Novel LARS2 variants in patients with Perrault syndrome: expanding the genetic spectrum and phenotypic heterogeneity

ZIBIN LIN¹Jiale Xiang²Xiangzhong Sun³Xinyu Shi⁴Xiaozhou Liu⁴Qinming Cai⁴Jing Yang³Nana Song³Haodong Ye³Jiangfan Xu³Jiguang Peng³Xianghong Ou^1*Yu Sun^4*Zhiyu Peng^2*

• ¹Guangdong Second Provincial General Hospital, Guangzhou, China
• ²University of Chinese Academy of Sciences, Beijing, China
• ³BGI Group, Shenzhen, China
• ⁴Huazhong University of Science and Technology Tongji Medical College, Wuhan, China

Background: Perrault syndrome (PS) is a rare autosomal recessive disorder characterized by sensorineural hearing loss (SNHL) and primary ovarian insufficiency in females. LARS2, encoding mitochondrial leucyl-tRNA synthetase, is the most common causative gene for PS. However, the genetic spectrum and clinical variability of PS remain underexplored. Expanding the catalog of LARS2 variants and correlating them with phenotypic data are critical for delineating genotype-phenotype relationships. Methods: Two unrelated Chinese probands with hearing loss were enrolled, and comprehensive clinical evaluations were performed. Whole-exome sequencing (WES) was used to identify genetic variants, followed by Sanger sequencing for family co-segregation verification. Minigene assays and RT-PCR were conducted to assess the splicing effect of the novel canonical splice-site variant LARS2 c.235-2A>G. For the novel missense variant LARS2 c.1661T>C, 3-D structural modeling and evolutionary conservation analysis were performed to evaluate its pathogenicity. Moreover, we comprehensively summarized all LARS2 variants associated with PS via an extensive literature review. Results: Proband 1 (12-year-old female) harbors compound heterozygous variants LARS2 c.235-2A>G (novel) and LARS2 c.880G>A, presenting with profound SNHL, primary ovarian insufficiency, and developmental delay. Proband 2 (7-year-old male) carries compound heterozygous variants LARS2 c.1661T>C (novel) and LARS2 c.1886C>T, manifesting severe SNHL with an unusual upsloping audiogram pattern and comprehension difficulties. Functional assays confirmed that LARS2 c.235-2A>G disrupts canonical splicing, leading to exon 4 skipping and in-frame deletions. 3-D structural modeling and conservation analysis revealed that LARS2 c.1661T>C likely impairs protein stability by altering residue interactions, with Val554 being highly conserved across species. According to the ACMG/AMP guideline, both novel LARS2 variants were classified as likely pathogenic. Conclusion: We identified two novel LARS2 variants associated with PS in Chinese patients, thereby expanding the LARS2 genetic spectrum and providing precise molecular evidence for clinical management and genetic counseling. This study enhances understanding of genotype-phenotype correlations in PS, thereby revealing the phenotypic heterogeneity of LARS2 variants.