CREBBP variants underlying Menke-Hennekam syndrome exhibit histone acetyltransferase hyperactivity with divergent phase behaviors

Menke-Hennekam syndrome (MKHK) is a neurodevelopmental disease characterized by specific pathogenic regions within the transcriptional coactivator CREB-binding protein (CREBBP). CREBBP regulates gene expression through histone acetyltransferase (HAT) activity and involves IDR-dependent transcriptional condensates. Although domain-specific phenotypes and distinct DNA methylation episignatures have been recognized in MKHK, the underlying molecular mechanisms remain widely unclear. In this study, we identified a recurrent missense variant, p.(R1868W) [R1868W] and a novel splice variant r.5963_5969del,p.(Cys1723Thrfs*19) [C1723fs] in two families clinically diagnosed with MKHK and manifesting developmental delay, characteristic facial features, and growth impairment. R1868W and C1723fs exhibited increased auto-, nonhistone protein, and histone acetylation. Despite these shared enzymatic abnormalities, the variants promoted divergent disruption in liquid-liquid phase separation. The recurrent CBP-ID4 variant R1868W activated the formation of low-mobility aberrant nuclear condensates, whereas the C-terminal, truncating variant C1723fs, impaired condensate formation and showed diffuse nuclear localization. Treatment with the selective p300/CBP HAT inhibitor A485 partially restored condensate dynamics and fusion-relaxation behavior in R1868W. Furthermore, R1868W recruited BRD4 around condensates in an acetylation-dependent manner, which was suppressed by the BET inhibitor JQ1. Together, these findings suggest that aberrant condensate material properties arising from disrupted CREBBP IDR-dependent regulation play a critical role in the molecular pathogenesis of MKHK. Significance StatementPathogenic variants in specific regions of the transcriptional coactivator CREBBP underlie the Menke-Hennekam syndrome (MKHK), but its molecular basis is poorly understood. Here, we show that two CREBBP variants responsible for MKHK share a common feature of increased histone acetyltransferase (HAT) activity but disrupt liquid-liquid phase separation in distinct ways. The recurrent CBP-ID4 missense variant R1868W promoted the formation of low-mobility aberrant condensates and acetylation-dependent recruitment of BRD4, as opposed to the C-terminal truncating variant C1723fs. Notably, HAT inhibition restored condensate dynamics in R1868W, suggesting that condensate properties are reversibly regulated by enzymatic activity. These findings reveal a framework linking pathogenic variants affecting CREBBP IDR-dependent regulation to aberrant condensate material properties in MKHK.