De novo variants in MAGED1 suggest a role in intellectual disability pathogenesis

Intellectual disability (ID) is a common neurodevelopmental disorder that severely affects cognitive function and social adaptability. Although its pathogenic factors are complex and diverse, genetic causes-particularly de novo variants-play a critical role in sporadic cases. Here we identified two de novo variants in the MAGED1 (Melanoma-Associated Antigen D1) in two independent ID families: a frameshift variant (NM_001005332.2: c.410dupT, Leu137PhefsTer4) and a missense variant (NM_001005332.2: c.932 A > G, Gln311Arg). Functional experiments revealed distinct molecular mechanisms by which these variants may contribute to ID pathogenesis. Our co-immunoprecipitation and immunofluorescence studies indicated that Leu137PhefsTer4 variant disrupted the interaction between MAGED1 and the E3 ubiquitin ligase Praja-1, impairing the degradation of the truncated variant protein and leading to its abnormal stabilization and elevated expression which proven by Western blot. Additionally, wound healing and transwell migration assays revealed Leu137PhefsTer4 abolished the wild-type (WT) MAGED's inhibitory effect on HeLa cell migration, suggesting potential interference with normal neuronal migration. In contrast, by detecting the cell cycle and apoptosis, we found that Gln311Arg variant significantly dysregulated apoptosis and cell cycle progression compared to the WT, implicating its role in disrupting neurodevelopmental homeostasis. Our findings establish a link between MAGED1 de novo variants and ID, expanding the genetic spectrum of ID. These results further highlight the critical role of MAGED1 in neurodevelopment and open new avenues for investigating the pathological mechanisms of ID.