The phenotypic spectrum associated with pathogenic ARID1B variants is remarkably broad, ranging from classic Coffin-Siris syndrome to non-syndromic intellectual disability and autism spectrum disorders. While speech delay, motor impairments and learning difficulties are well documented, brain imaging investigations remain scarce in this population. We combined multimodal neuroimaging and neuropsychological assessments in 12 patients carrying pathogenic ARID1B variants (age = 13.8 ± 4.7 years) and 34 age-matched healthy controls. Whole-brain voxel-wise analyses included arterial spin labelling to measure cerebral blood flow (CBF) at rest and voxel-based morphometry to assess grey matter density. To investigate white matter abnormalities, we performed fixel-based analysis in a subgroup of 7 patients and 17 age-matched controls. While patients showed pronounced language, motor and social impairments, their memory performance ( + 5 SD) largely exceeded other cognitive and motor skills. Whole-brain voxel-wise analyses showed a significant bilateral increase of CBF at rest in several limbic structures, including hippocampi and visual areas. They also showed significant decrease in grey matter density and fibre density in the same limbic structures, language, motor and social circuits. This paradoxical coexistence of hyperperfusion and structural deficits within memory networks suggests functional resilience or compensatory mechanisms. These preserved visual and memory functions strongly contrasted with their impaired language, motor, and social abilities. Patients appeared to rely on visual cues and memory to compensate for deficits in verbal communication. These findings support the development of individualized and innovative interventions that build on preserved visual and memory abilities in children with pathogenic ARID1B variants.

Autism spectrum disorder (ASD) is a heterogeneous condition in which genetically defined subtypes offered insights into underlying biological mechanisms and potential targeted treatments. Here, we investigate the clinical and pathogenic significance of GIGYF2 variants in ASD through an integrated approach combining clinical genetics, conditional knockout (cKO) mouse models, neurobiology, and molecular studies. Through targeted sequencing, large-scale genomic data analysis of neurodevelopmental disorder cohorts, and international collaborations, we identified ten affected individuals from eight families harboring de novo or dominantly inherited likely gene-disruptive (LGD) variants and 13 affected individuals from 13 families with de novo missense variants in GIGYF2. Clinical characterization of 16 probands with GIGYF2 variants revealed common features, including ASD, language problems, intellectual disability, and anxiety. In a Gigyf2 cKO mouse model, we observed pronounced autistic-like behaviors, cognitive deficits, and anxiety-like behaviors, mirroring phenotypes observed in affected individuals. Mechanistically, Gigyf2 deficiency disrupted synaptic homeostasis, as evidenced by altered spine density and miniature excitatory postsynaptic currents, and impaired IGF-1R/mTOR signaling, along with dysregulation of synapse-related genes such as Nrp2. Pharmacological inhibition of mTOR with rapamycin or Torin1, as well as Nrp2 knockdown rescued synaptic defects in Gigyf2 KO neurons. These findings define a novel ASD subtype associated with GIGYF2 variants and establish GIGYF2 as a key regulator of synaptic development and function, implicating GIGYF2 dysfunction in ASD pathogenesis and highlighting the IGF-1R/mTOR pathway as a potential therapeutic target for GIGYF2-related ASD subtype.

Background Pathogenic variants in FBXO11 cause a syndromic neurodevelopmental disorder characterised by intellectual disability, behavioural abnormalities, and subtle facial dysmorphism. The genotypic-phenotypic spectrum remains incompletely defined. Methods We describe 21 previously unreported individuals with heterozygous pathogenic or likely pathogenic FBXO11 variants identified through clinical exome/genome sequencing. Detailed phenotypic data were collected and compared with published cases. Facial similarity was assessed using GestaltMatcher. Based on aggregated data, we propose structured diagnostic criteria. Results Mild intellectual disability (86%), facial dysmorphism (67%), hypotonia (62%), and behavioural dysregulation (62%) were the most prevalent features. Microcephaly occurred in 24%, while seizures were present in 43%. Brain imaging abnormalities were nonspecific and did not consistently correlate with epilepsy. Variants included missense, truncating, and multi-exon deletions, supporting haploinsufficiency as the principal pathogenic mechanism. Computational facial analysis demonstrated measurable intra-cohort similarity. Conclusion FBXO11 -related neurodevelopmental disorder frequently presents with mild cognitive impairment and subtle dysmorphism, suggesting under-recognition in milder cases. We propose semi-quantitative diagnostic criteria to support phenotypic assessment and variant interpretation.

