ABSTRACT Objectives Mental wellbeing is lower in people with vision impairment (VI) but the mechanisms for this are not completely understood. Here we examined factors that limit and benefit wellbeing in children and young people with VI. Design Qualitative semi-structured interviews with children and young people with vision impairment and parents/carers of young people with VI. Interviews were recorded, transcribed and analysed by two researchers, working independently, using reflexive thematic analysis. Setting Low vision and genetic eye disease clinics in a tertiary eye hospital in London, England. Participants Young people aged 13-18 years with vision impairment (VI) caused by inherited macular disease and parents of young people with VI caused by inherited macular disease. Results Four overarching themes were developed: (1) Living in the aftermath of diagnosis , capturing participants’ internal experience of living with vision impairment from the time of diagnosis onward, including the psychological impact of negotiating the loss of vision and the challenge of accepting VI; (2) Fighting the system , reflecting how parents and CYP navigate both formal and informal support systems, highlighting the barriers they face; (3) Being seen and being misunderstood , encapsulating how VI influences the way that participants experience relationships, develop a sense of self and navigate their place within society; and (4) Building a life with vision impairment , centring on how participants function in everyday contexts whilst living with VI, alongside their aspirations for building their lives and living well in adulthood. Conclusions Vision impairment has emotional, social, and systemic consequences. Factors linking VI to reduced mental well-being included low acceptance of vision loss, low functional adaptation, reduced self-efficacy, effects of social stigma and discrimination. Strengths and limitations The study uses detailed interviews of wellbeing from two perspectives (young people and their parents/carers); Participants identified a broad range of positive and negative experiences which can be used to inform future interventions; All participants were under the care of a specialist eye clinic so they may not be fully representative of the broader population of people with vision impairment.

Purpose:To assess cross-sectional and longitudinal relationships between fundus autofluorescence (FAF) and visual acuity (VA) in ABCA4-associated Stargardt disease (STGD1). Methods:Secondary analysis used data from 301 STGD1 participants (566 study eyes) enrolled in the international ProgStar studies. The study reading center graded the FAF images qualitatively and quantitatively, including areas of atrophy reflected as definitely decreased autofluorescence (DDAF) and questionably decreased autofluorescence (QDAF). Linear models estimated cross-sectional and longitudinal associations between the growth of DDAF area and total DAF area (i.e., sum of DDAF and QDAF areas) and change in VA. Results:At the first visit, the median age was 30 years (range, 7-69); 55% were women. Mean ± SD VA was 0.73 ± 0.36 logMAR; mean total DAF area was 3.4 ± 3.8 mm2; and 42% of eyes had no DDAF. Cross-sectionally, increasing age and duration of symptoms, younger age of symptom onset, and larger QDAF area were significantly associated with worse VA (P < 0.05). Mean follow-up was 3.3 years (range, 0.5-10.3). There was no statistically significant relationship between growth of total DAF or DDAF areas and change in VA (P > 0.05). Conclusions:Characteristics other than DAF area (e.g., flecks presence) may influence VA. Some patients remained DDAF free longitudinally and thus would be excluded in STGD1 trials that use DDAF as the primary endpoint. The cross-sectional relationship between DAF and VA confirmed the association of VA with retinal pigment epithelium (RPE) structure. The lack of a significant association between growth in DAF areas with change in VA over follow-up points to challenges resulting from slow progression and large VA variability. Exploring outcome measures from other modalities is warranted for designing STGD1 trials.

