Human Mutation

BackgroundGenetic skeletal disorders (GSDs) comprise a heterogeneous group of rare, predominantly monogenic conditions that are increasingly diagnosed through high-throughput sequencing. While gene discovery has progressed rapidly, interpretation of pathogenic and uncertain variants remains a major bottleneck, in part because their functional consequences are determined at the protein structure level. However, a systematic assessment of structural knowledge across GSD-associated genes is currently lacking. Here, we present a comprehensive protein structure-centric analysis of 674 protein-coding genes implicated in GSDs. MethodsWe integrated experimental structures, AlphaFold2 (AF2) models, multimeric states, protein-protein interactions, and ClinVar variant annotations. ResultsWe quantify experimental structural availability and sequence coverage, revealing that 37% of GSD proteins lack any experimental structure and that, among proteins with structures, sequence coverage is often incomplete. We show that AF2 models provide high-confidence structural information for a substantial subset of proteins lacking experimental data, but that model reliability strongly correlates with existing structural coverage. Analysis of multimeric assemblies and co-occurring partners demonstrates that many GSD proteins function as obligate multimers, highlighting the importance of interface-level interpretation of variants. Finally, mapping clinically annotated missense variants onto representative protein structures illustrates how structural context can inform the interpretation of pathogenic and uncertain variants, particularly at interaction interfaces. ConclusionsTogether, this work provides a structure-aware reference framework for GSD genes, highlighting systematic gaps in current protein knowledge and demonstrating how integration of structural data can guide genomic variant interpretation. Our observations support a broader principle of structural equivalence, whereby distinct variants converge on shared structural perturbations that explain clustering patterns and enable mechanistic interpretation of nearby variants of uncertain significance.

Cancer Variant Interpretation Group UK was established in 2017 in response to the publication of the 2015 ACMG/AMP v3 guidance for the interpretation of sequence variants. Its initial purpose was to ensure consistency in the UK clinical-laboratory community implementation of ACMG/AMP v3 guidance for cancer susceptibility genes (CSGs). Still convening for monthly national meetings, the remit of CanVIG-UK now encompasses additional activities delivered under the following objectives: O_LICreation of a national multidisciplinary professional network and regular forum. C_LIO_LIDelivery of training and education. C_LIO_LIEstablishment of a consensus approach to the fundamentals of variant interpretation in cancer susceptibility genes. C_LIO_LIDevelopment and ratification of gene-specific frameworks for variant interpretation for cancer susceptibility genes. C_LIO_LIDevelopment and maintenance of an online platform to facilitate information sharing and variant interpretation within the UK clinical-laboratory community. C_LIO_LIFacilitation of UK contribution to international variant interpretation endeavours. C_LI A survey of CanVIG-UK members evaluating the impact of these activities conducted in November 2025 had 163 responses, including 113 clinical scientists/trainees and 27 Clinical Genetics consultants/trainees. The utility of the CanVIG-UK consensus recommendations for variant interpretation in cancer susceptibility genes was highly rated, with 89/145=61.4% of survey respondents reporting using the guidance at least weekly ([≥]4 times/month) and 124/128=96.9% rating it as extremely/very useful. The usage frequency and utility of the gene-specific guidance reported by survey respondents were similar to those reported for the main consensus specification. Both qualitative and quantitative survey responses clearly demonstrate the value of the CanVIG-UK activities to the clinical-diagnostic community. Key messagesO_LIWhat is already known on this topic: Cancer Variant Interpretation Group UK (CanVIG-UK) is a national subspeciality multidisciplinary network first established in 2017. It brings together members of the UK clinical-laboratory community to improve accuracy and consistency in the interpretation of variants in cancer susceptibility genes (CSG) C_LIO_LIWhat this study adds: this article presents the results of a survey of CanVIG-UK members, demonstrating the impact of CanVIG-UK activities on their services, as well as a review of progress in the six updated objectives of CanVIG-UK C_LIO_LIHow this study might affect research, practice or policy: this article presents current priorities and practices and potential future directions for variant interpretation in CSGs across the UK and Republic of Ireland C_LI

