A Novel Missense Variant in the CDH23 Gene is Segregated in an Iranian Family with Hearing Loss

Elham Alimoradi ^1,2,3,†, Parham Nejati ^4,†, Fatemeh Molavi ⁵, Setareh Isaee ⁵, Soudeh Ghafouri-Fard ^2,*, Reza Alibakhshi ^1,5,*

1. Department of Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran

2. Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran

3. Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran

4. Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran

5. Dr. Alibakhshi’s Medical Genetics Laboratory, Kermanshah, Iran

† These authors contributed equally to this work.

* Correspondences: Soudeh Ghafouri-Fard and Reza Alibakhshi

Academic Editor: Akbar Dorgalaleh

Received: November 25, 2025 | Accepted: March 10, 2026 | Published: April 13, 2026

OBM Genetics 2026, Volume 10, Issue 2, doi:10.21926/obm.genet.2602336

Recommended citation: Alimoradi E, Nejati P, Molavi F, Isaee S, Ghafouri-Fard S, Alibakhshi R. A Novel Missense Variant in the CDH23 Gene is Segregated in an Iranian Family with Hearing Loss. OBM Genetics 2026; 10(2): 336; doi:10.21926/obm.genet.2602336.

© 2026 by the authors. This is an open access article distributed under the conditions of the Creative Commons by Attribution License, which permits unrestricted use, distribution, and reproduction in any medium or format, provided the original work is correctly cited.

1. Introduction

Hearing loss is a highly prevalent sensory disorder. In fact, prelingual hearing loss has an approximate prevalence of 1 in 500 individuals [1]. This condition exhibits immense genetic and clinical heterogeneity, with approximately 150 genes implicated in its etiology [2,3]. For individuals with hearing loss and their relatives, a genetic diagnosis provides a comprehensive picture. It clarifies the expected progression of the condition, reveals whether it is isolated or part of a broader syndrome, guides appropriate habilitation and care, indicates whether specific treatments exist, and provides crucial data for family planning through genetic counseling [3]. Among the genes associated with autosomal recessive non-syndromic hearing loss and Usher syndrome type 1D is CDH23, which encodes the cadherin-related 23 protein [4]. This protein is a critical constituent of the stereocilia tip links in the inner ear, playing an essential role in the mechanotransduction pathway necessary for auditory function. It may contribute to congenital hearing loss by regulating purine metabolism [5]. A wide range of CDH23 variants has been reported in various populations, contributing to both congenital and progressive forms of hearing loss [6,7,8]. Recently, a homozygous variant within CDH23 (c.5149T>C) has been suggested as the probable causative mutation in an Iranian family [9]. Moreover, targeted exome sequencing of hearing loss-related genes has led to the identification of a homozygous c.2206C>T variant in this gene in another Iranian family with Usher syndrome type 1 [10].

In the present study, we investigated a large consanguineous Iranian family with several members affected by sensorineural hearing loss (SNHL). Using WES, we detected a novel homozygous missense variant in the CDH23 gene, which was subsequently confirmed and shown to co-segregate with the hearing loss phenotype in the family.

2. Case Presentation

2.1 Subjects

All steps were conducted in accordance with ethical guidelines. Parents signed informed consent forms. The study was permitted by the Ethics Committee of Kermanshah University of Medical Sciences (IR.KUMS.MED.REC.1403.178). Affected and healthy individuals of an extended inbred Iranian family with multiple consanguineous marriages from Kermanshah, West of Iran, were enrolled to study SNHL. During genetic counseling, family information was obtained to construct the pedigree (Figure 1). The pedigree included several patients with hearing loss, including both congenital (IV.5 and III.4) and progressive forms (other cases). In the latter cases, symptoms of deafness began between the ages of 4 (IV.12) and 17 (IV.6), respectively, and worsened progressively over time.

Figure 1 Family pedigree (A) and the results of Sanger sequencing for evaluation of segregation of the detected variant in the CDH23 gene (c.817T>C, p.Tyr273His) (B).

