Novel gnomAD missense mutations in the Ceruloplasmin gene result in ferroxidase impairment and are consistent with significant underdiagnosis of Aceruloplasminemia

Background: Aceruloplasminemia (ACP) is a ultra-rare autosomal recessive disease caused by mutations on the Ceruloplasmin (CP) gene, encoding the key plasma ferroxidase protein in mammals. The disease is characterized by the accumulation of iron in various organs including the brain, resulting in a clinical landscape characterized by anemia with hyperferritinemia, diabetes, neurological impairment and neurodegeneration. Importantly, although the reported prevalence is 0.5x106 (based on a single report on a very small Japanese population from 1999) the availability of recent population genomic datasets allows for a real-world assessment of pathogenic and potentially pathogenic Cp variants. Aims: To perform a real-world assessment of pathogenic and potentially pathogenic missense CP variants using gnomAD, identifying them and functionally characterizing their effect on CP structure and function, thus improving prevalence estimates for ACP. Methods: literature data was reviewed to identify CP residues crucial for CP function as well as ACP missense mutations. CP missense variants present in the latest gnomAD release (4.0) were identified and compared with literature-derived CP residues of interest. Candidate new pathogenic missense variants were identified and prioritized for further investigation based on allele frequency reported on the gnomAD database. Expression plasmids containing wild-type (WT) recombinant (r) human CP cDNA or rCP mutants encoding the selected variants (and known pathogenic variants as controls) were transiently transfected into HEK293T cell-line, followed by biochemical and functional characterization. Results: A number of novel gnomAD-derived CP missense variants displayed robust impairment of CP ferroxidase activity and protein expression/secretion. The prevalence (actual or predicted) of these variants in the homozygous state in the human population is significantly higher than current ACP estimates, with compound heterozygotes potentially further contributing to increase ACP prevalence. Summary/Conclusion: Within the human population, we identified new heterozygous and homozygous missense alleles in the CP gene which strongly impact CP ferroxidase activity and its biology, thus representing novel pathogenic variants. The actual or predicted prevalence of these variants in the homozygous condition is considerably higher than previous prevalence estimates for ACP, suggesting that a large number of individuals at risk of developing ACP remains undiagnosed.