Unraveling RP1-Associated Retinal Dystrophies: Comprehensive Genetic, Clinical, and Disease Progression Analysis in China

Abstract

Purpose

To characterize the clinical manifestations, genetic landscape, and natural history of RP1-associated retinopathy in a Chinese cohort.

Methods

This longitudinal cohort study enrolled and followed 49 patients with genetically confirmed RP1-associated retinopathy. Phenotyping included visual acuity (VA), visual field, full-field stimulus testing (FST), microperimetry, and multimodal imaging. Genetic analysis and variant interpretation followed American College of Medical Genetics and Genomics and Association for Molecular Pathology guidelines.

Results

The cohort predominantly presented with retinitis pigmentosa (RP, 91.8%) and bilateral involvement, with overall no significant interocular differences in major functional parameters (all P > 0.05). Median symptom onset age was 20 years (interquartile range, 7.25–33.75). On linear regression analysis, earlier onset age (P = 0.024) and longer disease duration (P = 0.019) correlated with worse VA. Kaplan–Meier analysis estimated that the median age at which patients reached blindness (>1.3 logarithm of the minimum angle of resolution [logMAR]) was 74 years. Quantified decline rates included VA (0.015 logMAR/year) and visual field index (−7.8%/year) in the first decade and FST (0.167 log cd·s/m²/year) and retinal sensitivity (−1.22 dB/year) over two decades. Classic bone-spicule pigmentation was absent in 33.3% of patients. Genetic analysis identified 46 variants; truncating mutations (71.7%) clustered in exon 4, with c.5797C>T as a founder variant (16.3% of alleles). Variants within the upstream one-third of exon 4 were associated with later onset (P = 0.049).

Conclusions

RP1-associated retinopathy manifests as bilateral, atypical RP with quantifiable, duration-dependent decline and a genotype–phenotype correlation linking upstream exon 4 variants to later onset.

Translational Relevance

Quantified progression rates and genotype–phenotype correlations inform clinical trial endpoints and patient counseling.

Introduction

Retinitis pigmentosa (RP) is a genetically heterogeneous disorder, with pathogenic variants in RP1 (OMIM: 603937) accounting for approximately 4% of cases in a reported Chinese cohort.¹ In autosomal dominant RP, RP1 is a major causative gene, accounting for approximately 4% to 8% of cases.^2–5 Located at 8q11.23-q12.1, RP1 encodes a doublecortin family protein that is critical for maintaining the stability and length of the photoreceptor axoneme, thereby ensuring the proper stacking of outer segment discs.^6,7 Mutations in this gene are associated with a spectrum of inherited retinal diseases, including retinitis pigmentosa type 1⁸ (RP1), cone-rod dystrophy (CRD),⁹ macular dystrophy,¹⁰ and Leber congenital amaurosis,¹¹ with the specific phenotype (https://monarchinitiative.org/HGNC:10263?associations=biolink:GeneToPhenotypicFeatureAssociation) likely influenced by the type of mutation and residual protein function.¹⁰

ClinVar (http://www.ncbi.nlm.nih.gov/clinvar, as of September 1, 2025) documents over 390 pathogenic or likely pathogenic variants in RP1, with recurrent mutations such as Arg677X and 2280del4 being well documented (http://www.sph.uth.tmc.edu/RetNet/). The genetic architecture reveals distinct patterns¹²: dominant RP1 mutations are predominantly located in exon 4 and often exert a dominant-negative effect,¹³ whereas recessive RP1 mutations are distributed differently¹⁰ and are associated with earlier onset¹⁴ and a more severe disease course.¹⁵

Despite significant progress in genotyping, the natural history and phenotypic characteristics of RP1-associated retinopathy remain inadequately defined, particularly in large cohorts and specific ethnic populations.^16,17 This gap in knowledge impedes prognosis counseling, clinical trial design, and the development of targeted therapies. Therefore, the present study aims to characterize the genetic landscape and detailed clinical course of RP1-related retinal degeneration in a large Chinese cohort to address this unmet need.

