Genetics in Medicine Open

The human opsin gene cluster at Xq28 contains highly similar OPN1LW and OPN1MW genes essential for red-green color vision. Current molecular methods cannot accurately analyze this complex locus, limiting diagnosis of color vision deficiencies (CVD) and detection of carrier status. We performed Nanopore long-read sequencing of 206 individuals, comparing alignment-based analysis with targeted de novo assembly. Alignment-based methods performed poorly, whereas targeted assembly achieved 99% concordance for OPN1LW and 92% for OPN1MW copy numbers and resolved gene order in all XY individuals and 87% of XX individuals. This approach detected CVD in 3.2% of XY individuals and identified 8% of XX individuals as carriers, consistent with population estimates. Moreover, it molecularly explained the phenotypic severity in a family with Bornholm eye disease and clarified carrier status in an XX individual suspected of carrying two CVD haplotypes. Our approach provides a comprehensive, reference-free method for accurate analysis of expressed opsin genes and reliable CVD carrier detection.

Variant databases ClinVar and gnomAD are the backbone of clinical variant interpretation, but their population composition is skewed toward European ancestry. Whether this skew creates systematic classification disadvantages for non-European patients with monogenic diabetes has not been examined at the database level. ClinVar variant_summary (GRCh38, April 2026; 4,421,188 variants) was cross-referenced with gnomAD v4.0 genome data for 17 monogenic diabetes genes. Annotation coverage and variant classification rates were computed stratified by genetic ancestry group (AFR, AMR, EAS, SAS, MID, NFE, FIN, ASJ). Of 14,691 gnomAD variants across the 17 genes, only 29.7% had any ClinVar classification (range: 12.7%-61.3% by gene). Among classified variants, non-Finnish European (NFE) variants had the highest variant of uncertain significance (VUS) rate (32.1%) and the lowest benign/likely benign fraction (41.6%), consistent with a large submission volume without functional follow-up. African-ancestry (AFR) variants showed the second-highest VUS rate (29.2%), not statistically distinguishable from NFE after Bonferroni correction, while all other non-European groups had significantly lower rates (all p < 0.001). GCK showed a pattern inversion - non-European VUS rate (18.5%) exceeding European (15.0%) - consistent with progressive reclassification in European populations absent in non-European cohorts. Annotation coverage and VUS divergence were uncorrelated (r = -0.15, p = 0.57). The primary equity problem is a 70% annotation gap combined with a non-European curation deficit, not a simple VUS excess. Ancestry-stratified evaluation of ClinGen Variant Curation Expert Panel (VCEP) criteria performance is warranted across disease domains.

Introduction: BEACONS-NBS (Building Evidence and Collaboration for GenOmics in Nationwide Newborn Screening) is the first research study to integrate whole genome sequencing into newborn screening (NBS) across multiple U.S. states and territorial public health laboratory programs (PHLPs). We developed a list of conditions for screening. Methods: We designed inclusion criteria and assembled an initial condition list from published resources. The list was revised by clinical experts, molecular geneticists, genetic counselors, PHLPs, rare disease advocacy organizations, the BEACONS-NBS Community Advisory Board, and project leadership from the National Institutes of Health. For each condition, we provided a rationale for early detection, diagnostic signs or biomarkers, and treatments or surveillance strategies. Results: The BEACONS-NBS condition list includes 777 conditions associated with 743 genes, one copy number variant, and two aneuploidies and is larger than those used in other genomic NBS research studies in the U.S. and United Kingdom. Most conditions are inborn errors of immunity (37.2%), inherited metabolic disorders (18.7%), or endocrine conditions (18.1%). Nearly all conditions (93.3%) can be confirmed using a non-genetic test. Discussion: BEACONS-NBS has established a condition list for implementation across multiple state and territorial PHLPs, enabling the prospective evaluation of feasibility of population-wide genomic NBS.