2.2 Clinical Evaluations

All affected individuals underwent a comprehensive clinical assessment to characterize their hearing loss and exclude syndromic etiologies. Pure-tone audiometry confirmed bilateral sensorineural hearing loss in all affected members, with air-bone gaps of less than 10 dB. Tympanometry revealed normal middle ear function (type A tympanograms) in all cases. The proband (IV.5) presented with congenital, profound SNHL (pure-tone average >90 dB). Individual III.4 also had a congenital profound loss. In contrast, individuals IV.6 and IV.12 showed progressive, severe-to-profound SNHL, with initial diagnoses at ages 17 and 4, respectively, and documented deterioration on subsequent audiograms. In addition, all affected individuals underwent a complete ophthalmic evaluation. No evidence of retinitis pigmentosa, such as bone-spicule pigmentation on fundoscopy or abnormal rod/cone responses on electroretinography, was observed in any subject. Furthermore, no individual reported symptoms of night blindness or visual field constriction. Finally, none of the affected individuals reported a history of balance difficulties or delayed motor milestones (e.g., sitting or walking). A general physical examination revealed no other abnormalities, including no cardiac, renal, or craniofacial anomalies. These comprehensive assessments confirm that the hearing loss in this family is non-syndromic and sensorineural.

2.3 Molecular Analyses

After obtaining informed consent from all individuals, 4 mL of peripheral blood was collected and preserved in EDTA-containing tubes. DNA extraction was accomplished using a commercial DNA extraction kit. Purity and concentrations of DNA were assessed using 1% agarose gel and a spectrophotometer (Nanodrop 2000 Thermoscientific, USA), respectively. The proband’s sample was subjected to WES by a commercial service provider (Centogene, Rostock, Germany). Genomic DNA was fragmented using enzymes. Then, capture probes targeting coding regions of about 6700 genes with recognized clinical impact were used to enrich for regions of interest. Libraries were made using the Illumina-compatible adaptors. Sequencing was accomplished using an Illumina platform. Coding exons in conjunction with flanking ±10 intronic bases were evaluated. Raw sequence data were analyzed using validated in-house software. This step included base calling, demultiplexing, alignment to the human reference genome (GRCH37), and variant calling. Relevant variants reported in HGMD, ClinVar, or CentoMD, in addition to all variants with minor allele frequency <1% in ExAc, were assessed. Eventually, family history and clinical data were used to appraise the identified variants. Variants were categorized in classes into Pathogenic, Likely Pathogenic, Variant of uncertain significance (VUS), Likely Benign, Benign, and Disease-associated variants. Variants correlated to the hearing loss, except benign or likely benign variants, were reported. As the primary bioinformatic analysis was conducted externally, we received a curated clinical report containing variants that passed the laboratory’s internal filtration criteria. According to the laboratory’s standard protocol, variants were sequentially filtered as follows: (1) removal of low-quality calls (depth <10×, mapping quality <40); (2) retention of nonsynonymous, stop-gain/loss, frameshift, and canonical splice-site variants; (3) exclusion of variants with a minor allele frequency (MAF) ≥ 0.01 in public databases (gnomAD, 1000 Genomes); (4) prioritization of variants consistent with autosomal recessive inheritance (homozygous or compound heterozygous), given the consanguineous pedigree structure; and (5) cross-referencing against a curated list of genes associated with hereditary hearing loss (based on the Hereditary Hearing Loss Homepage and OMIM). This step led to the detection of a novel homozygote variant in the CDH23 gene (c.817T>C, p.Tyr273His). No other rare, potentially pathogenic variants in known hearing loss genes were reported in the final analysis. The laboratory’s internal quality metrics confirmed that >98% of the target exome was covered at a depth sufficient for confident variant calling, minimizing the likelihood that a second causative variant was missed due to technical factors.

Key quality metrics, as provided in the laboratory’s quality control report, were as follows: Mean target coverage: 142×, Coverage uniformity: 98.5% of target bases were covered at 20×, Percentage of target bases covered at ≥10×: 99.2%, Mapping rate: 99.7% of reads successfully mapped to the reference genome (GRCh37/hg19).

Then, Sanger sequencing was used to confirm the result in the proband and other family members. The primers used for amplification of the region of interest are as follows: Forward Primer: 5’-TTGCCCTTGCAGCCAGGATCAG-3’, Reverse Primer: 5’-GAGGACTGTCCCTGTAGTCAGGT-3’. Molecular tests led to the identification of the following variant in the CDH23 gene (Table 1).