Materials and Methods

Participant Selection and Clinical Evaluation

This study was conducted in accordance with the tenets of the Declaration of Helsinki and approved by the Institutional Review Board of the Eye, Ear, Nose and Throat Hospital of Fudan University. Informed consent was obtained from all participants. An initial screening of the hospital's genetic database identified all participants with confirmed RP1 variants. From this cohort, 49 patients with a clinical diagnosis of RP1-associated retinal atrophy were recruited. Retrospective data were extracted from electronic health records, and a standardized prospective follow-up examination protocol was subsequently implemented for all available participants.

The clinical diagnosis was established by a senior geneticist based on comprehensive evaluations incorporating presenting symptoms, clinical history, ocular examination, and disease progression, in alignment with established international guidelines. Specific diagnostic criteria for RP, macular dystrophy, CRD, and atypical or segmental forms of RP were applied as previously described.^10,18,19 Disease staging of RP was based on a composite assessment of clinical manifestations.²⁰ Patients were classified into two subgroups based on their inheritance: autosomal recessive (AR) variants and autosomal dominant (AD) variants.

Ocular Examination Protocol

A standardized ophthalmic phenotyping protocol was prospectively performed in all available participants, comprising the following assessments. All collected clinical parameters were systematically classified into predefined categories for analysis (e.g., visual impairment per World Health Organization International Classification of Diseases, 11th Revision criteria, as detailed in Supplementary File S1).

Vision-related quality of life (VRQoL) was assessed using the National Eye Institute Visual Function Questionnaire–25 (NEI-VFQ-25).^21,22 Best-corrected visual acuity (BCVA) was assessed using a decimal chart and converted to the logarithm of the minimum angle of resolution (logMAR) unit for analysis.²³ Static perimetry (Humphrey Field Analyzer 30-2; Carl Zeiss Meditec, Jena, Germany) yielded the visual field index (VFI), mean deviation (MD), and pattern standard deviation (PSD). Kinetic perimetry (Goldmann Manual Perimeter; Haag-Streit, Bern, Switzerland) was quantified by the sum of degrees of the V4e isopter.²⁴

Full-field stimulus testing (FST; Espion V6; Diagnosys LLC, Lowell, MA, USA) was performed after 45 minutes of dark adaptation, reporting thresholds in log cd⋅s/m².²⁵ Microperimetry²⁶ (MP-3; NIDEK, Gamagori, Aichi, Japan) measured retinal sensitivity (dB) across the central 10°. A control group of 15 age-matched healthy individuals was enrolled to establish normative baseline values for FST and microperimetry. Full-field electroretinography (ffERG; Espion ffERG; Diagnosys LLC) adhered to the ISCEV standard protocol (www.iscev.org/standards).

Spectral-domain optical coherence tomography (OCT; Spectralis OCT; Heidelberg Engineering, Heidelberg, Germany) was employed to evaluate macular morphology, including quantitative assessment of ellipsoid zone width (EZW) and detection of pathologic features such as cystoid macular edema and epiretinal membrane.^27–29 Widefield fundus imaging and autofluorescence (CLARUS 500, single 133° field; Carl Zeiss Meditec) were acquired for panoramic retinal assessment.^30–35

Genetic Analysis

Genetic testing was performed on genomic DNA extracted from peripheral blood. Putative pathogenic variants in RP1 were identified using either whole-exome sequencing or targeted Sanger sequencing. For next-generation sequencing, libraries were prepared using KAPA HyperExome (Roche, Pleasanton, CA, USA) probes for exome capture, followed by sequencing on an MGISEQ-2000 platform. A mean coverage depth of >180× was achieved, with >95% of target regions covered at ≥20×.

Bioinformatic processing included alignment to the GRCh37 (hg19) reference genome using BWA, variant calling with GATK HaplotypeCaller, and copy number variant (CNV) detection using ExomeDepth. Identified variants were annotated and filtered against population frequency databases (gnomAD, 1000 Genomes, dbSNP) and disease-specific databases (ClinVar, HGMD, OMIM). Pathogenicity was assessed in accordance with the joint American College of Medical Genetics and Genomics and Association for Molecular Pathology (ACMG/AMP) guidelines. All reported variants were validated by Sanger sequencing.