Wolfram syndrome is a rare genetic disorder characterized by antibody-negative early-onset atypical diabetes mellitus, optic nerve atrophy, sensorineural hearing loss, diabetes insipidus (arginine vasopressin deficiency), and progressive neurodegeneration, with significant variability in disease severity. We assessed the accuracy of a genotype-based severity scoring system to predict the onset of cardinal symptoms in Wolfram syndrome. This system is based on the type of WFS1 variants (in-frame or out-of-frame) and their location relative to transmembrane domains. Severity scores were assigned to 324 patients with documented onset ages for diabetes mellitus, optic atrophy, hearing loss, and diabetes insipidus. Our analysis revealed a clear correlation between severity scores and earlier onset of diabetes mellitus and optic atrophy. Patients with in-frame variants outside transmembrane domains exhibited milder symptoms, especially WFS1 c.1672C>T (p.Arg558Cys) variant, whereas those with out-of-frame variants showed the earliest onset. Severity scores 3 and 4 did not follow the expected progression, suggesting that transmembrane domain involvement in both alleles may result in greater severity. These findings suggest that this scoring system provides valuable insights into the progression of Wolfram syndrome and may guide clinical care. Further refinement may improve its utility for predicting the onset of non-diabetic symptoms.

Interpreting HNF1B variants is challenging in clinical practice. We aimed to integrate functional, clinical, and family data to improve variant classification, describe clinical features of carriers and report registry-level prevalence of HNF1B alterations. Clinical, genetic, and family data were analyzed from the Norwegian MODY Registry (NMR) and the Norwegian Childhood Diabetes Registry (NCDR). Clinical features of sequence variant and 17q12 deletion (17q12del) carriers were summarized, and variants were classified using ACMG-AMP-ClinGen criteria. Registry-level prevalence was reported with 95% confidence intervals. HNF1B sequence variants were functionally assessed, showing that the lower transactivation (TA) was associated with higher clinical severity. Eleven variants demonstrated impaired functional activity, with TA inversely correlated with clinical burden ({varrho} = -0.701, p = 0.002). We identified 28 individuals with 17q12del (21 in NMR, seven in NCDR) and 15 individuals carrying 14 unique (LP/P) sequence variants, all detected in the NMR. Overall, 36/486 probands (7.4%) with genetically confirmed monogenic diabetes in the NMR carried an LP/P HNF1B sequence variant or 17q12del. In the NCDR, [~] 0.2% carried 17q12del (7/3,583; 3/7 GADA/IA-2A-positive). Functional data enabled reclassification of three variants. Since many pediatric 17q12del carriers in the NMR were referred for testing due to structural renal anomalies without diabetes, HNF1B screening should be considered in children with renal/extra-renal features, irrespective of diabetes or autoantibody status. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/26348894v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@41feforg.highwire.dtl.DTLVardef@ccc48borg.highwire.dtl.DTLVardef@17ba2e9org.highwire.dtl.DTLVardef@4919b_HPS_FORMAT_FIGEXP M_FIG C_FIG

Despite the multidimensional value of implementing genomic medicine, in terms of diagnostic yield, cost-effectiveness, and optimisation of care trajectories, its deployment in many African countries, including Algeria, remains constrained by major structural and interpretive challenges, compounded by the persistent underrepresentation of African populations in genomic databases with direct consequences for variant interpretation and clinical decision-making. We implemented a fully in-house whole-exome sequencing (WES) workflow structured through a clinically driven sequential framework in 14 unrelated patients with unexplained neurodevelopmental disorders, in a context of high consanguinity and enriched recessive inheritance. A definitive molecular diagnosis was established in 8 cases, with pathogenic or likely pathogenic variants identified in MECP2, PTPN11, FOXG1, ARV1, GNAO1, ATM, ROBO3, and CHD3. Five cases yielded variants of uncertain significance and one clinically relevant incidental finding was identified. Beyond its diagnostic contribution, this study reveals persistent interpretive limitations: a disproportionate VUS burden, complex incidental finding management, and reduced accessibility to classification criteria, reflecting database underrepresentation, the predominance of private variants, and the limits of current frameworks in consanguineous settings. These findings underscore the necessity of population-specific reference datasets, iterative phenotyping, adapted ethical frameworks, and strategies addressing territorial disparities in access. This work demonstrates that WES implementation requires a structured multidisciplinary ecosystem integrating clinical, bioinformatic, and ethical dimensions, and provides a transferable model for the sustainable integration of genomic medicine in under-resourced settings, while highlighting the global scientific value of incorporating underrepresented populations into genomic research.