Background : Phelan–McDermid syndrome (PMS) is a neurodevelopmental disorder caused by pathogenic variants involving the SHANK3 gene, a key postsynaptic scaffolding protein regulating synaptic function. SHANK3 alterations range from sequence variants to large chromosomal deletions on chromosome 22q13. While SHANK3 haploinsufficiency alone produces core PMS features, larger deletions encompassing adjacent genes are associated with more severe motor, speech, and cognitive phenotypes, whereas smaller deletions may lead to distinct neurobehavioral profiles. Methods : We conducted a multimodal study integrating molecular genetics and neuropsychological assessment with structural MRI, voxel-based morphometry (VBM) and arterial spin labeling (ASL) perfusion imaging in 36 individuals with de novo SHANK3 variants, including 21 sequence variants and 15 deletions ranging from (68.64 kb to 8.7 Mb). Deletions were stratified into Class I (involving SHANK3 only or with ARSA , ACR , and/or RABL2B ) and Class II (all other deletions). Results : Class II deletions were strongly associated with cortico-subcortical atrophy (10/15 vs. 0/21; p = 0.00001) and corpus callosum abnormalities. The group with larger deletions (Class II) showed a distinctive anomaly of the forceps minor, characterized by marked enlargement and dysmorphism (8/8 vs 0 in other groups; p < 0.001) and severe nonverbal social communication deficits. This feature was absent in Class I deletions and sequence variants. A minimal 760 kb critical region, including CERK , TBC1D22A , CELSR1 , and GRAMD4 , was implicated in these anomalies. VBM analyses revealed widespread reductions in gray and white matter volumes in carriers of Class II deletions, predominantly in frontotemporal and parietal regions, whereas sequence variants showed no significant volume loss. ASL imaging demonstrated reduced cerebral blood flow in key regions of the social brain network, particularly within the bilateral superior temporal cortex. Limitations : Multimodal MRI without premedication remains challenging in children older than 5 years due to motion, particularly with longer acquisition times. Conclusions : The identification of a minimal overlapping deleted region encompassing multiple candidate genes supports the contribution of additional loci within 22q13 to disease expression. These findings refine genotype–phenotype correlations in PMS and provide evidence that the disorder associated with larger deletions may be regarded as a contiguous gene syndrome.

Small nuclear RNAs (snRNAs) are essential components of the spliceosome. De novo variants in snRNA genes RNU4-2 (ReNU syndrome), RNU5B-1 and RNU2-2 have been linked to dominant neurodevelopmental disorders (NDDs), revealing a large unexpected contribution of noncoding RNA genes to genetic diseases. Here, through international collaborations, we analyze systematically 200 potentially functional snRNA genes in a French cohort of 34,329 people with rare disorders. We report RNU2-2 variants in 141 individuals, including 35 with recurrent dominant pathogenic variants and 91 affected members from 73 families with biallelic variants. Recessive RNU2-2 NDD is at least twice as frequent as the dominant form and often involves a de novo variant in trans with an inherited allele, consistent with the high mutability of snRNA genes. Dominant and recessive RNU2-2 NDDs share overlapping clinical features, with frequent epilepsy. Blood transcriptomics and DNA methylation analyses revealed subtle, variant-specific effects on splicing and episignatures. Our results support a gradient-of-impact model bridging dominant and recessive inheritance, and establish RNU2-2 variants as a principal contributor to NDDs, nearly as prevalent as ReNU syndrome.

Nuclear factor I (NFI) transcription factors regulate neural stem and progenitor differentiation during brain development. While NFIA, NFIB, and NFIX are linked to neurodevelopmental disorders, the role of NFIC (MIM: 600729) in human disease remains unclear. This study aimed to determine whether NFIC contributes to a neurodevelopmental syndrome, define its phenotype, and assess dosage-dependent effects. We established the first cohort of 11 individuals, including NFIC deletions and single nucleotide variants. Genotype-phenotype correlations, including critical region mapping, were performed. Murine data and bioinformatics were integrated to explore underlying pathomechanisms. We report 11 individuals with NFIC variants, including four with de novo SNVs and seven with deletions encompassing the gene, of whom nine have not been previously reported. A core phenotype of syndromic intellectual disability and macrocephaly was delineated. Opposing cranial phenotypes relative to proximal 19p13.3 duplication cases support a dosage-sensitive effect and a mirror-syndrome model. NFIC-related disorder represents a novel neurodevelopmental syndrome characterized by intellectual disability and macrocephaly, highlighting the importance of NFIC dosage supporting a mirror-syndrome model.

