Phenotypes and genotypes of mitochondrial diseases with mtDNA variations in Chinese children: A multi-center study

•96%-point mutations (30 alleles in 11 genes) and 4%-deletions were identified as the cause of 14 phenotypes in 262 patients of children with MDs caused by pathogenic mtDNA variants. To our knowledge, this is the largest multi-center study focused on mtDNA variations systematically.•We delineated the genotype and phenotype spectrum and their correlation of mtDNA-associated MDs.•For a suspected MELAS, m.3243A > G mutation is recommended to detect first in both blood and urine. For a suspected LS in clinical, trios-WES and mtDNA genome sequencing by NGS both in blood and urine are recommended first.•We highlight avoiding overdiagnosis and overtreatment through rigorous assessment of pathogenicity.