Identification and computational analysis of USH1C, and SLC26A4 variants in Pakistani families with prelingual hearing loss

Abstract

Hearing loss (HL) is clinically and genetically heterogeneous disorder and is the most frequent occurring sensory deficit in humans. This study was conducted to decipher the genetic cause of HL occurring in two large consanguineous Pakistani families (GCNF-01, GCNF-03). Family history and pure tone audiometry of both families suggested prelingual HL, while the affected individuals of GCNF-01 also had low vision and balance problems, consistent with cardinal features of Usher syndrome type I (USH1). Exome sequencing followed by segregating analysis revealed a novel splice site variant (c.877-1G > A) of USH1C occurring with USH1 phenotype in family GCNF01. While the affected individual of family GCNF-03 were homozygous for the c.716 T > A, p.(Val239Asp) previously reported pathogenic variant of SLC26A4. Both variants have very low frequencies in control database. In silico mutagenesis and 3-dimensional simulation analyses revealed that both variants have deleterious impact on the proteins folding and secondary structures. Our study expands the mutation spectrum of the HL genes and emphasizes the utility of exome sequencing coupled with bioinformatics tools for clinical genetic diagnosis, prognosis, and family counseling.

Keywords: Exome sequencing; Genetic heterogeneity; Prelingual hearing impairment; SLC26A4; Sensorineural hearing loss; USH1C; Usher syndrome.

Fig. 1. Pedigree structures and identified variants segregating with HL.

A. Known HL genes variants segregating with HL phenotype in two large consanguineous Pakistani families. Filled and empty squares represent the affected and normal males, respectively, while circles denote females. Double line defines the consanguinity. Genotypes of each participating individuals for the candidate variants are shown below the symbols. B. Air conduction bone audiometry data of two families GCNF-01 and GCNF-03 show severe to profound HL. C. Clustal-Omega multiple sequence-alignment of orthologous proteins shown in evolutionary conserved mutated residues across the species.

Fig. 2. 3-D molecular modeling and Ramachandran plots for OTOG and SLC26A4 proteins.

A. Wildtype and mutated residues of OTOG at position 50 are shown in orange and magenta, respectively. Protein strands, helix and coils are represented in green. B. Ramachandran plot analysis of OTOG with p.Gln50 and p.Glu50 variants indicate 94 and 93% of total 1497 analyzed residues lie in allowed region. However, as compare to wild type protein, in which 93 residues (labeled amino acids) are outliers, the p.Glu50 change predicted 100 residues in outlier region. C. Wild type and mutant residues of SLC26A4 at position 239 are shown in green and red, respectively. Yellow dotted line represents hydrogen bond interacting with neighboring residue shown in turquoise. Protein strands, helix and coils are represented in pink. D. Ramachandran plots of SLC26A4^p.Val239 and SLC26A4^p.Asp239 residues reveal that 96% of the analyzed amino acids are present in the allowed region.