Molecular Vision 2025; 31:306-317 <http://www.molvis.org/molvis/v31/306>
Received 16 February 2025 | Accepted 27 September 2025 | Published 29 September 2025

Genetic variants through exome sequencing in Spanish patients affected by primary congenital glaucoma and juvenile open-angle glaucoma

Javier Laguna,1 Sara Labay-Tejado,2 Míriam Potrony,1,3 Laura Pinyol,1 Cristina Vendrell,4 Aurora Sánchez,1,3 Celia Badenas,1,3 Valeria Opazo-Toro,5 Meritxell Jodar,1,6 Elena Milla2

1Department of Biochemistry and Molecular Genetics, CDB, Hospital Clínic de Barcelona, Barcelona, Spain; 2Department of Ophthalmology (ICOF), Hospital Clínic de Barcelona, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), Barcelona, Spain; 3CIBER of Rare Diseases, Barcelona, Spain; 4Department of Ophthalmology, Hospital de Viladecans, Barcelona, Spain; 5Skövde’s Ophthalmology Department, Skaraborg’s Hospital, Lövänsvägen, Sweden; 6Department of Biomedicine, Faculty of Medicine and Biomedical Sciences, University of Barcelona, Barcelona, Spain

Correspondence to: Meritxell Jodar, Department of Biochemistry and Molecular Genetics, CDB, Hospital Clínic de Barcelona, C/ Villarroel, 170, Esc. 7 Pl. 5. 08036 Barcelona, Spain. mjodar@clinic.cat

Abstract

Purpose: To evaluate the genetic characteristics using whole-exome sequencing (WES), aiming to assess the potential of this approach for accurate diagnoses and to explore the genetic factors underlying these conditions.

Methods: A total of 28 patients, including 6 with primary congenital glaucoma and 22 with juvenile open-angle glaucoma, were studied. Genetic analysis involved initial Sanger sequencing for the CYP1B1 and MYOC genes. WES was subsequently performed in 11 patients with negative initial results, using a panel of genes most associated with glaucoma and related ophthalmic syndromes. Variant interpretation was performed based on American College of Medical Genetics and Genomics guidelines. Segregation analysis was performed when possible.

Results: Pathogenic variants in CYP1B1 and MYOC genes were identified in three patients (10%). WES identified disease-causing variants in three additional patients (27% of those with negative results from the initial testing conducted so far), all of them with syndromic features. In families where segregation analysis was possible, variants were confirmed to segregate with the clinical presentation. The diagnostic yield was 21%.

Conclusions: WES is an effective diagnostic tool for early-onset glaucoma, enhancing clinical management and genetic counseling. It supports its use in routine diagnostics to enable early detection and intervention for at-risk relatives. Further research is needed to uncover additional genetic factors and refine testing guidelines.

Introduction

Glaucoma is a group of progressive optic neuropathies leading to blindness through optic disc neurodegeneration from retinal ganglion cell apoptosis [1,2]. Glaucoma is divided into early-onset glaucoma (before 40 years) and late-onset glaucoma (after 40 years). Early-onset includes primary congenital glaucoma (PCG), with neonatal (0-1 month) and infantile (1-24 months) subtypes, and juvenile open-angle glaucoma (JOAG) starting from age 3 years [3-5].

PCG and JOAG have strong genetic bases, with pathogenic variants in genes such as CYP1B1 and MYOC being among the most frequently identified, making them key targets for genetic testing [5-7]. Next-generation sequencing (NGS) and whole-exome sequencing (WES) have advanced the understanding of monogenic forms of PCG and JOAG by identifying genes linked to ocular balance and intraocular pressure (IOP) regulation [8,9]. These new techniques support accurate diagnosis and genetic counseling, sometimes enabling preventive measures to avoid visual loss. However, the cause remains unknown for many families. Early detection of glaucoma is crucial, as decreasing IOP is the only current tool to halt its progression [1,10]. Suspected cases require initial treatment with IOP-lowering eye drops; if ineffective, surgery may be needed. Early management improves prognosis and may prevent surgery. The objectives of this study are to genetically evaluate Spanish patients with PCG and JOAG. In addition, it aims to assess the potential of WES to provide accurate diagnoses and to explore the genetic factors contributing to these conditions.