PURPOSE:ZIC1 encodes a transcription factor with critical roles in vertebrate neural and skeletal development. Heterozygous deletions encompassing ZIC1 and ZIC4 cause Dandy-Walker malformation, whilst in the final exon heterozygous ZIC1 variants result in a distinct phenotype of craniosynostosis with variable intellectual disability via a gain-of-function mechanism. We describe the largest group of individuals harboring ZIC1 variants to date, significantly expanding the phenotypic spectrum and allowing genotype-phenotype correlation. METHODS:Through international collaboration we identified 18 different heterozygous ZIC1 variants from 22 families, comprising 30 individuals. RESULTS:Twelve families segregated a phenotype comprising craniosynostosis with facial dysmorphism, structural brain abnormalities and developmental delay, whereas 10 families had a neurodevelopmental disorder alone without craniosynostosis. Variants associated with craniosynostosis were clustered in the final exon (3) and were predominantly truncating variants predicted to escape nonsense-mediated decay. Variants associated with neurodevelopmental disorder alone included missense substitutions within exons 1 and 2 predicted to disrupt the normal function of the zinc-finger domain, leading to loss of ZIC1 function, which was confirmed in a functional assay. CONCLUSION:This study presents evidence for a ZIC1 genotype-phenotype correlation differentiating variants that cause a neurodevelopmental phenotype with and without craniosynostosis.

BACKGROUND: Recent advances in sequencing technologies have enhanced patient diagnosis; however, causal pathogenic variants remain unidentified for a significant number of patients due to limited understanding of certain variants, regulatory sequences, or sequencing challenges, such as complex rearrangements. Investigating the epigenetic landscape has become essential to improve the diagnostic yield. Diseases caused by pathogenic variants in epigenetic regulators, often associated with growth abnormalities, intellectual disability, and facial dysmorphism, are prime models for studying episignatures. Among them, Snijders Blok-Campeau syndrome (ORPHA:599082), caused by pathogenic variants in the CHD3 gene, remains largely understudied. METHODS: A European cohort of 23 patients displaying typical Snijders Blok-Campeau syndrome traits and carrying pathogenic/likely pathogenic CHD3 variants was analysed using the Illumina EPIC array, identifying 270 differentially methylated positions distinguishing patients from 62 healthy matched controls. A subset of these regions serves as diagnostic tools for complex cases or variants of uncertain significance and helps uncover deregulated pathways linked to this syndrome. Four patients carrying pathogenic/likely pathogenic variants but with atypical clinical presentation, as well as 10 patients with variants of uncertain significance, were analysed as the testing set. RESULTS: Comparing methylomes of patients carrying pathogenic variants in CHD3, CHD7 (CHARGE syndrome, ORPHA:138), and CHD8 (Intellectual developmental disorder with autism and macrocephaly, ORPHA:642675) genes allows us to identify distinct subgroups with unique methylation profiles. This CHD3 DNA methylation signature aids in reclassifying variants and diagnosing atypical cases. CONCLUSIONS: Our findings advance the field of epigenetic signatures in rare diseases. We have opened new avenues for further investigation into subtypes defined by methylome assays (such as in the context of chromatinopathies), which could refine the phenotype spectrum and help predict patient outcomes.