Heterozygous FOXL2 (non-)coding sequence and structural variants (SVs) lead to blepharophimosis, ptosis and epicanthus inversus syndrome (BPES), a rare, autosomal dominant developmental disorder characterized by a completely penetrant eyelid malformation and incompletely penetrant primary ovarian insufficiency (POI). We collected variants from our in-house database, generated via clinical genetic testing and downstream research testing in the Center for Medical Genetics Ghent, Belgium (2001-2024), and via literature and other resources in the same period. All retrieved variants were categorized using ACMG/AMP classifications to increase the knowledge of pathogenicity. We collected 413 unique genetic defects of the FOXL2 region, including 76 novel variants, in 864 index patients. Of these, 87% of patients were identified with a coding FOXL2 sequence variant. The polyalanine tract is a known mutational hotspot of FOXL2, illustrated here by the high percentage of pathogenic polyalanine expansions (24%). Furthermore, the molecular spectrum in typical BPES index patients is characterized by 8% coding deletions and 3% deletions located up- and downstream of FOXL2. The remaining 2% carry translocations along with chromosomal rearrangements of 3q23. This uniform and structured reclassification, incorporating the largest dataset of variants implicated in FOXL2-associated disease so far, will improve both the diagnosis as well as genetic counselling for individuals with BPES.

BackgroundWhile pancreatic cysts have been described in syndromic ciliopathies, the pancreas is not commonly recognized as a target organ. However, several ciliary gene knockout mouse models develop a pancreatic phenotype combining acinar atrophy and adipocyte accumulation, hereby called adipopancreatosis, suggesting a link between ciliary dysfunction and pancreatic disease. ObjectiveWe investigated whether mutations in ciliopathy-associated genes are linked to pancreatic dysfunction in humans. DesignWe analyzed a cohort of 341 patients with pediatric-onset pancreatic anomalies and characterized the pancreatic phenotype of new mouse models with conditional Nphp3 inactivation or bearing Nphp3 mutations recapitulating human mutations. In patients, pancreatic fat content was quantified using Dixon-MRI. ResultsMutations in the cilium-related HNF1B and NPHP3 were identified in patients presenting with both renal and pancreatic dysfunction. Nphp3 mutant mice developed acinar atrophy, adipopancreatosis, and moderate inflammation. Adipocytes in the pancreas exhibited a white adipocyte-like profile and likely originated from mesothelial-derived fibroblasts. Reduced numbers and altered length of ductal cilia were monitored. Interestingly, secretory canaliculi, typically unnoticed structures found within and between acinar cells and connected to the acinar lumen, exhibited a microcystic morphology. Consistent with the mouse phenotype, Dixon-MRI revealed significantly increased pancreatic fat content in patients with HNF1B and NPHP3 mutations. ConclusionWe describe a previously unrecognized pancreatic manifestation of ciliopathies, which we name ciliogenic pancreatopathy. Patients with known ciliopathy-causing mutations should be evaluated for this pancreatic condition, particularly those with kidney disease, as concomitant exocrine pancreatic insufficiency may further compromise renal function or the outcome of kidney graft. What is already known on this topicO_LICiliopathies, resulting from defects in primary cilia, are genetic disorders primarily affecting the kidney and liver. C_LIO_LIPancreatic cysts have been sporadically reported in syndromic ciliopathies. C_LIO_LIThe pancreas is not currently recognized as a major target organ of ciliary dysfunction. C_LIO_LIA clear link between ciliary gene mutations and pancreatic anomalies is still unknown. C_LIO_LIAnimal studies have suggested a possible association between ciliary dysfunction and pancreatic anomalies. C_LI What this study addsO_LIIdentifies HNF1B and NPHP3 mutations as genetic causes of a pancreatic phenotype characterized by acinar atrophy and adipose replacement (adipopancreatosis). C_LIO_LIDemonstrates the presence of defective ductal cilia and moderate inflammation in the pancreas of Nphp3 mutant mice. C_LIO_LIReveals that secretory canaliculi in the exocrine pancreas of Nphp3 mutant mice acquire a microcystic morphology. C_LIO_LIShows that patients with HNF1B or NPHP3 mutations have significantly increased pancreatic fat content by Dixon-MRI. C_LIO_LIDefines a new disease entity, ciliogenic pancreatopathy, as a pancreatic manifestation of ciliopathies. C_LI How this study might affect research, practice or policyO_LIEstablishes the pancreas as a novel and clinically relevant target of ciliopathies. C_LIO_LIExpands the phenotypic spectrum of HNF1B- and NPHP3-related diseases to include exocrine pancreatic dysfunction. C_LIO_LISuggests that patients with ciliopathy-causing mutations should be evaluated for exocrine pancreatic insufficiency. C_LIO_LIHighlights the need to consider pancreatic function monitoring in kidney disease and transplant settings. C_LIO_LIOpens new research avenues into the role of primary cilia in pancreatic homeostasis and disease. C_LI

