Orphanet Journal of Rare Diseases

The Vanishing White Matter (VWM) Registry is a single-center database containing longitudinal survey data from >470 untreated patients with DNA- and MRI-confirmed VWM. VWM is a rare genetic disorder of the brain's white matter with an estimated live birth incidence of 1 per 100,000 and prevalence of 1.3 per 1,000,000 people in the Netherlands. The Registry represents a remarkably extensive collection of systematically gathered information on this disease, enabling crucial research into the natural history of VWM and providing a valuable resource for control arms in clinical trials. Data, initially collected on paper from 2004, have been maintained electronically since 2018, and include validated scales alongside a disease-specific customized questionnaire covering clinical, functional, and psychosocial domains. Survey packages, available in eight languages, are sent one to four times a year, depending on patient age. Built-in validity checks and review by pediatric and adult neurologists ensure data quality. The dataset is continuously updated with questionnaires expanding its scope, and structured for analysis and reuse in research on VWM.

Background and objectives: Cerebral Autosomal Dominant Arteriopathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL) is the most common monogenic cerebral small vessel disease. Though neuropsychiatric symptoms (NPS) of CADASIL profoundly impact function and quality of life, these symptoms remain understudied. This analysis characterizes the prevalence, severity, and profile of NPS among individuals with CADASIL-causing NOTCH3 variants and non-carrier biological family controls in the United States CADASIL Consortium (USCC). Methods: This cross-sectional analysis used multimodal baseline data from 12 enrollment sites across the country. Statistical analyses used nonparametric tests and regression models to compare clinical and neuropsychiatric outcomes across CADASIL risk tiers and controls, adjusting for age, sex, race, and education where appropriate. The primary outcome measure was the Neuropsychiatric Inventory Questionnaire (NPI-Q), an informant-reported measure which assesses 12 categories of NPS. NPI-Q item severity and distress were evaluated for individuals with confirmed cysteine-altering NOTCH3 variants and compared with controls. Results: Four hundred fifty-nine USCC participants were included in the analytic cohort: 343 cases [256 high-risk (HR); 63 medium-risk (MR); 24 low-risk (LR)]; and 116 controls. Among participants with available NPI-Q data, at least one neuropsychiatric symptom was reported by 72.6% (n = 228/314) of cases compared with 53.2% (n = 58/109) of controls. Reported symptoms were more common among CADASIL cases than controls, occurring in 75.0%, 71.2%, and 72.7% of participants in the LR, MR, and HR groups, respectively, compared with 53.2% of controls. Compared with controls, participants in the MR group and HR group had higher NPI-Q severity scores. HR participants also had higher NPI-Q distress scores than controls. Discussion: Our findings support the notion that NPS are an important clinical manifestation of CADASIL. Beyond previously reported symptoms, additional neuropsychiatric manifestations were identified. Given the higher burden and variability in the neuropsychiatric presentation of CADASIL, the relationships among neuropsychiatric, neurological, and patient-reported outcomes merit further investigation. The NPS profile may enhance the evaluation of the safety and efficacy of different treatments to target these symptoms for CADASIL patients. Trial Registration Information: The study is registered at ClinicalTrials.gov (NCT05677880, 12/12/2022).

Background: Hereditary spastic paraplegia (HSP) comprises a heterogeneous group of neurodegenerative disorders characterized by progressive lower-extremity weakness and spasticity, with or without additional neurological symptoms. Objectives: To characterize the molecular genetic spectrum, inheritance patterns, molecular finding rate, and clinical characteristics of HSP within a multicenter Canadian cohort. Methods: We investigated 671 patients from 423 families who met clinical criteria for HSP identified through the Canadian HSP (CanHSP) registry from 7 medical centers across Canada. Patients were evaluated using known HSP and HSP mimic gene panels, whereas unsolved and more recent patients underwent whole-exome sequencing (WES). 435 individuals underwent gene-panel testing and 485 underwent WES. Copy-number variants (CNVs) were assessed using ExomeDepth, and candidate CNVs using multiplex ligation-dependent probe amplification (MLPA). Results: Molecular findings were identified in 426 of 671 individuals (63.5%): 351 (52.3%) had HSP-associated findings, 70 (10.4%) HSP-mimicking disorders, and five (0.7%) other molecular findings; 245 (36.5%) remained unresolved. Candidate variants were found in 80 relevant genes, 36 of which were HSP-associated genes. The most frequently implicated genes were SPAST (22.5%), SPG7 (5.7%), ATL1 (5.2%), SPG11 (3.6%), and SPG8 (3.3%). Phenotypically, SPAST, ATL1, and SPG8 w[zg1.1]ere predominantly associated with pure HSP, whereas SPG7 and SPG11 more often showed complicated phenotypes, with prominent cerebellar involvement in SPG7 and cognitive and developmental features in SPG11. Conclusion: Patients in CanHSP present with genetic and phenotypic heterogeneity. Reanalysis and complementary approaches, including whole-genome, RNA, and long-read sequencing, may increase diagnostic yield.

