Caroline Nava

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.

Retrotransposition has generated thousands of intronless gene copies in mammalian genomes, yet their contribution to brain development and evolution remains largely unexplored. RBMX encodes an X-linked RNA-binding protein involved in pre-mRNA splicing. RBMX has highly similar retrocopies, RBMXL1, which arose independently in primates and rodents, suggesting convergent evolutionary pressure and potential functional compensation. We identified individuals with RBMX variants through exome sequencing and GeneMatcher. We combined transcriptomic profiling, protein-protein and protein–RNA interaction studies both in human cellular models and mouse embryonic cortices to assess the functional redundancy between RBMX and its retrocopy RBMXL1. Finally, we use mouse genetics to dissect RBMX function and its compensation by RBMXL1 in corticogenesis. Hemizygous RBMX variants lead to neurodevelopmental disorders characterized by intellectual disability and variable brain, ocular, and genital malformations. N-terminal variants include missense changes and in-frame deletions, whereas truncating variants clustered in the final exon. RBMX pathogenic variants disrupt cortical development through both partial loss-of function (C-terminal variants) and gain-of-function (N-terminal variants) mechanisms. Despite severe phenotypes in humans, Rbmx-deficient mice display only mild cortical abnormalities. We demonstrate that RBMX and RBMXL1 share protein and RNA partners and act redundantly in brain development, with RBMXL1 buffering the impact of RBMX deficiency. Together, these findings establish RBMXL1 as a functional paralog of RBMX that is likely buffering deleterious variation in a context- and dosage-dependent manner. More broadly, these results identify retrocopies as active contributors to neurodevelopmental robustness and suggest that functional retrocopies may have facilitated the evolutionary diversification of the mammalian brain.

Context: A subset of metabolic diseases is caused by rare monogenic variants. Next-generation sequencing offers a promising approach for identifying such variants, but its application in clinical diagnostics for metabolic disease is limited and the diagnostic yield is unknown. Objective: To determine the diagnostic yield of clinical genome sequencing (GS) in adults presenting with common metabolic diseases. Methods: We performed clinical GS on 560 adults seen in New York clinical practices between August 2020 and December 2023. Participants presented with hyperlipidemia/hypertriglyceridemia (HLD/HTG), pre-diabetes, Type 2 diabetes mellitus (T2DM), and/or metabolic dysfunction-associated fatty liver disease/steatohepatitis (MAFLD/MASH). Variants in a curated set of 90 genes associated with monogenic forms of these conditions were classified as Pathogenic (P), Likely Pathogenic (LP), or Variant of Uncertain Significance (VUS) using ACMG/ClinGen guidelines. P/LP variants in ACMG secondary findings (v3.1) genes were also reported with participant consent. Results: The cohort had a female-to-male ratio of 1.7, with 18.6% African American and 22.6% Latino participants. The most common enrollment diagnoses were HLD/HTG (25%), T2DM (9%), pre-diabetes (7%), and MAFLD/MASH (4%). Many participants had multiple conditions (42% with two, 12% with three). Approximately one-third had reportable variants, with 6% classified as P/LP. The most common P/LP variants were in APOB and LDLR. Conclusion: The prevalence of clinically significant (P/LP) variants related to primary metabolic disease in this cohort was 6%. An additional 5.5% of participants had P/LP variants in ACMG secondary findings genes. Future studies should refine participant selection for genome sequencing to optimize its diagnostic and clinical value.

Recently, de novo variants in an 18-nucleotide region in the centre of RNU4-2 were shown to cause ReNU syndrome, a syndromic neurodevelopmental disorder that is predicted to affect tens of thousands of individuals worldwide ^1,2 . RNU4-2 is a non-protein-coding gene that is transcribed into the U4 small nuclear RNA component of the major spliceosome ³ . ReNU syndrome variants disrupt spliceosome function and alter 5′ splice site selection ^1,4 . Here we performed saturation genome editing (SGE) of RNU4-2 to identify the functional and clinical impact of variants across the entire gene. The resulting SGE function scores, derived from variants’ effects on cell fitness, discriminate ReNU syndrome variants from those observed in the population and markedly outperform in silico variant effect prediction. Using these data, we redefine the ReNU syndrome critical region at single-nucleotide resolution, resolve variant pathogenicity for variants of uncertain significance and show that SGE function scores delineate variants by phenotypic severity and the extent of observed splicing disruption. Furthermore, we identify variants affecting function in regions of RNU4-2 that are critical for interactions with other spliceosome components. We show that these variants cause a new recessive neurodevelopmental disorder that is distinct from ReNU syndrome. Together, this work defines the landscape of variant function across RNU4-2 , providing critical insights for both diagnosis and therapeutic development.