Statistical Analysis

Statistical analyses were performed using SPSS software (version 26.0; SPSS, Chicago, IL, USA). Statistical significance was set at P < 0.05. Descriptive statistics are presented as medians and interquartile ranges (IQRs). Group comparisons (e.g., interocular symmetry, patient vs. controls, and AD vs. AR subgroups) were performed using the Mann–Whitney U test. Correlations between continuous variables were assessed using Spearman's rank correlation coefficient. Univariate linear regression analyses were performed to evaluate the associations of functional parameters (visual acuity and visual field) with both demographic factors (age at onset, disease duration, and current age) and structural parameters. For time-to-event endpoints, Kaplan–Meier survival analysis estimated the median age at which patients reached visual impairment or blindness, with subgroup comparisons performed using the log-rank test. For ffERG parameters, amplitudes were log-transformed to correct for positive skewness before analysis.

Results

Cohort Demographics

The baseline cohort comprised 49 patients from 45 unrelated families, including eight individuals from multiplex families (pedigrees in Supplementary File S2). The cohort consisted of 29 men and 20 women, with a median age of 43 years (IQR, 35–47). The cohort had a median disease duration of 20 years (IQR, 8.25–30.75) and median age at symptom onset was 20 years (IQR, 7.25–33.75). A positive family history was reported in 53.1% (26/49) of patients, and consanguinity was documented in 6.7% (3/45) of families.

While patients originated from multiple regions across China, most were from East China (33/49, 67.3%), followed by Central China (8/49, 16.3%), Southwest China (4/49, 8.2%), North China (3/49, 6.1%), and Northwest China (1/49, 2.0%). No patients were registered from Northeast China or South China in this cohort.

Of these, 11 patients (22.4%) carried biallelic variants consistent with AR inheritance, while 38 patients (77.6%) carried monoallelic variants consistent with AD inheritance. When stratified by inheritance, the recessive subgroup showed a trend toward earlier onset (median 16 years; IQR, 6–29) compared with the dominant subgroup (median 23 years; IQR, 10–34.5); however, the difference did not reach statistical significance (P = 0.308).

Clinical Overview

RP was the predominant clinical diagnosis (91.8%, 45/49), while macular dystrophy and cone-rod dystrophy were observed in 3 patients and 1 patient, respectively. Common concomitant phenotypes included high myopia (63.3%, 31/49) and epiretinal membrane (44.9%, 22/49). Comprehensive cohort characteristics and detailed parameter classifications are provided in Supplementary Files S3 and S4.

No unilateral cases were observed. A key finding was the high degree of interocular symmetry (Supplementary File S5). No statistically significant interocular differences were observed in any of the measured functional or psychophysical parameters: BCVA (mean Δ = 0.17 logMAR, P = 0.452), MD (mean Δ = 0.60 dB, P = 0.209), retinal sensitivity (RS; mean Δ = 0.65 dB, P = 0.657), or FST (mean Δ = 0.34 log cd·s/m², P = 0.94). Figure 1 illustrates representative clinical phenotypes of RP1-associated retinopathy in our cohort. Longitudinal data on visual function progression are presented in Figures 2A–D.

Figure 1.

Clinical phenotypes in RP1-associated retinal dystrophy. Images from left to right include widefield fundus imaging, fundus autofluorescence (FAF), microperimetry (RS, dB), macular optical coherence tomography (OCT), and visual field pattern deviation (MD, dB) for patients with RP1-associated retinal dystrophy. (A) Macular dystrophy: patient 3 (man, aged 31–50 years) with a homozygous RefSeq NM_006269.2:c.5797C>T (p.Arg1933Ter) mutation, referred to as the Arg1933* mutation; high myopia (−10.75 D); and a 5- to 10-year history of progressive vision loss. BCVA: 1.3 logMAR; severe attenuation in the outer retinal layer on OCT; hypofluorescence with a ring of hyperautofluorescence in FAF; RS: 15.4 dB; MD: −5.69 dB. (B) Segmental RP: patient 20 (woman, aged 31–50 years) with a heterozygous Arg1933* mutation and a positive family history. Asymptomatic, but visual field defects were detected during routine examinations. BCVA: 0 logMAR; normal fundus without pigment deposition; absent ellipsoid zone in the superior temporal retina but intact in the macula; localized visual field defects and RS reduction in the superior temporal retina. (C) Nonpigmented RP: patient 19 (man, aged 31–50 years) with a heterozygous Arg1933* mutation, night blindness (5–10 years), and a positive family history. BCVA: 0.2 logMAR; no retinal pigmentation; ring of hyperautofluorescence in FAF; residual ellipsoid zone in the macula and diffuse retinal atrophy on OCT; MD: −32.26 dB; RS: 2.4 dB. (D) Minimal-pigmented RP: patient 9 (man, aged ≥51 years) with a heterozygous RefSeq NM_006269.2:c.1997C>A (p.Ser666Ter) mutation, night blindness (21–40 years). BCVA: 0.1 logMAR; mild periphery retina pigmentation; ring of hyperautofluorescence in FAF; residual ellipsoid zone in macula and diffuse retinal atrophy on OCT; MD: −31.05 dB; RS: 3.1 dB.

