Protein-truncating variants in the 3' region of a transcript, evading mRNA degradation and giving rise to aberrant truncated proteins, are an underrecognized cause in Mendelian diseases. Here, we report two individuals with heterozygous de novo nonsense variants in the penultimate and last exon of NUSAP1, both presenting with early-onset refractory epilepsy, global developmental delay, congenital microcephaly, and a recognizable facial gestalt. RNA sequencing performed in one individual did not show a reduction in expression, compatible with escape of aberrant transcripts from nonsense mediated mRNA decay (NMD). We systematically analyzed gnomAD population data to delineate a critical region at the 3' region of NUSAP1, where nonsense variants introduce a premature termination codon and escape NMD. Such variants are absent from healthy controls, while frameshift variants producing C-terminal elongations appear tolerated. This position-dependent model provides guidance for diagnostic variant interpretation.
ABCA13 encodes ATP-binding cassette subfamily A member 13, one of the largest members of the ABC transporter family. Rare ABCA13 variants have been reported in neuropsychiatric and neurodevelopmental phenotypes, including schizophrenia, bipolar disorder, autism spectrum disorder, intellectual disability, and developmental delay; however, the mode of inheritance remains uncertain, and most published cases have focused on heterozygous variants in the context of a possible dominant or susceptibility model. We report a 5-year-old boy with neurodevelopmental delay, skeletal foot deformities, nonspecific dysmorphic features, convergent strabismus, and behavioral abnormalities. Initial genome sequencing analysis was nondiagnostic. Reanalysis after 6 months identified two rare predicted loss-of-function variants in ABCA13 in trans: c.2510del, p.(Leu837TyrfsTer21), a frameshift variant, and c.12064C>T, p.(Arg4022Ter), a nonsense variant previously reported in a patient with unexplained intellectual disability. The identification of compound heterozygous predicted loss-of-function variants supports the possibility that biallelic disruption of ABCA13 may contribute to neurodevelopmental disease, whereas previously reported heterozygous variants may represent incompletely penetrant risk alleles, susceptibility factors, or candidate findings rather than fully penetrant dominant causes. This case expands the emerging clinical and genetic spectrum associated with ABCA13 and supports further evaluation of a recessive model in patients with intellectual disability and neurodevelopmental delay.
Pathogenic variants on the paternal allele of IGF2 are linked to Silver-Russell syndrome (SRS). This report describes two unrelated individuals-a 5-year-old girl and an adult female-with de novo IGF2 missense variants, both diagnosed with SRS. While one exhibited normal development, the other had intellectual disability, highlighting phenotypic variability. A review of 20 individuals with IGF2 variants revealed that SRS features, as defined by the Netchine-Harbison Clinical Scoring System, were most common. Additional recurrent traits included delayed speech and motor development, under-masculinized male genitalia, hand/foot anomalies, and congenital heart defects. Growth faltering patterns varied, and intellectual disability was seen in some. We also demonstrated that long-read sequencing can determine the allelic origin of de novo IGF2 variants using differentially methylated regions, eliminating the need for parental samples. This approach confirms long-read sequencing as a powerful tool for identifying de novo variant origins in imprinted genes like IGF2.
This research letter expands the phenotypic spectrum of ACTG2-associated autosomal dominant visceral myopathy to include isolated uterine involvement based on a case of an individual harboring a known pathogenic ACTG2 variant with uterine atony as her only symptom.
Pediatric cardiomyopathies (CM) are rare and heterogeneous heart disorders, including hypertrophic, dilated, restrictive, arrhythmogenic, and non-dilated CM. While their genetic basis is well characterized in adults, it remains less clearly defined in children particularly in early-onset apparently isolated and syndromic forms. We conducted a retrospective study (2018-2024) of 59 pediatric patients who underwent Whole-Exome Sequencing (WES) for CM at Amiens and Lille University Hospitals, aiming to characterize the genetic architecture of pediatric CM. WES identified at least one Variant Of Interest (VOI) in 62.7% of patients (37/59), including 45.8% (27/59) of P/LP variants, and 16.9% (10/59) of VUS. VOI identification yields for HCM and DCM were respectively 67.7% and 57.1%. Yield was higher in patients diagnosed before 1 year of age compared with those diagnosed later (72.7% vs. 56.7%). Variants were identified in classical CM genes, including sarcomeric genes, but also in less typical and syndromic genes. Among patients diagnosed before 6 months, 55% carried a variant in genes associated with syndromic cardiomyopathy, including cases with initially isolated cardiac phenotypes. These findings support the use of WES as a first-line approach in pediatric CM and highlight the contribution of complex and syndromic genetic architectures to early-onset and severe diseases.
