Novel Compound Heterozygous Variants in CDH3 Cause Congenital Hypotrichosis with Juvenile Macular Dystrophy: A Case Report with Longitudinal Imaging and Functional Validation

Abstract

Introduction

Hypotrichosis with juvenile macular dystrophy (HJMD) is a rare autosomal recessive disorder caused by biallelic CDH3 variants. We report a Chinese patient with HJMD carrying novel compound heterozygous CDH3 variants, providing functional validation and longitudinal imaging documentation of disease progression.

Case Presentation

We present an 18-year-old male with painless bilateral vision loss over 8 years and sparse scalp hair noted since 5 years of age. Multimodal imaging documented a severe maculopathy that progressed from outer retinal tubulations (ORTs) to diffuse atrophy within 2 years, accompanied by choroidal thinning and reduced choriocapillaris perfusion. The patient also exhibited the characteristic hypotrichosis. Whole exome sequencing revealed novel compound heterozygous variants in CDH3, including an intronic splicing variant c.391-3C>G, and a missense variant c.1625A>G (p.Asn542Ser), suggesting a diagnosis of HJMD. The minigene splice assay provided evidence that c.391-3C>G leads to aberrant splicing with intron 4 retention and exon 5 skipping. Structural modeling suggested that p.Asn542Ser disrupts a key hydrogen bond in the fourth extracellular cadherin repeat domain, potentially destabilizing the extracellular structure of P-cadherin.

Conclusions

This case demonstrates that intronic CDH3 variants require functional validation for accurate diagnosis, and that ORTs in HJMD can progress rapidly to diffuse atrophy, highlighting a potential window for future interventions.

Introduction

Congenital hypotrichosis with juvenile macular dystrophy (HJMD, OMIM #601553) is a rare autosomal recessive disorder characterized by sparse hair from infancy, progressive macular degeneration typically beginning in the first 2 decades of life, and causative mutations in the CDH3 gene [1–8]. CDH3 encodes P-cadherin, a calcium-dependent cell adhesion molecule critical for the development and maintenance of the retinal pigment epithelium (RPE) and hair follicles [2]. Loss of functional P-cadherin compromises RPE integrity, leading to secondary photoreceptor degeneration and the characteristic macular dystrophy [9, 10].

Since its initial description, over 40 pathogenic CDH3 variants have been identified, predominantly exonic missense, nonsense, or frameshift mutations that directly disrupt the protein coding sequence [11]. In contrast, the characterization of non-canonical intronic variants, particularly those affecting pre-mRNA splicing, remains less common, potentially leaving a proportion of cases genetically unsolved [12]. Furthermore, while the clinical features of HJMD have been described, detailed longitudinal descriptions of the retinal phenotype using modern multimodal imaging techniques are limited. Documenting the sequential structural changes is crucial for understanding the disease’s natural history, and identifying potential biomarkers for future therapeutic trials.

In this report, we present a patient with HJMD caused by novel compound heterozygous CDH3 variants, including a missense variant and an intronic splicing variant. We provide comprehensive functional validation of their pathogenicity and, notably, present a 2-year longitudinal follow-up that captures a dynamic progression in the macular pathology.

The CARE Checklist has been completed by the authors for this case report, attached as online supplementary material (for all online suppl. material, see https://doi.org/10.1159/000551989).

Case Presentation

Clinical History and Baseline Presentation

An 18-year-old Chinese male came to our eye center for evaluation of progressive, painless bilateral vision loss over 8 years, first noted around age 10. He also reported a history of sparse scalp hair, evident since 5 years of age. There was no family history of consanguinity or similar ocular or dermatological conditions.

At his initial presentation (age 18), best corrected visual acuity was 0.8 (Snellen equivalent, 20/25) in the right eye and 0.2 (Snellen equivalent, 20/100) in the left eye. Anterior segment examination was unremarkable. Dilated fundus examination revealed symmetrical, well-demarcated areas of retinal pigment epithelium (RPE) atrophy with underlying choroidal sclerosis in the macular region of both eyes (Fig. 1a).

Fig. 1.

Multimodal retinal imaging and dermatology examination. a Wide-field fundus photography showing severe macular dystrophy in both eyes. b, b’ Spectral-domain optical coherence tomography of both eyes. The right eye shows retinal atrophy with outer retinal tubulations (b, arrowhead) that progressed to further atrophy and thinning of the outer retina after 2 years (b’, arrowhead). Short-wavelength fundus autofluorescence at baseline shows hypoautofluorescent clusters (c) and 2-year follow-up revealed subtle enlargement of the hypoautofluorescent ring with decreased distance to a superotemporal retinal branch vein (c’). d OCTA images showing reduced density and impaired capillary perfusion in both the retinal and choroidal layers. e, e’ Dermoscopy of the scalp at the parietal and frontal regions (×50).