RNA sequencing (RNA-Seq) is increasingly used alongside exome and genome sequencing to identify causal variants underlying rare Mendelian disorders. We present short-read RNA-Seq data from 5,412 individuals with a diverse range of rare disorders recruited to Genomics Englands 100,000 Genomes Project. We show that the proportion of genes from gene panels applied to different disorders which are well captured (transcripts per million (TPM) [&ge;] 5) from blood RNA varies widely, highlighting differences in applicability across disorder types. Using OUTRIDER and FRASER2 to identify gene expression and splicing outliers respectively, we identify at least one outlier event in a disorder relevant gene in 20% of the cohort. To prioritise likely diagnostic candidates, we apply multiple strategies including focussing on outlier events in known haploinsufficient genes (n=78), integrating outliers with structural variant calls (n=19), and using strategies integrating phenotypic presentation (Exomiser, n=39). We present a series of candidate diagnoses involving diverse variant types and disease mechanisms, demonstrating the broad utility of RNA-Seq in identifying and prioritising diagnostic candidates in individuals with a variety of different rare conditions and no known genetic diagnosis. Our findings demonstrate that blood-based RNA-Seq can deliver clinically relevant findings across a broad range of rare disorders.

Wolfram syndrome is a rare autosomal recessive disorder caused by pathogenic variants in the WFS1 gene, characterized by early-onset diabetes mellitus, optic atrophy, sensorineural hearing loss, arginine vasopressin deficiency, and progressive neurodegeneration. The condition selectively affects pancreatic {beta} cells and neurons via chronic endoplasmic reticulum (ER) stress, and no proven disease-modifying therapy currently exists. Diabetes mellitus is typically the first manifestation, presenting at a mean age of 6 years as an insulin-dependent phenotype with preserved C-peptide and negative diabetes-related autoantibodies. Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) are well-established agents in the management of type 2 diabetes, augmenting glucose-dependent insulin secretion, suppressing glucagon, slowing gastric emptying, and promoting satiety. Preclinical evidence further suggests that GLP-1 RAs preserve {beta}-cell mass, attenuate ER stress, and confer neuroprotective effects, properties of particular therapeutic relevance to Wolfram syndrome. We conducted a retrospective cohort study of 84 participants with genetically confirmed Wolfram syndrome and insulin-dependent diabetes mellitus enrolled in the Washington University Wolfram Syndrome International Registry and Clinical Study. Clinical data were extracted from medical records; for participants concurrently enrolled in the Tracking Neurodegeneration in Early Wolfram Syndrome study, longitudinal data were obtained from that source as well. Thirty-five percent of eligible participants had received a GLP-1 RA at some point during follow-up. We characterize the prevalence of GLP-1 RA use, documented rationale for initiation, observed effects on glycemic control and visual outcomes, adverse effects, and reasons for discontinuation. No statistically significant changes in hemoglobin A1c (HbA1c) or body mass index (BMI) were observed. Visual acuity declined significantly at two years, consistent with expected disease progression. Gastrointestinal adverse effects were common and contributed to frequent discontinuation. These observational data provide important clinical context and a foundation for future prospective trials evaluating GLP-1 RAs as a potential disease-modifying strategy in Wolfram syndrome.