Background: Short-rib polydactyly syndrome type IV (Beemer-Langer syndrome) is a lethal skeletal ciliopathy that can result from biallelic pathogenic variants in KIAA0586 (TALPID3). Earlier clinical observations suggested an unusually high occurrence of this phenotype in Romani families from the Carpathian Basin. Methods: Whole-exome sequencing was performed in affected individuals from five independent families, and the frequency of KIAA0586 c.1815G>A was assessed in a Hungarian Romani genetic database of 500 individuals. Results: The affected individuals were homozygous for c.1815G>A, a splice-disrupting variant previously shown to cause exon 14 skipping. Four families self-identified as Roma from Hungary and one affected individual was from Turkey. Six heterozygous carriers were identified among 500 individuals in the Hungarian Romani cohort, corresponding to an allele frequency of 0.6%. This was markedly higher than the frequencies cited from ALFA (0.01%) and gnomAD (0.0014%). The Hungarian-Romani and Turkish affected individuals also shared genotypes at informative markers flanking the variant, supporting a shared ancestral haplotype. Conclusions: These observations strengthen evidence that KIAA0586 c.1815G>A is a founder allele enriched in at least some Romani populations. The data support consideration of ancestry-informed carrier testing in appropriately counseled families. Historical admixture may explain the occurrence of the same haplotype in a Turkish case, but this remains a hypothesis requiring broader population-genomic confirmation.

Background: Rapid genome sequencing (rGS) is a first-tier test in the neonatal intensive care unit (NICU). Implementation strategies to scale rGS for clinical care may change clinician roles. We analyzed the NICU rGS workflow to understand challenges rGS poses for clinical roles and responsibilities. Methods: The study took a qualitative approach to understanding the rGS workflow in Level III and Level IV NICUs. The five workflow phases studied included: i) identification of a patient with a suspected genetic disorder, ii) subspecialist consultation, iii) test selection and ordering, iv) return of results, and v) disclosure. Data were collected via job task journals, interviews, and workflow diagram construction with clinicians involved in rGS. Analysis included participant-guided workflow diagram refinement, qualitative thematic analysis, and identification of rGS workflow challenges. Results: We documented issues related to decision-making authority and scope of responsibility for clinicians, with the majority relating to complexities of subspecialist consultations. Issues included differences in: criteria for triggering consultations, expectations of consulted subspecialists' roles, test selection preferences, and responsibility for documenting clinical interpretations and disclosure. Conclusion: Subspecialist consultations in clinical rGS involved significant role ambiguity and communication challenges, requiring intentional implementation efforts to ensure clear clinical roles and responsibilities.

FBXO31 encodes the substrate receptor of an SCF (SKP1-CUL1-F-box) E3 ubiquitin ligase that recognizes C-terminal amide-bearing proteins (CTAPs) and targets them for proteasomal degradation, a function of particular importance in neurons. A recurrent de novo missense variant, c.1000G>A p.(Asp334Asn), reprograms FBXO31 substrate specificity and causes an autosomal-dominant neurodevelopmental disorder with spastic cerebral palsy through a neomorphic gain-of-function mechanism. By contrast, biallelic loss of function has tentatively been linked to a recessive disorder. Here we report a female patient, born to consanguineous parents, with moderate intellectual disability, developmental delay and dysmorphic features, who carries a homozygous 54.3 kb deletion removing exons 2-8 and the coding part of exon 9 of FBXO31. The deletion retains only the exon 1-encoded F-box domain, while removing the coding sequence for the entire C-terminal substrate-recognition region. It is predicted to result in loss of function. Segregation is consistent with autosomal-recessive inheritance, with both parents and three of five unaffected siblings being heterozygous carriers. Together with two previously reported recessive families and the experimentally established neomorphic action of p.(Asp334Asn), the homozygous deletion supports an FBXO31 allelic series comprising dominant gain of function and recessive biallelic loss of function.