Purpose To evaluate the repeatability and reproducibility of Starguage, a novel automated method compared with manual segmentation for measuring decreased autofluorescence (DAF) and definitely decreased autofluorescence (DDAF) in fundus autofluorescence (FAF) images of patients with Stargardt disease. Design Cross-sectional reproducibility and agreement study. Participants A total of 316 eyes from 158 genetically confirmed Stargardt patients were analyzed. For intra-grader repeatability, 114 FAF images were reassessed in a masked, repeated-measures design. Methods DAF and DDAF lesion areas were independently quantified by five certified graders using either manual delineation with Heidelberg RegionFinder or a threshold-based automated algorithm, with automated quantification and cross-method agreement analyses restricted to a prespecified central 6-mm fovea-centered region. Agreement and repeatability were assessed using intraclass correlation coefficients (ICC), standard error of measurement (SEM), minimal detectable change (MDC), Lin’s concordance correlation coefficient (CCC), Bland–Altman plots, and Passing–Bablok regression. Both raw and square-root-transformed lesion areas were evaluated. Main Outcome Measures Repeatability (intra-grader ICC, SEM, MDC), reproducibility (inter-grader ICC), and agreement (CCC, bias in regression analysis) between and within manual and automated methods. Results The automated method achieved excellent intra-grader repeatability for both DAF and DDAF (ICCs ≥0.988, SEM ≤0.71 mm2, MDC ≤1.98 mm2), with minimal operator influence. Manual measurements showed variable repeatability (DAF ICCs 0.909–0.974; DDAF ICCs as low as 0.837), with square-root transformation reducing SEM and MDC. Inter-grader reproducibility was highest for automated methods (ICC = 0.989–0.992), whereas manual methods ranged from 0.764–0.939 (raw) and 0.867–0.922 (transformed). Cross-method agreement was strong (CCC = 0.91–0.96), though minor proportional and constant bias was observed in raw DAF data. Conclusions The automated approach provides near-perfect repeatability and high agreement with manual grading, offering a scalable, objective alternative for quantifying hypo-auto-fluorescent lesions in Stargardt disease. Manual methods are generally reliable but more variable, especially for DDAF, and benefit from square-root transformation. Findings reflect a pediatric/adolescent single-trial predominantly Asian cohort.

Abstract Background Nucleic acid therapies (NATs) comprise engineered DNA- or RNA-based medicines that act through sequence-specific interactions to modify gene function. Among these, antisense oligonucleotide (ASO) therapies are designed to bind messenger RNA (mRNA) or pre-mRNA to alter splicing, transcript stability, or translation. Many patients with a rare genetic disease stand to benefit from these treatments and, as underlying technologies continue to advance, a critical barrier to care is the equitable selection of targets and patients. Owing to landmark progress in genomic health care, the UK is uniquely positioned to develop a national framework on NAT patient-selection infrastructure. The UK Platform for Nucleic Acid Therapies (UPNAT) has been launched, in part, to meet this goal, with a key output being a structured patient and target selection framework to support NAT development and clinical application, using ASO therapies as a pilot modality. Methodology and Results A multidisciplinary panel of UK-based experts established the UPNAT framework to enable systematic assessment of ASO amenability across modular domains encompassing disease understanding, functional models, variant characteristics, and the individual patient, incorporating the recently published N1C VARIANT guidelines. This modular structure supports consistent prioritisation of tractable targets while identifying biological, clinical, technical, or evidentiary gaps currently limiting ASO development. Designed for implementation within the UK healthcare infrastructure and amenable to future automation using open-access resources, the framework was iteratively refined through application to genomic and clinical data from approved ASO therapies and selected real-world patient case studies. Conclusion We present the first disease-agnostic framework to support structured prioritisation of patients and targets (diseases, genes, or variants) for ASO development and consideration within specialist healthcare services. Designed to accommodate rapid technological advances in NATs, the framework promotes transparent, equitable, and reproducible decision-making within the UK National Health Service (NHS), with principles transferable to other healthcare systems.

Importance:Substantial unexplained heritability remains for pathogenic inherited retinal disease (IRD) variants. Application of genome-wide association studies (GWAS) could help identify causal genes in rare diseases. Objective:To leverage a GWAS for the discovery of IRD-associated genes. Design, Setting, and Participants:This GWAS analysis was combined with replication of findings in 2 independent IRD cohorts. The study was conducted from January 2024 to December 2025 in a multicenter setting through FinnGen, 100 000 Genomes Project, and the National Health Service Genomic Medicine Service combined with clinical cohort from the Oulu University Hospital. Using IRD criteria from the International Classification of Diseases, 9th and 10th Revisions, 540 individuals with IRD and 473 945 control individuals were identified in the FinnGen study. For validation of FinnGen results, 49 patients were recruited from Oulu University Hospital. Results were further validated in 2 individuals identified from the UK cohort. Main Outcomes and Measures:The GWAS and proteomics analysis were performed in the FinnGen cohort. Sanger and whole-genome sequencing and RNA approaches were used in a clinical IRD cohort to validate pathogenicity of the identified XXYLT1 variant. Results:This GWAS identified 13 recessive loci reaching genome-wide significance (defined as P < 5 × 10-8). Of these, 4 (near or within XXYLT1, ANKRD10, DYM, and CBLN4) had not been associated with IRD, including the XXYLT1 c.505-1G>C founder variant. This variant was further genotyped in the clinical replication cohort, leading to identification of 5 more homozygous individuals from 4 families. The phenotype was consistent with a cone-rod or macular dystrophy, with visual deterioration, cystoid macular edema and/or schisislike macular abnormalities. The effect of the XXYLT1 c.505-1G>C variant was further investigated using RNA sequencing and complementary DNA amplicon sequencing, demonstrating exon 2 skipping and a loss-of-function effect. These findings were replicated in an independent population identifying 2 patients from the UK harboring a homozygous XXYLT1 c.766G>A, p.(Glu256Lys) missense variant. Conclusions and Relevance:This GWAS identified an association between XXYLT1 and IRD. These results affirm that GWAS in a founder population can be used as a potential tool for the discovery of rare mendelian disease genes and that XXYLT1 should be considered in clinical IRD gene panels.

