Spondyloepimetaphyseal dysplasia with joint laxity, type 2 (SEMDJL2) is a rare skeletal disorder caused by pathogenic variants in KIF22, a mitotic chromokinesin that generates polar ejection forces (PEFs) to ensure proper chromosome alignment and segregation. Although SEMDJL2-associated variants disrupt chromosome segregation in epithelial cells, their effects in chondrocytes remain poorly understood. Here, we examined the functional consequences of the hotspot, dominant variant R149Q, a recently reported recessive variant R49Q, and two new dominant variants, P144T and E222Q, in human chondrocytes. Both novel variants were found in individuals with classic SEMDJL2 phenotypes. P144T and E222Q retained PEF-generating activity, whereas R49Q displayed reduced PEFs, consistent with their inheritance patterns. Live-cell imaging revealed that all variants perturbed mitosis. The heterozygous variants (P144T, E222Q, and R149Q) dominantly impeded anaphase chromosome segregation and spindle pole separation, supporting classification as likely pathogenic. In contrast, R49Q produced milder, partially penetrant defects, consistent with reduced and dysregulated motor activity. These findings support a model that defines two mechanistic classes of KIF22 dysregulation: constitutive activation in heterozygous variants, which fail to inactivate KIF22 at anaphase onset, and mixed-state dysregulation in the recessive R49Q variant. This work broadens the mechanistic framework linking KIF22 variants to disrupted chondrocyte mitosis and SEMDJL2.

BACKGROUND:Achondroplasia is a genetic skeletal condition caused by FGFR3 pathogenic variants. Infigratinib, an oral FGFR1-3 tyrosine kinase inhibitor, down-regulates key pathways in the pathogenesis of achondroplasia. METHODS:In this phase 3, multicenter, double-blind, placebo-controlled trial, we randomly assigned children with achondroplasia (3 to 17 years of age) in a 2:1 ratio to receive infigratinib (at a dose of 0.25 mg per kilogram of body weight) or placebo once daily for 52 weeks. The primary end point was the change from baseline in the annualized height velocity in the infigratinib group as compared with the placebo group at week 52. Key secondary end points were the change from baseline in the height z score and in the upper-to-lower body segment ratio at week 52. The primary analysis evaluated the treatment effect at week 52 in the full analysis population, with missing data handled with a prespecified imputation approach. RESULTS:In all, 114 patients underwent randomization: 75 patients to receive infigratinib (with 1 withdrawal before treatment) and 39 patients to receive placebo. The difference between infigratinib and placebo in the least-squares mean change from baseline to week 52 was 1.74 cm per year (95% confidence interval [CI], 1.31 to 2.17; P<0.001) for the annualized height velocity, 0.32 (96% CI, 0.23 to 0.41; P<0.001) for the height z score, and -0.02 (96% CI, -0.06 to 0.01) for the upper-to-lower body segment ratio. Adverse events occurred in 71 of 74 patients (96%) in the infigratinib group and in 37 of 39 patients (95%) in the placebo group; serious adverse events occurred in 4 of 74 patients (5%) and 1 of 39 patients (3%), respectively. No serious adverse events or adverse events leading to treatment discontinuation were considered by the investigator to be related to infigratinib or placebo. CONCLUSIONS:In children with achondroplasia, treatment with once-daily oral infigratinib for 52 weeks resulted in a significantly greater increase from baseline in the annualized height velocity than placebo. (Funded by BridgeBio Pharma; PROPEL 3 ClinicalTrials.gov number, NCT06164951; EudraCT number, 2023-506130-67.).

BACKGROUND:Hypochondroplasia, a fibroblast growth factor receptor 3 (FGFR3)-related skeletal condition characterized by disproportionate short stature and a spectrum of clinical features, has no available targeted therapies. Vosoritide, a C-type natriuretic peptide analogue approved for the treatment of achondroplasia, is being investigated for hypochondroplasia. METHODS:In this phase 3, multicenter trial, children with hypochondroplasia who were 3 to less than 18 years of age were randomly assigned to receive once-daily subcutaneous injections of vosoritide or placebo for 52 weeks per weight-band dosing regimen. The primary end point was change from baseline in annualized growth velocity at week 52 versus placebo. Confirmatory statistical testing using hierarchical procedures to control for type I error at the one-sided 0.025 significance level (equivalent to the two-sided 0.05 level) was performed for the primary and six key secondary efficacy end points. The safety and side effect profile of vosoritide versus placebo was assessed. RESULTS:A total of 81 participants were randomly assigned to receive vosoritide (n=41) or placebo (n=40). At week 52, the least squares mean (LSM) change from baseline in annualized growth velocity was 1.95 cm/year with vosoritide versus -0.39 cm/year with placebo (LSM difference of 2.33 cm/year; 95% confidence interval, 1.85-2.82 cm/year; two-sided P<0.0001). Most participants in the vosoritide group (87.8%) and the placebo group (72.5%) experienced at least one adverse event (AE). There were no reports of grade 3 or higher AEs, AEs leading to treatment discontinuation, or deaths. CONCLUSIONS:One year of vosoritide treatment significantly increased linear growth in children with hypochondroplasia. (Funded by BioMarin Pharmaceutical; ClinicalTrials.gov number, NCT06455059.).

