PURPOSE. Inherited retinal diseases (IRDs) are a group of more than 50 clinically and genetically heterogeneous diseases caused by variants in more than 300 genes. The Israeli population is composed of multiple ethnic groups with variable prevalence of IRD-causing variants. In the current study, we analyzed IRDs in different Israeli ethnic groups to establish the genetic landscape. METHODS. Patients were recruited by five genetic centers, and eight ophthalmic centers, located throughout the country, and belonging to the Israeli inherited retinal disease consortium (IIRDC). The information regarding the cause of disease in each solved family was tabulated. For each ethnic group, we listed the causing variants and their frequencies. RESULTS. We identified a total of 1062 disease-causing variants in Israeli patients with IRDs from 20 ethnic groups (13 of which are Jewish), with a total of 4,728 familial pathogenic alleles. Founder variants contributed the largest proportion of alleles in Yemenite Jews (75%), followed by Turkish Jews (67%), and North African Jews (66%). The most common disease-causing variant was ABCA4-c.5882G>A, a pan-ethnic variant, followed by FAM161A-c.1355_1356del, a founder variant in multiple Jewish ethnic groups. By performing haplotype analysis, 21 additional founder variants were identified. We generated a searchable online database (https://www.eyes.org.il/genecal) based on this data depicting the most common variants for each ethnic group and IRD. CONCLUSIONS. Our analysis provides a comprehensive list of common and founder variants for each ethnic group in Israel and is likely to allow more accurate and informative genetic counseling for Israeli families with IRDs.

Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous group of disorders affecting millions worldwide, with limited therapeutic options for the majority of patients. Recent advances in RNA editing-particularly adenosine-to-inosine (A-to-I) editing mediated by adenosine deaminases acting on RNA (ADAR)- offer a promising approach for correcting pathogenic variants at the RNA level without altering the genome. This review presents a comprehensive overview of the molecular basis of ADAR-mediated RNA editing, its natural occurrence in retinal tissues, and the growing array of strategies that harness endogenous ADAR enzymes for site-directed RNA editing (SDRE). We discuss design principles and optimization strategies for guide RNAs (gRNAs), including linear, circular, and chemically modified formats such as LEAPER, RESTORE, CLUSTER, CadRNAs, and AIMers. Additionally, we explore high-throughput screening systems for guide selection, cellular models for assessing RNA editing efficiency, and current in vitro and in vivo approaches targeting IRD pathogenic variants. Finally, we highlight the translational potential of endogenous and exogenous ADAR-based RNA editing, emphasizing its relevance as a precision medicine strategy for IRDs and beyond.

Inherited retinal degenerations (IRDs) are a group of clinically and genetically heterogeneous blinding disorders. In this study, we describe five families clearly or which were presumed to be diagnosed with autosomal recessive non-syndromic IRD and one with mild syndromic IRD, in which affected probands carried rare bi-allelic variants in SCLT1, a gene previously associated with multiple autosomal recessive ciliopathies. Eight of the ten variants identified were novel; five variants affected splicing, including the known missense p.(Lys544Arg), detected in compound heterozygosity in three East Asian probands, and the novel, hypomorphic, deep-intronic variant c.290+2732A>G, leading to the inclusion of a 45-bp cryptic exon containing a premature termination codon. Analysis of the genomic data also revealed a large in-frame tandem duplication spanning exons 3-10, which was subsequently validated. Although no clear correlation was found between the severity of the SCLT1-associated phenotypes and the identified causal variants, this report expands the current knowledge of SCLT1-associated disease by enriching its mutational landscape and clearly supports its association with autosomal recessive non-syndromic IRD.

