Biallelic hexose-6-phosphate dehydrogenase variants cause mitochondrial dysfunction underlying Parkinson's disease

Parkinson's disease (PD) is a progressive neurodegenerative disorder influenced by complex genetic and environmental factors. We report that biallelic variants in hexose-6-phosphate dehydrogenase (H6PD), which encodes a key enzyme in the endoplasmic reticulum (ER) pentose phosphate pathway, contribute to PD and investigate its role in maintaining mitochondrial homeostasis. Through whole-exome sequencing of 2223 patients with PD and 1229 controls, together with whole-genome sequencing of 4010 patients and 6072 controls, we found 13 biallelic H6PD variants in eight probands, including two homozygous and six compound heterozygous cases (six early-onset PD, two late-onset PD). Functional studies were conducted using cultured cells, Drosophila, and AAV-shRNA-mediated H6PD knockdown mice. Mitochondrial function and redox status were assessed using confocal imaging, flow cytometry, and Seahorse metabolic flux analysis. ER-mitochondria contacts, Ca²⁺ dynamics, and mitophagy were evaluated using SPLICS sensors, calcium imaging, and PINK1-Parkin pathway assays. Our study revealed that H6PD depletion impaired NADPH generation, disrupted ER-mitochondria coupling, caused abnormal Ca²⁺ release, mitochondrial fragmentation, reduced respiratory capacity, and suppressed PINK1-Parkin-dependent mitophagy. PD-related H6PD variants lost the ability to maintain NADPH/redox balance and mitochondrial protective function. In Drosophila, H6PD loss induced dopaminergic neurodegeneration, locomotor deficits, and shortened lifespan, all partially rescued by human H6PD. Similarly, H6PD knockdown in mice aggravated MPTP-induced neuronal loss and mitochondrial abnormalities. In conclusion, our study identifies biallelic variants in H6PD as a novel cause of PD. H6PD maintains ER NADPH/redox homeostasis, stabilizes ER-mitochondria communication, and preserves mitochondrial function and mitophagy, thereby supporting dopaminergic neuron survival.