Estimating the occurrence of primary ubiquinone deficiency by analysis of large-scale sequencing data

Abstract

Primary ubiquinone (UQ) deficiency is an important subset of mitochondrial disease that is caused by mutations in UQ biosynthesis genes. To guide therapeutic efforts we sought to estimate the number of individuals who are born with pathogenic variants likely to cause this disorder. We used the NCBI ClinVar database and literature reviews to identify pathogenic genetic variants that have been shown to cause primary UQ deficiency, and used the gnomAD database of full genome or exome sequences to estimate the frequency of both homozygous and compound heterozygotes within seven genetically-defined populations. We used known population sizes to estimate the number of afflicted individuals in these populations and in the mixed population of the USA. We then performed the same analysis on predicted pathogenic loss-of-function and missense variants that we identified in gnomAD. When including only known pathogenic variants, our analysis predicts 1,665 affected individuals worldwide and 192 in the USA. Adding predicted pathogenic variants, our estimate grows to 123,789 worldwide and 1,462 in the USA. This analysis predicts that there are many undiagnosed cases of primary UQ deficiency, and that a large proportion of these will be in developing regions of the world.

Figure 1

Prevalence of primary UQ deficiency based on known and predicted pathogenic variants. (A) Predicted number of afflicted individuals due to compound heterozygosity or homozygosity of known or predicted pathogenic variants, as denoted on x-axis, for each population. (B) Frequency of afflicted individuals within each analyzed population. (C) Contribution of known or predicted pathogenic variants to the frequency or number of afflicted individuals within each population. The fold-difference between known pathogenic variants only, and the total of known and predicted pathogenic variants, is shown on the x-axis.