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.

BackgroundExome sequencing (ES) has become a key diagnostic tool for rare diseases (RDs). However, most evidence on ES performance comes from high-income countries and patients from European ancestry. In countries such as Chile, limited access to next generation sequencing amplifies health disparities and highlights the need to identify which patients are most likely to benefit from ES. MethodsThis study presents the second phase of the Chilean DECIPHERD project, in which we performed ES in a new group of patients with RDs presenting with multiple congenital anomalies (MCA), neurodevelopmental disorders (NDD), and/or suspected inborn errors of immunity. To identify clinical and demographic factors associated with an increased probability of obtaining an informative ES result, we conducted a logistic regression analysis, combining the results of the first and second phases of the project. We also objectively evaluated global ancestry measured using ADMIXTURE, as a potential factor. ResultsSixty-seven patients participated in this second phase of DECIPHERD with a median age of 6 years (range: 0-27); 55.2% were female, with an average ({+/-} s.d.) proportion of Native American ancestry of 0.615 {+/-} 0.18. Clinically, 52.2% presented with both MCA and NDD, and the rest had other phenotype combinations. An informative result, including pathogenic or likely pathogenic variants in genes consistent with the patients phenotype, was identified in 34.3% of the cohort; 61% of these variants had not been previously reported in databases such as ClinVar. By combining the two phases of the study, we reached a total of 167 patients, in whom the presence of NDD and/or MCA significantly increased the probability of achieving an informative ES outcome. In contrast, previous use of gene panel testing was associated with a decreased likelihood of receiving an informative result. Ancestry was not associated with diagnostic yield. ConclusionsThis study demonstrates the utility of ES in achieving a diagnosis in a clinically diverse cohort of Chilean patients with RDs, and characterized features associated with a higher diagnostic yield. These findings may contribute to evidence-based patient prioritization strategies in settings with limited access to NGS resources.

Loeys-Dietz syndrome (LDS) is an autosomal dominant connective-tissue disorder caused by genetic variants in TGF-{beta} pathway genes, most often TGFBR1/2. While pathogenic TGFBR2 genetic mutations usually cluster in the kinase domain and disrupt SMAD signalling, distinguishing with confidence those with functional impact on TGFBR2 function from rare benign genetic alterations represents one of the most important ongoing challenges for accurate genetic testing. Therefore, there is a pressing need to develop methods that can improve functional variant interpretation. Here, we describe and characterize the functional impact of a novel genetic variant in the TGFBR2 kinase domain (E431K), in a patient with the clinical diagnosis of syndromic genetic aortopathy. We assessed the structural and functional consequences of this variant using AI-driven molecular modelling and in vitro cell-based assays. A high-quality homology-based model of TGFBR2 was generated and computational mutagenesis based on the structural context and evolutionary conservation was used to forecast variant pathogenicity. Relative to wild type, the variant affects protein stability by disrupting intramolecular interactions and likely induces conformational changes that may affect kinase activity and thus TGF-{beta} signalling. This was experimentally confirmed by showing abnormal protein level and alteration of canonical TGF-{beta} pathway activation. Overall, our results establish that the E431K variant leads to aberrant TGF-{beta} signalling and confirm the diagnosis of Loeys-Dietz syndrome type 2 in this patient.