Pathogenic variants in AGO1 and AGO2, core components of the Argonaute family, have emerged as causes of rare neurodevelopmental disorders characterized by intellectual disability, marked language impairment, behavioral abnormalities, and distinctive craniofacial features. Reported variants cluster at the L1-PAZ boundary, a structurally sensitive region essential for guide-RNA engagement. We describe two unrelated Japanese individuals carrying de novo variants in AGO1(NM_012199.5):c.569T>C p.(Leu190Pro) or AGO2(NM_012154.6):c.544_546del p.(Phe182del), affecting structurally corresponding residues within this boundary. Both individuals exhibited global developmental delay, hypotonia, midface hypoplasia, thin upper lip, elongated facial shape, and reduced cerebral white matter volume, aligning with previously reported AGO1- and AGO2-related phenotypes. Structural assessment using AlphaFold2-based AGO1 models and the AGO2 crystal structure confirmed positional equivalence of the affected residues, supporting the concept of a shared structural vulnerability across Argonaute paralogs. These observations expand the phenotypic spectrum of Argonaute-related neurodevelopmental disorders in the Japanese population and highlight RNA-regulatory dysfunction as a coherent pathogenic axis. Recognition of this clinical gestalt may assist clinicians in prioritizing AGO1 and AGO2 during genomic evaluation of unexplained neurodevelopmental disorders.
Pathogenic variants in PORCN cause focal dermal hypoplasia (FDH/Goltz syndrome), an X-linked dominant disorder historically considered lethal in males, with milder presentations now recognized as PORCN non-Goltz spectrum (PONGOS). We report three male patients identified by exome sequencing: one with a mosaic de novo variant (c.727C>T; p.Arg243*) showing FDH features, and two siblings with an inherited non-mosaic variant (c.1315T>G; p.Trp439Gly) from their unaffected carrier mother with a PONGOS phenotype. These cases confirm that male survival is possible with both mosaic and non-mosaic PORCN variants and expand the clinical and molecular spectrum of the disease. Our findings highlight the role of residual protein function in clinical variability and have important implications for diagnosis, genetic counseling, and management in families with apparently unaffected carrier mothers.
Hereditary polyneuropathies (HPPs), including Charcot-Marie-Tooth disease (CMT), represent a genetically and clinically heterogeneous group of disorders. Overlapping phenotypes, genetics, and clinical heterogeneity, and more complex phenotypes mimicking CMT can complicate the diagnosis. This study evaluated the effectiveness of an algorithm-guided, broad genetic testing strategy in a tertiary neuromuscular center in Türkiye, where recessive disorders are relatively common. Sixty-seven patients from 63 families referred for suspected HPP (2018-2025) were clinically stratified by phenotype and electrophysiology, and a diagnostic workflow integrating PMP22 MLPA with clinical or whole-exome sequencing was applied. The overall molecular diagnostic yield was 73% (46/63). PMP22-related neuropathies accounted for 43.5% of all diagnosed cases, with a group-specific yield of 60%. Among the non-PMP22 CMT group, the predominant inheritance pattern was autosomal recessive (70%). Nine novel variants were identified. Two dual molecular diagnoses (PMP22/MCCC1; MPZ/CRYBB2) were established. Importantly, six patients initially labeled as "CMT-like" harbored non-CMT disorders, including CYP27A1-, BTD-, HEXB-, ZFYVE26-, C19ORF12-, and COA7-related diseases-several of which are treatable or actionable. In a population with high genetic heterogeneity and elevated consanguinity, reliance on narrow CMT-focused panels risks misdiagnosis and may miss therapeutic opportunities. An algorithm-driven approach integrating PMP22 CNV analysis with exome sequencing substantially improves diagnostic yield, reveals blended or digenic mechanisms, and helps distinguish non-CMT phenocopies. These findings underscore the importance of comprehensive genomic testing and careful phenotype-genotype correlation in the evaluation of hereditary polyneuropathies.