Figure 2.

Longitudinal decline of visual function in RP1-associated retinopathy. (A–D) Longitudinal changes in four visual function parameters over the disease course. The disease course was classified into the following ranges: ≤10 years, 11 to 20 years, 21 to 40 years, and ≥41 years. Data are presented as median with IQR. Asterisks indicate significant differences between consecutive disease course groups (≤10 years vs. baseline; 11–20 years vs. ≤10 years; etc.), as determined by post hoc pairwise comparisons (*P < 0.05; **P < 0.01; ***P < 0.001). (A) Visual acuity over the disease course (n = 49 patients). A gradual decline of 0.015 logMAR/year was observed during the first decade postonset, with a more rapid deterioration of 0.04 logMAR/year occurring in the second decade, after which visual acuity remained relatively stable for the following 20 years, with a subsequent decline beyond this phase. (B) VFI over the disease course (n = 49 patients). A rapid decline of 7.8%/year occurred during the first decade, followed by a slower decline of 1.7%/year in the second decade, with minimal change observed thereafter. (C) FST over the disease course (n = 29 patients). For each parameter, data were stratified by stimulus color (white, blue, and red) to illustrate the differential rate of decline. Data are presented as the amount of decline relative to normal threshold values. FST with a white stimulus declined rapidly during the second decade postonset (0.26 log cd·s/m²/year), more slowly during the first decade (0.074 log cd·s/m²/year), and continued at a slower rate between 20 and 40 years of disease course (0.04 log cd·s/m²/year). (D) RS on microperimetry over the disease course (n = 28 patients). RS showed a faster decline in the first two decades postonset, with a reduction rate of 1.22 dB/year, followed by a significantly slower decline in subsequent stages. (E, F) Survival analyses for visual function endpoints in RP1-associated retinopathy, stratified by inheritance mode (AR and AD). (E) Survival curves for visual impairment (BCVA >0.3 logMAR) and blindness (BCVA >1.3 logMAR) are shown. Survival analysis revealed a consistent temporal dissociation in visual decline: the median age of visual impairment onset (56 years) significantly preceded that of blindness (74 years) in the overall RP1 cohort, corresponding to a median disease duration of 25 versus 44 years between these endpoints (P < 0.001, log-rank test). For visual acuity endpoints, AR patients reached both visual impairment and blindness at significantly earlier ages compared with AD patients (P < 0.0001, log-rank test), indicating a more rapid decline of central vision in AR patients. (F) Survival curve for severe visual field loss, defined as MD ≤−12.01 dB, in RP1 patients (n = 49). The median survival age for severe visual field loss in the overall RP1 cohort was 48 years. When stratified by inheritance mode, the survival curves for severe visual field loss showed no significant difference between AR and AD subgroups (P = 0.7122, log-rank test).

Visual Acuity and Refractive Outcomes

Refractive error was common in this cohort, affecting 83.7% of eyes (82/98). Astigmatism was particularly frequent, observed in 70.2% of eyes (59/84), with moderate to severe astigmatism (≤–1.00 D) predominating. Significant changes in refractive status were observed in 12 of 17 participants with longitudinal data.

VRQoL, assessed by the NEI-VFQ-25 in 31 patients, was generally preserved; most (28/31, 90.3%) reported good or moderate scores. Furthermore, VRQoL composite scores showed a strong positive correlation with better visual acuity (r = –0.64, P < 0.001) and better visual field index (r = 0.57, P = 0.001).