Episignatures are increasingly valuable for variant interpretation in rare neurodevelopmental disorders, especially when optimized to capture the impact of specific variant types and locations across a gene. Here, we generated a next-generation DNA methylation (DNAm) episignature for Kabuki syndrome type 1 (KS1) using the largest cohort studied to date, aiming to clarify the epigenomic and phenotypic effects of diverse KMT2D variant types and positions. Genome-wide DNAm profiles were obtained for 110 individuals with KMT2D variants and 854 controls using microarrays and long-read sequencing (LRS). Differentially methylated loci were enriched in genes involved in embryonic and nervous system development and were leveraged to construct a support-vector machine classifier for detecting pathogenic KMT2D variants. The classifier achieved 97% sensitivity and 100% specificity in validation cohorts and outperformed in silico tools, demonstrating stronger concordance with clinical presentation. Missense variants in the C-terminal region (exon 48) of KMT2D and the N-terminal plant homeodomain (PHD)-type zinc fingers were predominantly classified as pathogenic, highlighting regions enriched for pathogenic variants. Missense variants in the central region (exons 31-39) were more often predicted benign for KS1, consistent with potential association with a different syndrome, highlighting the classifier's specificity for KS1. Test performance was consistent across array and LRS platforms, and classifier scores reflected levels of mosaicism detected by LRS. The KS1 episignature also positively classified pathogenic KDM6A variants associated with KS2. These findings represent a significant advance in the evolution of episignature development, demonstrating diagnostic and interpretive value of a KS1 signature in resolving uncertain or complex cases.

RNA-binding proteins (RBPs) regulate gene expression, and a number of RBPs have been implicated in brain function and behavior. Here, we report 16 individuals with a neurodevelopmental disorder and de novo heterozygous variants in ELAVL2, encoding an RBP not previously linked to Mendelian disease. Thirteen individuals were identified through GeneMatcher. Their ELAVL2 variants include two structural, five nonsense, and six missense variants, supporting haploinsufficiency as the primary disease mechanism. The cohort presented with developmental delay, intellectual disability, autism spectrum disorder, seizures, sleep problems, sensory processing issues, emotional instability, and difficulty with socialization. Three additional variants (two missense and one terminal exon truncation), each previously reported in a different large cohort study, were also included for follow-up investigations. We provide multiple lines of evidence linking variants in ELAVL2 to the observed neurodevelopmental and behavioral phenotypes. First, we show that common genetic variants in ELAVL2 are significantly associated with intelligence, motor development, sleep-related traits, and sociability in the general population. Drosophila loss-of-function models provide further independent evidence for a conserved role in the regulation of seizure-like behavior, sensory processing, and sleep. Molecular studies confirm that some of the missense variants are deleterious, leading to decreased protein levels. Together, our integrative study combining Mendelian genetics, clinical and association studies, and animal and molecular modeling supports variants in ELAVL2 as a cause of a neurodevelopmental disorder, with haploinsufficiency as the disease mechanism, and identifies crucial roles of ELAVL2 in neuronal function, cognition, and behavior.