PACS1-related disorder (PACS1-RD), also known as Schuurs-Hoeijmakers syndrome, is a rare autosomal dominant neurodevelopmental disorder predominantly caused by the recurrent de novo c.607 C > T p.(Arg203Trp) gain-of-function variant. Although core clinical features have been delineated, systematic data on developmental milestones, growth parameters, and clinical variability remain limited. We assembled a series of 24 previously unreported, unrelated individuals with PACS1-RD and compared their clinical and molecular features with 84 individuals from the literature. Genome-wide DNA methylation profiling was performed on peripheral blood DNA using bisulfite sequencing, interrogating ~860,000 CpG sites. Our study expands the phenotypic spectrum of PACS1-RD by reporting median age at independent walking and first spoken words (both 24 months), cross-sectional growth parameters, and previously undescribed clinical features, including congenital kidney malformations (25%) and feeding difficulties (75%). Compared with the literature, our series showed a higher prevalence of cryptorchidism (77.8%), congenital heart defect (45.8%), and hypotonia (75%). Methylation analysis identified a specific episignature for PACS1-RD, consistently observed in individuals carrying either the canonical p.(Arg203Trp) or the non-recurrent p.(Arg203Gln) variant. This episignature further enabled PACS1-RD diagnosis in one unsolved individual initially suspected of Kabuki syndrome. These findings refine the clinical delineation of PACS1-RD and establish an episignature that will support diagnosis in unresolved neurodevelopmental disorders and guide pathogenicity assessment of non-recurrent PACS1 variants.

Developmental language disorder (DLD) refers to children who present with language difficulties that are not due to a known biomedical condition or associated with autism spectrum disorder (ASD) or intellectual disability (ID). The clinical heterogeneity of language disorders, the frequent presence of comorbidities, and the inconsistent terminology used over the years have impeded both research and clinical practice. Identifying sub-groups of children (i.e. DLD cases without childhood apraxia of speech (CAS)) with language difficulties is essential for elucidating the underlying genetic causes of this condition. DLD presents along a spectrum of severity, ranging from mild speech delays to profound disturbances in oral language structure in otherwise typically intelligent children. The prevalence of DLD is 7-8

Variants in spliceosomal small nuclear RNA (snRNA) genes RNU4-2 (ReNU syndrome), RNU5B-1, and RNU2-2 have recently been linked to dominant neurodevelopmental disorders (NDDs), revealing a major, previously overlooked role for noncoding snRNAs in human disease. Here, we systematically analysed 200 potentially functional snRNA genes in a French cohort comprising 26,911 individuals with rare disorders and through international collaborations. We identify de novo and biallelic variants in RNU2-2 associated with both dominant and recessive NDDs in 126 individuals from 108 unrelated families. Recessive RNU2-2 NDD is at least twice as frequent as the dominant NDD caused by n.4G>A and n.35A>G, and often arises from a de novo variant in trans with an inherited allele, reflecting the high mutability of snRNA genes. Dominant and recessive RNU2-2-NDDs share overlapping clinical features with frequent epilepsy. Blood transcriptomics and DNA methylation analyses revealed subtle, variant-specific effects on splicing and episignatures. Our findings support a gradient-of-impact model and a continuum between dominant and recessive inheritance, establishing RNU2-2 variants as a frequent cause of NDDs, nearly as prevalent as ReNU syndrome.

Background Facial analysis tools can assist in diagnosing rare genetic syndromes, but their accuracy is limited in ultra-rare conditions and underrepresented ethnicities due to small, biased datasets. Synthetic facial images could enrich training data and improve equity in diagnostic performance. Methods We developed a synthetic face generation pipeline using diffusion models (DreamShaper XL Turbo), enhanced with LoRA-based syndrome-specific domain adaptation and pose conditioning via ControlNet. A total of 4432 synthetic faces were generated across ten rare syndromes, balanced by age (0-18 years), sex (50/50), and ethnicity (33% Caucasian, Afro-Caribbean, Asian). Synthetic and real data were used in four machine learning designs to train and test ArcFace R-100, a phenotyping algorithm for syndromic classification. Results Synthetic faces generated from real patient data achieved high phenotypic realism, with classification performance reaching top-1 accuracy of 0.823 and AUC of 0.991. Adding synthetic images to real training datasets increased accuracy on real test images from 0.766 to 0.869 and improved AUC from 0.988 to 0.993. Performance gains were most significant for ultra-rare syndromes and Asian individuals (top-1: 0.971). Training with synthetic images alone yielded lower accuracy (top-1: 0.606), underscoring their complementary role. Conclusion This study demonstrates that diffusion-generated synthetic faces can enhance inclusivity and accuracy in AI-based dysmorphology tools. These synthetic datasets provide a scalable, ethical solution to data scarcity, with applications in clinical training and telemedicine, especially in underserved regions.

