Clinical Exome Sequencing Identifies, Two Homozygous LOXHD1 Variants in Two Inbred Families With Pre-Lingual Hearing Loss From South India.

Abstract

In recent years, numerous genetic variants have been linked with prelingual hearing loss (HL). Variants in the LOXHD1 gene (lipoxygenase homology domain-1) associated with DFNB77 are highly heterogeneous, with different auditory characteristics varying from stable to progressive and mild to profound. To date, 168 DFNB77 cases have been recorded worldwide. Forty-one hearing-impaired (HI) probands, who were previously excluded for a set of four common deafness-causing genes (viz., GJB2, GJB6, SLC26A4, and CDH23) from 33 HI families, were subjected to clinical exome sequencing (CES) involving 285 genes associated with HL. This was followed by a segregation analysis of the available members in the family. We identified two pathogenic LOXHD1 variants in two unrelated inbred families. One is a novel homozygous pathogenic nonsense variant (c.3999C > A; p.C1333X), whereas the other is a likely pathogenic missense variant (c.6046G > T; p.E2046K). In silico tools such as SIFT, PolyPhen-2, Mutation Taster, CADD, and REVEL scores were used to predict variant pathogenicity. Furthermore, American College of Medical Genetics and Genomics guidelines specific to HL were applied to finally classify a variant as pathogenic or otherwise. The frequency of LOXHD1 variants identified in our study is 4.88% (2/41). This is the first LOXHD1 report associated with non-syndromic HL in South Indian families.