Background: Genetic variants impacting red blood cell biology disrupt the relationship between glycaemia and glycated haemoglobin (HbA1c), with implications for diagnosis and management of type 2 diabetes (T2D). Thalassaemia trait is estimated to affect 350 million people globally, but its impact on T2D and related outcomes is not clear. Methods: We explored associations between thalassaemia trait, HbA1c, and T2D diagnosis and complications in 43,088 British Bangladeshi and Pakistani participants in the Genes & Health study with linked multisource England National Health Service (NHS) electronic health record data and whole exome sequencing. Findings: 2,490 participants (5.8%) were heterozygous carriers of ClinVar pathogenic / likely pathogenic thalassaemia variants, however 3 in 4 of these were not diagnosed with thalassaemia in their NHS health records. rs33950507, a common variant causal for HbE thalassaemia, was associated with increased HbA1c (beta=0.13, 95%CI:0.08-0.18, p=7.8x10-8), but not glucose levels (beta=0.01, 95%CI:-0.04-0.06, P=0.72). rs33950507 was associated with increased hazards of prediabetes (HR=1.38, 95%CI:1.26-1.52, p=2.2x10-6) and T2D (HR=1.11, 95%CI:1.01-1.22, p=0.03), and reduced hazards of diabetic eye disease (HR=0.74, 95%CI:0.56-0.96, p=0.02) and cerebrovascular disease (HR=0.44, 95%CI:0.20-0.94, p=0.03). Sensitivity analyses suggested mediation by overdiagnosis and overtreatment of T2D. Interpretation: Alternatives to HbA1c, and/or precision medicine approaches to defining and managing hyperglycaemia, are needed, particularly on a global scale. This may be particularly relevant to individuals from ancestral groups among whom erythrocytic traits are more common but often undiagnosed. Funding: Wellcome Trust, MRC, NIHR, Barts Charity, Genes & Health Industry Consortium

There are few therapeutic options to treat patients with sickle cell disease (SCD), a blood disorder caused by mutations in the {beta}-globin gene that affects >7M individuals worldwide. Combining human genetics and high-throughput proteomics can help identify new drug targets. Here, we present results from a proteogenomic analysis of the plasma proteome in SCD patients. We measured the levels of 5,411 plasma proteins and tested their associations with common genetic variation in 343 SCD patients. After conditional analyses, we identified 560 protein quantitative trait loci (pQTL), including 58 (10%) that are novel. Many of these pQTL are not specific to SCD patients and associate with clinically relevant traits in non-SCD African Americans from the Million Veteran Program (e.g. hemoglobin concentration, triglycerides). The effect sizes of the pQTL is largely concordant between SCD and non-SCD individuals, although we found examples (e.g. APOL1, haptoglobin) with evidence of heterogeneity that suggests an interaction between the plasma proteome and the SCD genotype. Finally, we combine pQTL and genome-wide association study results for fetal hemoglobin (HbF) in a Mendelian randomization analysis to prioritize five proteins that may increase HbF production (ENPP5, LBP, NAAA, PT3X, ZP3).

Introduction: Accurate estimation of disease prevalence is crucial for public health and therapeutic development, but traditional methods are often inaccurate. Genetic prevalence, which estimates the proportion of a population with a causal genotype, using allele frequencies from population data, offers an important alternative. Methods: We partnered with 18 Rare As One patient organizations to estimate genetic prevalence for 22 autosomal recessive conditions using population data from two releases of the Genome Aggregation Database (gnomAD). To standardize and democratize these analyses, we developed the Genetic Prevalence Estimator (GeniE), a publicly available tool, for accessible calculations. Results: Conservative carrier frequencies in gnomAD v4.1 ranged from 1/164 to 1/11,888. The median change in genetic prevalence frequency between v2.1 to v4.1 was 0.806. Partnership with patient advocacy groups provided critical real-world context that refined the interpretation of these estimates. Discussion: These findings highlight that genetic prevalence is not a static figure but a dynamic, evolving measure with important caveats that need to be considered. Our study underscores the necessity of re-evaluations as databases expand. By integrating patient-partnered insights with the GeniE platform, we empower the genomics community to maintain transparent, up-to-date, and actionable data for rare disease advocacy and drug development.

To date, FBRSL1-related disorder has been reported in five individuals with congenital abnormalities and severe postnatal impairment with or without epilepsy; however, the full extent of the phenotypic and genotypic spectrum remains unclear. Previously reported cases involved small truncating variants apparently escaping nonsense-mediated decay, suggesting either a haploinsufficiency or a dominant-negative mechanism. We report the first case of a complex structural variant at the FBRSL1 locus, resulting in an additional, partially truncated copy of the gene, providing strong evidence for a dominant-negative mechanism. RNA-Seq supported the expression of the additional truncated gene copy. The patient is an infant girl with a profound developmental and epileptic encephalopathy (DEE). The child presented at birth with intrauterine growth restriction, respiratory insufficiency, severe swallowing dysfunction, spasticity, contractures, optic nerve hypoplasia, facial dysmorphism, and atrial septal defect. She developed severe postnatal growth restriction with microcephaly and profound developmental impairment. She has a DEE with frequent neonatal focal seizures evolving to infantile epileptic spasms syndrome (IESS). Our patient has congenital abnormalities in common with previously reported cases, along with a profound DEE, not associated previously with FBRSL1. Our case expands both the phenotypic and genotypic spectrum of FBRSL1-related disorder.