Table 1 Characteristics of the identified variant in the CDH23 gene.

The variant was classified as likely pathogenic as stated by the ACMG guidelines, since it met the following criteria: PM2 (Exceptionally low frequency in gnomAD population databases (Table 2)), PP3 (Computational prediction tools solidly supported a deleterious impact on the gene (Table 3)), PP5 (Pathogenic Moderate: Reliable source reports variant as pathogenic), PP1 (Supporting, based on the co-segregation with hearing loss in several affected family members).

Table 2 Frequency of identified variants in the gnomAD.

Table 3 The results of assessment of the pathogenicity of the identified variant by in silico tools.

The identified variant (c.817T>C, p.Tyr273His) was cosegregated with the phenotype in the family except for the III.5 case who had progressive hearing loss, but was normal for the identified variant (Figure 1B).

3. Discussion

We report a novel homozygous missense variant (c.817T>C, p.Tyr273His) in the CDH23 gene, identified through WES in a large Iranian family with a history of consanguinity and SNHL. The variant was found to co-segregate with the hearing loss phenotype in all but one affected family member, strongly supporting its pathogenicity.

The novelty of the c.817T>C (p.Tyr273His) variant is underscored by its complete absence from global population databases (gnomAD, GME Variome, Iranome), its lack of prior reporting in the literature, and its location within the functionally critical third extracellular cadherin (EC3) repeat domain of CDH23, where no other variants at this codon have been described. Crucially, this is the first report of a CDH23 variant at this specific residue associated with a rigorously confirmed non-syndromic phenotype, as a comprehensive ophthalmologic evaluation excluded Usher syndrome in all affected individuals.

In addition, the variant was classified as "Likely Pathogenic" according to the ACMG guidelines. This classification was based on several lines of evidence: its extreme rarity in population databases (PM2), consistent predictions of a deleterious impact from multiple in silico tools (PP3) and its segregation with the disease in the family (PP1). Furthermore, the affected tyrosine residue at position 273 is located in a highly conserved extracellular cadherin repeat domain of the protein [11], underscoring its functional importance. The disruption of this conserved residue is predicted to impair the protein’s adhesive function, essential for preserving the structure of hair cell stereocilia (Figure 2).

Figure 2 A schematic section of the CDH23 gene is presented, highlighting the location of the identified pathogenic variant (c. 817T>C) within the human genome. Additionally, the conservation of the region across various species is illustrated.

Our findings are consistent with the established role of CDH23 in hearing loss. Mutations in this gene are well documented as a cause of both syndromic and non-syndromic autosomal recessive hearing loss. The phenotypic spectrum in our family, which included both congenital and progressive hearing loss, aligns with the variable expressivity often observed in CDH23-related hearing impairment. The single exception to the segregation pattern (individual III.5) suggests phenotypic heterogeneity or a different genetic etiology in this individual, which is not uncommon in large families, especially those with consanguineous backgrounds.

Different variants in the CDH23 gene have been associated with autosomal recessive SNHL. For instance, 6 missense CDH23 variants have been detected in 5 families segregating this type of hearing loss [4]. Additionally, 5 siblings with SNHL, born to consanguineous parents, have been found to harbor a homozygous F1888S substitution in this gene [12]. Homozygosity or compound heterozygosity for 4 different missense variants in this gene has been detected in several Japanese patients from different families with autosomal recessive hearing loss, indicating that CDH23 variants may account for approximately 5% of nonsyndromic hearing loss among Japanese patients [13]. A novel variant in this gene (c.2961T>G) has been suggested to be the basis of congenital profound progressive hearing loss in an Iranian family [14].

CDH23 plays an essential role in establishing and maintaining the proper structure of the stereocilia bundle in cochlear and vestibular hair cells during late embryonic and early postnatal development. It interacts with USH1C, USH1G, and MYO7A to form the tip link complex, and these interactions are critical for mediating mechanotransduction in cochlear hair cells (Figure 3). Disruption of this complex, as predicted for the p.Tyr273His variant, which affects a highly conserved residue in an extracellular cadherin repeat domain, would impair hair cell function and lead to sensorineural hearing loss.