Methylmalonic aciduria (MMA) is caused by deficiency of methylmalonyl-CoA mutase (MMUT), which catalyses the final step of propionate catabolism and fuels the tricarboxylic acid cycle for energy production. Previous studies reported disrupted mitochondrial homeostasis in MMA, including reduced mitochondrial membrane potential and increased oxidative stress, especially in energetically demanding and chronically affected tissues like brain and kidneys. However, how these changes impact mitochondrial energy production remains unclear. Here, we systematically investigated mitochondrial energy production using extracellular flux analysis in cellular models of MMA, including 293T cells, patient-derived fibroblasts, urine-derived epithelial kidney cells and induced pluripotent stem cells (iPSCs) as well as iPSC-derived neurons harbouring either complete loss (knockout, KO) or pathogenic missense variants in MMUT. We found no impact on mitochondrial energy production in MMUT-KO 293T cells and fibroblasts compared to controls. In contrast, fibroblasts and 293T cells expressing the pathogenic MMUT-p.N219Y variant showed decreased energy production. This corresponds to the altered mitochondrial membrane potential in 293T cells, but contrasts with their unchanged mitochondrial abundance. Depletion of glucose, glutamine and pyruvate from the media or provision of each individually as sole fuel source exacerbated the phenotype of MMUT-p.N219Y clones, but did not induce a phenotype in MMUT-KO 293T cells. Finally, we confirmed reduced mitochondrial energy production in patient-derived kidney cells but found no evidence in MMUT-p.N219Y iPSCs and their derived neurons. Overall, our work suggests that the impact of MMUT-deficiency on mitochondrial energy production is cell type- and variant-dependent. Further investigations should clarify molecular mechanisms and their clinical impact.

Background: To determine the crude and age-adjusted point prevalence of motor neuron disease (MND) and its phenotypes (classical amyotrophic lateral sclerosis [ALS], primary lateral sclerosis [PLS] and progressive muscular atrophy [PMA]) using a comprehensive multi-source case ascertainment strategy. Methods: Cross-sectional population-based study with a prevalence date of 1 January 2025. Cases were identified through five complementary regional data sources and confirmed by clinical review against the revised El Escorial and Gold Coast criteria. Cases were classified by phenotype as ALS, PLS or PMA. The reference population was the population aged 15 years or older in Valencian Community (n=4,433,999). Crude prevalence was calculated per 100,000 with 95% Poisson confidence intervals; age-adjusted rates were obtained by direct standardisation to the 2013 European Standard Population. Results: A total of 374 confirmed MND cases were identified. The overall crude prevalence of MND was 8.43 per 100,000 (95% CI: 7.60-9.29) and the age-adjusted prevalence was 7.85 per 100,000 (95% CI: 7.05-8.65). By phenotype, ALS accounted for 325 cases (86.9%; crude prevalence 7.33 per 100,000), PLS for 26 (7.0%; 0.59 per 100,000) and PMA for 23 (6.1%; 0.52 per 100,000). Prevalence was consistent across provinces. Mean age was 65.9 years, the male-to-female ratio was 1.37:1, and 83.4% were receiving riluzole. Conclusions: This is the first comprehensive, multi-source population-based estimate of MND prevalence and its subtypes in the Valencian Community. The estimate is higher than the previous single-unit figure and consistent with recent European data, underscoring the value of multi-source ascertainment.