Background Familial exudative vitreoretinopathy (FEVR) is an inherited eye disease characterised by the incomplete development of the retinal vasculature. Over 10 genes have been associated with FEVR, but there are still a substantial number of genetically unsolved cases. The aim of this study was to analyse whole genome sequencing (WGS) data from the FEVR cases in the Genomics England (GEL) 100 000 genomes project to identify the causative variants. Methods WGS was performed by GEL and accessed within the GEL Research Environment. FEVR cases were identified using LabKey and candidate variants were extracted using the ‘gene-variant workflow’ and ‘CNV/SV workflow’ and by using BCFtools in unfiltered VCF files. Results Fifty-nine FEVR probands were submitted to GEL. We found six novel and eight previously reported pathogenic variants in six genes known to underlie FEVR ( TSPAN12, LRP5, FZD4, CTNNB1, KIF11 and NDP ), as well as structural variants in TSPAN12 and KIF11 . These accounted for 15/59 (25.4%) of FEVR cases. We also found candidate heterozygous variants in CTNND1 in three unsolved FEVR cases. Expanding the list of genes examined to include all genes reported to be mutated in ocular disorders likely solved a further four cases, indicating that these individuals may be misclassified as FEVR in GEL. Conclusion By performing bespoke reanalysis of the FEVR GEL cohort, this study has highlighted additional heterozygous variants in CTNND1 in FEVR cases and increased the diagnostic yield from 20% solved by the GEL analysis pipeline to 37% (22/59), but the majority of FEVR cases remain without a molecular diagnosis.

Purpose:To evaluate the repeatability and reproducibility of Starguage, a novel automated method, compared with manual segmentation for measuring decreased autofluorescence (DAF) and definitely decreased autofluorescence (DDAF) in fundus autofluorescence (FAF) images of patients with Stargardt disease. Design:A cross-sectional reproducibility and agreement study. Participants:A total of 316 eyes from 158 genetically confirmed Stargardt patients were analyzed. For intragrader repeatability, 114 FAF images were reassessed in a masked, repeated-measures design. Methods:Decreased autofluorescence and DDAF lesion areas were independently quantified by five certified graders using either manual delineation with Heidelberg RegionFinder or a threshold-based automated algorithm, with automated quantification and cross-method agreement analyses restricted to a prespecified central 6-mm fovea-centered region. Agreement and repeatability were assessed using intraclass correlation coefficients (ICCs), standard error of measurement (SEM), minimal detectable change (MDC), Lin's concordance correlation coefficient (CCC), Bland-Altman plots, and Passing-Bablok regression. Both raw and square-root-transformed lesion areas were evaluated. Main Outcome Measures:Repeatability (intragrader ICC, SEM, and MDC), reproducibility (intergrader ICC), and agreement (CCC and bias in regression analysis) between and within manual and automated methods. Results:The automated method achieved excellent intragrader repeatability for both DAF and DDAF (ICCs ≥0.988, SEM ≤0.71 mm2, MDC ≤1.98 mm2), with minimal operator influence. Manual measurements showed variable repeatability (DAF ICCs 0.909-0.974; DDAF ICCs as low as 0.837), with square-root transformation reducing SEM and MDC. Intergrader reproducibility was highest for automated methods (ICC = 0.988-0.992), whereas manual methods ranged from 0.764-0.939 (raw) and 0.867-0.922 (transformed). Cross-method agreement was strong (CCC = 0.91-0.96), though minor proportional and constant bias was observed in raw DAF data. Conclusions:The automated approach provides near-perfect repeatability and high agreement with manual grading, offering a scalable, objective alternative for quantifying hypo-auto-fluorescent lesions in Stargardt disease. Manual methods are generally reliable but more variable, especially for DDAF, and benefit from square-root transformation. Findings reflect a pediatric/adolescent single-trial predominantly Asian cohort. Financial Disclosures:The authors have no proprietary or commercial interest in any materials discussed in this article.

