Genotype–Phenotype Correlations in RPGRIP1 -Associated Retinal Dystrophy in a Nationwide Japanese Cohort

Purpose

To investigate genotype–phenotype correlations in a nationwide Japanese cohort of patients with RPGRIP1 -associated retinal dystrophy.

Design

Retrospective, multicenter cohort study.

Methods

Japanese patients with biallelic pathogenic RPGRIP1 variants diagnosed with Leber congenital amaurosis (LCA) or achromatopsia (ACHM) were recruited from university hospitals throughout Japan. Genetic analyses included polymerase chain reaction for detection of the exon 18 deletion variant (exon 18-DEL), whole-exome sequencing, and whole-genome sequencing. Ophthalmic evaluations comprised best-corrected visual acuity (BCVA), visual field testing, full-field electroretinography, and multimodal retinal imaging.

Results

Thirty-four patients from 26 families (23 [18 families] with ACHM and 11 [8 families] with LCA) were included. Fourteen distinct RPGRIP1 variants were identified, with exon 18-DEL being the most prevalent (43 of 68 alleles, 63.2%). In ACHM, variants were predominantly clustered around exon 18, whereas LCA showed more diverse variant combinations. BCVA was significantly worse in LCA than in ACHM, although the rate of BCVA decline did not differ between phenotypes. Multimodal imaging demonstrated relatively preserved macular structure even in older patients with LCA, while ACHM showed age-dependent progressive outer retinal degeneration. Electroretinography revealed near-complete loss of rod and cone function in early infancy in LCA, whereas rod function was initially preserved in ACHM but gradually deteriorated.

Conclusions

RPGRIP1 variants cause two distinct clinical phenotypes, LCA and ACHM, with clear genotype–phenotype correlations. The exon 18-DEL, observed in both phenotypes, likely represents a founder variant in the Japanese population. These findings expand the clinical spectrum of RPGRIP1 -associated retinal dystrophy and have implications for molecular diagnosis, prognostic counseling, and future therapeutic development.

INTRODUCTION

L eber congenital amaurosis (LCA) and achromatopsia (ACHM) are two major forms of congenital inherited retinal diseases (IRDs), both characterized by severe visual impairment from birth or early infancy. To date, more than 25 genes have been identified as causes of LCA, whereas 7 genes ( CNGA3, CNGB3, GNAT2, PDE6C, PDE6H, ATF6 , and RPGRIP1 ) have been associated with ACHM. ^,^,^,^,^,^,^,^, However, no single gene had been definitively established as causative for both phenotypes until recently.

The retinitis pigmentosa GTPase regulator (RPGR) interacting protein 1 ( RPGRIP1 ) gene (NM_020366.4), composed of 25 exons, encodes a large multidomain protein localized to the centrioles, basal bodies, and the connecting cilium in photoreceptor cells. RPGRIP1 plays a key role in ciliary function, including the regulation of RPGR localization, vesicle trafficking, directional transport of nascent proteins from the inner to the outer segments, and photoreceptor disc morphogenesis.

Biallelic pathogenic variants in RPGRIP1 have been associated with a wide clinical spectrum of IRDs, including LCA, retinitis pigmentosa (RP), cone dystrophy (COD), and cone-rod dystrophy (CORD). ^,^, More recently, RPGRIP1 -associated cone dysfunction with a normal fundus appearance has been reported, further expanding the phenotypic spectrum. Our previous studies have revealed distinct genetic and clinical features in Japanese patients with RPGRIP1- associated ACHM, ^, including a high prevalence of a homozygous deletion involving exon 18 (exon 18-DEL). These studies were the first to establish a relationship between ACHM and RPGRIP1 variants. ^, In addition, we have reported the exon 18-DEL in combination with a truncating variant in 4 of 10 Japanese patients with LCA, suggesting that this exon 18-DEL may underlie both ACHM and LCA phenotypes.

The aim of the present study was to elucidate genotype–phenotype correlations in Japanese patients with RPGRIP1- associated retinal dystrophy presenting with ACHM or LCA, using a nationwide cohort.