CBX1-related syndrome is characterized by developmental delay, hypotonia, autistic features, and mild dysmorphic features. This syndrome is caused by heterozygous missense variants in CBX1, which encodes heterochromatin protein 1 beta (HP1{beta}). These variants are situated within the chromodomain of HP1{beta}, a critical region that mediates the interaction between HP1{beta} and trimethylated H3K9. While a prior study identified three individuals with pathogenic CBX1 variants, the variant and clinical spectrum of CBX1-related syndrome remains largely unknown. Here we report three patients with novel de novo heterozygous variants in CBX1. Patients with CBX1 p.(Leu40Pro) and p.(Cys60Arg) manifested with global developmental delay, while the patient with CBX1 p.(Cys60Gly) primarily exhibited speech delay without concurrent motor developmental delay. All variants reside within chromodomain of the HP1{beta} protein. Interestingly, in vitro cellular assays revealed that CBX1 p.(Cys60Gly) variant showed an intermediate cellular phenotype between the wild type and the CBX1 p.(Leu40Pro) and p.(Cys60Arg) variants, suggesting a possible genotype-phenotype correlation. This report provides further evidence that missense variants within the chromodomain of HP1{beta} cause a syndromic neurodevelopmental disorder, CBX1-related syndrome.

Background: CADASIL caused by cysteine-altering NOTCH3 variants, the most frequent hereditary cerebral small vessel disease worldwide, is characterized by marked phenotypic variability. Mutation location within the EGFr domains of the NOTCH3 receptor has emerged as a key determinant of this variability. We investigated phenotypic variability and potential modifiers of CADASIL expression by comparing individuals harbouring the same pathogenic NOTCH3 variant across distinct recruitment settings in three European countries. Methods: We compared clinical features, MRI markers, and cardiovascular risk factors among individuals harbouring the p.Arg1231Cys NOTCH3 mutation across three distinct recruitment settings: a multigenerational founder population from Cilento, Italy (CILCAD), a population-based cohort from the UK Biobank (UKB), and a clinically referred cohort from a national referral centre in Lariboisiere Hospital, Paris, France (LRB). In addition, CILCAD carriers were compared with NON-Carriers from the same population. The NOTCH3 locus was finally analysed to define the shared haplotype in CILCAD and explore potential genetic contributions to phenotypic variability. Findings: By comparing populations from three European countries, this study showed marked context-dependent phenotypic variability associated with the sole pathogenic p.Arg1231Cys NOTCH3 variant. In CILCAD, a multigenerational founder population, the haplotype carrying the NOTCH3 mutation also predisposes to decreased LDL levels, resulting in an unusually low LDL cholesterol profile in this sample. Strikingly, these very low LDL levels were associated with a higher likelihood of stroke. Interpretation: In European carriers of NOTCH3 p.Arg1231Cys, factors beyond mutation location, including genetic background, may substantially shape disease expression, while exceptionally low LDL levels could paradoxically be associated with greater disease severity.

Myotonic dystrophy type 1 (DM1) is caused by a CTG expansion in the 3' untranslated region of the DMPK gene that results in the expression of expanded CUG RNA which trap splicing factors resulting in widespread alternative splicing dysregulation. A panel of these splicing events, or splicing index (SI), is currently used to measure splicing dysregulation in DM1 patients. Despite significant interest in splicing, little is known about its progression over time in DM1. The objective of this study was to evaluate the changes in SI over 3 years in a well-phenotyped cohort of DM1 participants and identify factors contributing to these changes. RNA was extracted from vastus lateralis (VL) biopsies of 20 DM1 participants taken 3 years apart and the SI score was measured using targeted RNA sequencing. Baseline SI scores correlated with percent predicted muscle strength of the ankle dorsiflexors, knee extensors and hand grip. On average, SI scores worsened over 3 years, but the progression varied markedly among participants. Adult/juvenile phenotypes and lower baseline SI scores were among the factors associated with higher progression of SI scores over time. These findings emphasize the importance of integrating clinical phenotype and baseline molecular severity when interpreting longitudinal SI change, particularly in the context of clinical trials.