Figure 3 CDH23 has an essential role in the establishment and/or preservation of the appropriate structure of the stereocilia bundle of cochlear and vestibular hair cells. Its interactions with other proteins establish a functional system that contributes to the function of cochlear hair cells (https://string-db.org/cgi/network?taskId=bzO0FXwSIc3c&sessionId=bOoGsk0aGVZK).

The identification of a novel likely pathogenic variant in CDH23 provides this extended Iranian family with several tangible benefits that directly address the principles outlined in the introduction. First, the genetic diagnosis clarifies the expected progression of hearing loss for the affected individuals. For the younger affected members, genetic diagnosis enables appropriate planning for educational and communication needs. Second, the comprehensive clinical evaluation that accompanied this genetic testing confirmed the non-syndromic nature of the hearing loss. The normal ophthalmologic examinations and the absence of vestibular symptoms provide critical reassurance to the family that their children are not at risk for the progressive vision loss associated with Usher syndrome type 1D, which is also caused by CDH23 mutations. This distinction profoundly alters clinical management, as it eliminates the need for regular ophthalmologic surveillance specifically for retinitis pigmentosa, though routine eye care remains important. Third, the genetic diagnosis guides appropriate habilitation. With a confirmed genetic etiology and no contraindications, the affected individuals are excellent candidates for cochlear implantation if hearing aids prove insufficient, and the genetic information may inform candidacy for future gene-based therapies as they become available. Finally, and perhaps most importantly for this consanguineous family, the identification of the specific causal variant enables precise genetic counseling and informed reproductive decisions. Carrier testing can now be offered to at-risk relatives, and preimplantation genetic testing is now feasible for couples in this family who wish to avoid having another affected child. The single exception to segregation (individual III.5) adds an important layer of complexity to genetic counseling, as it demonstrates that not all hearing loss in this family is attributable to the CDH23 variant, underscoring the need to carefully evaluate each individual’s genetic status before making assumptions about recurrence risk.

Finally, the identification of this novel CDH23 variant is particularly significant within the context of Iran’s unique genetic landscape. Iran has a high rate of consanguineous marriage, estimated at up to 38.6% in the general population [15], which directly contributes to a higher prevalence of autosomal recessive disorders, including non-syndromic hearing loss (NSHL). Previous studies have established that CDH23 is a major contributor to NSHL in Iran, accounting for approximately 6.9% of cases [16]. Our findings add a novel variant to this known mutational spectrum, expanding the catalog of mutations relevant for genetic screening in the region. The variant’s absence from population-specific databases like the Iranome project underscores the importance of comprehensive family-based studies to capture rare, pathogenic variants that may be unique to individual pedigrees. This discovery has direct implications for genetic counseling in this high-risk population, enabling precise carrier detection and prenatal diagnosis for the affected family and potentially others.

To sum up, we have identified a novel likely pathogenic variant in the CDH23 gene as the probable genetic cause of hearing loss in an extended Iranian family. This discovery expands the mutational spectrum of CDH23 and highlights its role in hereditary hearing loss. A confirmed genetic diagnosis provides important information for this family, enabling accurate genetic counseling and informed reproductive decisions. Future functional studies are warranted to explain further the mechanistic impact of this specific variant on the CDH23 protein and its role in hair cell function.

Author Contributions

Elham Alimoradi and Parham Nejati evaluated the medical records and assessed the patient. Fatemeh Molavi and Setareh Isaee performed the experiments. Soudeh Ghafouri-Fard wrote the manuscript. Reza Alibakhsi supervised the study.

Competing Interests

The authors have declared that no competing interests exist.

AI-Assisted Technologies Statement

Artificial intelligence (AI) tools were used solely for basic grammar correction and language refinement in the preparation of this manuscript. Specifically, OpenAI’s DeepSeek was employed to improve the readability and linguistic clarity of the English text. All scientific content, data interpretation, and conclusions were developed independently by the author. The authors have thoroughly reviewed and edited the AI-assisted text to ensure its accuracy and accept full responsibility for the content of the manuscript.