PURPOSE:To describe the radial outer retina reflectivity (RORR) sign in patients carrying pathogenic variants in the X-linked lysosome-associated membrane protein-2 (LAMP2) gene and to review the histologic characteristics of LAMP2 expression in the human retina. METHODS:International multicentre observational case series and experimental laboratory study of patients with LAMP2 deficiency. Baseline demographics and multimodal retinal imaging including colour and fundus autofluorescence (FAF), optical coherence tomography (OCT) with en face reconstruction and fluorescein angiography were obtained. Sections through the retina of a human donor eye were processed for immunofluorescence combining antibodies against LAMP2 with markers for Müller glia, rod and cone photoreceptors. Sections were imaged using high-resolution multichannel confocal microscopy. Assessment of en face OCT reflectivity profiles at 5-50 μm internal to the plane of external limiting membrane (ELM) was performed as well as histologic localisation of LAMP2. RESULTS:We recruited 11 cases with pathogenic variants in LAMP2 across five countries. Six cases demonstrated peripheral radial streaks of hyper- and hypopigmentation with UWF imaging. The RORR sign was best visualised 10-25 μm internal to ELM in 9 cases. We hypothesise the radial pattern to be secondary to X-chromosome inactivation. LAMP2 immunoreactivity was observed internal and external to the ELM. CONCLUSION:Our findings expand the phenotypic spectrum of LAMP2-associated retinopathy by demonstrating the RORR sign using en face OCT. Histologic sections revealed LAMP2 expression in the neuroretina.

Purpose:The purpose of this study was to estimate lens opacity (LO) and associated risk factors in patients with ABCA4 associated Stargardt disease (STGD1). Methods:This is a secondary analysis of the multicenter ProgStar study. Patients with molecularly confirmed STGD1 aged ≥6 years from the United States and Europe were enrolled and followed for 2 years. LO was graded using the Age-Related Eye Disease Study (AREDS) protocol during slit lamp examinations. Baseline prevalence and 2-year incidence of LO were estimated. Logistic regression with generalized estimating equation was used to identify risk factors associated with LO. Results:Of the 259 participants, 54% were women, 86% were Caucasian, and the median age of STGD1 symptom onset was 19 years. At baseline, median age = 31 (interquartile range [IQR] = 21-44, range = 6-68) years; LO prevalence = 14.3% (69/483) of study eyes. Older age and later disease symptom onset were significantly associated with LO prevalence: for every decade older, adjusted odds ratio (adjOR) = 4.6 (95% confidence interval [CI] = 2.6-7.9); adjOR for every decade later in symptom onset = 0.7 (95% CI = 0.4-1.0). Among the 354 eyes without LO at baseline, 2-year incidence was 5.6%. Older age was associated with incidence: adjOR for every decade older = 4.1 (95% CI = 1.8-9.1). Posterior-subcapsular cataract was rare and nuclear cataract was the most prevalent or incident type. Conclusions:LO prevalence in ProgStar is higher than in age-matched general population. Age and age of symptom onset were risk factors of LO, suggesting both biological and accelerated aging due to retinal degeneration in STGD1. Trials of STGD1 should closely monitor safety in the anterior segment and consider excluding patients expecting cataract surgery soon.

