Recessive LOXHD1 variants cause a prelingual down-sloping hearing loss: genotype-phenotype correlation and three additional children with novel variants

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

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.

Rare Case with Pathogenic Variant in DHX16 Gene Causing Neuromuscular Disease and Oculomotor Anomalies

The DEAD/DExD/H-box RNA helicases are a group of RNA-binding proteins involved in the metabolism of mRNAs. They coordinate gene expression programs and play a role in cellular signaling, fate, and survival. We describe a case of a 36-year-old female with neuromuscular disease, sensorineural hearing loss, retinitis pigmentosa, and primary ovarian insufficiency harboring a heterozygous de novo missense pathogenic variant in the DEAH-box helicase 16 (DHX16) gene. This is the first case exhibiting a high intellectual level and the highest survival outcome so far. Eight previous cases of DHX16 disease-causing variant carriers have been described with common features, including muscle weakness with hypotonia, myopathy or peripheral neuropathy, sensorineural hearing loss, abnormal retinal findings, and infantile spasms or epilepsy. Increasing evidence associates RNA-binding proteins, including the DEAD/DExD/H-box helicase family genes, with neuropsychiatric or neurodevelopmental disorders. DHX16 genetic analysis should be considered early when diagnosing a child or young adult with muscular disease, severe hearing loss, and ocular anomalies.

Genetic Analysis of the LOXHD1 Gene in Chinese Patients With Non-Syndromic Hearing Loss

Non-syndromic hearing loss (NSHL) is a common neurosensory disease with an extreme genetic heterogeneity which has been linked to variants in over 120 genes. The LOXHD1 gene (DFNB77), encoding lipoxygenase homology domain 1, is a rare hearing loss gene found in several populations. To evaluate the importance of LOXHD1 variants in Chinese patients with NSHL, we performed genetic analysis on LOXHD1 in 2,901 sporadic Chinese patients to identify the aspect and frequency of LOXHD1 causative variants. Next-generation sequencing using a custom gene panel of HL was conducted on 2,641 unrelated patients and whole-exome sequencing on the remaining 260 patients. A total of 33 likely causative variants were identified in 21 patients, including 20 novel variants and 13 previously reported pathogenic variants. Each of the 20 novel variants was evaluated according to ACMG criteria. These findings showed that causative variants in LOXHD1 were found in about 0.72% (21/2,901) of Chinese NSHL patients. This study is by far the largest number of novel variants identified in this gene expanding the range of pathogenic variants in LOXHD1, and suggests that variants in this gene occur relatively commonly in Chinese NSHL patients. This extensive investigation of LOXHD1 in Chinese NSHL patients proposed six recurrent LOXHD1 variants. These findings may assist in both molecular diagnosis and genetic counseling.