Unraveling the Genetic and Molecular Architecture of Autism Spectrum Disorder: Implications for Clinical Genetics and Genomic Diagnostics

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.