A Novel Biallelic Variant in CDH23 Gene in a Family with Atypical USH1D Manifestation

A Literature Review and Investigation of Genotype-Phenotype Correlation

  • Khorram, Erfan
  • Iravani, Omid
  • Khorrami, Mehdi
  • Amini, Masoomeh
  • Jahanian, Sara
  • Nilforoush, Mohammad Hossein
  • Mousavi, Seyyed Reza
  • Ehsanifard, Mahsa
  • Kheirollahi, Majid
Audiology and Neurotology 28(4):p 317-326, August 2023. | DOI: 10.1159/000529420

Introduction: Usher syndrome (USH) is an autosomal recessive disorder that predominantly affects hearing, vision, and, in some cases, vestibular function. USH, according to the onset age, severity, and progression of symptoms, is categorized into four main types. In addition, there are a significant number of reports that patients’ manifestations deviate from canonical phenotypic criteria of main types of USH, which are named atypical USH. CDH23 is the second most common USH gene in which its defects result in USH1D, non-syndromic autosomal recessive deafness-12 (DFNB12), and in a few cases, atypical USH1D. While some studies have suggested that missense and truncating damaging variants in the CDH23 gene cause DFNB12 and USH1D, respectively, no genotype-phenotype correlation for atypical USH1D has been established. Methods: Using whole-exome sequencing, we studied an Iranian family with two affected siblings who manifested congenital bilateral hearing loss, late-onset nyctalopia, retinitis pigmentosa, and normal vestibular function, indicating that their clinical symptoms are consistent with USH2. Results: Whole-exome data analysis revealed a novel bi-allelic nonsense variant (c.6562G>T; p.Glu2188Ter) in the CDH23 gene, which was confirmed by Sanger sequencing. Surprisingly, CDH23 is a member of the USH1 genes; therefore, our patients suffered from atypical USH1D. Also, by conducting a literature review, we provided a clinical and mutational profile of all reported patients with atypical manifestations or those who refuted the claimed genotype-phenotype correlation. Conclusion: By reporting a novel damaging variant, we expand the mutational spectrum of the CDH23 gene that leads to atypical USH1D. Also, reviewing the literature shows that, contrary to previous claims, different genotypes occur in the CDH23 gene allelic disorders, and there is no clear-cut genotype-phenotype correlation.

Introduction

Usher syndrome (USH), the most common cause of combined deaf-blindness in humans, is a group of autosomal recessive disorders characterized by congenital sensorineural hearing loss (HL), retinitis pigmentosa (RP), and with or without vestibular dysfunction [Nolen et al., 2020]. The prevalence of USH varies in different populations but is estimated to range from 3.5 to 6 per 100,000 people [Yan and Liu, 2010]. Genetically and clinically, USH is a heterogeneous disorder [Yan and Liu, 2010], and according to the OMIM database, up to now, three loci and fifteen genes (fourteen causatives and one modifier) for USH have been reported. Most USH patients, according to the age of onset of the visual and auditory symptoms and the presence/absence of vestibular dysfunction, are categorized into four distinct types [Abad-Morales et al., 2020; Peter et al., 2021], with each type based on the causative gene being divided into several subtypes (Table 1). USH1, the most severe form, is featured by severe to profound congenital HL, childhood RP, and congenital vestibular dysfunction. To date, seven genes and three loci associated with the USH1 type have been reported, including MYO7A, USHIC, CDH23, PCDH15, USHIG, CIB2, ESPN, 21q21, 15q22-q23, and 10p11.21-q21.1, respectively (Table 1) [French et al., 2020]. USH2, the most common form, is characterized by moderate to severe congenital HL, late-onset RP (in the second decade of life), and normal vestibular function, which is the result of damaging variants in the USH2A, ADGRV1, and WHRN genes [Besnard et al., 2014; Toms et al., 2020]. Furthermore, PDZD7 has been suggested as a modifier gene for patients with USH2A, whose damaging variants result in earlier onset and more severe retinal disease [Ebermann et al., 2010]. A variant in CLRN1 or HARS1 genes leads to USH3, which is characterized by progressive HL, variable RP onset age, and varying vestibular abnormalities [Puffenberger et al., 2012; Toms et al., 2020]. USH3 is extremely rare, but it is prevalent in some populations, such as the Finish, Acadian, and Ashkenazi Jewish [Besnard et al., 2014]. The USH4 is a newly introduced type that is caused by a damaging variant in the ARSG gene [Khateb et al., 2018; Peter et al., 2021]. USH4 patients generally showed late-onset HL (∼40) and RP with normal vestibular function [Abad-Morales et al., 2020; Peter et al., 2021]. Some USH genes, including PDZD7, HARS, ABHD12, CIB2, ARSG, and ESPN, due to a few reported affected cases, are called ultra-rare USH genes [Nolen et al., 2020]. In addition to monogenic inheritance, some studies report digenic inheritance in USH, including PCDH15/CDH23 and GPR98/PDZD7 [Zheng et al., 2005; Ebermann et al., 2010]. The classification of USH based on clinical symptoms does not apply to all patients, and there are several reports that patients’ manifestations deviate from the canonical criteria of the USH main types, which is called atypical USH [Aparisi et al., 2014; Igelman et al., 2021]. These deviations may occur in the severity or age of onset of RP, HL, or the presence/absence of vestibular dysfunction. Genetic studies in these patients revealed that they had damaging variants in well-known or ultra-rare USH genes [Nolen et al., 2020].