RNA-binding proteins play a key role in post-transcriptional events, such as mRNA splicing, transport, stability, translation and decay. Dysregulation of RNA life can have dramatic consequences. CELF RNA-binding proteins appear to be essential during embryo development. In this study, we identified 15 patients with heterozygous missense or loss-of-function variants in the CELF4 gene by exome or genome sequencing. All variants affecting the N-terminus of the protein are essential and sufficient for the RNA-binding and splicing activity or RRM domains. Most patients presented with neurodevelopmental disorders including global developmental delay/intellectual disability (11/14), seizures (9/15) and overweight/obesity (10/14) that began in childhood. Clinical features are similar to the reported celf4-mouse mutant phenotype. This study highlights the essential role of CELF4 in development and its involvement as a novel etiology of neurodevelopmental disorders with obesity.

The CCR4-NOT complex, crucial in gene expression regulation, includes CNOT3, a subunit linked to neurodevelopmental disorders when mutated. This study investigates 51 patients from 42 families with heterozygous CNOT3 variants, aiming to expand the understanding of CNOT3-related neurodevelopmental disorders and explore genotype-phenotype correlations. Patients originated from various countries, reflecting the disorder’s global significance. All patients exhibited developmental delays, particularly in the language area. Intellectual disability was found in 87% of patients and was typically mild to moderate. Behavioral issues, including autism spectrum disorders and attention deficits, were common, affecting over half of the patients. Dysmorphic features were highlighted and may help establishing the diagnosis. Epilepsy was uncommon (10%). Twenty-eight novel variants were identified, including missense, nonsense, frameshift, intronic variations and a deletion of 12 exons. Missense variants clustered at the N- and C-terminal regions of the protein, indicating critical functional roles. No clear genotype-phenotype correlation was observed, suggesting that all identified variants resulted in a loss-of-function effect. Finally, this work delineates the clinical and molecular spectrum of CNOT3-related disorders thanks to an in-depth characterization of a large cohort. Further research will be necessary to understand the functional consequences of the variants and enhance patient long-term outcomes.

The major spliceosome contains five small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) essential for splicing. Variants in RNU4-2, encoding U4, cause a neurodevelopmental disorder called ReNU syndrome. We investigated de novo variants in 50 snRNA-encoding genes in a French cohort of 23,649 individuals with rare disorders and gathered additional cases through international collaborations. Altogether, we identified 145 previously unreported probands with (likely) pathogenic variants in RNU4-2 and 21 individuals with de novo and/or recurrent variants in RNU5B-1 and RNU5A-1, encoding U5. Pathogenic variants typically arose de novo on the maternal allele and cluster in regions critical for splicing. RNU4-2 variants mainly localize to two structures, the stem III and T-loop/quasi-pseudoknot, which position the U6 ACAGAGA box for 5' splice site recognition and associate with different phenotypic severity. RNU4-2 variants result in specific defects in alternative 5' splice site usage and methylation patterns (episignatures) that correlate with variant location and clinical severity. This study establishes RNU5B-1 as a neurodevelopmental disorder gene, suggests RNU5A-1 as a strong candidate and highlights the role of de novo variants in snRNAs.

BackgroundAarskog-Scott syndrome (AAS) is a rare condition with multiple congenital anomalies, caused by hemizygote variants in theFGD1gene. Its description was based mostly on old case reports, in whom a molecular diagnosis was not always available, or on small series. The aim of this study was to better delineate the phenotype and the natural history of AAS and to provide clues for the diagnosis and the management of the patients.MethodsPhenotypic characterisation of the largest reported AAS cohort, comprising 111 male patients with proven causative variants inFGD1, through comprehensive analyses of clinical data including congenital anomalies, growth and neurodevelopment. Review of photographs and radiographs by experts in dysmorphology and skeletal disorders.ResultsThis study refines the phenotypic spectrum of AAS, with the description of new morphological and radiological features, and refines the prevalence of the features. Short stature is less frequent than previously reported and has a prenatal onset in more than half of the patients. The growth has a specific course with a catch-up during the first decade often leading to low-normal stature in adulthood. Whereas intellectual disability is rare, patients with AAS have a high prevalence of specific learning difficulties and attention hyperactivity disorder. In light of this better knowledge of AAS, we provide management recommendations.ConclusionA better knowledge of the natural history and phenotypic spectrum of AAS will be helpful for the clinical diagnosis and for the interpretation ofFGD1variants using a retrophenotyping strategy, which is becoming the most common way of diagnosis nowadays. Recommendations for care will improve the management of the patients.