Autism spectrum disorder (ASD) is a neurodevelopmental condition that occurs in early childhood, characterized by a broad range of clinical manifestations and impairments in social communication. It represents one of the most prevalent neurodevelopmental disorders, affecting approximately 1% of the general population. The phenotypic heterogeneity of ASD arises from different genetic causes, including chromosomal abnormalities, copy number variants (CNVs), and single-nucleotide variants (SNVs), which may occur as de novo or inherited events. Moreover, the polygenic and multifactorial nature of ASD, together with epigenetic regulation and environmental influences, contributes substantially to its complex genetic architecture. Molecular diagnosis remains challenging and relies on multiple genomic approaches, such as array comparative genomic hybridization (array-CGH), whole-exome sequencing (WES), and whole-genome sequencing (WGS); however, the diagnostic yields of these methods remain limited, reflecting the complexity of ASD’s genetic architecture. Notably, ASD-associated genes converge on key biological pathways, particularly those involved in transcriptional regulation, chromatin remodeling, synaptic function, and neuronal signaling. These include well-established risk genes such as CHD8, ADNP, ARID1B, SHANK3, SYNGAP1, SCN2A, GRIN2B, FOXP1, and DYRK1A, among others. This review summarizes the current knowledge on the genetic basis of ASD, highlighting key aspects of its complex genetic architecture. By integrating evidence from major clinical and research databases, it provides a clearer understanding of the underlying mechanisms, supporting improved diagnosis and future research and therapeutic strategies.

Neurotrimin (NTM) (OMIM #607938), a member of the IgLON family, collaborates with other neural cell adhesion proteins to regulate neurite outgrowth, axonal fasciculation, and synapse formation. Disruption of NTM function in animal models has been associated with deficits in emotional learning and increased anxiety-like behaviours. In this study, we examined an individual presenting with mild intellectual disability, anxiety-like behaviours, and low frustration tolerance, along with generalised hypotonia. Trio-based whole exome sequencing (WES) identified a de novo nucleotides insertion, c.788_791dup, in the NTM (NM_001144058) gene. NTM currently lacks a MIM phenotype entry linking it to a specific disorder, and has been predicted to follow both autosomal dominant and recessive inheritance patterns. The variant was classified as pathogenic according to ACMG guidelines and displays a very low frequency in the gnomAD population (0.000006829). It is located at a highly conserved site (PhyloP: 7.674). In-silico analysis predicted that the variant induces nonsense-mediated decay (NMD) of the transcript, resulting in loss of NTM protein production. However, if the transcript escapes NMD, the insertion is expected to cause a frameshift, altering codons beyond amino acid 262, resulting in Ile263, a novel Asp264, and a premature stop codon (TGA) in position 265. This mutation is predicted to disrupt NTM homodimerization and heterodimerization with other IgLON family proteins (OPCML, LSAMP, NEGR1, and IgLON5), regardless of whether degradation of the transcript occurs or a truncated protein is produced. These findings suggest a potential link between NTM dysfunction and neurodevelopmental phenotypes and highlight its possible role as a candidate gene for mild cognitive and behavioural disorders.

Zinc finger proteins are frequently implicated in a wide range of neurodevelopmental disorders (NDDs). In this study, we report a case of mild intellectual disability (ID), global developmental delay (GDD), and developmental coordination disorder (DCD) in an individual with unaffected parents. Trio-based whole-exome sequencing (WES) identified a de novo variant (c.1530dup, p.Glu511ArgfsTer16) in the ZNF496 gene of the proband. According to ACMG guidelines, this novel variant is classified as pathogenic. It creates a frameshift that introduces a premature stop codon, resulting in a truncated protein of 525 amino acids (compared to the wild-type 587 residues). Notably, NMDEscPredictor analysis predicted that the transcript escapes nonsense-mediated decay (NMD) despite the frameshift. Computational analyses suggest the potential pathogenetic effects of the identified variant. As documented, ZNF496 interacts with JARID2, a gene associated with NDDs, ID and facial dysmorphism (MIM: #620098). In silico analyses suggest that the identified mutation disrupts this interaction by deleting ZNF496’s C2H2 domain, potentially dysregulating JARID2 target genes. To our knowledge, this is the first reported association between ZNF496 and NDDs, and the variant has been submitted to the ClinVar database (SCV006100880). Functional studies are imperative to validate ZNF496’s role in NDDs and confirm the mutation’s impact on ZNF496-JARID2 interactions.

Neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD), are increasingly recognized as conditions with a complex, multisystemic origin. ASD frequently co-occurs with other neurological conditions, such as epilepsy. We report a female patient, born to unrelated healthy parents, presenting with a complex clinical phenotype characterized by ASD level 1 with fluent speech, borderline intellectual functioning (BIF), coordination disorder, and epilepsy. Trio-based whole-exome sequencing (WES) revealed a de novo variant in the USP24 gene (c.3155G>T; p.Ser1052Ile), classified as likely pathogenic according to ACMG criteria (PS2, PM2, PP2, BP4). USP24 has previously been associated with Parkinson’s disease and has recently emerged as a candidate risk gene for ASD. In addition, WES detected two variants of uncertain significance (VUS), both inherited from the clinically unaffected father: c.388G>C (p.Gly130Arg) in NRXN2 and c.6395C>A (p.Ser2132Tyr) in LRP2. Although neither gene shows a fully penetrant causal relationship with the observed phenotype, both have been implicated in neurodevelopmental disorders. Array-CGH analysis did not reveal pathogenic copy number variants; however, the presence of additional genetic contributors not detectable by WES cannot be excluded. Overall, the de novo USP24 variant likely represents the primary genetic driver of the phenotype, while the potential contribution of the inherited NRXN2 and LRP2 variants remains plausible. This case underscores the complexity of the genetic architecture underlying NDDs and supports a model involving cumulative effects of multiple variants rather than a strictly multigenic interaction.

Background/Objectives: Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental condition characterized by a complex and multifactorial genetic architecture. In this study, we report a male patient, born to non-consanguineous healthy parents, presenting with ADHD and oppositional defiant disorder (ODD). Methods: Trio-based whole-exome sequencing (WES) was performed in the proband and both parents. Variant classification was performed according to American College of Medical Genetics and Genomics (ACMG) guidelines, and the potential pathogenicity of the identified variant was further assessed through multiple in silico prediction algorithms and protein structural analyses. Results: WES identified a homozygous variant in the LNX2 gene (NM_153371.4: c.1165G>A, p.Ala389Thr), classified as a variant of uncertain significance (VUS) and supported by multiple in silico predictions. LNX2 is expressed during brain development and encodes an E3 ubiquitin ligase involved in neuronal differentiation and synaptic function. The identified variant is located within the PDZ2 domain, a functionally relevant region involved in protein–protein interactions. Although the variant is reported in population databases (gnomAD ID: rs148429804), it has not been associated with any clinical phenotype, and its presence in the homozygous state has been reported only once, remaining extremely rare and lacking clinical annotation. Structural modelling predicted localized rearrangement of the hydrogen-bonding network within the PDZ2 domain without major conformational changes. Integrative transcriptomic, and single-cell analyses further supported the biological relevance of LNX2 in neurodevelopment, highlighting its preferential association with neuronal projection-cell networks, synaptic vesicle trafficking pathways, and neuron-specific regulatory programs. Conclusion: Although the identified LNX2 variant cannot be considered causative for the patient’s phenotype and a definitive disease–gene relationship cannot be established based on a single individual, the complementary genetic, structural, and transcriptomic findings support the biological plausibility of LNX2 as a candidate gene for neurodevelopmental disorders. Additional independent patients and functional studies will be required to clarify its contribution to human disease.