Bi-allelic ATG12 variants impair autophagy and cause a neurodevelopmental disorder

Macroautophagy/autophagy is an essential developmental and homeostatic process, defined by the endolysosomal degradation of intracellular components and pathogens. Dysfunctional autophagy is implicated in complex human disease, yet reports of congenital autophagy disorders were considered exceedingly rare until the recent report of several unrelated families with bi-allelic variants in ATG7, encoding a core autophagy effector complementing the report of two individuals harbouring ATG5 variants. We now report six affected individuals from five families with bi-allelic ATG12 variants with complex neurological phenotypes overlapping those of ATG5 and ATG7 patients, including developmental delay, congenital ataxia and cerebellar hypoplasia. Structural modelling implicated a potential disruption of the important ATG12-ATG5-ATG16N-ATG3 complex. Biochemical analyses of patient-derived primary fibroblasts from members of two affected families confirmed the loss of stable ATG12-ATG5 conjugate in one family and altered autophagic flux in one unrelated family. HeLa cell models demonstrate a decrease in ATG12-ATG5 conjugate and reduced autophagic flux in response to starvation using the Halo Tag processing assay. Yeast complementation studies demonstrated that equivalent missense atg12 variants were unable to fully recover the biochemical defect in atg12 null yeast and also demonstrated a reduced delivery of autophagy substrates to the yeasts degradative compartment. Functional studies in zebrafish models demonstrated global developmental delay, impaired brain function, and pre-adulthood lethality. Our findings underscore the pivotal role of efficient autophagy in maintaining human neural integrity and emphasise the importance of this emerging group of congenital autophagy disorders, thereby expanding our understanding of adaptive homeostasis in human health and disease.