METHODS

ethics statement

The Institutional Review Boards of the Jikei University School of Medicine (approval number 24-231 6997), Nagoya University Graduate School of Medicine (approval number 2020-0598), National Center for Child Health and Development (approval number 686, 1532), Hamamatsu University School of Medicine (approval number 14-040), the National Hospital Organization Tokyo Medical Center (approval number R18-029), Kindai University (approval number 22-132, R5-071, R06-155), Hokkaido University Hospital (approval number 021-0120), The University of Osaka Graduate School of Medicine (approval number 719-5), Kobe City Eye Hospital (approval number E19002), and Juntendo University Graduate School of Medicine (approval number 2013052 and M08-0468) approved this study. The study protocol followed the Declaration of Helsinki, and all participants provided written informed consent.

inclusion criteria and molecular genetic analysis

The study included Japanese patients who met the following inclusion criteria and were examined at 10 university hospitals and research institutions. These patients were recruited from university hospitals and other medical facilities across the country. The inclusion criteria for patients were (1) clinical findings; diagnosed as IRDs, (2) genetic findings; homozygous or compound heterozygous (biallelic) pathogenic variants in the RPGRIP1 gene (NM_020366.4). Molecular genetic analysis, including polymerase chain reaction with Sanger sequencing for detection of RPGRIP1 exon 18-DEL, whole-exome sequencing, or whole-genome sequencing, was performed for patients with IRDs. Detailed methods of molecular genetic analysis were described previously. ^,^,^,^,^,^, Nucleotide and structural variants were called using our in-house pipelines as previously described. ^, The pathogenicity of the RPGRIP1 variants was evaluated using the Human Gene Mutation Database Professional (HGMD, http://www.hgmd.cf.ac.uk/ ), ClinVar ( https://www.ncbi.nlm.nih.gov/clinvar/ ), Genome Aggregation Database (gnomAD, https://gnomad.broadinstitute.org/ ), and the Japanese Multi Omics Reference Panel (jMorp; https://jmorp.megabank.tohoku.ac.jp/ ).

clinical examinations

Comprehensive ophthalmic examinations were performed, including a detailed medical history review (such as age at onset and chief complaint), measurement of decimal best-corrected visual acuity (BCVA), fundus photography, and fundus autofluorescence imaging (FAF) using the Spectralis HRA (Heidelberg Engineering) and/or the ultrawidefield retinal imaging system Optos 200Tx/California (Optos). Spectral-domain optical coherence tomography (OCT) was conducted using one or more of the following devices: Cirrus HD-OCT (Carl Zeiss Meditec AG), RS-3000 Advance (Nidek), Spectralis OCT (Heidelberg Engineering), or swept-source OCT (DRI OCT-1, Topcon Corporation). Full-field electroretinography (ERG) was recorded with a Ganzfeld dome using the Neuropack 2 system (Nihon Kohden) or a light-emitting diode built-in electrode (LE-4000, Tomey). ERG recordings followed the standardized protocols of the International Society for Clinical Electrophysiology of Vision. Detailed procedures and recording conditions have been described in previous studies. ^,^,

In the present study, the following two aspects were clarified. First, genotype–phenotype correlations were evaluated; clinical phenotypes (LCA or ACHM) were determined based on a combination of medical history (including symptoms such as poor visual acuity, nystagmus, and photophobia, and/or night blindness from birth or early infancy), longitudinal changes in BCVA, multimodal retinal imaging findings, and ERG results. Second, the progression of clinical findings in each phenotype was assessed; ophthalmic examinations, including BCVA, multimodal retinal imaging, and ERG results, were analyzed at first and last examinations. In addition, OCT analysis was specifically performed in patients with ACHM. The correlation between central retinal thickness (CRT) at the fovea and patient age at the time of examination was investigated in patients with ACHM whose OCT data were available. Eyes with ocular conditions that could affect CRT measurements, such as significant refractive errors (hyperopia >+2.0 diopters or myopia <−6.0 diopters), glaucoma, or the presence of an epiretinal membrane, were excluded from the analysis. Additionally, eyes in which CRT could not be reliably measured at the foveal center were also excluded. CRT was defined as the distance from the inner limiting membrane to the inner border of the retinal pigment epithelium (RPE). All measurements were manually performed by the first author (K.M.) and independently verified by the corresponding author (T.H.) to ensure consistency.

statistical analysis

All statistical analyses were performed using R (version 4.4.2; R Foundation for Statistical Computing) and RStudio ( http://www.r-project.org ). Spearman’s rank-order correlation was used to identify the significance of the correlation between CRT and patient age at the time of examination. The Mann–Whitney U test was applied to determine the significant differences in the age at onset and BCVA at the first and last examinations between the two phenotypes. Furthermore, we used a linear mixed-effects model (random intercept model) to estimate the longitudinal changes of BCVA between the two phenotypes. The linear mixed-effects model was specified as follows: objective variable (the difference in BCVA at the first and last examinations), fixed effects (phenotype, age at last examination, disease duration), and random effect (patients). For statistical analyses, decimal BCVA values were converted to logMAR units. BCVA values of count fingers, hand motion, light perception, and no light perception were converted to 2.6, 2.7, 2.8, and 2.9 logMAR units, respectively. A P value less than.05 was considered statistically significant.