Methods

Patients

We studied 28 patients with PCG (6 patients) or JOAG (22 patients). Patients with angle-closure glaucoma and secondary glaucoma were excluded. The diagnostic criteria for PCG and JOAG were based on the European Glaucoma Society Guidelines [11] and the Childhood Glaucoma Research Network guidelines [12]. PCG was diagnosed in patients who had an onset before 2 years of age, presented with elevated IOP, and had a medical history of corneal enlargement, Haab striae, and optic nerve cupping. JOAG was defined by onset after early childhood, with open angles on gonioscopy, elevated untreated IOP, glaucomatous optic nerve damage, and often a family history, frequently involving MYOC variants.

All patients underwent a complete ophthalmic examination, including slit-lamp evaluation of the anterior segment and IOP measurement with a Goldmann tonometer. In addition, ancillary tests were performed, such as gonioscopy, pachymetry, Humphrey visual field, and Cirrus optical coherence tomography of the optic nerve and macula. Glaucoma stage was categorized by the mean deviation (MD) from the visual field test using the Hoddap-Parrish-Anderson criteria: early (MD ≥ −6 dB), moderate (−6 dB > MD ≥ −12 dB), and severe (MD < −12 dB) stages [13]. Both eyes were taken into consideration unless there was phthisis bulbi, ocular hypertension or lack of pathology, or a missing fellow eye due to evisceration or enucleation. The investigation followed the principles established in the Declaration of Helsinki. The research protocol received approval from the ethics committee (HCB/2023/0220).

Genetic studies

Written informed consents for genetic testing were obtained from all patients and relatives when necessary. CYP1B1 and MYOC genes were amplified by specific oligonucleotides (Appendix 1) and directly sequenced. WES was performed in a subset of patients who tested negative for pathogenic or likely pathogenic variants in CYP1B1 and MYOC. These families were selected based on clinical and familial criteria suggestive of a stronger genetic component. Specifically, selection was guided by features such as early age of onset, high familial burden, high penetrance, a severe disease course with poor visual prognosis, the need for multiple surgical interventions, and poor response to conventional treatments. Moreover, three patients (11%) exhibited syndromic features (additional physical or developmental anomalies suggestive of an underlying syndrome).

Additionally, the Nextera Flex for Enrichment massive sequencing protocol was followed with complete exome probes (Illumina, San Diego, CA, USA) and subsequent sequencing on the NextSeq550 platform. Primary and secondary bioinformatic analysis of the data obtained was performed using the coreBM-EX-1.1.0 pipeline, developed at the Hospital Clínic de Barcelona. WES analysis relied on a virtual custom panel, including genes commonly linked to glaucoma and glaucoma-related syndromes (Appendix 2). The virtual panel of genes was assembled based on a comprehensive review of the literature and curated databases, including OMIM, Orphanet, HGMD, and PanelApp. Genes were selected for their known association with early-onset glaucoma or glaucoma-related syndromes, as well as for their biologic relevance to ocular development and IOP regulation.

The Jnomics platform was used for annotation and variant prioritization according to frequency, quality, coverage, and possible pathogenicity. A rare variant filter (allele frequency <0.5%) was applied to coding exons and flanking intronic regions (15 pb) of the analyzed exons. Untranslated regions were not analyzed. The coverage of the analyzed regions was a minimum of 20×. Furthermore, copy number variants were studied using the ExomeDepth tool [14] in Jnomics. Population allele frequencies were obtained from the gnomAD database (version 4.1.0), using general population data as the reference. Final interpretation of variants was performed based on the American College of Medical Genetics and Genomics guidelines [15], classifying variants as benign, likely benign, uncertain significance (VUS), likely pathogenic, or pathogenic.

