Analysis of whole-exome sequencing data from nearly 10,000 Iranian individuals: identification of recessive mitochondrial disease variants and proposal of a population-specific carrier screening panel

Mitochondrial diseases, often stemming from recessive nuclear gene mutations, represent a heterogeneous group of disorders with significant morbidity and mortality. Carrier screening for these conditions is population-specific, yet data on the pathogenic variant burden in the Iranian population remain limited. This study aimed to analyze whole-exome sequencing (WES) data from 9989 Iranian individuals to identify the spectrum and frequency of recessive mitochondrial disease variants and to develop a population-specific carrier screening panel. We analyzed WES data from 9989 unrelated Iranian individuals. Variants in 1,564 nuclear genes associated with mitochondrial function were filtered for rarity (minor allele frequency < 0.01 in public databases), predicted pathogenicity, and recessive inheritance patterns (homozygous or compound heterozygous). Clinically relevant variants were manually curated, and carrier frequencies for significant recessive mitochondrial conditions were calculated. Our analysis identified variants across 15 groups of mitochondrial-related nuclear genes in 345 individuals recognized as carriers. Of these, 123 variants (35.6%) were classified as Pathogenic, and 154 variants (44.6%) were classified as Likely Pathogenic according to ACMG guidelines. This study provides the first large-scale WES-derived assessment of recessive mitochondrial disease carrier burden in the Iranian population. The high estimated carrier rate supports implementing population-specific preconception screening. The results of this study can be used for design of targeted panels of nuclear mitochondrial genes to identify at-risk couples, facilitating genetic counseling and reproductive decision-making in Iran. Mitochondrial disorders are clinically and genetically heterogeneous, with autosomal recessive forms being particularly prevalent in populations with high consanguinity rates like Iran. However, the specific spectrum and population frequency of pathogenic recessive variants in nuclear mitochondrial genes have never been systematically characterized at a large scale in the Iranian general population, leaving a critical gap for evidence-based carrier screening. This study provides the first large-scale, WES-derived analysis of nearly 10,000 Iranian individuals, revealing that approximately 3% carry at least one pathogenic or likely pathogenic recessive variant for a mitochondrial disease. It identifies multiple founder-like variants (e.g., in NDUFA9, PCK2, and a novel SURF1 frameshift insertion) that are significantly enriched in Iranians compared to global populations, and quantifies carrier frequencies across 15 functional categories of mitochondrial genes. These findings directly inform the design of a population-specific preconception carrier screening panel for recessive mitochondrial disorders in Iran, with a proposed first-tier panel of five high-priority genes (NDUFB3, NDUFS1, SURF1, POLG, PCK2) capturing over 19% of detectable carrier risk. Implementing such targeted screening could facilitate genetic counseling, at-risk couple identification, and informed reproductive decision-making within the Iranian healthcare system.