Adenine base editing for MECP2 c.380G>A (p.Arg127His): direct correction of a methyl-CpG binding domain missense variant in Rett syndrome

For MECP2 c.380G>A (p.Arg127His), a pathogenic missense variant in the methyl-CpG binding domain (MBD) of MeCP2, adenine base editing (ABE) offers a theoretically precise correction strategy. This G>A transition (C>T on the coding strand) creates a classic ABE target: the pathogenic adenine on the antisense strand can be converted back to guanine, restoring the wild-type arginine codon. Unlike gene replacement, which faces the critical MECP2 dosage problem (both deficiency and overexpression are pathogenic), base editing corrects the endogenous gene under its native regulatory control, preserving physiological expression levels and X-inactivation-dependent regulation. This eliminates the risk of MECP2 overexpression in neurons that already express wild-type MeCP2 from the other X chromosome — the fundamental challenge for gene replacement in female Rett patients.

ABE converts A-to-G with high efficiency and specificity in the editing window (protospacer positions 4-8). For c.380G>A, the target adenine on the antisense strand could be edited back to guanine, restoring the wild-type CGC (Arg) codon from the mutant CAC (His). Arg127 is within the MBD (residues ~78-162) and directly contacts methylated CpG dinucleotides in the DNA major groove; R127H disrupts this interaction and impairs MeCP2 chromatin binding (Ho et al., Mol Cell 2008; PMID:18243107). ClinVar classifies this variant as Pathogenic. Preclinical studies have demonstrated that AAV-delivered base editors can achieve efficient editing in mouse brain neurons (Levy et al., Nat Biomed Eng 2020; PMID:32514169). The key advantage over gene replacement for MECP2 is that editing preserves native regulation: the corrected gene remains subject to endogenous promoter control and X-inactivation, so neurons that already express wild-type MeCP2 (from the active wild-type X) are not exposed to supraphysiological levels. Split-intein dual-AAV delivery systems can package the large ABE construct across two AAV vectors for CNS delivery.

No base editing therapy for any neurological disease has entered clinical trials. Delivery of ABE to sufficient neurons throughout the brain is the primary challenge — MECP2 is expressed in virtually all neurons, and widespread CNS coverage is needed for meaningful phenotype rescue. Split-intein dual-AAV systems reduce per-cell editing efficiency compared to single-vector delivery. In female Rett patients with random X-inactivation, only ~50% of neurons express the mutant allele; editing needs to target these specific cells, but AAV does not distinguish between neurons expressing the mutant vs wild-type X. Editing wild-type neurons (which express Arg127 already) would have no phenotypic effect, effectively halving the functional editing rate. Off-target editing in the brain is particularly concerning given the irreversibility of DNA changes in post-mitotic neurons. The therapeutic window is uncertain: whether base editing in postnatal/childhood neurons can reverse established Rett phenotype or only prevent progression requires preclinical validation. Guide RNA specificity must be confirmed to avoid editing at homologous sites elsewhere in the genome.