Purpose:To describe the use of a model eye-mounted retinal phantom to support adaptive optics scanning light ophthalmoscope (AOSLO) imaging in a multicenter clinical trial (NCT05537220). Methods:Six three-dimensional-printed retinal phantoms were mounted in model eyes. These phantoms contain equally spaced arrays of reflective "cone-like" structures mimicking foveal cone photoreceptor spacing. Intrasession repeatability of phantom imaging was assessed for all six phantoms on two custom AOSLOs. One phantom was also imaged on two additional AOSLOs to assess interdevice reproducibility. Lastly, each of the six phantoms was imaged longitudinally at their respective trial sites. Results:Intrasession repeatability of phantom-derived horizontal "cone" spacing measures was high for two different AOSLOs. However, intersystem differences were found in the average horizontal "cone" spacing of five of eight patches assessed. Across four unique AOSLOs, intersystem differences were found in the average horizontal "cone" spacing of seven of eight patches assessed. A linear regression analysis of longitudinal phantom imaging with a single AOSLO revealed few significant changes in horizontal "cone" spacing over the course of about 2 years. Similar results were observed for vertical "cone" spacing measures across the three experiments. Conclusions:Longitudinal spacing measurements were generally stable in our study. However, small but significant differences in spacing were observed between systems. The approach described here may facilitate combining cone metrics extracted from images acquired using different AOSLOs in multicenter studies. Translational Relevance:Cross-system validation strategies can support the use of AOSLO imaging in multicenter clinical trials.

Doyne honeycomb retinal dystrophy is an incurable juvenile macular dystrophy that leads to visual impairment by early to mid-adulthood. It is an autosomal dominant disorder caused by a c.1033C>T, p.(Arg345Trp) variant in EFEMP1, and is characterized by the early onset of extracellular deposition of drusen between the retinal pigment epithelium and underlying Bruch’s membrane. In this study, we developed an antisense oligonucleotide approach to target EFEMP1. We reprogrammed patient-derived renal epithelial cells to induced pluripotent stem cells, followed by directed differentiation to retinal pigment epithelium and compared the phenotype to gene-corrected and EFEMP1 knockout patient-derived retinal pigment epithelium. In the patient-derived disease model, remodeling of the extracellular matrix (ECM) occurred with progressive accumulation of the drusen-associated proteins apolipoprotein E and collagen IV, in addition to the intracellular accumulation and extracellular deposition of lipids. We developed an allele-specific antisense oligonucleotide which specifically and effectively promoted the clearance of the EFEMP1 c.1033C>T transcript in the patient-derived disease model following assisted or gymnotic delivery. Gymnotic delivery rescued remodeling of the ECM, reduced intracellular accumulation of lipids, and cleared extracellular deposits, even after the onset of the disease phenotype, suggesting that this could be a practical and effective therapeutic approach.

Purpose To determine whether mutation class (truncating versus non-truncating) modifies clinical penetrance in heterozygous female carriers of pathogenic FRMD7 variants. Design Retrospective multi-cohort pedigree analysis with cluster-aware statistical modelling. Subjects 560 heterozygous female carriers from 126 pedigrees with pathogenic or likely pathogenic FRMD7 variants: 100 pedigrees (477 carriers) from 40 published reports identified by systematic literature search and 26 pedigrees (83 carriers) from two UK institutional clinical genetics cohorts. Methods Heterozygous female carriers were classified as affected or unaffected for infantile nystagmus based on clinical examination, and variants were stratified into truncating and non-truncating classes. Penetrance was compared between variant classes using generalised estimating equations with a logistic link and pedigree as the cluster variable. Sensitivity analyses comprised a mixed-effects logistic regression with a pedigree-level random intercept, together with leave-one-pedigree-out and leave-one-publication-out influence diagnostics. Main Outcome Measures Clinical penetrance of infantile nystagmus, defined as the proportion of heterozygous female carriers meeting clinical criteria, compared between mutation classes. Results Pooled penetrance was 30.1% (74/246; Wilson 95% CI 24.7–36.1%) for truncating variants and 49.7% (156/314; Wilson 95% CI 44.2–55.2%) for non-truncating variants. Cluster-aware analysis confirmed higher odds of clinical manifestation for non-truncating compared with truncating variants (OR 2.12, 95% CI 1.32–3.40, P = 0.002). The result was robust to leave-one-pedigree-out (OR range 2.02–2.28) and leave-one-publication-out (OR range 1.84–2.28) sensitivity analyses and was directionally concordant in literature and institutional cohorts (interaction P = 0.49). Conclusions Mutation class is a robust modifier of clinical penetrance in heterozygous female carriers of pathogenic FRMD7 variants. These variant-class specific estimates may refine genetic counselling in FRMD7-associated infantile nystagmus beyond the conventional single penetrance figure.