Background: Facioscapulohumeral muscular dystrophy (FSHD) is a common hereditary neuromuscular disorder. The Russian FSHD Patient Registry was established in 2019 following the development of a PCR-based method for genetic confirmation of the diagnosis. Results: The registry included 470 participants (51% male). Genetic confirmation was obtained for 76% (n=356), the remainder were included based on clinical and anamnestic data. Clinical assessment forms and patient-reported questionnaires were analyzed for 310 and 142 patients, respectively. D4Z4 repeat unit (RU) distribution showed patterns consistent with European cohorts, with a predominance of patients with 3 RUs. A moderate inverse correlation was found between RUs number and clinical severity scales. Periscapular weakness was the most common onset manifestation (46.8%), followed by facial weakness (31.6%) which was often unnoticed by patients. The mean age in the Russian cohort was 37.8 years (range 0-97), indicating a younger cohort compared to international data. A delta-adjusted cluster analysis (n=215) identified three distinct trajectories: a classic phenotype with onset before age 14 and early involvement of various muscle groups (n=177), and two clusters characterized by either facial or periscapular onset with slow progression. Conclusion: The Russian FSHD registry provides a comprehensive characterization of a large national cohort, revealing a predominance of patients with 3 D4Z4 repeats and a younger demographic profile compared to international data. Cluster analysis identified three heterogeneous disease trajectories, offering a framework for improved patient stratification.

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.

Background and objectivesA pathogenic GGC repeat expansion in the zinc finger homeobox 3 (ZFHX3) gene, encoding a pure polyglycine tract, is the cause of spinocerebellar ataxia type 4 (SCA4). Intermediate expansions of other SCA loci contribute to the risk of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease involving the progressive loss of motor neurons. There is increasing awareness of the role of short tandem repeat (STR) motif composition and configuration in disease pathogenicity. Given the genetic pleiotropy between ALS and SCA, this study aimed to evaluate whether ZFHX3 GGC expansions were associated with ALS and to characterise repeat motif composition. MethodsExpansionHunter v5 was used to genotype ZFHX3 GGC repeat sizes in short-read whole genome sequencing data from people with ALS and healthy controls of European ancestry. Repeat sizes were visually inspected using REViewer v2. Repeat motif configurations of Australian ALS cases were manually derived from REViewer images. Receiver operating characteristic (ROC) curve analysis and Youdens J statistic were performed to find a candidate repeat size threshold for association testing using Fishers exact test. ResultsAnalysis of 5,785 people with ALS and 7,982 healthy controls found no association between ZFHX3 GGC repeat expansions and disease risk. However, more than 30 unique repeat motif compositions were identified across 802 people with ALS. Of these, seven distinct configurations coded a pure polyglycine tract which, when expanded, is canonical to SCA4. DiscussionAlthough no association was observed between ZFHX3 GGC repeat expansions and ALS, this study established the dynamic nature of ZFHX3 repeat motif composition and configuration. Unique motif compositions were identified both within and between repeat sizes, including the presence of pure polyglycine repeats in ALS. Consideration of repeat motif composition and configuration, in addition to repeat allele length, may be important for assessing neurodegenerative disease risk.

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.

Copy number variants (CNV) contribute significantly to the pathogenic variation associated with developmental disorders. CNV detection is often not included in standard exome sequencing (ES) analysis. Complementary methods such as chromosomal microarray are typically offered in diagnostic laboratories to diagnose pathogenic CNV. In this study, we aimed to develop an optimal approach for incorporating CNV detection within our ES analysis process for the Deciphering Developmental Disorders in Africa (DDD-Africa) cohort. We analyzed ES data from 505 probands with a developmental disorder, applying a CNV detection approach that assessed data generated using the tools CANOES and XHMM. When available, parental ES data was used to assess inheritance patterns. We confirmed a diagnosis in 42/505 (8,3%) patients with 44 pathogenic CNV identified in the probands. There were 31 deletions and 13 duplications. Among the 27 probands with parental data, all identified CNV were de novo. The addition of CNV analysis to our ES analysis pipeline resulted in an 8.3% increase in diagnostic yield in the DDD-Africa cohort without additional laboratory cost. This approach offers a feasible approach which is likely to reduce analytical cost and is suitable for low- and middle-income countries where funding and resources for genomic medicine initiatives are limited.