OBJECTIVE:To evaluate a novel image-based deep learning method for the automated identification of inherited retinal diseases (IRDs) and to explore the feasibility of predicting selected causative gene groups using a multimodal analysis of wide-field fundus autofluorescence (FAF) and pseudocolor fundus (pCF) images. DESIGN:The method was evaluated using a retrospective dataset of patient studies containing FAF and pCF images, as well as genetic tests for IRD. PARTICIPANTS:Patients with confirmed IRD for which both wide-field FAF and pCF images and genetic tests for IRD performed at Hadassah University Medical Center were included. The dataset consisted of 409 patients (330 patients with IRD with the 25 most commonly affected genes in our population and patients without IRD, and 79 patients without IRD). METHODS:Nine EfficientNet-V2-m convolutional neural networks were trained for the following three classification tasks: a binary IRD vs. non-IRD classification, and classification into two groups of five causative genes (Groups 1 and 2). For each task, three models were trained on the FAF images only, the pCF images only, and both the FAF and pCF images. The performance of the models was then evaluated and compared using 5-fold cross-validation. MAIN OUTCOME MEASURES:Accuracy, precision, F1 scores, AUC, and confusion matrices. RESULTS:The multimodal classification models that were trained on both the FAF and pCF images yielded the best results. The binary classification model had a mean (±SD) accuracy of 0.95 ± 0.01, a mean precision of 0.92 ± 0.01, and a mean F1 score of 0.90 ± 0.02. The Group 1 classification model had a mean accuracy of 0.92 ± 0.03, a mean precision of 0.93 ± 0.03, and a mean F1 score of 0.89 ± 0.03. Finally, the Group 2 classification model had a mean accuracy of 0.85 ± 0.03, a mean precision of 0.87 ± 0.04, and a mean F1 score of 0.83 ± 0.04. CONCLUSIONS:Our results indicate that determining whether a patient has IRD can be performed with high accuracy within this retrospective cohort based on FAF and pCF images using image-based deep learning classifiers. This image-based approach may assist clinicians during the patient's initial visit by providing decision support prior to genetic testing. It may also help prioritize patients for genetic workup, particularly in settings in which genetic testing is not readily available. Further prospective and external validation is required before clinical implementation.

PRCD is a ∼6 kDa protein localized to the cytosolic surface of rod and cone outer segment discs. Pathogenic variants in the PRCD gene cause autosomal recessive retinal degeneration in human patients and in over 65 dog breeds. We characterized the natural history and phenotype of PRCD-associated retinal disease in dogs and compared it with the human condition. Human patients with PRCD-associated retinitis pigmentosa, p.R22∗ variant, exhibited severe, retina-wide degeneration, abnormal electroretinograms, and constricted visual fields. However, visual acuity and foveal photoreceptor structure could be preserved into the second decade of life. In dogs, four homozygous mutants (p.Cys2Tyr variant, PRCDMis/Mis), one heterozygous, and 24 wild-type dogs were evaluated from 0.4 to 4.8 years of age using serial in-vivo imaging modalities, complemented by histological quantification, Western blotting, and immunohistochemistry. OCT revealed significant outer nuclear layer (ONL) thinning in all quadrants by 0.8 year, with the fovea-like region (FLR) spared until 2.3 years in PRCDMis/Mis dogs. The inferior retina showed the most severe thinning, with 92% loss by 4.8 years, whereas the cone-rich visual streak and FLR showed 22% loss by 4.8 years. Scotopic a-wave ffERG amplitudes were significantly reduced at all time points, while photopic responses remained stable. At early stages of disease, the preferential involvement of the inferior quadrant was confirmed by histology. Western blot and immunostaining confirmed absence of PRCD protein in mutant retinas. Together, these findings demonstrate a rod-dominant degeneration with a distinct spatial pattern and relative central preservation, closely mirroring the human phenotype.

Nonsense variants cause 18% of inherited retinal diseases (IRDs), yet current therapies require variant-specific development, leaving most patients untreated. Here, we combined a large-scale genetic analysis literature survey of >37,500 IRD patients with anticodon-edited (ACE)-tRNA engineering to create a single, gene-agnostic therapy targeting Arg>Ter nonsense variants which are the most prevalent subclass (35%) of premature stop codons (PTCs). We developed an optimized ACE-tRNA (V3) that achieved up to 86% readthrough across 13 clinically relevant variants, restored native PRCD localization in the arRP-causing p.R22* mutant, and demonstrated activity in photoreceptor-like cells. To enable translation, we established an AAV2/7m8 production platform and defined 1*10⁹ GC/eye as the safe dose in mice. This patient genetics-guided strategy positions ACE-tRNA_V3 as a promising candidate for preclinical development, offering a precision medicine approach that targets the most common nonsense variant class with a single therapeutic molecule.