The CDH23 gene is the second most common USH gene, in which few atypical USH patients due to its damaging variants have been reported [Millán et al., 2011; Schultz et al., 2011] (Table 2). CDH23 gene encodes a calcium-dependent cell-cell adhesion glycoprotein with 27 Extracellular (EC) domains, a transmembrane domain, and a cytoplasmic domain [Pan and Zhang, 2012]. CDH23 and other USH proteins interact with each other and form an interaction network, which is called the USH interactome. USH interactome proteins are mainly colonized in stereocilia and the synaptic region of hair cells in the inner ear. The murine model revealed that the USH interactome is crucial for morphogenesis and development of the retina and hair bundle in the inner ear [Yan and Liu, 2010]. In addition to atypical USH, damaging variants in the CDH23 gene cause other allelic disorders, including USH1D and non-syndromic autosomal recessive deafness-12 (DFNB12) [Schultz et al., 2011]. Although it has been suggested that missense and truncating damaging variants in the CDH23 gene result in DFNB12 and USH1D, respectively [Valero et al., 2019], to the best of our knowledge, no genotype-phenotype correlation has yet been established in association with CDH23 damaging variants and atypical USH1D.

In this study, we used whole-exome sequencing (WES) to investigate 2 patients from an Iranian family and identified a novel homozygous nonsense variant (c.6562G>T; p.Glu2188Ter) in the CDH23 gene, which manifested atypical USH1D. Moreover, by collecting all atypical USH1D cases and those that violated the proposed genotype-phenotype correlation for the CDH23 gene allelic disorders, we found that there was no clear-cut genotype-phenotype correlation and nearly all types of genotypes in USH1D, atypical USH1D, and DFNB12 have been reported.

Material and Methods

Subjects

A consanguineous Iranian family with 2 affected patients whose manifesting phenotypes were consistent with USH was referred for genetic counseling. A comprehensive questionnaire was taken regarding family history, pregnancy complications, environmental risks, developmental milestones, and disease progression.

Genomic DNA Preparation

Venous blood samples were collected in ethylenediaminetetraacetic acid-containing tubes from the patients (IV-1 and IV-2), parents (III-1 and III-2), and healthy sibling (IV-3) (shown in Fig. 1). Genomic DNA was extracted following standard procedures (QIAGEN). The concentration and quantity of the extracted DNA were determined by agarose gel electrophoresis and a NanoDrop 2000 Spectrophotometer [NanoDrop 2000, Thermo Scientific, USA].

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Fig. 1

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Pedigree and electropherogram of the family. a Healthy, carrier, and affected individuals are represented as hollow, semi-black, and black circles or squares, respectively. b The father, mother, and healthy siblings were heterozygous for the c.6562G>T variant. The proband and his affected brother were homozygous for the c.6562G>T variant.

WES and in silico Analysis

WES was performed on high quality DNA sample of the IV-1 (shown in Fig. 1), and interpretation of the identified variants was performed according to the ACMG guidelines [Richards et al., 2015]. Exome-enriched genomic libraries was performed using SureSelect Human All Exon V7. Captured DNA fragments were sequenced using Illumina HiSeq 2500 (Illumina, Inc) with coverage of 100 × mean depth. Burrows-Wheeler Aligner software (http://bio-bwa.sourceforge. net/) was used for the alignment of reads with the human reference sequence (hg19 assembly). Variant calling was done by GATK software (https://gatk.broadinstitute.org/), and subsequent annotation was performed using ANNOVAR software. All analytical methods were done in accordance with the previous reports [Khorrami et al., 2021].