PurposeFuchs endothelial corneal dystrophy (FECD) is a common corneal disease and a leading indication for endothelial keratoplasty (EK). Although CTG18.1 repeat expansion is a major genetic risk factor, the contribution of polygenic background to disease progression remains unclear. We evaluated whether combining CTG18.1 expansion status with a FECD-specific polygenic risk score (PRS) enables genomic prediction of progression to EK. MethodsWe retrospectively analysed 589 individuals with FECD from two European centers, with replication in an independent cohort of 185 individuals. Association of CTG18.1 expansion ([&ge;]50 repeats) and PRS with time to EK were evaluated using Cox models adjusted for sex and ancestry. ResultsExpansion-positive status was associated with earlier EK (HR 2.30; 95% CI 1.62- 3.26; P<.001). Addition of PRS improved prediction (C-index 0.614 vs 0.602; P=.014). Each 1-SD increase in PRS was associated with earlier EK (HR 1.16; 95% CI 1.03-1.30; P=.015), with replication in the validation cohort (HR 1.42; 95% CI 1.15-1.75; P=.001). ConclusionIntegration of monogenic and polygenic risk enables genomic prediction of FECD progression, supporting clinical genomic risk stratification to inform individualized monitoring and timing of intervention.

Robinow Syndrome is a polygenic, rare skeletal disorder characterized by craniofacial and limb defects. The genes involved are in the Wingless-related Integration site-1 (WNT) pathway and DVL1 (Dishevelled 1) is the most commonly affected gene. In all pathogenic variants of DVL1, a frameshift replaces the C terminus with a novel peptide. We tested whether the variant DVL11519{Delta}T was sufficient to alter development in vivo and in vitro in two animal models. We compared phenotypes to wtDVL1 or DVL1 with a stop codon at position 1519. Misexpression of DVL11519{Delta}T in the developing face of chicken embryos with an avian retrovirus, leads to a widening of the frontonasal mass similar to the human facial phenotype and ultimately to inhibition of skeletogenesis that was also verified in primary cultures of frontonasal mass mesenchyme. In luciferase assays carried out in facial mesenchyme, the wtDVL1 activated canonical and JNK PCP WNT signalling however the DVL11519* and the DVL11519{Delta}T variant removed some but not all of the signaling activity. We also determined that there is mislocalization of the protein expressed from DVL11519{Delta}T in the nucleus while the other two constructs were mainly found in the cytoplasm. In complementary Drosophila experiments using a variety of readouts, only the DVL11519{Delta}T variant impacted morphogenesis and signaling. This is the first study to clarify the pathogenesis of Robinow syndrome is due to the novel C-terminus of DVL1 which exerts dominant interference on morphogenesis, skeletogenesis and WNT signaling.

PIK3CA-related overgrowth spectrum (PROS) comprises a heterogeneous group of disorders caused by postzygotic activating variants in PIK3CA, leading to mosaic activation of the PI3K pathway. PROS natural history is highly variable across patients and depends on the timing and distribution of the somatic mutation. To better characterize this natural history, we analyzed a cohort of patients with PROS. This multicenter study was conducted at Hopital Femme Mere Enfant (Lyon, France) and Hopital Necker-Enfants Malades (Paris, France). We included pediatric and adult patients with PROS who had a documented PIK3CA variant and at least two MRI examinations performed at least 2 months apart. Patients undergoing interventional surgical or radiological procedures, or receiving targeted therapies were excluded. In all patients, target lesions were identified on baseline MRI scans, and assessed on follow-up scans according to the RECIST criteria. Among 67 PROS patients screened from 2008 to 2021, 30 met the inclusion criteria, including 43.3% female patients. The median age at first MRI was 19 years (interquartile range, 5 to 34) and the median interval between the two scans was 75.7 months (range, 2.1 to 160.3 months). Recurrent localizations included the face (n = 6; 20%), ear, nose and throat region (n = 3; 10%), upper limbs (n = 5; 16.7%), thorax (n = 3; 10%), abdomen (n = 4; 13.3%), pelvis (n = 5; 16.7%), and lower limbs (n = 10; 33.3%), with some patients presenting multisite involvement. During the observation period, 86.6% (n = 26) of patients exhibited an increase in target lesion volume, with a median progression of 37.8% (range, 2.6 to 233.0%) and a mean progression of 52% (standard error of the mean, 7.2%), reflecting a right-skewed distribution driven by a subset of rapidly enlarging lesions. In conclusion, this study provides the first radiological description of the natural history of PROS, demonstrating that tissue malformations most often enlarge over time, with sustained progression persisting into adulthood.

