Systematic analysis of mitochondrial genes associated with hearing loss in the Japanese population: dHPLC reveals a new candidate mutation

Using denaturing high-performance liquid chromatography combined with direct sequencing and cloning-sequencing, Japanese patients with prelingual (N = 54) or postlingual (N = 80) sensorineural hearing loss not having pathogenic mutations of m.1555A > G and m.3243A > G nor GJB2 were subjected to mutational analysis of mtDNA genes (12S rRNA, tRNALeu(UUR), tRNASer(UCN), tRNALys, tRNAHis, tRNASer(AGY), and tRNAGlu).We discovered 15 variants in 12S rRNA and one homoplasmic m.7501A > G variant in tRNASer(UCN); no variants were detected in the other genes. Two criteria, namely the low frequency in the controls and the high conservation among animals, selected the m.904C > T and the m.1105T > C variants in 12S rRNA as candidate pathogenic mutations. Alterations in the secondary structures of the two variant transcripts as well as that of m.7501A > G in tRNASer(UCN) were predicted.The m.904C > T variant was found to be a new candidate mutation associated with hearing loss. The m.1105T > C variant is unlikely to be pathogenic. The pathogenicity of the homoplasmic m.7501T > A variant awaits further study.Hearing loss manifests in more than 1 in 1000 persons at birth, and the frequency increases subsequently to 3 in 1000 by 4 years of age [1,2]. Approximately 50 to 70% of congenital and childhood deafness is estimated to be due to genetic mutations. In adults, the prevalence of hereditary hearing impairment has been estimated to be approximately 3.2 in 1000 [3]. Some of the mitochondrial DNA (mtDNA) genes, such as 12S rRNA, tRNALeu(UUR), and tRNASer(UCN), are known to be responsible for hereditary hearing loss [4]. Among them, the m.1555A > G mutation in 12S rRNA is found relatively frequently (0.6-16%, depending on the ethnic group) in aminoglycoside-induced, congenital, and late-onset nonsyndromic hearing loss [4,5]. The m.1494C > T mutation in 12S rRNA is also associated with aminoglycoside-induced and nonsyndromic hearing loss [6,7]. The m.3243A > G mutation in tRNALeu(UUR)