Rare AFG3L2 and POLG Variants Suggest a Role for Mitochondrial Dysfunction in Enteric Neuronal Vulnerability in Idiopathic Achalasia

Idiopathic achalasia is a rare esophageal motility disorder characterized by the selective degeneration of inhibitory myenteric neurons. Its genetic basis remains poorly defined. We investigated whether rare coding variants may contribute to disease susceptibility. Exome sequencing was performed in 31 individuals with idiopathic achalasia and seven unaffected relatives. Candidate variants were prioritized using phenotype-driven filtering and assessed through in silico and structural analysis of publicly available gene expression and single-cell transcriptomic datasets. No pathogenic or likely pathogenic variants were identified in achalasia-associated genes. A gene-agnostic analysis identified two rare heterozygous missense variants in unrelated patients: AFG3L2 c.2105G>A (p.Arg702Gln) and POLG c.1760C>T (p.Pro587Leu). Both genes encode mitochondrial proteins involved in neuronal homeostasis. The variants affected conserved residues, mapped to functionally relevant protein regions, and were predicted by multiple computational approaches to affect protein stability and function. Both genes were highly expressed in esophageal tissue, with AFG3L2 showing enrichment in enteric neuronal populations. These exploratory findings support a potential link between mitochondrial dysfunction, enteric neurodegeneration, and idiopathic achalasia. Rare mitochondrial-related variants may contribute to disease susceptibility in selected individuals by increasing vulnerability of inhibitory enteric neurons, although functional validation and larger studies are required. Accordingly, our findings should be considered hypothesis-generating rather than evidence of causality.