Segregation analysis was performed in available relatives (families 1 to 5). Relatives were unavailable for families 6 and 7. Primers used are listed in Appendix 1.

Results

Of the 28 patients included in the study, 22 patients had a family history of glaucoma (79%), and 25 patients had bilateral glaucoma (89%). Information about the stage of glaucoma and surgery per eye is summarized in Table 1. Pathogenic or likely pathogenic variants in CYP1B1 and MYOC were identified in three patients (10%). The clinical and epidemiological characteristics of the probands from each family with genetic variants are summarized in Table 2. Since WES is newly implemented in our laboratory, it was performed on only 11 (44%) patients with negative CYP1B1 and MYOC results, identifying disease-causing variants in 3 patients (27%; Table 3), all of whom had syndromic features. In addition, a VUS was found in one patient without other pathogenic or likely pathogenic variants. No copy number variants were detected.

Genetic variants were detected in four patients with PCG (one neonatal and three infantile cases) and in three patients with JOAG (Table 3). Figure 1 and Figure 2 show the detected variants and the pedigrees of each family, respectively.

Family 1

A 22-year-old woman with neonatal glaucoma (PCG) underwent goniotomy and trabeculectomy in both eyes as an infant, followed by cataract–Ahmed valve surgery in her right eye (RE). She had severe refractory glaucoma in her left eye (LE), despite medication leading to a successful Paul device implantation with satisfactory IOP control since then. Genetic testing revealed two pathogenic CYP1B1 variants in compound heterozygosity: c.840C>A (p.Cys280Ter; Figure 1A) and c.1064_1076del (p.Arg355HisfsTer69; Figure 1B), both classified as disease-causing with a low population frequency (0.001% and 0.02%, respectively). Segregation studies confirmed that the patient inherited the CYP1B1 c.840C>A variant from her mother and the c.1064_1076del variant from her father (Figure 2A). Both parents were asymptomatic, and the brother did not carry any pathogenic variant.

Family 2

A 66-year-old woman with severe JOAG was diagnosed at age 20 years. She had a family history of glaucoma (father and siblings) and required trabeculectomy in her RE and sclerectomy in her LE (Figure 3). We identified the variant c.1139A>C (p.Asp380Ala) in heterozygosity in the MYOC gene (Figure 1C). A previous study showed that this variant has reduced secretion levels compared to wild-type myocilin protein [16], which has a deleterious effect on the protein function. This variant, reported in several patients with glaucoma, was detected in all affected relatives and absent in symptom-free relatives (Figure 2B), supporting its classification as pathogenic.

Family 3

A 23-year-old man was diagnosed with JOAG at age 7 years and initially managed his IOP with timolol-dorzolamide in both eyes. However, his IOP spiked to 38 mm Hg in the RE and 34 mm Hg in the LE. Despite a preserved optic nerve head appearance (Figure 4A), an initial optic nerve fiber loss was detected (Figure 4B). Finally, the patient was scheduled for trabeculectomy in both eyes, resulting in controlled IOP without further medication. Genetic testing revealed the variant c.1150G>A (p.Asp384Asn) in heterozygosity in the MYOC gene (Figure 1D). This variant, with a low population frequency (0.0007%), had only been reported in Chinese affected families [17-19]. Segregation studies confirmed its presence in affected relatives and absence in healthy individuals (Figure 2C). Hence, the variant was classified as likely pathogenic. The patient’s nieces (aged 5 and 2 years), while carrying the familial variant, have not shown any glaucoma manifestation to date.

