8 , and others. Conclusion: Our study highlights the improved diagnostic yield and clinical utility of combining genomic and epigenomic profiling in patients with clinically and/or genetically suspected chromatinopathies. Integration of EpiSign analysis facilitated variant reclassification, delineated genotype-epigenotype-phenotype correlations, and expanded the episignature atlas for rare neurodevelopmental disorders.