A novel CLPP variant in a Pakistani family with Perrault syndrome associated with recurrent fevers

Perrault syndrome (PRLTS) is an autosomal recessive disease with sensorineural hearing loss and ovarian dysfunction in girls, and either a fluctuating neurological phenotype or not. PRLTS type 2 is known to be caused by pathogenic variants of the CLPP gene that encodes mitochondrial ATP-dependent protease. This paper involved clinical and genetic studies on a Pakistani family with PRLTS. Whole-exome sequencing identified a novel homozygous CLPP missense mutation (NM_006012.4: c.250 A > C; p.Ile84Leu). Its pathogenicity was assessed with the help of multiple sequence alignment, AlphaFold protein modeling, and docking with CLPX with the help of ClusPro. Auditory brainstem responses and tympanometry were in clinical assessment. The individuals were found to have a uniform phenotype of severe sensorineural hearing loss, mild intellectual disability, ataxia and frequent fever. There was one patient in whom the unilateral Eustachian tube dysfunction was hinted at by Tympanometry. At the molecular level, the identified CLPP variant involved a highly conserved residue. Structural modeling showed preserved protein architecture, whereas docking simulations revealed disrupted CLPP-CLPX interaction, suggesting a basis for impaired proteostasis. We report a novel CLPP missense variant (p.I84L) in a Pakistani family with PRLTS, expanding the mutational spectrum of CLPP. To the best of our knowledge, recurrent fever was reported in PRLTS for the first time, which expanded the PRLTS phenotype spectrum.