Family 4

A 33-year-old man was diagnosed with infantile PCG glaucoma at age 1 year, requiring multiple interventions. He also exhibited micrognathia, dental crowding, hypertelorism, a broad forehead, impaired balance (possibly related to cerebellar vermis hypoplasia), and severely impaired visual acuity. His brother had a similar clinical presentation. NGS analysis revealed the heterozygous variant c.257T>C (p.Leu86Pro) in the FOXC1 gene (Figure 1E), associated with Axenfeld-Rieger syndrome. This variant has not been previously described in the general population but was recently reported in a patient with glaucoma, congenital nasolacrimal duct obstruction, corectopia, posterior embryotoxon, and iridocorneal adhesions [20]. Furthermore, multiple variants at the same position (p.Leu86) had been reported, all of them causing disease [21,22]. Although the p.Leu86Pro variant results in a stable protein product, it still has the potential to disrupt FOXC1 function and severely affect the nuclear localization of the protein, affecting DNA binding [21]. Segregation analysis confirmed the variant in the brother but not in the unaffected mother, while the father was not available for the study (Figure 2D). Consequently, the variant was classified as pathogenic.

Family 5

A 36-year-old woman was diagnosed with JOAG at age 4 years. She underwent combined cataract-trabeculectomy surgery in late childhood and recently had a Paul device implanted in her LE due to glaucoma progression. The patient showed significant lordosis, leading to joint pain and bowlegs. Her mother and brother also exhibited similar clinical manifestations. The c.3137dup (p.Gly1047TrpfsTer11) variant was detected in the COL2A1 gene (Figure 1F), associated with Stickler syndrome type I. Loss-of-function variants in the COL2A1 gene have been considered pathogenic [23]. This variant has not been found in the general population but was identified in a patient with Stickler syndrome [23]. Additionally, it was confirmed to be present in both the affected mother and brother (Figure 2E), leading to its classification as pathogenic.

Moreover, the variant c.1103G>A in the CYP1B1 gene was detected in heterozygosity in the index case and her mother (but not her brother). Prediction programs suggest possible pathogenicity, but this variant is present, even in homozygosity, in the general population (0.2%), mainly in South Asian populations [24]. For this reason, it was classified as a VUS.

Family 6

A 39-year-old woman with severe PCG in her LE and pupillary seclusion due to her condition (Figure 5) was diagnosed at age 1 year. She also had ocular hypertension in her RE and a history of collapsing focal and segmental glomerulosclerosis (cFSGS). The variant c.2683C>T (p.Arg895Cys) was detected in heterozygosity in the TRPC6 gene. This variant has not been described in the general population and has been reported as a de novo occurrence in other patients with cFSGS [25]. Although an association between the TRPC6 gene and glaucoma has been suggested in the literature [26], evidence is insufficient to support this link. Therefore, the variant was classified as likely pathogenic, pending further validation of its association with glaucoma.

Family 7

The heterozygous variant c.1311+5G>C in the COL18A1 gene was found in a 33-year-old woman with infantile-onset PCG detected at 4 months. She underwent trabeculectomy in both eyes in early infancy, followed by cataract extraction and retinal detachment surgery in the LE. This variant has a low frequency of 0.02%. Prediction programs for splice-affecting variants have been inconsistent, and their impact on splicing needs confirmation via RNA analysis, so this variant was classified as a VUS.

Discussion

Currently, there are no established guidelines for genetic testing in glaucoma. The American Academy of Ophthalmology suggests testing only if it impacts treatment or surveillance, prioritizing patients with clinical signs of Mendelian disorders. Thus, genetic testing is ideal for those with PGC or JOAG during childhood or young adulthood [27].

Our center initially offered genetic testing of CYP1B1 and MYOC, key genes in early-onset glaucoma [5,6]. However, WES has emerged as a comprehensive and cost-effective approach for identifying pathogenic variants, making direct WES testing feasible for patients with suspected genetic early-onset glaucoma [28,29]. The diagnostic yield in our sequenced cohort was 21%, aligning with the 19% reported by others [7]. However, we acknowledge that this is a preliminary diagnostic rate, as WES was performed in only 11 patients who were negative for CYP1B1 and MYOC. Therefore, the overall yield is expected to increase as WES is extended to the remaining unsolved cases.