Background As part of Singapore's effort towards precision medicine tailored to Asian diversity, we describe the implementation of a nationwide reproductive carrier screening program. Using a customised 112-gene panel, incorporating population-specific recessive genetic diseases, we outline the overall program design, and initial efforts of community and stakeholder engagement, to inform culturally appropriate implementation. Methods Participants receive culturally tailored online education regarding our reproductive screening program and are provided results with genetic counselling and reproductive options. Community and stakeholder perspectives were assessed through questionnaires and consultations with religious leaders. Results Recruitment is nation-wide, and since initiation of our pilot phase in September 2024, 1,619 couples have registered interest, with 60% uptake of those deemed eligible. Among the 456 couples that have received results to date, four couples (0.9%) were identified to be at increased risk. Community questionnaire responses (n=1002), involving couples who participated in the program as well as the general public, indicated interest is high (59%) across the cohort but awareness, intent to participate and implications for reproductive options differed by sociodemographic factors such as ancestry and religion. Healthcare professional respondents (n=113) acknowledged carrier screening will be routine in medical care, but report limited confidence and resources. Engagement with religious leaders indicated support for the program. Conclusion These early program outcomes and community engagement are guiding the implementation of expanding population-based carrier screening in Singapore, contingent on addressing practical challenges through equitable outreach and professional training.

Background: Saudi Arabia bears a disproportionate burden of autosomal recessive genetic disorders, driven by consanguineous marriage rates of 50 to 58% and elevated carrier frequencies for conditions such as sickle cell disease (carrier rate up to 25%), betathalassemia (12%), and spinal muscular atrophy (6%). The existing premarital screening program screens for only two conditions. We developed SafeGene, a computational platform that expands predictive genetic screening to 50+ conditions using region specific population genetics. Methods: SafeGene integrates five risk calculation engines: (1) Mendelian inheritance models for AR, AD, XR, and XD conditions; (2) Hardy Weinberg equilibrium based carrier probability estimation using Saudi, Gulf, and global databases; (3) a six level consanguinity coefficient calculator (F = 0 to 1/8) with risk amplification multipliers; (4) multifactorial polygenic risk models for 12 complex diseases; and (5) maternal age dependent trisomy risk curves. Built using React.js, Node.js/Express, and MongoDB with bilingual Arabic/English support. Results: The platform encompasses 50 genetic conditions across 12 categories. Validation against published Saudi data demonstrated concordance with observed disease frequencies. Economic modeling projects that expanding screening could prevent 2,800 to 4,200 affected births annually, yielding savings of SAR 1.2 to 2.8 billion ($320 to 746 million USD) per year. Conclusions: SafeGene represents a scalable, evidence-based digital health solution for comprehensive genetic screening addressing the unique population genetics of consanguineous Gulf societies. The platform is protected under pending patent applications in South Africa (CIPC) and Saudi Arabia (SAIP).