Inherited retinal diseases (IRDs) encompass a broad spectrum of genetic conditions leading to visual impairment. In this study, we identify KATNA1, encoding the catalytic p60 subunit of the microtubule-severing enzyme katanin, as a previously unrecognized cause of autosomal dominant macular dystrophy (adMD), a form of IRD. Specifically, we could ascertain the presence of 10 heterozygous missense changes affecting six conserved amino acids in 21 individuals from 16 unrelated families from various parts of the world, all presenting with non-syndromic MD of variable severity. Structure-guided analyses indicated that the identified variants potentially disrupt katanin's assembly into hexamers or its ability to bind or hydrolyze ATP, thus compromising its microtubule-severing function. Characterization of patient-derived fibroblasts revealed accumulation of acetylated microtubules both in the cytoplasm and within the primary cilium, together with an altered subcellular distribution of KATNA1. Immunostaining of human retinal tissue showed that KATNA1 specifically localizes to photoreceptors, with distinct distribution patterns between rod and cone photoreceptors. Immunogold transmission electron microscopy confirmed this finding, revealing KATNA1 distribution along the rod axoneme and predominantly within the cone connecting cilium. Together, these results establish KATNA1 as a novel gene associated with adMD, possibly accounting for ~4% of all unresolved MD cases, and associate defective microtubule severing and cytoskeletal dysregulation with macular degeneration.

Our understanding of the genetic landscape of inherited optic neuropathies has grown significantly over the past decades, and it is now known to involve many genes found in both the nuclear and mitochondrial genomes, exhibiting all possible inheritance patterns. Furthermore, pathogenic variants in nuclear genes of mitochondrial respiratory Complex I (CI) subunits have been identified in some cases of ION, in addition to the more common severe presentation of CI deficiencies, usually with early onset. We conducted NGS screening of CI genes to identify potential causative variants in patients with optic atrophy, also performing comprehensive clinical assessments, including neuroimaging studies (MRI) and neurological evaluations. Detailed molecular structure modeling was performed to better evaluate the damaging effects of both novel and previously reported variants in the relevant CI subunits. We identified and characterized candidate causative variants in 31 patients from 23 unrelated families, with biallelic or hemizygous variants in 11 different nuclear CI-related genes encoding polypeptides involved in the structure of CI, including 3 core subunits (NDUFS7, NDUFV1, NDUFV2), 4 accessory subunits (NDUFA1, NDUFA10, NDUFA12, NDUFB11), and 4 assembly factors (NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF8). Notably, defects in core CI subunits in this cohort lead to isolated optic atrophy, while defects in accessory CI subunits and assembly factors resulted in a spectrum of phenotypes, from isolated to syndromic optic atrophy. For 12 cases, the subacute onset of vision loss enabled us to associate or confirm novel genes (NDUFS7, NDUFV1, NDUFAF2, NDUFAF4, NDUFAF8) with the autosomal recessive Leber Hereditary Optic Neuropathy (arLHON) phenotype. Moreover, in the NDUFS7 subunit a partial spatial segregation was noted for missense variants causing either Leigh syndrome or isolated optic atrophy, hinting at possible disease-specific molecular defects. Our case series broadens the genetic spectrum of inherited optic neuropathies, emphasizing the crucial role of nuclear CI genes in its pathogenesis. The arLHON phenotype emerges as linked to numerous nuclear CI genes for which an insidious onset of optic atrophy is also reported, and in some cases the same variant may underlie both phenotypes. Overall, we highlight the possibly so far underestimated prevalence of CI nuclear subunits in the molecular diagnosis of ION, prompting to include all CI-related genes in the standard diagnostic screening.