Multimodal imaging was critical for characterizing the patient’s phenotype. Spectral-domain optical coherence tomography demonstrated foveal photoreceptor loss, a subretinal pigment epithelium scar, and uneven atrophy of the outer retina and choroid bilaterally. A distinctive finding was the presence of outer retinal tubulations (ORTs) in the parafoveal area of both eyes, suggesting the rearrangement of photoreceptors in a configuration that was relatively more continuous temporally compared to the central fovea (Fig. 1b, arrowhead). Short-wavelength fundus autofluorescence revealed confluent hypoautofluorescence corresponding precisely to the areas of macular atrophy, indicative of RPE loss (Fig. 1c). Optical coherence tomography angiography showed profound attenuation of the choriocapillaris flow signal beneath the macular lesion in both eyes, with relative preservation of the superficial and deep retinal capillary plexuses outside the atrophic zone (Fig. 1d).

A concurrent dermatological examination confirmed the diagnosis of congenital hypotrichosis. Scalp inspection showed diffusely sparse hair, and dermoscopic evaluation at ×50 magnification highlighted reduced hair density, a predominance of single-hair follicular units, and the presence of hairs with variable calibers (Fig. 1e, e’).

Two-Year Longitudinal Follow-Up

The patient was re-evaluated after 2 years and subjectively reported further blurring of vision in his right eye, while the left eye remained stable. Functionally, best corrected visual acuity had declined to 0.5 (Snellen equivalent, 20/40) in the right eye but remained stable at 0.2 in the left eye.

Serial spectral-domain optical coherence tomography provided the most significant insight into structural progression. In the right eye, the previously well-defined parafoveal ORTs observed at baseline were no longer distinct. Instead, this area had evolved into a zone of more homogeneous and diffuse outer retinal atrophy, with further thinning of the outer nuclear layer, complete disruption of the ellipsoid zone, and flattening of the RPE band (Fig. 1b’, arrowhead). This represented a clear morphological transition from a stage characterized by photoreceptor reorganization to advanced degeneration. In contrast, the structural architecture in the left eye showed minimal change. Follow-up short-wavelength fundus autofluorescence at 2 years revealed subtle progression, with mild enlargement of the hypoautofluorescent ring and decreased distance between the ring and a superotemporal retinal branch vein (Fig. 1c’), indicating slow expansion of RPE atrophy that paralleled the OCT-documented structural changes.

Genetic Findings

Whole exome sequencing performed on the proband’s DNA identified two novel heterozygous variants in the CDH3 gene (NM_001317195.3): c.391-3C>G in intron 4, and c.1625A>G in exon 12 that results in the amino acid substitution p.Asn542Ser. These findings, in conjunction with the patient’s clinical features, confirmed the diagnosis of HJMD. Both variants were absent or had extremely low allele frequencies in population databases including gnomAD and 1000 Genomes. Sanger sequencing of family members confirmed their trans configuration and autosomal recessive inheritance. The proband’s mother and a younger brother were heterozygous carriers of the c.391-3C>G variant, while the father was a heterozygous carrier of the c.1625A>G variant (Fig. 2).

Fig. 2.

Pedigree chart, genetic findings, and minigene assay in vitro for the splicing variant c.391-3C>G. a The pedigree of a Chinese family with HJMD. The arrow indicates the proband. b Sanger sequencing of the two variants.

Functional Characterization of Variants

To determine the impact of the intronic variant c.391-3C>G on splicing, a minigene assay using the pSPL3 vector was performed (Fig. 3a). A genomic fragment encompassing the variant site was cloned and expressed in COS7 cells. Reverse transcription-PCR analysis revealed that the wild-type construct produced a single, correctly spliced product. In contrast, the c.391-3C>G mutant construct yielded two aberrant transcripts: a larger product due to partial retention of intron 4, and a smaller product due to complete skipping of exon 5 (Fig. 3b). Sequencing confirmed these events (Fig. 3c). These variants predict severe molecular consequences. Intron retention leads to a frameshift and premature termination codon (p.Leu131Valfs*32), likely triggering nonsense-mediated decay, while exon skipping results in an in-frame deletion of 52 amino acids (p.Lys132_Leu183del) within the first extracellular cadherin repeat (EC1), a domain critical for cadherin adhesion.

Fig. 3.

Minigene splicing assay for c.391-3C>G and structural modeling of p.Asn542Ser. a PCR fragments were cloned into the EcoRI and BamHI sites of the pSPL3 vector using recombinant primers. SDc, splice donor vector; SAv, splice acceptor vector. b Electrophoresis of RT-PCR products of minigene transcripts in COS7 cells. Lane 1: marker; lane 2: empty pSPL3 vector (263 bp); lane 3: c.391-3C>G (931 bp* and 552 bp**); lane 4: WT (708 bp); lane 5: no-template control. c Direct sequencing of the RT-PCR products revealed that the 931 bp* fragment inserted a sequence corresponding to intron 4, while the 552 bp** fragment skipped exon 5. d Structural modeling of the p.Asn542Ser mutant P-cadherin showing the weakened Ser542-His575 hydrogen bond (dashed yellow line; distance: 3.8 Å).