Neuromuscular oculoauditory syndrome (NMOAS; OMIM# 618733) is a rare neurodevelopmental disorder caused by heterozygous variants in DHX16, a gene in the DExD/H-box RNA helicase family. Despite increasing reports of DHX16-related NMOAS, the functional impact of specific variants on RNA splicing remains poorly understood. In this study, whole-exome sequencing identified a de novo DHX16 variant (c.1360C>G, p.Arg454Gly) in a 2-year-old boy with NMOAS. In vitro assays revealed aberrant intron retention in HSPH1 and FOS transcripts in cells expressing the mutant DHX16-1360G, suggesting impaired splicing efficiency. Longitudinal clinical follow-up uncovered progressive multisystem involvement, including delayed gonadal development and autism spectrum disorder phenotypes not previously linked to DHX16. These findings expand the genotypic and phenotypic spectrum of NMOAS, confirm the pathogenic role of this variant in splicing dysregulation, and emphasize the need for long-term monitoring of emerging comorbidities in affected patients.
Noonan syndrome (NS) is a clinically heterogeneous condition caused by pathogenic variants in genes of the RAS/MAPK signaling pathway, presenting as a spectrum of phenotypic features rather than a single uniform disorder. We report two unrelated female pediatric patients evaluated for LZTR1-related NS following whole-exome sequencing. The first patient presented with isolated short stature, subtle dysmorphic features, and normal neurodevelopment. The second displayed multisystem involvement including developmental delay, skeletal abnormalities, and auditory processing disorder. A heterozygous pathogenic variant in LZTR1 was confirmed in the first patient, while the second carried a heterozygous LZTR1 variant of uncertain significance, rendering her diagnosis provisional. Neither patient had congenital heart defects. These cases illustrate the marked phenotypic variability of LZTR1-related NS and underscore that, while cardiac defects may be absent in some individuals, appropriate cardiac surveillance remains necessary.
A 29-year-old woman with a novel homozygous VPS13A frameshift variant presented with drug-resistant temporal-lobe epilepsy and severe sensory neuronopathy, but no acanthocytes on repeated blood smears-expanding the phenotypic spectrum of chorea-acanthocytosis beyond its defining haematological feature.
We report a 7-year-old boy with NF1-negative optic pathway glioma harboring a novel germline ELP1 splice-acceptor variant (NM_003640.5:c.2205-2A>G) identified by whole-exome sequencing. The variant was likely pathogenic (ACMG/AMP: PVS1, PM2) and inherited from an asymptomatic father, consistent with incomplete penetrance, expanding the limited evidence linking germline ELP1 variation to gliomas.
Neurodevelopmental disorders (NDDs) are a group of developmental brain disorders caused by various genetic or acquired factors. OMIM has only recently associated the KCNK3 gene with developmental delay associated with sleep apnea (DDSA). Most prior studies on the KCNK3 gene have focused on PAH and cardiovascular diseases. In a 2-year-old girl presenting with generalized hypotonia and delayed language development, we identified a de novo missense variant in KCNK3 through the reanalysis of trio-whole exome sequencing (trio-WES) data. To further explore the relationship between KCNK3 and neurodevelopmental phenotypes, we conducted bidirectional expression regulation of the homologous gene Task7 based on the Drosophila model. Both overexpression and knockdown of the Task7 gene induced anxiety-like behaviors and impaired learning and memory. Notably, Task7 overexpression also led to reduced climbing ability and abnormal sleep patterns; collectively, these four phenotypes recapitulate the characteristic hallmarks of human neurodevelopmental disorders. This study represents the first application of a Drosophila model to demonstrate that KCNK3 functions as a dosage-sensitive regulator of neurodevelopment. While the underlying mechanisms remain to be fully elucidated, these findings position KCNK3 as a candidate gene for molecular screening and pave the way for future functional studies and therapeutic exploration in NDDs.
Multiple morphological abnormalities of the flagella (MMAF) is a severe form of male infertility characterized by immotile spermatozoa with absent, short, coiled, or irregular flagella. Despite advances in whole-exome sequencing, many cases remain genetically unexplained. Here, we identify a homozygous truncating variant in LRGUK (c.1063C>T; p.Arg355Ter) in an infertile man presenting with a typical MMAF phenotype. The variant, identified by whole-exome sequencing in a cohort of 168 MMAF patients and confirmed by Sanger sequencing, is predicted to result in loss of the C-terminal guanylate kinase-like domain. Immunofluorescence showed absence of LRGUK protein in patient spermatozoa, supporting a loss-of-function effect. Semen analysis revealed impaired motility and complete teratozoospermia. Morphological and ultrastructural analyzes demonstrated severe defects affecting both sperm head and flagellum, including disorganized axonemal architecture and central pair abnormalities. Nuclear analyzes showed increased nuclear size, defective chromatin compaction, and elevated DNA fragmentation. Immunostaining further indicated alterations of central apparatus-associated proteins, supporting a role for LRGUK in C1b projection organization. These findings identify LRGUK as a novel gene involved in male infertility, essential for spermatid morphogenesis and flagellum assembly.