IntroductionNeuromuscular disorders (NMDs) encompass a broad group of conditions that primarily affect the peripheral nervous system. They are often caused by genetic alterations that impair skeletal muscle function and result in debilitating symptoms. Obtaining an accurate molecular diagnosis remains a challenge, potentially because variants in genes that have yet to be identified as causal. We therefore used advanced computational methods to study the genetic architecture of NMDs and to identify key features that distinguish NMD genes from other genes in the broader genome. MethodsCurated genes implicated in NMDs (n = 639; GeneTable of NMDs) were obtained and merged with a comprehensive set of genomic features for human autosomal protein-coding genes. Machine-learning-based feature selection and ranking were performed using Boruta, along with complementary analytical approaches. These analyses were used to identify the most important genic features (n = 134, subcategories: gene complexity, genetic variation, expression patterns, and other general gene traits) for discriminating NMD genes from other genes in the genome ResultsNMD genes exhibit enriched expression in disease-relevant tissues, including skeletal muscle and heart. Additionally, compared with other protein-coding genes, these genes exhibit increased transcriptomic complexity (e.g., longer transcripts and more unique isoforms), contain more short tandem repeats, and show greater variation in conservation across model organisms. ConclusionsThis study identified several key genomic features that may distinguish NMD genes from the rest of the genome. This may enhance the identification of novel causal genes and could ultimately facilitate earlier diagnosis and medical management for affected individuals.

Saul-Wilson syndrome (SWS) is a skeletal dysplasia characterized by primordial dwarfism and progeroid features caused by a recurrent dominant COG4 variant (p.G516R). We previously showed that this mutation accelerates Golgi retrograde trafficking and disrupts glycosylation of the proteoglycan decorin, while zebrafish models revealed defects in chondrocyte elongation and intercalation. We have also shown that the SW1353 chondrosarcoma cells carrying the SWS variant exhibit reduced secretion of extracellular matrix (ECM) components. While these results indicate a critical function of COG4 in Golgi processing, the developmental process leading to skeletal dysplasia in SWS patients remains unknown. Here, we generated patient-derived iPSC cartilage organoids (SWS organoids), modeling early human chondrogenesis. SWS organoids failed to produce cartilage structures and displayed poor expression of chondrogenic markers. Time-course RNA-seq analysis of the chondrogenic process revealed reduced activation of gene networks involved in skeletal development, ECM organization, ossification, and glycosaminoglycan metabolism. Spatial multiomic analysis of protein and glycosylation by CODEX and GLYPH imaging revealed an altered chondrogenic trajectory, persistence of mesenchymal states, global glycosylation changes, and reduced deposition of chondroitin sulfate proteoglycans. These results indicate that the COG4 mutation disrupts ECM glycosylation and chondrogenic commitment, and that SWS organoids model early defects in cartilage formation underlies impaired skeletal growth in SWS. HighlightsO_LIPatient iPSC-derived cartilage organoids model development defects in Saul-Wilson syndrome C_LIO_LISWS organoids show defective extracellular matrix deposition and attenuated chondrogenic gene expression C_LIO_LIGlycan profiling reveals global glycosylation defects and deficient proteoglycan GAG chains C_LIO_LIAn early developmental impairment in chondrogenesis alters skeletal formation in Saul-Wilson syndrome C_LI