Structural variants (SVs) can disrupt gene function and contribute to pathogenesis of rare disorders. Here, we created a genome-wide knockout dataset across 125,730 individuals with genome sequencing data in the UK's National Genomic Research Library by leveraging the distinct read-depth signal associated with homozygous deletions. We curated 535,699 rare high-confidence homozygous deletion SVs, of which 48,735 were rare. These deletions collectively covered 213Mb or 6.92% of the human genome (4.58% of autosomal sequence), revealing substantial tolerance to complete sequence loss. From a subset of 58,022 individuals with rare disease, we identified 295 individuals with likely diagnostic homozygous deletions impacting protein-coding regions of known disease genes. A further 32 individuals had candidate non-coding SVs in or near to known disease genes, 19/32 (59.37%) of which disrupted 5'-UTR/promoter regions, revealing promoter deletion as an underappreciated cause of rare disorders. Finally, we identify 43 genes with no known rare-disease association but with exonic homozygous deletions in two or more individuals with consistent phenotypes. We describe in detail PDC (phosducin) in Leber Congenital Amaurosis, GCG (glucagon) for a syndromic neurodevelopmental disorder with gastrointestinal involvement, and ENTPD3 for intellectual disability with autism, as candidate novel disease-associated genes. Overall, we create a genome-wide map of homozygous deletions and demonstrate the power of this dataset for rare disease diagnosis and novel disease-gene discovery.

Purpose To characterize the long-term natural history, retinal phenotypic variability, and treatment outcomes in incontinentia pigmenti (IP), and to explore the association between fluorescein angiography (FA)–guided management and retinal outcomes. Design Retrospective interventional case series. Subjects Medical records of patients with IP seen at Moorfields Eye Hospital between 2000 and 2023 were reviewed. Methods Diagnosis was confirmed by dermatologic findings, histopathology, and/or genetic testing. All patients underwent ophthalmic examination, with wide-field imaging and FA performed when feasible. Main outcomes included retinal stage, visual acuity, genotype–phenotype correlations, laser treatment outcomes, incidence of retinal detachment (RD), and vitreoretinal surgery outcomes. Results Seventy-six eyes of 38 patients (36 female) were included, with a mean follow-up of 14.1 years. Retinal involvement was identified in 45 eyes (59.2%), ranging from retinal pigment epithelium changes to total RD. Fourteen eyes (18.4%) of 12 patients had tractional RD at presentation, most commonly in children presenting before 1 year of age. Fifteen eyes (19.7%) underwent laser photocoagulation for peripheral avascular retina and/or neovascularization, with a mean of 1.9 treatment sessions per eye. Among eyes with attached retinae at presentation that received FA-guided laser, none progressed to RD. In contrast, four eyes with untreated peripheral avascular retina developed RD, including patients older than 1 year. Surgical outcomes for RD were generally poor. Increased use of FA identified subclinical peripheral vascular abnormalities not evident on clinical examination alone. Genetic testing most commonly identified the recurrent IKBKG exon 4–10 deletion, with marked interocular and intrafamilial variability in retinal severity. Conclusion IP retinopathy carries lifelong risk of RD, highest in infancy but persisting beyond 1 year of age. FA identified peripheral vascular abnormalities that were not evident on color fundus examination alone. Angiography-based assessment provides advantages over color fundus-based staging alone. The observed outcomes support the use of early angiographic assessment and suggest a potential benefit of FA-informed surveillance and laser treatment.

PURPOSE:To analyze the clinical spectrum and natural history of MERTK-associated retinal dystrophy. METHODS:Clinical data from molecularly-confirmed patients and retinal imaging were extracted from an in-house database. The main outcome measurements were retinal imaging parameters and clinical findings, including age of onset, symptoms, best-corrected visual acuity (BCVA), outer nuclear layer (ONL) thickness, ellipsoid zone width (EZW) and area of definitely decreased autofluorescence (DDAF). RESULTS:Twenty-five patients were identified, harboring 30 variants in MERTK, with 6 being novel. The mean (range; ±SD) age of symptom onset was 9.4 years old (±3.4, 4-15), with all being symptomatic before 16 years old. The most common visual symptom at presentation was nyctalopia. The mean BCVA (±SD, range, median) at baseline was 1.2 LogMAR (±0.95, 0.1-3, 0.9) at a mean age of 22.6 years (±11, 6-52, 20); with all patients being legally blind by 39 years of age. Subjects were slightly myopic and 44% of the cohort had early-onset posterior subcapsular cataracts. The rate of EZW and ONL thickness loss, as well as the qualitative changes in retinal imaging, were indicative of a rapid rate of structural progression, suggesting a relatively small window of macular preservation. CONCLUSIONS:MERTK-associated retinal dystrophy represents a severe form of retinal dystrophy. Further prospective studies are needed for standardization and to evaluate the disease from a functional perspective.

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.