Objective To investigate and analyze the distribution characteristics and genetic variation of mitochondrial encephalomyopathy (ME) in children in Hainan province.

Methods According to the principle of capture-recapture (C-R) method, a mathematical model was established to investigate suspected and confirmed cases of ME in children treated in Hainan Province from January 2012 to January 2023. The representative hospitals in Haikou and Sanya were selected as sample sources. The Morava mitochondrial disease criteria scale was used for the initial screening of children suspected of having ME. Subsequently, further follow-up and comprehensive gene sequencing were conducted to identify confirmed ME cases. Finally, the confirmed cases were aggregated and incorporated into the mathematical model to estimate the prevalence of ME among children in Hainan Province, and their genetic variation characteristics were also analyzed.

Results A total of 238 children with suspected ME were screened using the Morava scale, and 64 children with ME were diagnosed through gene sequencing. The prevalence of ME in children in Hainan Province was estimated to be 5.58/100 000(95% CI: 3.12/100 000-8.04/100 000) by taking the confirmed cases from the survey into the C-R mathematical model. A total of 13 disease types were involved in the confirmed cases. There were 32 cases of mtDNA mutation, involving 10 pathogenic genes. Additionally, there were 32 cases of nDNA variation, involving 23 pathogenic genes. A total of 21 new mutation sites were found, and pathogenicity analysis was performed on 14 variants of uncertain significance among them. Apart from 3 mutations for which the evidence of pathogenicity was still insufficient, the remaining mutations were predicted by the computer to be harmful and associated with alterations in protein structure. Conclusions This study estimated the prevalence of a regional rare disease (ME in children in Hainan Province) based on the principle of the C-R method, providing references for further large-scale rare disease investigations in China. The comprehensive use of the Morava scale, genetic sequencing, and pathogenicity analysis tools is helpful for clarifying the characteristics of genetic variations in children with ME and achieving early diagnosis and treatment.