C9orf72 encodes a protein that is important for both typical neurodevelopment and homeostatic processes across the lifespan. Pathogenic C9orf72 repeat expansions constitute the most common genetic cause of frontotemporal lobar degeneration (FTLD). Collectively, preclinical models and clinical neuroimaging studies have observed smaller thalamic volumes in C9orf72-associated FTLD, including in asymptomatic young adult C9orf72 repeat expansion carriers across 18 to 30 years old, supportive of potential neurodevelopmental origins. However, it is unknown whether asymptomatic young adult C9orf72 expansion carriers demonstrate volume differences in specific thalamic nuclei, as reported in older asymptomatic carriers and symptomatic patients; if so, normative transcriptomic patterns could reveal relevant neurodevelopmental and/or FTLD-related neurodegenerative processes. This study investigated volumetric MRI differences of the thalamic nuclei in asymptomatic young adult C9orf72 expansion carriers compared to non-carriers, and examined spatial associations with normative thalamic transcriptomics from 8 weeks post-conception through middle age. Young adult C9orf72 expansion carriers (n=72) and non-carriers (n=48) were enrolled in the Frontotemporal Dementia Prevention Initiative across Europe, Canada, and the USA (ages: 18-30 years; sex: 57% female). Spatial associations between young adult thalamic nuclei volumes and normative transcriptomics from the Allen Human Brain Atlas were examined using complementary data-driven and hypothesis-driven approaches. Spatial expression patterns of transcripts of interest were characterized across prenatal and postnatal neurodevelopment using BrainSpan data. Smaller volumes of the pulvinar, mediodorsal, and lateral nuclei were observed in young adult C9orf72 expansion carriers compared to non-carriers. These nuclei showed higher normative expression of transcripts involved concurrently in neurodevelopmental and C9orf72-associated FTLD neurodegenerative processes (including lysosomal, autophagic, and small GTPase functions), and lower normative expression of CALB1, a marker of prenatal human thalamic development. Normative expression of CALB2 (another human thalamic development marker) yielded positive correlations with C9orf72 across prenatal development to adulthood. These findings identify candidate transcripts that may provide insight into the molecular architecture leading to smaller thalamic nuclei volumes in C9orf72-associated FTLD.

Purpose Children with suspected rare genetic disorders often remain undiagnosed after exome, gene panel, or chromosomal microarray testing. We sought to define recurrent missed-diagnosis mechanisms and evaluate an integrated clinical-genomic reanalysis framework. Methods We studied 75 participants with rare or striking pediatric-onset phenotypes who remained undiagnosed after prior genetic testing. Trio genome sequencing evaluated SNVs, indels and copy-number variants. RNA sequencing was performed in 63 participants to assess aberrant expression and splicing, with targeted follow-up assays used selectively for prioritized variants. Clinician-genome scientist review integrated longitudinal phenotyping, physician input, and inheritance. Unresolved cases underwent research-level candidate prioritization. Results Clinically reportable findings were returned in 9, including two with multilocus findings: 5 explained the primary phenotype and 4, while not fully explanatory, were clinically relevant and informing surveillance, management, or family follow-up. Previously missed findings reflected technical limitations, including deep intronic splice-altering variants supported by transcriptome analysis and a genomic deletion, and interpretive limitations related to incomplete phenotype integration or narrowly scoped prior testing. Research-level analysis prioritized six candidate genes, including biallelic ACHE variants with reduced enzymatic activity. Conclusion Integrated clinical-genomic reanalysis framework identified diagnostic gaps, recovered care-informing findings, and prioritized candidate genes for rare disease discovery.