Based on genetic findings, patients in our cohort can be classified into two groups: (1) those with isolated PCG or JOAG linked to pathogenic variants in CYP1B1 (family 1) and MYOC (families 2 and 3) and (2) those with syndromic forms of early-onset glaucoma (families 4, 5, and 6). Notably, three of the six genetically diagnosed cases with pathogenic or likely pathogenic variants were associated with syndromic glaucoma, highlighting the added diagnostic value of WES beyond isolated ocular findings. These results emphasize the importance of adopting a broader genetic approach in patients with atypical phenotypes or systemic involvement. Early identification of syndromic conditions can guide multidisciplinary management and genetic counseling. Prior to genetic testing, a comprehensive evaluation of family history and associated clinical features is essential to identify potential syndromic presentations.

After genetic testing, a visit to a genetic counselor is essential to identify at-risk relatives for early diagnosis and treatment, understand inheritance patterns, and explore family planning options [6]. For example, the index case in family 1 will transmit a mutated CYP1B1 allele to all offspring, but disease manifestation depends on the other parent’s carrier status. In contrast, other index cases had early-onset glaucoma with autosomal dominant inheritance, giving offspring a 50% risk of inheriting the altered allele and developing the disease.

Cascade genetic testing enables targeted testing and surveillance for relatives of patients with early-onset glaucoma with the same pathogenic variant as the index case, while reassuring those without the variant that their glaucoma risk is no higher than the general population. For instance, in family 1, the index case had two pathogenic CYP1B1 variants (one from each parent), but her brother did not inherit either, placing him at no increased risk. Similarly, in family 2, descendants of individuals with MYOC mutations did not carry the familial variant, meaning they are not at higher risk for JOAG.

It is noteworthy that, in family 3, genetic testing allowed presymptomatic diagnosis in two nieces of the index case, aged 5 and 2 years, who carried the variant but showed no glaucoma signs. Early diagnosis will allow prompt treatment before irreversible damage occurs. This case underscores the benefits of genetic testing for relatives of patients with PCG or JOAG, especially minors, with parental consent [30]. For positive cases without optic nerve or visual field damage, regular IOP monitoring is essential. In the case of a positive genetic test result, Leysen et al. [6] recommend four exams in the first year, followed by every 6 months for 2 years, and annually thereafter if no signs of glaucoma appear. While these follow-up recommendations are derived from PCG surveillance protocols, their application in MYOC-related JOAG may require adaptation, given the broader range of age of onset and variable expressivity associated with this form of glaucoma.

In family 5, a pathogenic variant in COL2A1 (associated with Stickler syndrome) was identified, along with a heterozygous CYP1B1 variant (c.1103G>A). Although CYP1B1 typically causes primary congenital glaucoma through autosomal recessive inheritance, several studies have proposed that heterozygous loss-of-function or hypomorphic variants may increase susceptibility to adult-onset primary open-angle glaucoma, rather than causing early-onset forms of the disease [31-33]. These variants have been shown to impair enzymatic activity and alter protein stability, suggesting a possible modifying effect on glaucoma risk. Nonetheless, as noted by Nolan et al. [34], the clinical interpretation of such variants remains difficult and must be approached with caution. In a recent study by our group, heterozygous CYP1B1 variants were found in 5 of 61 patients with primary late-onset open-angle glaucoma, making it the most frequently affected gene in that cohort [35]. In the case of family 5, the coexistence of the CYP1B1 variant with a pathogenic COL2A1 mutation complicates interpretation, but the COL2A1 variant is the most plausible explanation for the phenotype. Interestingly, the CYP1B1 variant was absent in the patient’s affected brother, prompting us to explore phenotypic differences within the family; however, follow-up was not possible due to relocation.