RESULTS

Our group has previously reported patients with RPGRIP1 -associated retinal dystrophy presenting with LCA or ACHM. ^, These studies demonstrated that structural variants, including exon 18-DEL, are prevalent in the Japanese population, and that retinal structure is relatively preserved as a characteristic clinical feature in each phenotype. Expanding upon these findings, the present study comprehensively evaluated genotype–phenotype correlations and disease progression in a larger cohort, including age at onset, longitudinal changes in BCVA, multimodal retinal imaging findings, and ERG data.

molecular genetic findings

A total of 34 patients, including previously reported 26 patients, ^,^,^,^, who met the inclusion criteria were examined. In total, 14 distinct RPGRIP1 variants were identified, including one novel p.Gln125Ter variant ( Figure 1 and Supplemental Table 1). These consisted of 6 stop-gain variants (p.Gln125Ter, p.Arg267Ter, p.Arg563Ter, p.Cys765Ter, p.Arg888Ter, and p.Arg1189Ter), three frameshift variants (c.871_872ins, p.Glu455LysfsTer2, and p.Arg1189GlyfsTer7), one canonical splice-site variant (c.1467 + 1G > T), and four large structural variants (exon 1-DEL, exon 1-3-DEL, exon 18-DEL, and exon 22-24-DUP). Among these, the exon 18-DEL was the most frequently observed (43/68 alleles; 63.2%).

phenotype classification

All patients in the cohort reported visual impairment that was present from birth or early infancy. No extraocular manifestations were identified in any of the patients. Based on clinical characteristics, all cases were diagnosed as nonsyndromic IRDs and were classified into two distinct phenotypes: ACHM and LCA. Twenty-three patients were diagnosed as ACHM when rod system function was relatively preserved on ERG, regardless of the patient’s age at the time of examination or abnormal fundus findings. In contrast, 11 patients were diagnosed as LCA when ERG demonstrated severe impairment in both rod and cone system functions.

Importantly, the phenotype referred to as “ACHM” throughout this manuscript is characterized by congenital, severe cone dysfunction with relatively preserved rod responses on ERG, consistent with the ERG-based definition used in prior studies of RPGRIP1 -associated retinal dystrophy. However, this phenotype differs from classical ACHM in several respects, including disease progression, visual acuity decline beyond the typical range for stationary ACHM, and macular atrophy in a subset of patients. Therefore, this phenotype may more accurately be described as an “ACHM-like” phenotype or very early-onset COD. The term “ACHM” is retained throughout this manuscript for consistency with prior literature and for clarity.

genotypes of achm and lca

The genotypes of all 34 patients from 26 families, including 23 (18 families) with ACHM and 11 (8 families) with LCA, are summarized in Figure 1 .

In the ACHM group, the homozygous exon 18-DEL was identified in 18 of the 23 patients (Patient IDs: A1, A2, A3, A4, A5, A6, A7, A8, A9, A10, A11, A12, A13, A14, A15, A16, A17, and A18). Among the remaining 5 patients, three (A19, A20, and A21) carried the exon 18-DEL in combination with another truncating variant: p.Arg888Ter (exon 18), exon 22-24-DUP, or c.1467 + 1G > T (intron 11). The other two patients (A22 and A23) had a homozygous truncating variant, p.Cys765Ter in exon 16.