Small nuclear RNAs (snRNAs) combine with specific proteins to generate small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. U4 snRNA forms a duplex with U6 and, together with U5, contributes to the tri-snRNP spliceosomal complex. Variants in RNU4-2, which encodes U4, have recently been implicated in neurodevelopmental disorders. Here we show that heterozygous inherited and de novo variants in RNU4-2 and in four RNU6 paralogs (RNU6-1, RNU6-2, RNU6-8 and RNU6-9), which encode U6, recur in individuals with nonsyndromic retinitis pigmentosa (RP), a genetic disorder causing progressive blindness. These variants cluster within the three-way junction of the U4/U6 duplex, a site that interacts with tri-snRNP splicing factors also known to cause RP (PRPF3, PRPF8, PRPF31), and seem to affect snRNP biogenesis. Based on our cohort, deleterious variants in RNU4-2 and RNU6 paralogs may explain up to ~1.4% of otherwise undiagnosed RP cases. This study highlights the contribution of noncoding RNA genes to Mendelian disease and reveals pleiotropy in RNU4-2, where distinct variants underlie neurodevelopmental disorder and retinal degeneration.

Inherited retinal diseases (IRDs) are a genetically heterogeneous group of Mendelian disorders that often lead to progressive vision loss and involve approximately 300 distinct genes. Although variants in these loci account for the majority of molecular diagnoses, other genes associated with IRD await molecular identification. In this study, we uncover bi-allelic assortments of 23 different (22 loss-of-function) variants in AP5Z1, AP5M1, and AP5B1 as independent causes of recessive IRD in members of 19 families from nine countries. Affected individuals, regardless of their genotypes, exhibit a specific form of macular degeneration, sometimes presenting in association with extraocular features. All three genes encode different subunits of the vesicular fifth adaptor protein (AP-5) complex, a component of the intracellular trafficking system involved in maintaining cellular homeostasis and ensuring the proper functioning of lysosomal pathways. The retinal pigment epithelium (RPE), a cellular monolayer located posteriorly to the neural retina, is characterized by intense lysosomal and phagocytic activity. Immunostaining of RPE cells revealed a punctate pattern of AP5Z1, AP5M1, and AP5B1 staining and co-localization with markers of late endosomes and the Golgi, suggesting a role of AP-5 in the normal physiology of this tissue. Overall, the identification of independently acting variants in three distinct proteins within the same macromolecular complex reveals AP-5 as having an important function in the preservation and maintenance of normal macular functions.

Purpose: The Foundation Fighting Blindness (FFB) Consortium is a collaboration of 41 international clinical centers that manage patients affected with inherited retinal diseases (IRDs). The annual Consortium gene poll was initiated in 2020 to capture the genetic cause of disease in patients with IRD and associated clinical practices of Consortium sites. Data from the 2022 gene poll are reported here. Methods: In 2022, academic, private practice, and government ophthalmology clinics that are members of the Consortium centers were polled to identify per-case IRD genetic causality from a list of 387 syndromic and nonsyndromic IRD genes. The survey also assessed how genetic testing was obtained and clinical practices of the sites. Results: Thirty centers responded and reported genetic data from 33,834 patients (27,561 families). Disease-causing variants were reported in 293 of 387 genes. The most common genetic etiologies were ABCA4 (17%), USH2A (9%), RPGR (6%), PRPH2 (5%), and RHO (4%). The top 100 genes accounted for the genetic cause of disease in 94.4% of patients. Two-thirds of the centers had at least one genetic counselor. In the 21 US sites, genetic testing was commonly obtained through sponsored programs (95%, FFB-My Retina Tracker Programs or Spark-ID Your IRD), whereas in the 9 non-US sites, genetic testing was commonly obtained using either patient- or public health system-funded testing pipelines. Clinical work-up of patients with IRD most commonly included updating history, eye examination, and optical coherence tomography. Conclusions: This report provides the largest assessment of genetic causality in the IRD patient population across multiple continents to date.