Genetic variants in RNU4-2 , which is transcribed into the U4 small nuclear RNA component of the major spliceosome, were recently shown to cause ReNU syndrome, a prevalent dominant neurodevelopmental disorder (NDD). These variants almost exclusively arise de novo and cluster within 18 nucleotides of RNU4-2 . Here we describe a new recessive NDD associated with homozygous and compound heterozygous variants in RNU4-2 . We identify 38 individuals with biallelic variants outside the 18-nucleotide ReNU syndrome region that cluster within other functionally important elements of U4: Stem II, the k-turn and the Sm protein binding site. We characterize the clinical phenotype in 31 individuals, demonstrating that the recessive disorder is clinically distinct from ReNU syndrome and is associated with distinctive white matter abnormalities, including enlarged perivascular spaces. Finally, we find reduced RNU4-2 transcript levels in individuals with the recessive disorder, suggesting a loss-of-function disease mechanism that is distinct from the mechanism underlying ReNU syndrome. Together, these findings expand the genotypic and phenotypic spectrum of RNU4-2 -associated NDDs.

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.

Vertebrate brain development is associated with prominent neuronal cell death and DNA breaks, but their causes and functions are not well understood. DNA transposable elements could contribute to somatic genome rearrangements; however, their contributions to brain development are largely unknown. PiggyBac transposable element derived 5 (PGBD5) is an evolutionarily conserved vertebrate DNA transposase–derived gene with DNA remodeling activities in human cells. Here, we show that PGBD5 contributes to normal brain development in mice and humans, and its deficiency causes disorder of intellectual disability, movement disorders, and epilepsy. In mice, Pgbd5 is required for the developmental induction of postmitotic DNA breaks and recurrent somatic brain genome rearrangements. In the cerebral cortex, loss of Pgbd5 leads to aberrant neuronal gene expression, including of specific types of glutamatergic neurons, which partly explains the features of PGBD5 deficiency in humans. Thus, PGBD5 is a transposase-derived gene required for brain development in mammals.

The UNC13A gene encodes a presynaptic protein that is crucial for setting the strength and dynamics of information transfer between neurons. Here we describe a neurodevelopmental syndrome caused by germline coding or splice-site variants in UNC13A . The syndrome presents with variable degrees of developmental delay and intellectual disability, seizures of different types, tremor and dyskinetic movements and, in some cases, death in early childhood. Using assays with expression of UNC13A variants in mouse hippocampal neurons and in Caenorhabditis elegans , we identify three mechanisms of pathogenicity, including reduction in synaptic strength caused by reduced UNC13A protein expression, increased neurotransmission caused by UNC13A gain-of-function and impaired regulation of neurotransmission by second messenger signalling. Based on a strong genotype–phenotype-functional correlation, we classify three UNC13A syndrome subtypes (types A–C). We conclude that the precise regulation of neurotransmitter release by UNC13A is critical for human nervous system function.

Anomalies of the corpus callosum (AnCC) are congenital malformations associated with highly variable neurodevelopmental outcomes. We performed prenatal exome sequencing (pES) on a cohort of 352 fetuses diagnosed with AnCC, analysing the diagnostic yield, the implicated genes based on the type of anomaly (partial or complete agenesis, short corpus callosum, or callosal dysgenesis) and assessing the impact on pregnancy outcomes. The overall diagnostic yield of pES was 23%, with pathogenic or likely pathogenic variants identified in 49 different genes, most of which linked to intellectual developmental disorders. The highest diagnostic yield (46%) was observed in fetuses with callosal dysgenesis. Notably, in cases of corpus callosum agenesis, variants in the DCC gene were the most frequently identified aetiology (3.2%, n = 9), associated with a favourable neurodevelopmental outcome. All couples with a fetal DCC variant decided to continue the pregnancy to term. In contrast, 73% of couples with other genetic diagnoses chose pregnancy termination, compared to 17% in cases without a genetic diagnosis. Prenatal decision-making and care are supported by essential prognosis information provided by pES. The identification of genes associated with favourable outcomes, along with the integration of pES into prenatal diagnosis, enhances informed decision-making for parents and improves the clinical management of AnCC.