Using exome sequencing, we diagnosed a Japanese patient with LS and identified the patient as a compound heterozygote for a novel variant of ECHS1, consisting of NM_004092.4:c.23T>C (p.Leu8Pro) and NM_004092.4:c.176A>G (p.Asn59Ser). This evidence concerns the gene ECHS1 and Leigh syndrome.