Background/Aaims Congenital stationary night blindness (CSNB) is an inherited retinal disease that is often associated with high myopia and can be caused by pathological variants in multiple genes, most commonly CACNA1F, NYX and TRPM1. High myopia is associated with retinal degeneration and increased risk for retinal detachment. Slowing the progression of myopia in patients with CSNB would likely be beneficial in reducing risk, but before interventions can be considered, it is important to understand the natural history of myopic progression.Methods This multicentre, retrospective study explored CSNB caused by variants in CACNA1F, NYX or TRPM1 in patients who had at least 6 measurements of their spherical equivalent of refraction (SER) before the age of 18. A mixed-effect model was used to predict progression of SER overtime and differences between genotypes were evaluated.Results 78 individuals were included in this study. All genotypes showed a significant myopic predicted SER at birth (-3.076D, -5.511D and -5.386D) for CACNA1F, NYX and TRPM1 respectively. Additionally, significant progression of myopia per year (-0.254D, -0.257D and -0.326D) was observed for all three genotypes CACNA1F, NYX and TRPM1, respectively.Conclusions Patients with CSNB tend to be myopic from an early age and progress to become more myopic with age. Patients may benefit from long-term myopia slowing treatment in the future and further studies are indicated. Additionally, CSNB should be considered in the differential diagnosis for early-onset myopia.

Inherited retinal diseases (IRDs) are rare disorders, typically presenting as Mendelian traits, that result in stationary or progressive visual impairment. They are characterized by extensive genetic heterogeneity, possibly the highest among all human genetic diseases, as well as diverse inheritance patterns. Despite advances in gene discovery, limited understanding of gene function and challenges in accurately interpreting variants continue to hinder both molecular diagnosis and genetic research in IRDs. One key problem is the absence of a comprehensive and widely accepted catalog of disease-associated genes, which would ensure consistent genetic testing and reliable molecular diagnoses. With the rapid pace of IRD gene discovery, gene catalogs require frequent validation and updates to remain clinically and scientifically useful. To address these gaps, we developed RetiGene, an expert-curated gene atlas that integrates variant data, bulk and single-cell RNA sequencing, and functional annotations. Through the integration of diverse data sources, RetiGene supports candidate gene prioritization, functional studies, and therapeutic development in IRDs.

Inherited retinal diseases (IRDs) are clinically and genetically complex disorders that cause blindness in about one in 3450 individuals worldwide. More than 350 genes have been implicated in IRDs showing all possible inheritance patterns. Despite the advancement of several genetic therapies, there is currently no cure for the vast majority of IRDs. By converting a sense codon into a nonsense codon, premature termination codon (PTC) variants cause abrupt termination of protein synthesis, leading to loss of protein function in most cases. Nonsense variants account for approximately 18 % of all disease-causing variants in IRDs, and there is currently no effective treatment available to correct them. In recent years, anticodon engineered tRNAs (ACE-tRNAs) or suppressor tRNAs have emerged as potential therapeutic option for treating rare diseases caused by nonsense variants. This review critically summarizes the spectrum of nonsense variants in the genetics of IRDs and examines the promise of ACE-tRNA therapy as a treatment. We focus on the therapy's mechanism of action, current advancements, and its specific advantages and limitations for addressing nonsense variant-induced IRDs.