Objectives Systemic inflammatory diseases (SIDs) are characterized by non-infectious multisystem inflammation. Genetic panels diagnose only 25% of suspected SID patients, due to SIDs’ clinical and genetic heterogeneity. We hypothesize that unsupervised machine learning and multifactorial data integration of clinical and laboratory data will improve the diagnosis and management of SIDs by identifying clinically based patient phenotypes. Methods We included pediatric genetically undiagnosed SID patients (symptom onset <18 years old) with clinical, laboratory, and whole-exome sequencing data. Genetic ancestry was inferred using principal components and PEDDY with 1K Genomes as a referent. Disease manifestations were divided into clinical and laboratory data sets, weighted by missingness and the data set size, then input into similarity network fusion (SNF) to identify patient clusters. Fisher’s exact test (Bonferroni corrected P<0.0004) identified variables with different distributions between clusters. Clusters were validated with 1000 independent simulated SNFs (simSNF). In each simSNF, we randomly used 70% of the cohort, thereafter the results across all iterations were aggregated. We tested autosomes (n=17443) and chromosome X (n=737) gene-level associations between SNF-clusters, adjusted for sex and ancestry, using SKAT-O (SAIGEv1.4.5). We completed gene set enrichment pathway analysis aggregated with SKAT-O genetic associations across all Biological Process Gene Ontology pathways. We estimated the effective number of independent pathways (Galwey method, P<4.9x10-5; 0.05/3571 independent pathways). Results We included 104 patients with undifferentiated SID (Figure 1A). SNF revealed 2 clusters. The median age of symptom onset in cluster 1 (n=72) was 5.7 years (Q1-Q3: 3.3-11.2) and cluster 2 (n=32), 6 years (Q1-Q3: 1-13.6). Cluster 2 included patients with consistently higher prevalence (>946/1000 simSNFs) of elevated levels of IgG antibodies (according to each laboratory’s reference standard), transaminitis, anti-nuclear antibodies, anemia, and macrophage activation syndrome compared to patients in cluster 1 (P<4.9×10^-5; Figure 1B). Laboratory manifestations predominantly characterized the clusters. Sensitivity analysis demonstrated that 89% of patients consistently clustered together over 1000 simSNFs. Individually, none of the tested genes were associated with cluster membership (P>2.5×10^-6). Pathway analysis demonstrated a significant association between ”flavonoid metabolic process” GO:0009812 and cluster membership (NES=1.94; P=3.7×10^-6). This metabolic process is a known anti-inflammatory pathway responsible for arachidonic acid metabolism, inhibiting NF-κB and MAPK signaling, and suppressing dendritic and mast cell activation. Figure 1: (A) Demographic and clinical characteristics of the SID cohort (n=104). (B) Clinical and laboratory manifestations with different prevalences between SNF clusters. Clinical manifestations are labelled in blue and laboratory manifestations are labeled in purple. “MAS” stands for macrophage activation syndrome. Difference in manifestation prevalence between clusters was determined with a fisher’s exact test. A Bonferroni corrected threshold for significance was set at P <0.0004 (0.05/125 independent tests). Conclusion We identified 2 robust patient clusters from clinical and laboratory manifestations in a heterogeneous SID cohort with SNF. Cluster differences were primarily influenced by laboratory manifestations. Future work will use imputed gene expression to determine the role of flavonoid metabolism on SID pathogenesis.

[This corrects the article DOI: 10.1016/j.bonr.2025.101857.].

Dysregulation of genes encoding the homologous to E6AP C-terminus (HECT) E3 ubiquitin ligases has been linked to cancer and structural birth defects. One member of this family, the HECT-domain-containing protein 1 (HECTD1), mediates developmental pathways, including cell signaling, gene expression, and embryogenesis. Through GeneMatcher, we identified 14 unrelated individuals with 15 different variants in HECTD1 (10 missense, 3 frameshift, 1 nonsense, and 1 splicing variant) with neurodevelopmental disorders (NDDs), including autism, attention-deficit/hyperactivity disorder, and epilepsy. Of these 15 HECTD1 variants, 10 occurred de novo, 3 had unknown inheritance, and 2 were compound heterozygous. While all individuals in this cohort displayed NDDs, no genotype-phenotype correlation was apparent. Conditional knockout of Hectd1 in the neural lineage in mice resulted in microcephaly, severe hippocampal malformations, and complete agenesis of the corpus callosum, supporting a role for Hectd1 in embryonic brain development. Functional studies of select variants in C. elegans revealed dominant effects, including either change-of-function or loss-of-function/haploinsufficient mechanisms, which may explain phenotypic heterogeneity. Significant enrichment of de novo variants in HECTD1 was also shown in an independent cohort of 53,305 published trios with NDDs or congenital heart disease. Thus, our clinical and functional data support a critical requirement of HECTD1 for human brain development.

BACKGROUND Achondroplasia is a genetic skeletal condition that results in disproportionately short stature and medical complications throughout life. Infigratinib is an orally bioavailable FGFR1-3 selective tyrosine kinase inhibitor in development for achondroplasia. METHODS In this phase 2 dose-finding study, we evaluated the safety and efficacy of oral infigratinib in children with achondroplasia between the ages of 3 and 11 years. A total of 72 children were enrolled in five sequential cohorts to receive daily infigratinib at doses of 0.016 mg per kilogram of body weight (cohort 1), 0.032 mg per kilogram (cohort 2), 0.064 mg per kilogram (cohort 3), 0.128 mg per kilogram (cohort 4), and 0.25 mg per kilogram (cohort 5) for 6 months, followed by 12 months of extended treatment in which the dose in cohorts 1 and 2 could be escalated to the next ascending level at months 6 and 12. The primary safety outcome was the incidence of adverse events that led to a decrease in the dose or discontinuation of infigratinib. The primary efficacy outcome was the change from baseline in the annualized height velocity. RESULTS During treatment, all the children had at least one adverse event, most of which were mild or moderate in severity; none resulted in treatment discontinuation. In cohort 5, an increased annualized height velocity was observed, which persisted throughout the duration of the study, with a mean change from baseline at 18 months of 2.50 cm per year (95% confidence interval [CI], 1.22 to 3.79; P=0.001). The mean change from baseline in height z score was 0.54 (95% CI, 0.35 to 0.72) relative to an untreated achondroplasia reference population at 18 months; the mean change from baseline in the upper-to-lower body segment ratio was -0.12 (95% CI, -0.18 to -0.06). CONCLUSIONS The administration of oral infigratinib did not result in any apparent major safety signal and increased the annualized height velocity and z score and decreased the upper-to-lower body segment ratio at 18 months of treatment in cohort 5.