Visual acuity data were available for all 49 patients, with longitudinal follow-up in 24 individuals. When analyzed as continuous variables, earlier age at onset (P = 0.024) and longer disease duration (P = 0.018) were significantly associated with worse visual acuity, whereas current age showed no such correlation (P > 0.05). No significant decline in visual acuity was detected during follow-up in the longitudinal subgroup (P > 0.05).

Survival analysis (Fig. 2E) revealed a consistent temporal dissociation in visual decline: the median age of visual impairment onset (56 years, BCVA >0.3 logMAR) significantly preceded that of blindness (74 years, BCVA >1.3 logMAR). For visual acuity endpoints, AR patients reached both visual impairment (BCVA >0.3 logMAR) and blindness (BCVA >1.3 logMAR) at significantly earlier ages compared with AD patients (P < 0.0001, log-rank test), indicating a more rapid decline in central vision in recessive cases.

At the final visit (median age 43 years), most eyes (74.5%, 73/98) maintained visual acuity of 0.9 logMAR or better, reflecting a notable overall preservation of central vision. For descriptive purposes, patients who were categorized as having advanced disease based on clinical staging (n = 41) had a median visual acuity of 0.4 logMAR (IQR, 0.1–0.6). Even among those with disease duration exceeding 40 years (n = 6) or age 50 years or older (n = 18), median BCVA remained relatively preserved at 0.85 logMAR (IQR, 0.53–1.78) and 0.5 logMAR (IQR, 0.3–1.1), respectively. Notably, one patient with macular dystrophy (patient 3) experienced a vision decline of 0.6 logMAR over 6 years, accompanied by a reduction of 3.89 dB of MD and an expansion of 1.28 mm of the macular atrophy area.

Visual Field Assessment

Static perimetry was performed in 34 patients (68 eyes). The patterns of visual field loss were heterogeneous, including central visual field loss, peripheral constriction, generalized depression, and localized defects. Cross-sectional analysis revealed no significant correlation between the severity of visual field loss (as measured by MD) and age at disease onset, disease duration, or current age (P > 0.05 for all). Survival analysis (Fig. 2F) for severe visual field loss in RP1 patients, defined as MD ≤−12.01 dB, showed a median survival age of 48 years. For visual field endpoints, however, no significant difference was observed between the AR and AD subgroups (P = 0.7122, log-rank test).

Most eyes (57/68, 83.8%) presented with severe visual field defects (defined as MD <−20 dB). These severe defects were associated with a median logMAR BCVA of 0.4 (IQR, 0.1–0.7), a median disease duration of 20 years (IQR, 9–25), and a median patient age of 31 years (IQR, 25–37). In contrast, moderate defects (patients 3, 5, and 20) were less common and typically manifested as central visual field loss in patients with macular dystrophy (two eyes from one patient) or localized defects in atypical RP (four eyes from two patients).

Longitudinal data were available for 19 patients over a median follow-up of 4 years (IQR, 2–6). A significant progression of visual field loss was observed, with the MD deteriorating at a rate of −0.82 dB/year (P = 0.003). In contrast, neither the VFI nor the PSD showed significant change over time (P > 0.05). A subgroup of seven patients from this cohort also exhibited a concurrent, significant decline in BCVA at a rate of 0.10 logMAR/year.

Visual Function Assessment

FST thresholds were measured using white, blue (rod-mediated), and red (cone-mediated) stimuli. FST thresholds for white, blue, and red stimuli were significantly higher (worse) in RP1 patients (n = 58 eyes) compared with healthy participants (n = 30 eyes) (all P < 0.001, Mann–Whitney U test). Blue-light thresholds showed a higher median elevation (2.77 log cd·s/m²; IQR, 0.96–3.99) compared with red-light thresholds (1.82 log cd·s/m²; IQR, 1.17–2.36). However, this difference did not reach statistical significance (P = 0.098, Wilcoxon signed-rank test), likely due to the limited sample size. Correlations between FST and other clinical parameters are detailed in Supplementary File S6. Similar stage-dependent patterns were observed across white, blue, and red stimuli: significant elevations were seen only in the late stage for all three stimuli (each P < 0.001), whereas no significant differences were detected in the early or middle stages for any of the three stimuli (all P > 0.05).