Variant Verification and Co-Segregation Analysis

Primer3 (http://primer3.ut.ee) was used for designing specific primers (F: 5′- GTAATGCCACCATCGACAGAG -3′ and R: 5′- GATATTCACAGCAAAGGCGTC - 3′) flanking the candidate variant. The primer pair checked for SNP absence with the BLAT (https://genome.ucsc.edu/cgi-bin/hgBlat). These primers amplify PCR products with 323 bp length, which were visualized using 1% agarose gel. Sanger sequencing was performed by an ABI 3130 sequencer (Applied Biosystems, USA), and the result was compared with the CDH23 gene reference sequence (NM-022124).

Results

Clinical Presentation

Parents stated that both patients had not responded to sounds since birth. Audiometry showed the proband and his affected brother both had severe HL at the age of 4 and 3 years old, respectively. Currently, the proband and his affected brother have 28 and 27 years old, respectively, and their audiometry showed that they both had severe sensorineural hearing loss (SNHL). Videonystagmography (VNG) test results indicated normal balance systems in both cases. Furthermore, the proband, at the age of 27 years, and his affected brother, at the age of 26 years, both showed night blindness (nyctalopia), and fundus photography revealed that both patients had mild RP (shown in Fig. 2).

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Fig. 2

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Audiometry, VNG, and fundus photography of the patients. Fundus photography of the proband (a) and his affected brother (b) showed the RP diagnostic triad, including disc pallor, bone spicule view, and arterial attenuation. c, d Audiograms of the proband at 4 and 28 years which show the patients had severe SNHL. e, f Audiograms of the other affected brother, at ages 3 and 27 years, which show the patient had severe SNHL. g, h Proband’s and the affected brother’s VNG test results, which showed that their balance systems were normal.

WES Detected a Novel Nonsense Variant (c.6562G>T; p.Glu2188Ter)

Analysis of the proband’s (IV-1) annotated VCF file revealed 70,145 variants, of which 1,865 occurred in coding regions with MAF ≤0.01. The mean depth of coverage was 100X for greater than 93.3% of the variants. Subsequent data filtering determined a nonsense variant c.6562G>T (p.Glu2188Ter) in the CDH23 gene, which results in a truncated protein (PVS1). The identified variant using Sanger sequencing was co-segregated with the disease (PP1). The variant was not reported in any population databases like ExAC, gnomAD and was not submitted in the ClinVar (PM2). Also, this variant was neither present in 50 healthy, ethnically matched controls nor in the Iranom project, in which 800 healthy individuals from eight major ethnic groups in Iran went through WES. No other pathogenic or likely pathogenic variant matching the clinical manifestation of the studied patient was found. The Combined Annotation Dependent Depletion score (CADD) of this variant was 46. Therefore, the detected variant was evaluated as pathogen according to ACMG guidelines.