Classical homocystinuria is an inherited metabolic disease of homocysteine metabolism due to biallelic pathogenic variants in CBS. The biochemical hallmark is elevated homocysteine and methionine levels. The treatment consists of betaine supplementation and protein restricted diet. We report two adult siblings with late diagnosis of classical homocystinuria, a variable phenotype and good response to the treatment. Patient 1 is a 29-year-old female with a history of myopia, Marfanoid habitus with significant kyphoscoliosis, anxiety and a psychotic episode. Clinical exome sequencing identified compound heterozygous pathogenic variants in CBS (c.209+1G>A; c.992C>T (p.Ala331Val)). She had markedly elevated homocysteine (298 μmol/L) and methionine (1040 μmol/L) levels. Her brain magnetic resonance spectroscopy revealed a low n-acetyl-aspartic acid peak. She was started on betaine supplementation, and a protein-restricted diet (0.8 g/kg/day) leading to significant decrease in her homocysteine (37 μmol/L) and methionine (49 μmol/L) levels. Patient 2 is a 27-year-old female (younger sibling) with a history of anxiety, one generalized tonic-clonic seizure and a dural sinus thrombosis in neuroimaging. She had both familial CBS variants and markedly elevated homocysteine (152 μmol/L) and methionine (560 μmol/L) levels, which were improved significantly on betaine supplementation and the protein-restricted diet. Both siblings had average range intellectual abilities. Higher homocysteine levels may result in severe skeletal, and central nervous system phenotypes.

Poly(rC)-binding protein 1 (PCBP1), a splicing factor and key member of the hnRNP E family, was initially characterized for its tumor suppressive properties. More recently, its role in regulating gene expression in the brain and nervous system has attracted growing interest. Through an international multicenter collaboration, we identified 13 de novo pathogenic variants in PCBP1 across 13 unrelated families. All affected individuals exhibited intellectual disability (ID), with autism spectrum disorder (ASD) as a prominent feature. Functional analysis in primary hippocampal mouse neuron cultures demonstrated that PCBP1 variants impair dendritic arborization, underscoring their deleterious effects. Transcriptomic profiling by RNA sequencing of subjects-derived T cells showed a distinctive signature characterized by significantly increased exon skipping. These results highlight the essential role of PCBP1 in neurogenesis and neuritogenesis, revealing the impact of loss-of-function variants in cells harboring PCBP1 pathogenic variants, thereby confirming the link between splicing defects and neurodevelopmental disorders. Collectively, our findings demonstrate the critical role of PCBP1 in neurodevelopment, reaffirming the importance of splicing regulation in mammalian neurodevelopment.

Family mapping is a useful tool for tracking the inheritance of rare inherited diseases, including hypophosphatasia (HPP), through generations. We show the inheritance of HPP in 6 affected families, describing genetic variants, biochemical hallmarks, and clinical manifestations among family members. Mapping families with HPP is warranted in clinical practice to better understand monitoring needs for potentially affected individuals over time, since manifestations of HPP can arise throughout a patient's lifespan.

Osteofibrous dysplasia (OFD) is a rare, benign, fibro‐osseous lesion that occurs most commonly in the tibia of children. Tibial involvement leads to bowing and predisposes to the development of a fracture which exhibit significantly delayed healing processes, leading to prolonged morbidity. We previously identified gain‐of‐function mutations in the MET gene as a cause for OFD. In our present study, we test the hypothesis that gain‐of‐function MET mutations impair bone repair due to reduced osteoblast differentiation. A heterozygous Met exon 15 skipping (MetΔ15‐HET) mouse was created to imitate the human OFD mutation. The mutation results in aberrant and dysregulation of MET‐related signaling determined by RNA‐seq in the murine osteoblasts extracted from the wide‐type and genetic mice. Although no gross skeletal defects were identified in the mice, fracture repair was delayed in MetΔ15‐HET mice, with decreased bone formation observed 2‐week postfracture. Our data are consistent with a novel role for MET‐mediated signaling regulating osteogenesis.