The median RS was 21 dB lower in patients than in healthy participants. Adult patients exhibited a median RS of 6.2 dB (IQR, 3.8–11.75; n = 15), which was higher than that of elderly patients (median, 2.7 dB; IQR, 2.3–14.6; n = 9). A significant negative correlation was observed between RS and disease duration (r = −0.525, P = 0.004; n = 28), indicating that shorter disease duration was associated with greater preserved sensitivity. Further correlation analyses are presented in Supplementary File S7.

In this cohort of 44 participants (56 electroretinography [ERG] assessments), severe generalized retinal dysfunction was consistently observed. Scotopic (rod) ERG responses were extinguished in 35 cases (79.55%), with residual activity detected in only 9 (20.45%). Photopic (cone) ERG responses were similarly affected, with 88.64% (n = 39) extinguished and minimal residual activity in merely 11.36% (n = 5). Regression analysis established that visual field loss (quantified by VFI) significantly predicted reductions in most ffERG parameters (P < 0.0001). Longitudinal follow-up in a subset of 12 patients (median 6 years; IQR, 4.75–6.5) revealed progressive deterioration of scotopic and photopic responses, accompanied by a trend toward a pronounced prolongation in the Photopic 3.0 Flicker 30 Hz ERG implicit time (P = 0.055).

Ophthalmic Imaging Findings

Longitudinal macular OCT data were available for 24 patients over a median follow-up of 5 years (IQR, 2–6). Progressive structural degeneration, manifested as a significant reduction in the EZW or an expansion of the area of retinal atrophy, was observed in five patients (20.8%), who represented the entire subset of the cohort meeting our predefined progression criteria (EZW reduction ≥50 µm) (Fig. 3). No other patients showed such progression. One patient (4.2%) developed new-onset cystoid macular edema during the follow-up period.

Figure 3.

Longitudinal progression in patients showing significant changes on macular OCT during follow-up. This figure presents longitudinal OCT images of the entire subset of five patients (20.8% of the cohort) with RP1-associated retinal dystrophy who met our predefined criterion for significant structural progression on macular OCT (EZW reduction ≥50 µm); no other patients in the cohort showed such progression. Patient has a macular dystrophy phenotype, while patients 7, 8, 9, and 19 have an RP phenotype. Over a follow-up period ranging from 5 to 9 years, an increase in the macular dystrophy area was observed in patient 3, while a reduction in the preserved ellipsoid zone in the macular area was observed in patients 7, 8, 9, and 19. Each row corresponds to different patients, labeled with patient number (No.), age (years), visual acuity (logMAR), and disease progression rate (mm/year). The scale bar indicates 200 µm. The green line indicates the measured width in millimeters. These five cases represent the complete progressor subgroup.

Widefield imaging identified a spectrum of characteristic peripheral patterning in RP1-related retinopathy, manifesting as variable severity of bone spicule pigmentation, ranging from minimal to moderate deposits (Fig. 4). When comparing patients with minimal or absent pigment deposition (31/45, 68.89%) to those with moderate to marked pigment deposition (14/45, 31.11%), the two groups were comparable in terms of age at examination (median 42 vs. 45 years, respectively; P = 0.791). However, patients with moderate to marked pigment deposition had a significantly longer disease duration (median 26 vs. 13 years; P = 0.006, Mann–Whitney U test) and significantly worse visual acuity (median 0.5 vs. 0.2 logMAR; P = 0.018, Mann–Whitney U test). For pigment deposition patterns, the distribution of minimal/absent versus moderate/marked pigmentation did not differ significantly between AR and AD subgroups (Fisher's exact test, P = 0.672). We also identified three cases presenting with a rare segmental or sectoral RP phenotype, as illustrated in Supplementary File S8. However, in the subset of patients with available longitudinal widefield fundus imaging data (n = 2), no significant progressive increase in peripheral retinal pigmentation was documented.

Figure 4.