Background: Diabetes poses a major global health and economic burden, and effective self management is essential for preventing complications. The National Health Service in England has recently announced plans to shift from analogue to digital services in their 10-year plan. However, digital health technology may also risk widening existing inequalities. MyWay Diabetes is a digital self-management intervention implemented in three regions across England. Understanding the acceptability of online and digital tools to support diabetes self-management, particularly among non users and underserved groups, is essential to ensure equitable engagement and implementation. Objectives: To (1) explore barriers to using online and digital support across diverse demographic groups with type 1 and type 2 diabetes who had not used the MyWay Diabetes platform, and (2) identify factors that could improve uptake and continued engagement. Design: Cross-sectional qualitative study. Methods: We conducted six focus groups with n=35 people living with diabetes (27F, 8M; 40% Asian British Pakistani) across three regions in England. The Theoretical Framework of Acceptability (TFA) informed data collection and analysis. Data were transcribed and analysed thematically using template analysis, mapped onto constructs of the TFA. Results: Digital engagement in diabetes self management was shaped by intersecting personal, social, and healthcare system factors. Participants' confidence with navigating digital environments was constrained by the emotional and practical burden of living with diabetes. Social and structural barriers, including cultural mismatch, accessibility challenges, financial constraints, and reliance on family further limited meaningful use of digital tools. Engagement was strongly influenced by trust in healthcare professionals and services; digital tools were considered acceptable when they complemented person-centred care, but resisted when perceived as replacing personalised, face to face support. Conclusions: Digital support for diabetes self management is more likely to be acceptable when it aligns with people's capabilities, social circumstances, and trusted healthcare relationships. Therefore, to prevent widening inequalities, digital tools should be accessible, culturally relevant, and embedded within supportive, person centred models of care. Lived Experience or Public Contribution: Public contributors with lived experience of diabetes (3F, 3M) reviewed participant materials and pseudonymised focus group transcripts, providing feedback on recruitment, data collection, and interpretation. Their insights informed analysis and theme development, ensuring a lived-experience perspective. Our public co-applicant is a co-author on this manuscript.

BackgroundPersistent postural-perceptual dizziness (PPPD) is a chronic functional dizziness disorder characterized by unsteadiness, hypersensitivity to motion and visually complex environments. Although increasingly investigated, the role of the different factors involved remains unclear. This study aims to comprehensively characterize PPPD across clinical, biological, and behavioral domains. MethodsData from 18 PPPD patients and 20 age- and sex-matched healthy control volunteers (HC) were analyzed, including clinical and psychological questionnaires, a neuropsychological battery, salivary markers, posturography under different conditions, and gait analysis under single- and dual-task demands. ResultsPatients reported greater depressive symptoms, higher perceived stress, and reduced quality of life than HC, but showed no neuropsychological deficits and comparable past psychological trauma and personality traits. Salivary stress marker levels were similar to HC. Gait analysis revealed a slower, cautious gait in patients, which worsened without vision, with no differences in automaticity (stride time variability). Postural assessments showed greater sway and enhanced low-frequency oscillations, exacerbated by absence of visual input in PPPD. Visual reliance for postural control correlated negatively with subjective symptom severity, but not other symptom-related measures. ConclusionPPPD patients have lower mood and increased perceived stress, with no increase in biological stress markers compared to HC. Cognition, personality, and exposure to past trauma might be less relevant than previously hypothesized. Patients show visual dependence for gait and postural control, likely a maladaptive compensatory mechanism. These findings support interventions targeted at reducing visual dependence and at improving mood, rather than interventions focusing on psychological trauma. SummaryO_LIWhat is already known on this topic - PPPD (Persistent Perceptual Postural Dizziness) is a functional dizziness disorder characterized by different biopsychosocial factors, often investigated in isolation. C_LIO_LIWhat this study adds - PPPD patients have higher depression and perceived stress scores, lower quality of life, but show no differences in past trauma, personality traits, and biological stress markers, compared to healthy controls. They also show a reliance on vision both for gait and for postural control, with increased low-frequency oscillations in the anteroposterior direction. Visual dependence is likely maintained by its perceived role in symptom reduction. C_LIO_LIHow this study might affect research, practice or policy - These findings support rehabilitation strategies aimed at reducing reliance on vision and increasing reliance on vestibular inputs, but not interventions focusing on past traumatic experiences. C_LI

