New Results
, View ORCID ProfileMelinda K. Wheelock, View ORCID ProfileRachel L. Powell, View ORCID ProfileZiyu R. Wang, View ORCID ProfileDaniel L. Holmes, View ORCID ProfileShawn Fayer, View ORCID ProfileGabriel E. Boyle, View ORCID ProfileAllyssa J. Vandi, View ORCID ProfileAbby V. McGee, View ORCID ProfileClara J. Amorosi, View ORCID ProfileNick Moore, View ORCID ProfileAlan F. Rubin, View ORCID ProfileDouglas M. Fowler, View ORCID ProfileMaitreya J. Dunham
doi: https://doi.org/10.1101/2025.08.11.669723
Abstract
G6PD deficiency is one of the most common enzyme deficiencies worldwide, and increases the likelihood of adverse reactions to certain drugs and foods. Identifying people at risk is challenging, since most are asymptomatic until they encounter a trigger. This is further complicated since over 60% of 1,559 known genetic variants in G6PD are variants of uncertain significance and thus cannot guide drug prescribing and dosing. To resolve which variants are clinically meaningful and avoid harm from adverse drug reactions, we conducted two high-throughput functional assays: one for G6PD activity, and one for abundance. We measured the function of 9,527 missense, nonsense, and synonymous G6PD variants. The patterns of variant effect on activity and abundance confirmed the importance of structural NADP+ for G6PD activity and abundance, and G6PD dimerization for G6PD activity. Based on the ability of our functional assay scores to accurately classify G6PD variants of known clinical effect, we generated evidence that 4,870 missense variants contribute to G6PD deficiency and 2,245 are unlikely to contribute to G6PD deficiency. Our data can be used to deepen our understanding of G6PD as a protein, and to close the gap in classification for variants of uncertain significance to improve implementation of genetic medicine for G6PD deficiency.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Updated functional scoring so that variants without activity scores only received a functional score if their abundance score was low (less than z-score of -3 from the average synonymous variant abundance score), indicating a likely loss of function due to low abundance. ClinVar variant interpretations used for calibration were re-accessed September 25, 2025
Funder Information Declared
National Cancer Institute, https://ror.org/040gcmg81, P30 CA015704
National Institute of General Medical Sciences, https://ror.org/04q48ey07, R01 GM132162, F32 GM143852
National Human Genome Research Institute, UM1 HG011969, T32 HG000035
Pharmacogenomics Global Research Network
Momental Foundation
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.