Introduction

The NEUROD2 gene (OMIM #601725) encodes a neuronal basic helix-loop-helix (bHLH) transcription factor that plays a critical role in neuronal differentiation, synaptic maturation, and maintenance of excitatory-inhibitory balance within the central nervous system. Experimental studies have shown that NEUROD2 is essential for the development and maturation of cortical neurons, and its dysfunction can disrupt neuronal circuit formation and synaptic plasticity [1–4].

Pathogenic NEUROD2 variants have recently been implicated in a rare autosomal dominant neurodevelopmental disorder (OMIM #618374) characterized by variable expressivity, including global developmental delay, intellectual disability (ID), epilepsy, behavioral abnormalities, and, in some cases, structural brain changes [5–10].

To date, only a limited number of NEUROD2 variants have been described, and most are clustered in the highly conserved bHLH domain, which is crucial for DNA binding and dimerization. Reported clinical presentations usually begin during infancy or childhood, often with infantile seizures, developmental delay, and abnormal electroencephalogram (EEG) findings. However, the phenotypic spectrum is still being defined, and neonatal presentation is unreported [5–10]. Expanding the number of well-characterized cases is essential for improving our understanding of genotype-phenotype correlations and the underlying disease mechanisms.

Here, we report the case of a newborn girl carrying a de novo heterozygous missense variant NM_006160.4:c.790G>A in the NEUROD2 gene, associated with early neonatal hypotonia, feeding difficulties, and electrographic seizures. This case report is notable for the very early onset of symptoms, beginning immediately after birth, and for the identification of a novel variant located outside the typical mutational hotspot. It provides additional insight into the clinical variability and genetic landscape of NEUROD2-related disorders.

Timeline

Table 1 shows the timeline, giving a clear and concise roadmap of the case.

Narrative

The baby girl was born at term via vaginal delivery with meconium-stained amniotic fluid. The pregnancy progressed normally, with a prenatal finding of a right pelvic kidney. At birth, she presented respiratory depression and was therefore ventilated, with subsequent recovery. Apgar scores were 2–6 and 7. Birth weight was 3,200 g (20th centile), length 51 cm (48th centile), and head circumference 33 cm (13th centile). Due to respiratory distress, she was admitted to the neonatal intensive care unit. Since the first days of life, she showed signs of altered neurological status, including hypotonia, hypo-reactivity, and feeding difficulties. During hospitalization, the baby presented with persistent hypotonia, hypo-reactivity, with a predominant behavioral state of sleep/drowsiness and crying episodes with stereotyped and abnormal movements. Repeated EEG evaluations showed an excessively discontinuous baseline EEG pattern and recorded isolated electrographic seizures with minimal clinical correlation (stereotyped movements like rowing and pedaling). Antiepileptic therapy with levetiracetam was therefore administered. The infant required non-invasive respiratory support for several days and prolonged orogastric tube feeding due to poor or absent sucking, although swallowing capacity was substantially preserved. By 2 months of age, she was able to feed herself with a bottle. She was therefore discharged and followed up (see Table 1). At 24 months of age, the patient presented normal growth and epilepsy control with levetiracetam. At 30 months of age, a comprehensive neurodevelopmental assessment was performed by a multidisciplinary team comprising a child neuropsychiatrist and a clinical psychologist, both with expertise in neurodevelopmental disorders. The patient demonstrated persistent deficits in social communication and social interaction across multiple contexts, as well as restricted patterns of behavior, meeting diagnostic criteria for autism spectrum disorder (ASD), according to DSM-5 clinical criteria. The assessment included clinical observation, developmental history, and standardized diagnostic instruments. The diagnosis was supported by the Autism Diagnostic Observation Schedule (ADOS-2, administered by clinicians) and the Autism Diagnostic Interview-Revised (ADI-R), completed with the primary caregiver. Thus, at 30 months of age, the patient exhibited a neurodevelopmental disorder characterized by global developmental delay and ASD. Ongoing multidisciplinary follow-up continues to monitor developmental progress and therapeutic interventions.

Diagnostics

Several diagnostic investigations were carried out in the neonatal period, including brain magnetic resonance imaging (MRI), which revealed hyperintensity of the subcortical white matter, and genetic testing. Array CGH, Prader-Willi, and myotonic dystrophy genetic tests resulted in normal. Trio exome sequencing revealed a heterozygous missense variant in exon 2 of the NEUROD2 gene: NM_006160.4:c.790G>A, leading to the amino acid substitution p.(Ala264Thr). The variant was confirmed by Sanger sequencing and was shown to be de novo (absent in both parents) (Table 2). In silico predictive tools consistently indicated a deleterious effect: SIFT predicted “damaging” (score 0.00), PolyPhen-2 predicted “probably damaging” (score 0.999), and the CADD score was 28.9 (strongly suggestive of pathogenicity). Splice AI predicted no significant impact on splicing (max score 0.02). The affected residue (alanine at position 264) is highly evolutionarily conserved across species, supporting its functional importance. Population database analysis showed that the variant is absent in gnomAD v4.0 (including all subpopulations), consistent with a rare disease-causing allele. Applying the ACMG/AMP guidelines [11, 12], the variant met the following criteria: PS2 (de novo in a patient with the disease and no family history), PM2 (absent from population databases), and PP3 (multiple lines of computational evidence supporting a deleterious effect). The overall classification framework is consistent with subsequent recommendations [13]. Collectively, these data support the classification of the variant as likely pathogenic. Monoallelic variants in the NEUROD2 gene have recently been associated with a neurodevelopmental disorder (OMIM #618374) with autosomal dominant inheritance and variable expressivity. The NEUROD2 NM_006160.4:c.790G>A variant has been submitted to ClinVar (SUB15787434) and is under processing (accession number SCV007105870). Parental consent for clinical description has been obtained.