Fanconi anemia (FA) is a rare genetic disorder of impaired DNA repair characterized by progressive bone marrow failure, congenital malformations, and cancer predisposition. Early identification of individuals with FA is critical for timely clinical management, yet phenotype-driven approaches to FA identification are hindered by inconsistencies in existing phenotypic profiles. We compared the Human Phenotype Ontology (HPO) annotations for FA in OMIM (215 terms across 22 complementation group entries) and Orphanet (106 terms in a single entry, ORPHA:84), quantifying overlap and anatomical system coverage. To address identified gaps, we developed a comprehensive custom HPO profile by extracting phenotypic terms from the entire Fanconi Cancer Foundation (FCF) Clinical Care Guidelines using OntoGPT, an LLM-based ontology extraction tool, followed by manual curation to ensure accuracy and clinical relevance. OMIM and Orphanet shared only 36 HPO terms (12.6% of their combined 285 unique terms), demonstrating substantial discordance. Our custom profile comprises 264 unique HPO terms, of which 161 (61.0%) are novel and not present in either existing source. The novel terms expand coverage particularly in musculoskeletal (39 terms, 23.8%), genitourinary (26 terms, 15.9%), limb (26 terms, 15.9%), head or neck (20 terms 12.2%), and digestive system (17 terms, 10.4%) phenotypes. Community-curated phenotypic profiles derived from clinical practice guidelines can substantially augment existing disease annotations. Our FA profile, the most comprehensive HPO-based phenotypic characterization of FA to date, is publicly available and provides a foundation for improved clinical decision support and EHR-based computable phenotyping that can accelerate diagnosis for individuals with FA. Furthermore, the LLM-assisted approach offers generalizable methods to improve the diagnostic odyssey for all rare diseases.

Severe combined immunodeficiency (SCID) is a heterogeneous, recessive disorder, associated with the onset of severe, recurrent infections in the first few months of life. SCID is fatal if left untreated, but outcomes can be significantly improved by prompt diagnosis and treatment, particularly prior to onset of infection. Consequently, SCID is already included in many newborn screening programmes around the world, as well as multiple international genomic newborn screening (gNBS) research programmes. However, there is a vital need to estimate penetrance of SCID variants in population cohorts, to mitigate the potential consequences of reporting low penetrance variants in a genotype-first gNBS setting. This study aimed to assess the penetrance and prevalence of these variants in the UK Biobank population cohort. Whole genome sequencing data from 490,640 individuals was used to interrogate 16 SCID genes for potentially causal variation. We identified 4206 carriers of single heterozygous pathogenic variants ([~]1% of cohort), but only 6 individuals double heterozygous, homozygous or hemizygous for relevant pathogenic variants. 3 individuals would be expected to require further testing had they been identified by gNBS, suggesting that fewer than 1 in 100,000 newborns might require follow-up testing due to SCID variants. Following detailed variant curation, we were able to identify only 2 unabected individuals likely to be harbouring biallelic pathogenic variants, potentially indicative of reduced penetrance. Nonetheless, SCID remains an excellent candidate for inclusion in gNBS studies, due its severity, clinical actionability and expected low false positive rate, although care should be taken when reporting hypomorphic variants.

The ryanodine receptor (RYR) genes encode evolutionarily conserved calcium release channels involved in a wide range of calcium-dependent biological processes. Here we show that the sole Drosophila RYR gene (dRyR) functions in differentiated somatic and cardiac muscle as well as in developing embryonic myotubes. In the larval body wall muscles, dRyR protein localizes at the SR membranes and dRyR knockdown adversely affects muscle contractility, suggesting its conserved role in calcium-triggered E-C coupling. After dRyR attenuation, sarcomere and mitochondrial patterns are severely impaired, showing dRyR involvement in structural muscle properties. However, dRyR is also prominently expressed and functionally required in growing embryonic muscles. dRyR loss of function leads to myotube growth defects and thin myofiber phenotypes, while its overexpression induces myofiber splitting. Given the structural and functional conservation of dRyR, we used Drosophila to test the impact of one human RYR1 variant of unknown significance (VUS). Larvae carrying p.Met4881Ile RYR1 VUS showed impaired mobility and altered structural muscle properties reminiscent of those seen in dRyR knockdown, thus indicating it is likely pathogenic. Overall, we show that Drosophila dRyR plays a conserved role in setting muscle contractility and structural muscle features. Our findings underline the still under-investigated role of dRyR as a promyogenic factor and provide a first example of the impact assessment of a human RYR1 VUS in Drosophila.