The U4 small nuclear RNA (snRNA) forms a duplex with the U6 snRNA and, together with U5 and ~30 proteins, is part of the U4/U6.U5 tri-snRNP complex, located at the core of the major spliceosome. Recently, recurrent de novo variants in the U4 RNA, transcribed from the RNU4-2 gene, and in at least two other RNU genes were discovered to cause neurodevelopmental disorder. We detected inherited and de novo heterozygous variants in RNU4-2 (n.18_19insA and n.56T>C) and in four out of the five RNU6 paralogues (n.55_56insG and n.56_57insG) in 135 individuals from 62 families with non-syndromic retinitis pigmentosa (RP), a rare form of hereditary blindness. We show that these variants are recurrent among RP families and invariably cluster in close proximity within the three-way junction (between stem-I, the 5' stem-loop and stem-II) of the U4/U6 duplex, affecting its natural conformation. Interestingly, this region binds to numerous splicing factors of the tri-snRNP complex including PRPF3, PRPF8 and PRPF31, previously associated with RP as well. The U4 and U6 variants identified seem to affect snRNP biogenesis, namely the U4/U6 di-snRNP, which is an assembly intermediate of the tri-snRNP. Based on the number of positive cases observed, deleterious variants in RNU4-2 and in RNU6 paralogues could be a significant cause of isolated or dominant RP, accounting for up to 1.2% of all undiagnosed RP cases. This study highlights the role of non-coding genes in rare Mendelian disorders and uncovers pleiotropy in RNU4-2, where different variants underlie neurodevelopmental disorder and RP.

PURPOSE:Variants in untranslated genomic regions are difficult to identify as pathogenic but are capable of causing disease by interfering with gene expression. This study aimed to characterize the effect of variants identified in the 5'-untranslated region of EYS in patients with autosomal recessive retinitis pigmentosa (RP). METHODS:Variant screening included gene panels, Sanger, exome, and genome sequencing. Functional validation included an electrophoretic mobility shift assay and various luciferase assays. RESULTS:Patients with RP from 6 EYS biallelic Arab-Muslim families harbored a 5' noncoding EYS variant, c.-453G>T, and 4 harbored a structural variant affecting the 5' noncoding exons. Electrophoretic mobility shift assay analysis revealed an effect on binding of transcription factors for c.-453G>T and a neighboring variant c.-454G>T. Dual luciferase assays using overexpression of various transcription factors showed distinct effects on expression. c.-453G>T was associated with higher luciferase expression with CRX overexpression and c.-454G>C with OTX2 overexpression. In addition, the 2 variants were found to influence translation by affecting upstream initiation codons. Interestingly, visual function of EYS RP patients who harbor c.-453G>T are better than those with biallelic null EYS variants. CONCLUSION:Our analysis revealed both single-nucleotide and structural variants in the EYS promoter as the cause of autosomal recessive RP. These variants may affect EYS expression via a dual mechanism by altering transcription factor binding affinity at the EYS promoter and by affecting upstream open reading frames.

Background: Syndromic inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous group of disorders, involving the retina and additional organs. Over 80 forms of syndromic IRD have been described. Methods: We aimed to phenotypically and genotypically characterize a cohort of 171 individuals from 140 Israeli families with syndromic IRD. Ophthalmic examination included best corrected visual acuity, fundus examination, visual field testing, retinal imaging and electrophysiological evaluation. Most participants were also evaluated by specialists in fields relevant to their extra-retinal symptoms. Genetic analyses included haplotype analysis, homozygosity mapping, Sanger sequencing and next-generation sequencing. Results: In total, 51% of the families in the cohort were consanguineous. The largest ethnic group was Muslim Arabs. The most common phenotype was Usher syndrome (USH). The most common causative gene was USH2A. In 29% of the families, genetic analysis led to a revised or modified clinical diagnosis. This included confirmation of an atypical USH diagnosis for individuals with late-onset retinitis pigmentosa (RP) and/or hearing loss (HL); diagnosis of Heimler syndrome in individuals with biallelic pathogenic variants in PEX6 and an original diagnosis of USH or nonsyndromic RP; and diagnosis of a mild form of Leber congenital amaurosis with early-onset deafness (LCAEOD) in an individual with a heterozygous pathogenic variant in TUBB4B and an original diagnosis of USH. Novel genotype–phenotype correlations included biallelic pathogenic variants in KATNIP, previously associated with Joubert syndrome (JBTS), in an individual who presented with kidney disease and IRD, but no other features of JBTS. Conclusions: Syndromic IRDs are a highly heterogeneous group of disorders. The rarity of some of these syndromes on one hand, and the co-occurrence of several syndromic and nonsyndromic conditions in some individuals, on the other hand, complicates the diagnostic process. Genetic analysis is the ultimate way to obtain an accurate clinical diagnosis in these individuals.