RASopathies comprise a group of congenital malformation syndromes with predominant neuro-cardio-facial-cutaneous involvement resulting from pathogenic variants in RAS/mitogen-activated protein kinase (MAPK) signaling pathway genes. In this study 33 patients are presented with their clinical and molecular findings as an RASopathy cohort including a family with an AMMECR1-related disorder. The diagnostic distribution of the cohort included Noonan syndrome (n = 18), neurofibromatosis type 1 (n = 8), and single cases of cardiofaciocutaneous syndrome, Costello syndrome, neurofibromatosis-Noonan syndrome, NF1 microdeletion syndrome, Noonan syndrome-like disorder with loose anagen hair, Noonan syndrome with multiple lentigines and AMMECR1-related midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (MIM# 300990). The most prevalent clinical manifestations were dermatological findings (90.9%), skeletal features (84.4%), cardiovascular involvement (75.8%), and typical craniofacial dysmorphism suggestive of RASopathy (72.7%). Variants were most frequently identified in PTPN11 and NF1, followed by single cases involving the BRAF, HRAS, LZTR1, RAF1, RIT1, SHOC2, and SOS1. Notably, one patient harbored a variant in AMMECR1, which is not involved in the RAS/MAPK pathway. Overall, this study delineates the clinical and molecular landscape of a cohort from Türkiye and underscores that the AMMECR1-related phenotype represents a distinct entity that closely mimics Noonan syndrome.
Arthrogryposis multiplex congenita (AMC) is a group of conditions with congenital joint contractures in at least two body regions. ACTC1 variants cause heart disorders but have also been reported in six families with AMC. We report on two individuals with AMC who were heterozygous for ACTC1 missense variants (NM_005159.5; c.325G>A, p.Glu109Lys and c.650A>C, p.Lys217Thr). Individual 1 had scoliosis and no reported cardiac phenotype. Individual 2 had Shone's complex with coarctation of the aorta, which has not been reported in ACTC1-related AMC before. In vitro testing demonstrated that p.Glu109Lys caused impaired actin filament assembly and reduced ACTC1 protein levels, effects not apparent for p.Lys217Thr. Our findings characterize two novel variants that cause ACTC1-related AMC and expand the list of phenotypes observed in this disorder.
CLDN11 has recently been associated with hypomyelinating leukodystrophy caused by de novo stop-loss variants. Here, we present a new case involving a homozygous variant in order to expand the genetic and clinical spectrum of the disease. We performed a comprehensive clinical, neuroradiological, and genetic evaluation in a child presenting with global developmental delay. Brain MRI and MR spectroscopy were obtained, and next-generation sequencing with parental segregation analysis was conducted. The patient presented with developmental delay, hypotonia, limb hypertonia, esotropia, and an absence of early developmental milestones in infancy, followed by partial motor improvement and persistent language and cognitive impairment. Brain MRI revealed diffuse supratentorial hypomyelination with stability over time. Genetic analysis identified a novel homozygous CLDN11 start-loss variant (c.1A>G; p.Met1Val), which is predicted to result in biallelic loss of function. Both parents were found to be heterozygous carriers. This case supports an autosomal recessive mechanism of CLDN11-related disease, which differs from the dominant stop-loss variants reported previously. The phenotype partially overlaps with that of earlier cases, but is characterized by milder motor involvement and more pronounced cognitive impairment. These findings broaden the mutational spectrum and suggest distinct pathogenic mechanisms, with important implications for diagnosis and genetic counselling.