Background: Artificial intelligence (AI)-driven variant prioritization has demonstrated substantial utility in expediting genetic diagnosis by ranking the most likely causative variants. While a variety of tools have been developed, few address the unique clinical and technical constraints in prenatal genetic diagnosis. Methods: We introduce Berrylyzer, a novel, end-to-end variant prioritization system applied to prenatal diagnosis.Inspired by clinician's reasoning process during variant interpretation, Berrylyzer applies a modular, stepwise scoring architecture that jointly integrates phenotypic and genomic evidence and delivers a ranked list of candidate variants, achieving high computational efficiency without compromising analytical rigor. Moreover, Berrylyzer natively supports both structured ontologies and free-text clinical narratives, enabling flexible integration into diverse clinical environments. Its performance was rigorously evaluated across two independent, real-world prenatal cohorts and benchmarked against three state-of-the-art methods: Xrare, Exomiser, and PhenIX. Results: Across the two datasets, Berrylyzer ranked 56.41% and 58.12% of diagnostic variants first, and achieved recall rates of 94.02% and 97.42% within top 20, respectively. Berrylyzer outperformed Xrare (85.19% and 87.08%), Exomiser (84.90% and 85.98%), and PhenIX (82.05% and 88.93%). Stratified analysis consistently demonstrated superior performance across diverse disease categories, inheritance patterns, and analytical strategies. Notably, Berrylyzer exhibited robustness regardless of phenotype forms, yielding comparable top 20 recall rates for free-text descriptions and standardized terminologies. Conclusion: Berrylyzer represents an accurate, interpretable, and computationally lightweight variant prioritization system for prenatal genetic diagnosis. The superior performance across heterogeneous diagnostic contexts enables it as a practical solution for seamless integration into clinical pipelines, thereby advancing precision medicine in prenatal settings.

Interpretation of germline variants in cancer susceptibility genes (CSGs) requires the collation of variant-level data from diverse sources, as well as the assembly of comprehensive clinical data, often necessitating sharing of information between genomic testing centers. Although a number of variant interpretation tools exist, there remains a need for a CSG-focused platform tailored to the diverse range of ClinGen variant curation expert panel guidance in these difficult-to-interpret genes. Here, we describe CanVar-UK, a freely-accessible web platform to assist in the interpretation of germline CSG variants. CanVar-UK contains variant-level data for over 1.7 million single nucleotide variants, comprising all coding variants in 115 established CSGs. These data include: in silico scores from 11 tools of clinical relevance; population allele frequencies from gnomAD v4.1 and case counts from NHS genomic testing via linkage to the National Disease Registration Service; variant-level readouts from 31 different functional and splicing studies across 13 CSGs; genetic epidemiology studies of the BRCA1/2 genes; and live linkage to existing consensus classifications in the ClinVar database. CanVar-UK additionally has a diagnostic discussion forum functionality, via which users are able to email the rest of the user base with queries and/or suggested classifications, facilitating the exchange of clinical and classification data between diagnostic centers. Already widely used by the NHS clinical workforce in the CSG space (with 879 registered NHS users), CanVar-UK has a rapidly growing international user base, with 607 registered users based outside the UK. We believe CanVar-UK to be an invaluable resource for germline CSG variant interpretation.

Accurate HLA typing is critical for transplantation, pharmacogenomics, and disease risk prediction, yet short-read approaches cannot resolve the HLA region's extreme polymorphism. Long-read sequencing improves resolution, but its adoption has been limited by higher cost, reduced base accuracy, limited throughput, and reliance on long-range PCR. To overcome these limitations, we present a multiplexed long-read hybrid capture workflow for PacBio and Oxford Nanopore sequencing that enriches all classical HLA loci and the complete HLA Class III region. A single-step enzymatic fragmentation and barcoding strategy enables automated library prep. We also introduce HLA-Resolve, an HLA typing program optimized for HiFi reads, and validate workflow performance against the Genome in a Bottle, Human Pangenome Reference Consortium, and International Histocompatibility Working Group benchmarks using 32 geographically diverse samples. These advances offer a cost-effective approach for high-resolution HLA typing with clinical applicability and enable investigation of the role of HLA Class III variation in disease.