ObjectiveTo evaluate usability and workflow implications of Pheno+, an electronic health record- (EHR) embedded natural language processing tool that extracts patient phenotypes and maps them to Human Phenotype Ontology (HPO) terms. Materials and MethodsThis study performed a mixed-methods formative evaluation of Pheno+ in the context of rapid genome sequencing in the neonatal intensive care unit. Two rounds of think-aloud interviews and surveys were conducted with neonatologists, advanced practice providers, medical geneticists, genetic counselors, non-genetics pediatric subspecialists and laboratory molecular geneticists. Usability was assessed using the System Usability Scale (SUS). Structured data were analyzed descriptively. Qualitative data underwent hybrid deductive-inductive thematic analysis. ResultsTwenty-eight interviewees participated in two rounds of data collection. Users retained an average of 24.2 HPO terms from an average of 45.6 terms per patient. Mean time curating terms was 8:59 per patient. Final SUS score was 76 (above scale mean). Qualitative themes included: burden of curating terms; interpretation of phenotypes; adding information to phenotypes; role of genetics expertise; and tool uses beyond the original core use case for Pheno+. DiscussionPheno+ demonstrated positive usability but required curation effort to reduce erroneous terms. Participant responses indicate that effective use may depend on knowledge of HPO structure and laboratory workflows. Automated phenotyping seems likely to reduce net clinician workload, while also reshaping clinical responsibilities, expertise requirements, and communication in genetic testing. ConclusionTools like Pheno+ can support scalable genomic medicine. Design and implementation may benefit from addressing curation burden, phenotype contextualization, expertise requirements, and other workflow needs.

Background: Dysfunction of the KCND3-encoded Kv4.3 channel, which carries the transient outward potassium current (Ito), has long been suspected to contribute to the pathophysiology of Brugada Syndrome (BrS). Although recent genome-wide association studies (GWAS) have implicated KCND3, the role of rare variation in this gene remains uncertain and clinically unactionable. Methods: Genome sequencing was performed in 983 BrS probands from Europe and Thailand. Putative gain-of-function (GoF) rare variants in KCND3 identified in patients were functionally characterized by patch-clamp analysis of Kv4.3 current properties using a HEK293 cell heterozygous model. Biobank datasets were utilized to evaluate rare-common variant interaction at the KCND3 locus. Results: Eight BrS cases carried six different rare KCND3 variants which clustered at the Kv4.3 C-terminus, with terminal exon rare variants significantly enriched in cases versus study (p=0.004) and population (p=2.0e-6) controls. Four of the five KCND3 case variants studied demonstrated significant GoF effects versus wild-type and putative benign variants, including increased Ito amplitude (p.Leu586Val, p.Ala634Thr) and slower inactivation (p.Gly600Arg, p.Ala654Thr, p.Ala634Thr). Analysis of p.Gly600Arg carriers in the UK Biobank and All of Us revealed a significant enrichment of the protective KCND3 expression-reducing allele of the GWAS lead single-nucleotide polymorphism rs12090194, suggesting a possible epistatic common-rare variant interaction modifies penetrance in carriers. Conclusions: GoF rare variants at the C-terminus of KCND3 are associated with BrS in a small proportion of cases. Determination of the rare and common variant status in BrS patients and their relatives may provide information about disease risk.

We investigated the genetic basis of a previously unclassified congenital vascular anomaly in a patient with multifocal cutaneous vascular tumors. Through genomic analysis, we identified a novel heterozygous de novo germline variant in GA-binding protein-alpha (GABPA), an ETS family transcription factor. Histopathologic evaluation demonstrated capillary-venous lesions lacking glucose transporter 1 expression, distinguishing this entity from common infantile hemangioma. Notably, the tumor vasculature exhibited a prominent alpha-SMA-positive perivascular cell layer, with nuclear localized GABPA detected in endothelial and perivascular cells. The GABPA c.509T>G (p.L170R) variant is absent from large population databases, including gnomAD, DeCAF, and RGC-MCPS databases, indicating it is extremely rare. The affected leucine residue is highly conserved across species and located within the Pointed (PNT) domain, a critical region mediating GABPA protein-protein interactions. AlphaMissense predicts this substitution to be highly damaging. Structure-based analysis using an AlphaFold-predicted approach, combined with in silico mutagenesis and molecular interaction analyses, revealed that the L170R substitution introduces new electrostatic interactions while disrupting native hydrophobic contacts within the PNT domain. Functional assessment in zebrafish demonstrated that mosaic stromal expression of GABPA-L170R caused abnormal vascular architecture compared with GABPA-wild-type controls, establishing a direct link between this variant and disrupted vascular development. Collectively, the genetic rarity, evolutionary conservation, predicted structural perturbation, and disruptive effects on vascular development establish GABPA-L170R as likely disease-causing variant. These findings define a new molecular mechanism underlying congenital vascular tumor formation and expand the role for ETS-family transcriptional regulation in human vascular anomalies.