Widefield fundus imaging characteristics in patients with RP1-associated retinal dystrophy. This figure presents the widefield fundus imaging findings observed in the cohort with RP1 variants, alongside key visual function parameters. The images and data illustrate the severity and varying patterns of retinal pigment deposition. VA, visual acuity (logMAR); VFI, visual field index (%); MD, mean deviation (dB); PSD, pattern standard deviation (dB); sum degree (°). The VFI reflects overall health status of the visual field, while the MD and PSD indicate the extent of visual field impairment. A higher sum degree indicates a larger visual field. (A) Absence of retinal pigment and ring of hyperautofluorescence. (B) Minimal retinal pigment deposition in the peripheral retina and ring of hyperautofluorescence. (C) Minimal retinal pigment deposition in the mid-peripheral retina and patchy hyperautofluorescence. (D) Moderate retinal pigment deposition in the peripheral retina and diffuse hypoautofluorescence. (E) Minimal retinal pigment deposition and irregular autofluorescence in one quadrant of the retina. (F) Diffuse retinal pigment deposition in the whole retina and a ring of hyperautofluorescence.

Genetic Landscape and Genotype–Phenotype Correlations

Comprehensive molecular analysis of the RP1 locus in our cohort identified 46 distinct variants, with their spectrum and distribution detailed in Figure 5. A significant mutational hotspot was observed, with 76.1% (35/46) of variants clustering within exon 4. Notably, half of these (23/46, 50% of all variants) were further concentrated within the exon 4 hotspot located in the upstream one-third of the exon, suggesting this region is particularly susceptible to mutational events. Twenty-four variants (52.2%) were novel, not previously reported in public databases (comprehensive details are provided in Supplementary File S9).

Figure 5.

Genetic profile of RP1 variants. RP1, which consists of four exons and encodes 2156 amino acids, is illustrated here. Different types of mutations are represented by various colored fonts, indicating changes in protein structure: missense mutations are highlighted in red, frameshift mutations in yellow, nonsense mutations in green, and splice acceptor mutations in blue. Variants of uncertain significance and likely benign variants are listed below the gene, while pathogenic and likely pathogenic mutations are listed above the gene. "#" denotes reported mutations. Gene segments encoding the doublecortin (DCX) domain (amino acids 36–114 and 154–229) are shown in red; segments encoding the polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain (amino acids 264–381 and 392–510) are shown in green; and segments encoding the fibroblast growth factor (FGF) domain (amino acids 544–578) are shown in blue.

Striking genotype–phenotype correlations were observed. All six variants associated with macular dystrophy or CRD were mainly located within the exon 4 cluster (5/6). Furthermore, variant position within exon 4 was a significant predictor of clinical severity. Variants within the exon 4 hotspot located in the upstream one-third of the exon were significantly associated with later symptom onset (median age >20 years; 15/23 patients). In contrast, variants outside this subregion conferred a more severe, early-onset disease course (median age <20 years; 15/26 patients; P = 0.049, Fisher's exact test).

The most frequent variant was the nonsense mutation c.5797C>T (p.Arg1933*), which was recurrently identified in eight probands from six unrelated families. This variant exhibited considerable pleiotropy, manifesting as typical RP, segmental RP, or macular dystrophy, both within and across families.

In accordance with ACMG/AMP guidelines, most variants were classified as pathogenic (11/46) or likely pathogenic (22/46). Fifteen of the novel variants met these stringent criteria. Variants were categorized based on their predicted impact. Nonsense variants were the most prevalent type, accounting for 41.3% (19/46) of all alterations. At the molecular level, most variants (31/46, 67.4%) were single-nucleotide substitutions. The spectrum of observed genotypes was predominantly heterozygous (77.6%, 38/49), with compound heterozygous (18.4%, 9/49) and homozygous (4.1%, 2/49; patients 3 and 6) genotypes observed in the remainder.

Discussion

This study provides a comprehensive characterization of RP1-associated retinopathy in a Chinese cohort by quantifying functional decline rates and establishing a genotype–phenotype correlation. The median age of symptom onset was 20 years, with retinitis pigmentosa as the predominant diagnosis (91.8%). Despite early onset and progressive peripheral field loss, central vision was relatively preserved, with 74.5% of eyes maintaining BCVA ≥0.9 at a median age of 43 years. In contrast, visual field loss progressed more rapidly, with a mean VFI loss of −7.8% per year during the first decade. Genetic analysis identified 46 variants, with a notable genotype–phenotype correlation linking upstream exon 4 variants to later onset.