Background Glycated haemoglobin (HbA1c) underpins type 2 diabetes (T2D) and prediabetes management worldwide and reflects both glycaemia and erythrocyte biology. A missense variant in PIEZO1 (rs563555492T), carried by 1 in 12 South Asians, has been associated with a nonglycaemic reduction in HbA1c. We aimed to further characterise this association and evaluate its clinical consequences. Methods We undertook genetic and linked health data analyses across two cohorts: 19,898 (37.4% female) South Indians from the Madras Diabetes Research Foundation (MDRF) and 43,011 (54.4% female) British Bangladeshis and British Pakistanis in Genes & Health. In MDRF, we tested associations with glycaemic and erythrocytic traits using additive genetic models. In Genes & Health we modelled diagnosis of prediabetes, T2D, and diabetic eye disease using flexible parametric survival models. Ten-year absolute risks were estimated for a population aged 40-50 years. Findings PIEZO1 rs563555492T was associated with erythrocytic traits and lower HbA1c, but not with fasting glucose, postprandial glucose, or C-peptide. This variant reduced risk of prediabetes (HR 0.63, 95% CI 0.58-0.69) and T2D (0.85, 0.78-0.93) diagnosis, and increased risk of diabetic eye disease among individuals with T2D (1.20, 1.01-1.43). Modelling suggested approximately 1,019 missed prediabetes and 303 missed T2D diagnoses per 100,000 adults over 10 years. Interpretation An ancestry-enriched PIEZO1 variant is associated with lower HbA1c independent of glycaemia, reduced prediabetes and T2D diagnosis suggesting delayed detection, and increased complication risk. Reliance on HbA1c may systematically underestimate glycaemic risk in a substantial minority of South Asians. Funding The Wellcome Trust; NIHR

Genotype-phenotype databases are essential for variant interpretation and disease gene discovery. Genetic variation differs among human populations, mainly in allele frequencies and haplotype patterns shaped by ancestry and demographic history. Population-specific genotypes can influence traits and disease risk; this makes population specific characterization important. Most existing resources focus on the characterization of a population's genetic background, but do not represent the resulting phenotypes. We have developed PAVS (Phenotype-Associated Variants in Saudi Arabia), a curated, publicly accessible database that integrates 5,132 Saudi clinical cases from four Saudi cohorts and 522 cases from analysis of a mixed-population cohort, together with 1,856 cases from the Deciphering Developmental Disorders study (DDD) and 9,588 literature phenopackets. Each case record describes patient-level phenotypes, encoded with the Human Phenotype Ontology (HPO), and links them to genomic variants, gene identifiers, zygosity, pathogenicity classifications, and disease diagnoses mapped to standardized disease terminologies. The data is represented in Phenopackets format and as a knowledge graph in RDF. Additionally, a web interface provides phenotype-based similarity search, gene and variant browsers, and an HPO hierarchy explorer. We evaluate the utility of the phenotype annotations for gene prioritization using semantic similarity. While there are clear differences to global literature-curated databases, phenotypes in PAVS can successfully rank the correct gene at high rank (ROCAUC: 0.89). PAVS addresses a gap in population-specific genotype-phenotype resources and provides a benchmark for phenotype-driven variant prioritization in under-represented populations.

Abstract Background Understanding the phenotypic spectrum of disease-associated genes is essential for accurate diagnosis and targeted therapy. FRMPD4 (FERM and PDZ Domain Containing 4) has previously been associated with intellectual disability and epilepsy. However, its potential role in non-syndromic hearing loss has not been explored. Methods We performed genetic analysis in two unrelated families presenting with non-syndromic sensorineural hearing loss, identifying maternally inherited missense variants in FRMPD4. Clinical phenotyping included audiological assessment and evaluation for neurodevelopmental involvement. Cross-species expression analyses were conducted in Drosophila, zebrafish, and mouse. Functional characterization included quantitative evaluation of sound-evoked responses in Drosophila nicht gut hoerend (ngh) mutants, assessment of neuronal development and acoustic startle responses in zebrafish loss of function models, and morphological cochlear analyses with auditory brainstem response measurements in knockout mice. Results Three affected males from two unrelated families presented with prelingual, bilaterally symmetrical sensorineural hearing loss, with confirmed congenital onset in one individual and no evidence of neurodevelopmental abnormalities. Cross-species analyses demonstrated evolutionarily conserved expression of FRMPD4 in auditory structures. In Drosophila, quantitative analysis of sound-evoked responses in ngh mutants revealed impaired auditory function. Zebrafish loss of function models exhibited reduced neuronal populations in the otic vesicle and posterior lateral line, abnormal neuromast development, and diminished acoustic startle responses. In mice, Frmpd4 knockout resulted in high-frequency hearing loss and cochlear abnormalities consistent with the human phenotype. Conclusions Our findings expand the phenotypic spectrum of FRMPD4 to include non-syndromic sensorineural hearing loss and establish its evolutionarily conserved role in auditory function. These results have direct implications for genetic diagnosis and variant interpretation in patients with hearing loss.