Background: Cervical spinal cord (CSC) compression and myelopathy are frequent, severe complications in mucopolysaccharidosis (MPS) types I and VI. Early detection is critical to prevent irreversible neurological deficits and preserve quality of life. This prospective study aimed to identify quantitative neuroimaging biomarkers of structural CSC damage and myelopathy in MPS I and VI. Methods: Structural and diffusion magnetic resonance imaging (MRI) of the CSC was analyzed in 17 MPS I patients, 3 MPS VI patients (19{+/-}7 years), and 19 case-matched healthy controls (20{+/-}7 years). CSC macrostructure (cross-sectional area, diameters) and microstructure (fractional anisotropy [FA], radial [RD], mean, axial diffusivities) were evaluated within and beyond the maximal compression areas. Results: MPS patients demonstrated reduced CSC cross-sectional area and anterior-posterior diameter at upper cervical levels, alongside widespread microstructural alterations (lower FA, higher RD) throughout the CSC versus controls (pFDR<0.05). Restricted foramen magnum space was associated with microstructural damage at lower cervical levels without overt macrostructural compression. Morphological and microstructural metrics were sensitive to CSC compression and myelopathy severity (pFDR<0.05). Lower CSC integrity correlated with more advanced growth retardation (p<0.001). Among patients receiving hematopoietic stem cell transplantation, earlier treatment correlated with preserved upper CSC morphology (p<0.05). Distinct neuroimaging phenotypes were observed across MPS genotypes (pFDR<0.05). Conclusions: CSC MRI provides candidate neuroimaging biomarkers for early detection and characterization of myelopathy in MPS I and VI. Structural damage extends beyond primary maximal compression areas, highlighting these markers for clinical monitoring and future therapeutic trials.

Purpose A significant proportion of cases with rare inherited retinal disease (IRD) remain genetically unresolved following short-read whole genome sequencing (WGS). This study aimed to increase the diagnostic yield of two cohorts in a research setting. One cohort was previously screened by short-read WGS (n=120 cases), while the second cohort (n=28 cases) was not included in any previous short-read WGS studies. In contrast to the larger cohort, these cases only underwent either exome sequencing (ES) or single-molecule molecular inversion probe (smMIPs) sequencing as pre-screening in earlier studies. For all cases, we performed a stepwise, case by case reanalysis in which short-read WGS was generated (n=28 cases) and (re)analyzed short-read WGS data using an optimized approach. For a subset of cases (n=20) that remained unresolved, this was followed by long read WGS. Together, these steps aimed to improve the diagnostic yield in these cohorts. Methods Short-read WGS data of 148 IRD-cases were (re)analyzed using updated allele frequency databases, new variant caller and variant predictor tools, as well as updated and extended gene-panels to identify causal single nucleotide variants (SNVs) and structural variants (SVs). For 20 genetically unresolved cases with sufficient high-quality DNA available, long-read WGS was performed. Results The (re)analysis of short-read WGS data in the 120 previously WGS-screened unresolved cases resulted in a diagnostic yield of 15% (18/120). For the 28 individuals without prior WGS, performing WGS analysis within this study provided an additional yield of 32% (9/28). Furthermore, long-read WGS contributed two genetic diagnoses among the 20 long-read WGS-sequenced probands. Amongst other reasons, new genetic diagnoses were attributed to pathogenic variants in genes newly associated with IRDs and in genes that were not included in the gene panels applied in previous WGS studies. The Mobile Element Locator Tool facilitated the identification of two pathogenic Alu insertions in short-read WGS. Long-read WGS identified two additional pathogenic variants. Conclusion These results support periodic reanalysis of existing short-read WGS data as a key component of IRD genetic diagnostics, with selective long-read WGS representing a valuable additional approach for unresolved cases. Together, these complementary strategies offer a practical framework for improving molecular diagnosis and narrowing the remaining diagnostic gap in IRDs.