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, Ca 2 ⁺ 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 Ca 2 ⁺ 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.