Structural bioinformatics analysis was performed for the p.Asn542Ser variant, which resides in EC4. Homology modeling using the mouse P-cadherin structure (PDB: 1Q55) and validation with AlphaFold2 predicted that Asn542 in the wild-type protein forms a stabilizing hydrogen bond of approximately 3.5 Å with His575 in EC5. In silico introduction of the p.Asn542Ser mutation demonstrated that substitution with the smaller serine residue increased this distance to approximately 3.8 Å, effectively disrupting this critical interdomain bond (Fig. 3d). This perturbation is predicted to compromise the structural integrity and stability of the P-cadherin extracellular region, leading to a partial loss of protein function.

Discussion

This report elucidates a case of HJMD through integrated clinical phenotyping, genetic discovery, and functional validation, offering novel insights on multiple aspects. The most distinctive contribution of this case is the longitudinal documentation of retinal changes over a 2-year period. The initial presence of parafoveal ORTs is a significant observation. ORTs are believed to represent a final common pathway of photoreceptor reorganization, forming microtubular structures as a response to severe RPE dysfunction in various retinal dystrophies [13, 14]. In HJMD, where CDH3 is exclusively expressed in the RPE, their presence underscores the primary defect at the RPE level. The follow-up imaging captured a critical progression: the resolution of these ORTs and their replacement by diffuse outer retinal atrophy in the right eye, which correlated with a measurable decline in visual acuity. The transition from ORTs, indicative of stressed but reorganizing photoreceptors, to their disappearance and substitution by atrophy, indicative of photoreceptor cell death, provides key insights into the natural history of HJMD. It suggests that ORTs may represent a transient, pre-atrophic stage in this disorder. The observed inter-eye asymmetry in progression further highlights the potential role of modifying factors or random biological variation in disease course.

Genetically, we identified two novel CDH3 variants in compound heterozygosity. The c.391-3C>G variant, located three nucleotides upstream of exon 5, is a putative pathogenic splice-altering variant. Our minigene assay demonstrated that it leads to intron 4 retention and exon 5 skipping. This finding underscores the importance of investigating noncoding variants beyond the canonical splice sites in genetically unsolved inherited retinal diseases, as they can cause significant loss-of-function through hidden splice site activation. The p.Asn542Ser missense variant affects a conserved residue. Structural modeling suggests that it disrupts a key hydrogen bond between EC4 and EC5 domains, likely compromising protein stability. The combination of a putative loss-of-function allele (splicing variant) and a structurally disruptive missense allele provides a plausible explanation for the autosomal recessive phenotype.

This study has several limitations. First, electrophysiological assessment was not performed; multifocal ERG would have provided more detailed topographic functional correlation with the structural changes documented on OCT. Second, while our minigene assay provides strong supportive evidence for the pathogenicity of the c.391-3C>G variant, in vivo confirmation using patient-derived RNA would offer greater certainty. Nevertheless, the combination of functional data, variant segregation, and consistent clinical phenotype provides robust support for the diagnosis.

In conclusion, we expand the mutational spectrum of CDH3 with novel, functionally validated variants and provide rare longitudinal phenotypic data that describes the progression of retinal pathology in HJMD. These findings highlight the importance of comprehensive genetic testing coupled with functional assays for accurate diagnosis. Furthermore, the documented imaging progression offers valuable reference points for patient prognosis and future monitoring of therapeutic interventions.

Statement of Ethics

This retrospective study was approved by the Ethics Committee of the Second Affiliated Hospital, Zhejiang University School of Medicine (Approval No. 20260242), and adhered to the tenets of the Declaration of Helsinki. Written informed consent was obtained from the patient for publication of this case report and any accompanying images. All identifiable patient information is kept strictly confidential and is not reported.

Conflict of Interest Statement

The authors have no conflicts of interest to declare.

Funding Sources

This study was supported by the Zhejiang Provincial Natural Science Foundation of China (LQ23H120004) and the National Natural Science Foundation of China (82401264), which provided assistance with patient follow-up, data collection, and data analysis.

Author Contributions

Yuchen Lin: conception, design of the work, data acquisition, and manuscript editing. Ping Yu: data analysis and review and editing. Sunliang Cui: in silico structural modeling, data analysis, and manuscript editing; Sijie Xiong: in silico structural modeling and data analysis. Yuan Zhou: dermatological examination and review and editing. Yuhong Chen: dermatological examination and data analysis. Jijian Lin: conception, design of the work, and review and editing. All authors agreed to be accountable for all aspects of the work.

Funding Statement

This study was supported by the Zhejiang Provincial Natural Science Foundation of China (LQ23H120004) and the National Natural Science Foundation of China (82401264), which provided assistance with patient follow-up, data collection, and data analysis.

Data Availability Statement

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