In contrast, a more diverse spectrum of variants was identified among the patients with LCA. Five of the 11 patients (L1, L2, L3, L4, and L9) had biallelic truncating variants located near the 5′ or 3′ ends of the RPGRIP1 gene, including exon 1-DEL, p.Arg1189GlyfsTer7 (exon 23), p.Arg1189Ter (exon 23), and exon 22-24-DUP. Four patients (L5, L6, L7, and L8) carried the exon 18-DEL in combination with another truncating variant, such as exon 1-DEL, exon 1-3-DEL, or p.Gln125Ter (exon 4), located near the 5′ end of the gene. The remaining 2 patients (L10 and L11) had biallelic truncating variants in compound heterozygous states: p.Arg267Ter (exon 6)/p.Arg563Ter (exon 13) and c.871_872ins (exon 7)/p.Glu455LysfsTer2 (exon 12), both located more centrally within the gene.

clinical findings

Detailed clinical findings, including age at onset, visual acuity measurements, multimodal retinal imaging, and electroretinographic findings, are presented in Figures 2 to 5 , Supplemental Figures 1 to 4, and Supplemental Table 1.

age at onset and visual acuity findings

All patients exhibited visual symptoms from birth or early infancy. There was no significant difference in the age at onset between patients with LCA (0.36 years; range, 0-3 years) and ACHM (1.05 years; range, 0-6 years) ( P =.279). In terms of visual acuity, patients with LCA exhibited significantly worse mean logMAR BCVA compared to those with ACHM at the time of the first examination ( Figure 2 , A). For the right eye, the mean logMAR BCVA was 0.96 (approximately 20/180) in ACHM patients and 2.02 (approximately 20/2000) in LCA patients ( P <.001). Similarly, for the left eye, the mean logMAR BCVA was 1.05 (approximately 20/220) in ACHM patients and 2.06 (approximately 20/2300) in LCA patients ( P <.001). At the last examination, these differences remained significant ( Figure 2 , A). For the right eye, the mean logMAR BCVA was 1.05 (approximately 20/220) in ACHM patients and 2.05 (approximately 20/2200) in LCA patients ( P <.001). For the left eye, the mean logMAR BCVA was 1.08 (approximately 20/240) in ACHM patients and 2.15 (approximately 20/2800) in LCA patients ( P <.001). According to the linear mixed-effects model, the change in visual acuity over the course of the disease (from the first to last examination) showed no significant difference between the two phenotypes (adjusted mean difference, 0.013, 95% CI, −0.267 to 0.293, P =.927). Notably, patients with LCA consistently exhibited poorer BCVA (logMAR > 1.0) than those with ACHM throughout the observation period ( Figure 2 , B).

multimodal retinal imaging

Patients with ACHM

In 17 younger patients (A1, A2, A3, A5, A6, A7, A9, A10, A11, A12, A13, A15, A16, A17, A18, A20, and A21), fundus photography and FAF findings revealed a normal appearance, while OCT consistently showed an indistinct ellipsoid zone (EZ) in all patients ( Figure 3 and Supplemental Figure 1). In 6 patients (A4, A8, A14, A19, A22, and A23) aged 37 years or older, retinal degeneration became more pronounced and exhibited various patterns: minimal or inconspicuous retinal degeneration (A8), retinal degeneration or atrophy confined to the macula with hypo-autofluorescence (AF) (A14) and ring-shaped hyper-AF (A19) on FAF findings (A14 and A19), retinal degeneration extending to the posterior pole (beyond the arcade vessels and optic disc) corresponding to a hypo-AF area (A4), and retinal degeneration restricted to the pericentral retina with hypo-AF at retinal degeneration area and hypo-AF at macula (A22 and A23). OCT findings indicated that disruption of the EZ was observed in patients with macular degeneration or atrophy (A4, A14, and A19) ( Figure 3 and Supplemental Figure 1). In contrast, an indistinct EZ was noted in patients with retinal degeneration restricted to the pericentral retina (A8 and A23) (Supplemental Figure 1). Furthermore, the CRT at the fovea was measured in 21 patients with ACHM (A1, A2, A3, A4, A5, A6, A7, A8, A9, A10, A11, A12, A13, A14, A15, A16, A17, A18, A19, A20, and A21) (Supplemental Figure 1). Among these, 17 patients showed no signs of retinal degeneration, while 4 patients (A4, A8, A14, and A19) exhibited retinal degeneration. The mean age at the time of examinations was 28.58 ± 18.65 (range, 4-68 years). A significant negative correlation was observed between age at the time of examination and the CRT ( r = −0.570, P <.001, Spearman’s rank-order correlation) ( Figure 5 ).

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Tags: American Journal of Ophthalmology Volume 288

Sep 20, 2026 | Posted by drzezo in OPHTHALMOLOGY | Comments Off

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