Survival analysis quantified the trajectory of visual acuity decline in the overall cohort: the median age at which visual impairment occurred was 56 years, whereas that for blindness was 74 years. The recessive subgroup reached both endpoints significantly earlier than the dominant subgroup, which likely reflects earlier disease onset rather than a faster rate of decline, as visual field progression and pigmentary patterns were comparable between the two subgroups. However, this finding should be interpreted with caution given the small number of recessive cases and the lack of multigenerational segregation data in some families.

Visual field loss showed a more rapid and severe trajectory than central vision decline. Most eyes (83.8%) exhibited severe defects (MD <−20 dB) at a median disease duration of 20 years, with longitudinal MD deterioration of −0.82 dB/year. FST thresholds were significantly elevated in patients versus controls for all stimuli, with significant elevations confined to the late stage, suggesting that FST may be more sensitive to advanced disease. The ffERG data revealed profound dysfunction, with scotopic responses extinguished in 79.6% and photopic responses in 88.6% of assessed patients. The preservation of flicker signals in some patients with extensive structural loss suggests that ERG may detect residual cone function even in eyes with advanced structural loss, although the substantial variability and limited longitudinal assessments preclude definitive conclusions.

Genetic analysis identified 46 distinct variants, of which 24 (52.2%) were novel, expanding the mutational spectrum of RP1.³⁶ Most clustered within exon 4 (76.1%), with half concentrated in the upstream one-third of this exon.³⁷ Variants within this upstream hotspot were significantly associated with later onset compared with variants outside this region, suggesting regional functional importance of this protein domain. The recurrent c.5797C>T (p.Arg1933*) variant exhibited marked phenotypic pleiotropy, manifesting as typical RP, segmental RP, or macular dystrophy, even among individuals sharing the same genotype, pointing to unidentified modifying factors.

Our findings are consistent with previous observations in several respects and have direct implications for patient counseling.^13,38–41 However, several clinical findings diverged from prior reports.^42,43 The absence of high myopia in our cohort contrasts with a previous suggestion linking RP1 to myopia.⁴⁴ While this discrepancy may reflect differences in cohort composition or measurement methods, it also raises the possibility that the two cohorts carry distinct mutational spectra with differential effects on axial elongation—a hypothesis requiring direct biometric investigation. Additionally, classic bone-spicule pigmentation was commonly absent or minimally present (nonpigmented: 33.3%; minimal: 35.56%), suggesting that RP1-related retinopathy may present with atypical fundus features. This atypical presentation underscores the importance of considering RP1 genetic testing in young patients with early-onset visual field constriction and relatively preserved central acuity, even in the absence of classic pigmentary retinopathy. Patients with moderate to marked pigmentation had significantly longer disease duration and worse VA than those with minimal or absent pigmentation, indicating that pigment deposition may serve as a crude marker of disease chronicity rather than a primary pathologic feature.

The quantified decline rates reported here—VA (0.015 logMAR/year), VFI (−7.8%/year), FST (0.167 log cd·s/m²/year over two decades), and retinal sensitivity (−1.22 dB/year)—provide clinically relevant benchmarks for natural history comparisons and sample size calculations in future interventional trials. The genotype–phenotype correlation linking upstream exon 4 variants to later onset may inform individualized prognostic counseling and guide genetic testing strategies. Furthermore, the predominantly nonpigmentary fundus features, together with RP1’s known role in photoreceptor axoneme stabilization, suggest that therapeutic development should prioritize photoreceptor-specific gene replacement over broader neuroprotective strategies—a distinction with direct translational relevance.

Several limitations merit consideration. First, the modest sample size and single-center design may limit the generalizability of our findings, particularly for subgroup analyses with limited statistical power. Second, the variable follow-up durations and incomplete longitudinal data across some modalities may have introduced attrition bias; our progression estimates are therefore more likely to be conservative, as patients with more severe disease tended to return for follow-up more consistently. Third, inheritance patterns were inferred from variant zygosity and family history, and multigenerational segregation data were not available for all families, leaving the possibility that some presumed dominant cases may represent recessive disease with heterozygous carriers. Despite these limitations, the consistency of our findings across multiple functional modalities supports their robustness.

Conclusions

This study provides a comprehensive characterization of RP1-associated retinopathy in a Chinese cohort. The quantified functional decline rates and the genotype–phenotype correlation identified here inform prognostic counseling and provide reference data for trial design in RP1-related disease.