Patient perspective

The parents of the infant were actively involved throughout the diagnostic and therapeutic journey. They provided written informed consent for all procedures, including genetic testing, and for the publication of this report. Upon learning of the de novo NEUROD2 variant and its likely pathogenicity, the parents expressed a mixture of relief at having a definitive diagnosis and concern regarding their daughter’s long-term neurodevelopmental prognosis. The parents reported that the most challenging aspects during the neonatal period were the infant’s prolonged hypotonia, feeding difficulties requiring orogastric tube feeding, and the emotional distress associated with the hospital stay. They appreciated the structured communication from the neonatal intensive care unit staff and the early involvement of the psychology unit, which offered emotional support and facilitated bonding. Following discharge, the family engaged in an early intervention program comprising physiotherapy and speech therapy.

Discussion

The present case of a newborn carrying a de novo heterozygous NM_006160.4:c.790G>A NEUROD2 variant contributes to the expanding phenotypic and genotypic spectrum associated with NEUROD2-related neurodevelopmental disorders. Pathogenic variants in this gene have been linked to an autosomal dominant neurodevelopmental disorder characterized by variable expressivity, including developmental delay, ID, epilepsy, and behavioral abnormalities. In most reported cases, clinical manifestations begin during infancy, and variants tend to cluster in the bHLH domain, which is essential for DNA binding and dimerization [5–10]. Compared to previously described patients, our case shows an unusually early and severe neonatal presentation (Table 2). The patient manifested cardiorespiratory depression at birth, required respiratory support, and exhibited neurological abnormalities, including hypotonia, hyporeactivity, feeding difficulties, and early-onset seizures. Brain MRI revealed hyperintensity of the subcortical white matter, consistent with previous reports of white matter signal abnormalities and delayed myelination in NEUROD2-related disorders. However, in contrast to many previously published cases in which symptoms typically become apparent during early infancy, our patient displayed significant neurological impairment since birth, suggesting that the pathogenic effect of this variant may interfere with neuronal development at very early stages. Two additional clinical findings merit comment. The meconium-stained amniotic fluid is likely attributable to perinatal distress rather than a direct effect of the NEUROD2 variant. The right pelvic kidney is not a recognized feature of NEUROD2-related disorders and is considered an incidental finding. A comparison of this case with prior literature highlights both shared and distinctive features (Table 2). Reported patients with NEUROD2 variants frequently presented with developmental delay and epilepsy, often manifesting as infantile spasms during the first months of life (developmental epileptic encephalopathy). EEG abnormalities, such as multifocal spikes or hypsarrhythmia, were common. MRI findings were usually nonspecific, including white matter hyperintensity and delayed myelination, without major structural malformations. Treatment responses were variable; some patients showed temporary improvement with vigabatrin and steroids, whereas others required multiple antiepileptic drugs. Developmental outcomes were generally poor, with persistent cognitive and motor impairment, although severity varies considerably even among individuals carrying variants affecting similar domains [5–10]. The NM_006160.4:c.790G>A NEUROD2 variant identified in this case has been rarely reported and is located further downstream from the most frequently mutated residues, which typically cluster in the core bHLH domain [1, 5–10]. Its presence in a highly conserved region, absence from population databases, de novo occurrence, and predicted functional impact support its classification as likely pathogenic. The severe and early neurological phenotype observed here may suggest that variants outside the canonical hotspot regions can still profoundly disrupt NEUROD2 function. Previous functional analyses of other NEUROD2 variants demonstrated reduced transcriptional activity and impaired neuronal differentiation, supporting a loss-of-function mechanism as the pathogenic basis. Notably, the Ala235Thr variant reported by Mis et al. [6] shares key structural features with the present case—both are alanine substitutions in the C-terminal region outside the bHLH domain—yet is associated with a substantially milder phenotype, underscoring the complexity of genotype-phenotype correlations within this region. The clinical course of this patient also highlights the heterogeneity and variable expressivity of NEUROD2-related disorders. Some reported individuals have milder phenotypes with developmental delay but no epilepsy, whereas others present with severe epileptic encephalopathy and profound neurological deficits. This variability may be influenced by the location and nature of the variant, modifier genes, and epigenetic factors.

Overall, this case reinforces the importance of including NEUROD2 in the differential diagnosis of neonates presenting with unexplained hypotonia, feeding difficulties, and early-onset seizures [1, 5–10, 14]. It also highlights the value of early exome sequencing in identifying de novo variants in genes associated with neurodevelopmental disorders, enabling accurate diagnosis and counseling [15–17].

Conclusions

In conclusion, we report a newborn with a de novo heterozygous NM_006160.4:c.790G>A NEUROD2 variant presenting with neonatal onset, thereby expanding both the phenotypic and mutational spectrum of NEUROD2-related neurodevelopmental disorders. This case introduces a novel missense change associated with severe early presentation, demonstrating that pathogenic NEUROD2 variants can exert profound clinical effects even when located outside the most well-characterized functional domains. As additional cases are identified, further refinement of genotype-phenotype correlations, improved prognostic accuracy, and the development of targeted therapeutic strategies will become increasingly feasible for this rare but clinically significant disorder.