Discussion

Atypical USH is a poorly defined clinical type in which patients’ symptoms do not meet the canonical criteria for main types of USH. In atypical USH, patients generally show a discrepancy in severity or age of onset of RP, HL, or the presence/absence of vestibular dysfunction [Nolen et al., 2020]. In this paper, we studied an Iranian family with two affected siblings who manifested congenital bilateral HL, late-onset nyctalopia and RP (in their late twenties), and normal vestibular function, indicating that their clinical symptoms are consistent with USH2. Using WES, we found a novel homozygous nonsense damaging variant (c.6562G>T; p.Glu2188Ter) in the CDH23 gene, which was confirmed by Sanger sequencing and co-segregated with the disease. Despite having the damaging variants in the CDH23 gene, our patient’s clinical symptoms deviated from typical manifestation of the USH1D; therefore, both patients are classified as having atypical USH1D. Patients with a damaging variant in the CDH23 gene may show significant variability in their phenotypes. In other words, damaging variants in the CDH23 gene cause different allelic disorders, including USH1D, atypical USH1D, and DFNB12 [Astuto et al., 2002]. Furthermore, there is a report of pituitary adenoma due to a missense damaging variant in the CDH23 gene [Zhang et al., 2017]. Since no genotype-phenotype correlation has yet been reported for atypical USH1D, we collected all the reported atypical USH1D cases in order to find a definite genotype-phenotype correlation. In previous reported atypical USH cases harboring damaging variants in the CDH23 gene, clinical deviations such as mild/late-onset RP, progressive HL, and normal vestibular function have been described (Table 2). In the analysis of damaging variants revealed in atypical USH1D, different types of genotypes, including missense/missense, nonsense/missense, missense/duplication, frameshift/frameshift, and splice-site/splice-site, have been reported. Also, these damaging variants do not cluster in a specific domain and distribute from the N-terminal to the C-terminal of the CDH23 gene (Table 2). Therefore, we found no correlation between the severity or clinical spectrum of the symptoms and the type and location of the damaging variants. Although no genotype-phenotype correlation for atypical USH1D has yet been reported, several papers have proposed a genotype-phenotype correlation for DFNB12 and USH1D, which are other allelic disorders for the CDH23 gene, i.e., a truncating damaging variant causes USH1D and a missense damaging variant results in DFNB12 [Fuster-García et al., 2021]. By reviewing the literature, we found many cases that refute this correlation (Table 2). As can be deduced from Table 2, there are many reports of homozygous or compound heterozygous missense damaging variants in patients with USH1D manifestation. Some of these missense damaging variants are located in the first or last nucleotide of exons, which may be involved in splicing (indicated by the asterisk in Table 2). Exon trapping experiments established that some of these damaging variants impaired splicing (indicated by a in Table 2), while others did not affect the splicing pattern of the CDH23 gene transcripts. Moreover, other types of genotypes such as missense/splice-site, missense/frameshift, and missense/nonsense in USH1D patients have been reported. On the other hand, there are several DFNB12 patients with genotypes such as frameshift/frameshift, homozygous in-frame deletion, missense/nonsense, and missense/frameshift (Table 2). Our investigations also show that some CDH23 gene damaging variants are involved in a wide range of phenotypes. For example, the c.5237G>A (p.R1746Q) damaging variants in the compound heterozygous state with the c.3016G>A (p.E1006K) missense damaging variants result in USH1D [Schultz et al., 2011]. It can also cause atypical USH1D in the homozygous state or in the compound heterozygous state with the c.7466G>A (p.R2489H) missense damaging variants [Bolz et al., 2001; Astuto et al., 2002; Zhao et al., 2015]. Also, the homozygous c.6050-9G>A splice site damaging variants occur in many patients, resulting in USH, but there is also a report that they cause a non-syndromic HL phenotype [Besnard et al., 2014; Valero et al., 2019]. By and large, there is no clear-cut genotype-phenotype correlation, and we suppose that there are unknown modifier genes or epigenetic factors that alter the phenotypic consequences of damaging variants and cause different clinical manifestations. We recommend that clinicians and medical geneticists consider this issue and inform families about the possibility of RP occurrence in patients with CDH23 gene missense damaging variants.

In summary, we used WES and Sanger sequencing to investigate two siblings manifesting clinical symptoms consistent with USH2 and identified a novel nonsense damaging variant (c.6562G>T; p.Glu2188Ter) in the CDH23 gene. Since the patient’s symptoms deviated from those of USH1D, they were categorized as atypical USH1D. By reviewing the literature, we endeavored to find a genotype-phenotype correlation between the type or position of the CDH23 gene damaging variants and atypical USH1D, but we figured out there is no correlation. Furthermore, we demonstrate that different genotypes may occur in other allelic disorders of the CDH23 gene, and there is no definite genotype-phenotype correlation.

Acknowledgments

Hereby, we would like to express our special thanks to our patients and their family for participating in this study.

Statement of Ethics

The study was performed according to the Declaration of Helsinki and with the approval of the Institutional Review Board of Isfahan University of Medical Sciences (IR.MUI.MED.REC.1398.186). Also, written informed consent was obtained from all participants. Indeed, for children under the age of 18 years, written informed consent was obtained from the participants’ legal guardian.

Conflict of Interest Statement

The authors report no conflict of interest.

Funding Sources

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.

Author Contributions

Erfan Khorram, Mehdi Khorrami, and Omid Irvani performed in silico analysis, investigation, visualization, and writing the draft. Sara Jahanian examined the patients and provided their clinical information. Mohammad Hossein Nilforoush conducted patients’ audiological evaluation. Masoomeh Amini, Seyyed Reza Mousavi, and Mahsa Ehsanifard contributed to the isolation of genomic DNA and Sanger sequencing. Majid Kheirollahi supervised the study. All authors have read, edited, and approved the final version of the manuscript.

Data Availability Statement

All data generated or analyzed during this study are included in this article. Further inquiries can be directed to the corresponding author.

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