Noonan syndrome (NS) and related RASopathies form a clinically and genetically heterogeneous group of disorders caused by germline dysregulation of the RAS/MAPK pathway. Pathogenic variants in PTPN11 account for roughly half of classical NS, but the contribution of non-PTPN11 genes in patients referred with NS or Noonan-like phenotypes remains incompletely defined in several populations, including Russia. We characterized the spectrum of non-PTPN11 variants in a large Russian cohort referred for suspected NS or Noonan-like phenotypes and examined gene-specific clinical patterns. We analyzed 456 unrelated patients with clinically diagnosed NS or Noonan-related syndromes using a targeted panel of 23 RAS/MAPK pathway genes. PTPN11 variants (23% of cases) were reported previously; here we focused on the remaining patients. Pathogenic or likely pathogenic variants were identified in 19% of cases (85/456), with NF1, SOS1, SHOC2, and BRAF being the most frequently mutated genes, together accounting for 50% of the non-PTPN11 diagnoses. Novel variants were observed in 12.1% of cases (7/58 unique variants). Several genotype-phenotype associations emerged: SOS1 mutations were associated with a high prevalence of cardiac defects, especially pulmonary stenosis and atrial septal defects (64% of patients, p = 0.01), whereas NF1 and SPRED1 cases had significantly fewer cardiac anomalies (p < 0.001 and p < 0.05, respectively). Lentigines were predominantly seen in NF1 and SPRED1 patients (p < 0.01), and all three evaluable males with MAP2K1 variants had cryptorchidism (3/3). Conversely, BRAF-mutated patients showed lower incidence of chest deformity (p < 0.01) but higher rates of developmental delay. NF1, SOS1, SHOC2, and BRAF together accounted for half of the non-PTPN11 molecular diagnoses in this Russian cohort, and the observed gene-specific clinical patterns align with previous series, although limited subgroup sizes preclude firm individual associations.
Pathogenic variants in AMMECR1 have been associated with a rare multisystem disorder characterized by midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (MFHIEN). To date, most reported cases involve copy number variants or presumed loss-of-function alterations, with only a single prior report describing a missense variant supported by functional studies. Here, we report a patient with a heterozygous de novo AMMECR1 missense variant, NM_015365.3:c.649G>A p.(Val217Met) presenting with clinical features consistent with MFHIEN, including midface hypoplasia, partial hearing impairment, nephrocalcinosis, and elliptocytosis identified on peripheral blood smear. Comparative review of the literature highlights that while previously reported missense variants in AMMECR1 demonstrated altered intranuclear protein distribution and reduced expression in functional assays, clinical evidence supporting pathogenicity of non-truncating variants remains limited. The phenotypic overlap between our patient and prior report strengthens the association between missense variations and the MFHIEN phenotype. Our findings support the pathogenic relevance of missense variation in AMMECR1 and emphasize the importance of integrating detailed phenotyping, including hematologic evaluation, with genomic data in the diagnosis of rare multisystem disorders. Additional cases and functional studies are needed to clarify genotype-phenotype correlations and underlying disease mechanisms.
Pathogenicity predictors exceed AUROC 0.97 on expert-curated ClinVar, yet the monogenic-epilepsy variant-of-uncertain-significance backlog persists because pathogenicity alone provides no direction-of-effect, no scalable mechanism-to-treatment mapping, and no evidence that updates as ClinVar grows. SeizeVar couples a consensus pathogenicity head (random forest plus ESM-2 LoRA cross-attention) to a gain-versus-loss-of-function mechanism classifier and a deterministic sodium-channel mechanism-direction rule. The framework was trained on a 49-gene epilepsy panel (n = 4576 labelled variants) and evaluated on six pairwise-disjoint held-out cohorts (n = 11 274) plus an external functional cohort with patch-clamp/TEVC labels (T2, n = 415). SeizeVar's mechanism head reaches honest leave-one-gene-out AUROC = 0.736 at 100% panel coverage and matches the proteome-wide specialist LoGoFunc on fair full-coverage comparison (0.770 vs. 0.760), whereas general-purpose pathogenicity predictors are mechanism-blind (AUROC ≤ 0.62). Applied to 29 293 epilepsy VUS, the pipeline returned 4708 consensus Likely-Pathogenic candidates, of which 1500 sodium-channel variants received predicted mechanism-direction labels (679 LoF-leaning, 821 GoF-leaning). By integrating pathogenicity, mechanism, and dynamic evidence on a shared probability scale, SeizeVar produces a mechanism-annotated prioritisation list to support-not replace-expert variant curation; the outputs are computational predictions and a natural next step is prospective clinical validation. Reclassified-VUS is released as a community benchmark for reclassification-aware evaluation.
