Functional interpretation, cataloging, and analysis of 1,341 glucose-6-phosphate dehydrogenase variants

Abstract

Glucose-6-phosphate dehydrogenase (G6PD) deficiency affects over 500 million individuals who can experience anemia in response to oxidative stressors such as certain foods and drugs. Recently, the World Health Organization (WHO) called for revisiting G6PD variant classification as a priority to implement genetic medicine in low- and middle-income countries. Toward this goal, we sought to collect reports of G6PD variants and provide interpretations. We identified 1,341 G6PD variants in population and clinical databases. Using the ACMG standards and guidelines for the interpretation of sequence variants, we provided interpretations for 268 variants, including 186 variants that were not reported or of uncertain significance in ClinVar, bringing the total number of variants with non-conflicting interpretations to 400. For 414 variants with functional or clinical data, we analyzed associations between activity, stability, and current classification systems, including the new 2022 WHO classification. We corroborated known challenges with classification systems, including phenotypic variation, emphasizing the importance of comparing variant effects across individuals and studies. Biobank data made available by All of Us illustrate the benefit of large-scale sequencing and phenotyping by adding additional support connecting variants to G6PD-deficient anemia. By leveraging available data and interpretation guidelines, we created a repository for information on G6PD variants and nearly doubled the number of variants with clinical interpretations. These tools enable better interpretation of G6PD variants for the implementation of genetic medicine.

Keywords: glucose-6-phosphate dehydrogenase; personalized medicine; pharmacogenetics.

Graphical abstract

Figure 1

G6PD variant interpretation (A) A total of 1,341 G6PD variants found from variant database and PubMed queries. Clinical or molecular data indicate the variant is interpreted on ClinVar (as benign, likely benign, likely pathogenic, or pathogenic) or has activity or stability data available from published studies. (B) Of 1,341 variants, 214 variants have interpretations other than VUS currently available on ClinVar, and an additional 186 were interpreted by applying ACMG guidelines to published reports. VUS includes variants interpreted as uncertain or with conflicting interpretations, including five previously interpreted on ClinVar. (C) Concordance between variant interpretations for all variants reported on ClinVar, including VUSs, and by our application of ACMG guidelines for 510 total G6PD variants.

Figure 2

Classification systems for G6PD variants (A and B) Average G6PD activity by effect on the coding sequence (A) and by type of genetic alteration in the variant (B), with most severe reported clinical presentation associated with each variant (“deficiency” indicates further information on anemia was not collected). (C–F) Average G6PD variant activity by 1985 (C) and 2022 (D) WHO classification, ClinVar interpretation (E), and by our application of ACMG guidelines (F). In ClinVar review status, 0 indicates least supporting evidence, and increasing numbers indicate increasing support. All average activities are from red blood cell extracts and weighted by number of hemizygotes per study. p value by one-way ANOVA with Tukey’s HSD, except (A) by t test, ^∗∗p < 0.01, ^∗∗∗p < 0.001, ^∗∗∗∗p < 0.0001.

Figure 3

G6PD structure and variant effects (A–C) G6PD variant activity (A) and stability (B) across the structural domains (C), with most severe clinical presentation associated with each variant (“deficiency” indicates further information on anemia was not collected). Only single missense and synonymous variants shown. (D and E) Variant stability compared to activity (D) and phenotypic severity (E). All average activities are from red blood cell extracts and weighted by number of hemizygotes per study. p value by one-way ANOVA with Tukey’s HSD, ^∗∗∗∗p < 0.0001.

Figure 4

Variation in activity and clinical presentation for G6PD variants across studies (A) Average G6PD activity (normalized to G6PD B activity) per study for all variants with at least 5 independent reports. (B) Average G6PD variant activity by most severe clinical presentation in each study. Nondeficient group is significantly different from each other group (p < 0.0001). All average activities are from red blood cell extracts of hemizygotes, and boxplots weighted by number of hemizygotes per study. p value by one-way ANOVA with Tukey’s HSD, ^∗∗p < 0.01, ^∗∗∗∗p < 0.0001. (C) G6PD activity measured in blood or serum 10 individuals with the code “Deficiency of glucose-6-phosphate dehydrogenase” or “Glucose-6-phosphate dehydrogenase deficiency anemia” in All of Us. Some individuals with B variant have noncoding variation. Individuals are grouped by nonsynonymous coding variants. Data are shown in accordance with a Data and Statistics Dissemination Policy exception granted by the All of Us Resource Access Board.