Background Aceruloplasminemia (ACP) is a rare recessive disease caused by loss of ceruloplasmin activity due to pathogenic variants in the ceruloplasmin (CP) gene. ACP causes iron accumulation in various organs, leading to neurodegeneration, anaemia, and diabetes. Estimating ACP prevalence is challenging, particularly as missense variants are not readily identified as pathogenic. Methods Heterozygous missense variants likely to impact function were mapped in gnomAD and representative examples analysed for effects on CP activity. This knowledge was complemented by prediction of destabilizing effects of potentially pathogenic missense variants and integrated with loss-of-function mutations. Global ACP prevalence was predicted and compared with a more traditional method. Findings Several as yet uncharacterised missense CP variants of pathogenic interest were identified by structure-function in-silico analysis. A representative subset was functionally validated, together with known ACP missense variants. Insights on the relative importance of copper ions coordinating centres in CP and its substrate specificity were discovered. Overall, a destabilizing effect was predicted for 130 missense CP variants. This information, integrated with known ACP missense and loss-of-function CP variants in gnomAD, allowed an estimation of ACP prevalence of 12.6/106. An alternative analysis based on minor allele frequency <= 0.01 resulted in an ACP prevalence as high as 8/106. Interpretation These prevalence estimates for ACP are 20-25-fold higher than previously estimated and underscore the applicability of structure-function based analyses of real-world genetic variability to provide an alternative method for representing the frequency of rare disease variants. Copyright (c) 2025 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
Functional characterisation of missense ceruloplasmin variants and real-world prevalence assessment of Aceruloplasminemia using population data
Ziliotto N.;Cirinciani M.;Da Pozzo E.;
2025-01-01
Abstract
Background Aceruloplasminemia (ACP) is a rare recessive disease caused by loss of ceruloplasmin activity due to pathogenic variants in the ceruloplasmin (CP) gene. ACP causes iron accumulation in various organs, leading to neurodegeneration, anaemia, and diabetes. Estimating ACP prevalence is challenging, particularly as missense variants are not readily identified as pathogenic. Methods Heterozygous missense variants likely to impact function were mapped in gnomAD and representative examples analysed for effects on CP activity. This knowledge was complemented by prediction of destabilizing effects of potentially pathogenic missense variants and integrated with loss-of-function mutations. Global ACP prevalence was predicted and compared with a more traditional method. Findings Several as yet uncharacterised missense CP variants of pathogenic interest were identified by structure-function in-silico analysis. A representative subset was functionally validated, together with known ACP missense variants. Insights on the relative importance of copper ions coordinating centres in CP and its substrate specificity were discovered. Overall, a destabilizing effect was predicted for 130 missense CP variants. This information, integrated with known ACP missense and loss-of-function CP variants in gnomAD, allowed an estimation of ACP prevalence of 12.6/106. An alternative analysis based on minor allele frequency <= 0.01 resulted in an ACP prevalence as high as 8/106. Interpretation These prevalence estimates for ACP are 20-25-fold higher than previously estimated and underscore the applicability of structure-function based analyses of real-world genetic variability to provide an alternative method for representing the frequency of rare disease variants. Copyright (c) 2025 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