Regarding family 6, a likely pathogenic variant in the TRPC6 gene was identified. This gene, along with other TRPC channels and transmembrane proteins such as podocin, forms mechanosensitive complexes that are involved in sensing glomerular pressure. This pressure-sensing function is critical in the pathogenesis of glomerular diseases such as cFSGS, where TRPC6 variants lead to abnormal calcium influx and podocyte damage. Given the shared pressure-related mechanisms in both the kidney and the eye, it is plausible that similar TRPC6-mediated pathways may contribute to retinal ganglion cell damage in glaucoma. In both contexts, elevated mechanical stress—glomerular pressure in the kidney and IOP in the eye—can lead to cellular dysfunction and degeneration via calcium overload [36,37]. Therefore, TRPC6 may represent a common molecular link between glomerular disease and glaucoma [26,38], supporting its role as a potential therapeutic target in pressure-related neurodegeneration, but further investigation is needed.

This study highlights the value of genetic analysis in diagnosing early-onset glaucoma. In our cohort, 21% of patients were diagnosed (6 of 28, corresponding to families 1 to 6), but many cases remain undiagnosed (22 of 28), indicating unidentified disease-causing variants.

Currently, therapies are focused on lowering IOP with medication, laser, or surgery. However, technological advances have brought gene therapy to the forefront. Recently, CRISPR/Cas9 system has emerged as a promising genome-editing tool in many medical fields, including glaucoma [39]. Jain et al. [40] used CRISPR/Cas9 to disrupt mutant MYOC genes in human and mouse trabecular meshwork cells and in a mouse model (Tg-MYOCY437H). This disruption reduced IOP by decreasing the accumulation of misfolded protein inside trabecular meshwork cells. Additionally, since the accumulation of misfolded protein causes MYOC-associated JOAG, chaperones that assist in proper protein folding may offer an alternative treatment strategy [41]. In this context, genetic studies will become increasingly relevant in identifying candidates for future gene-based therapies and enabling more personalized approaches to glaucoma management. Given the limited sample size and partial application of WES, this work is presented as a pilot descriptive case series. It is intended to generate preliminary insights into the genetic landscape of early-onset glaucoma.

In conclusion, the advent of NGS has improved the diagnosis of early-onset glaucoma by allowing the study of a larger number of genes. In some cases, it enables presymptomatic diagnosis in at-risk relatives, before glaucoma symptoms appear. This represents a clinical benefit, as in a state where optic nerve alterations are not yet present, it is crucial to conduct regular assessments to measure IOP, facilitating early diagnosis of glaucoma and preventing vision loss.

Appendix 1. Supplementary Table 1.

Appendix 2. Supplementary Table 2.

Acknowledgments

The authors thank all the participants who took part in this study, as well as all the medical staff and technicians who helped in obtaining and/or processing the human samples. E Milla is the co-corresponding author (emilla@clinic.cat) with Meritxell Jodar (mjodar@clinic.cat). There are no sources of support that require acknowledgment. The authors have no conflicts of interest to declare. All authors have seen and agreed with the contents of the manuscript and there is no financial interest to report. Author contributions: J Laguna: Data curation, Formal analysis, Investigation, Writing – original draft. S Labay-Tejado: Data curation, Investigation, Writing – review and editing. M Potrony: Formal analysis, Investigation, Writing – review and editing. L Pinyol: Methodology, Writing – review and editing. C Vendrell: Investigation, Writing – review and editing. A Sánchez: Investigation, Writing – review and editing. C Badenas: Investigation, Writing – review and editing. V Opazo-Toro: Investigation, Writing – review and editing. M Jodar: Conceptualization, Formal analysis, Investigation, Project administration, Resources, Supervision, Visualization, Writing – review and editing. E Milla: Conceptualization, Formal analysis, Investigation, Project administration, Resources, Supervision, Visualization, Writing – review and editing.

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