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Conducting the first comprehensive whole\u2010genome sequencing (WGS) analysis of Japanese ASD trios, this study aimed to elucidate the clinical significance of pathogenic variants and enhance the understanding of ASD pathogenesis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>WGS was performed on 57 Japanese patients with ASD and their parents, investigating variants ranging from single\u2010nucleotide variants to structural variants (SVs), short tandem repeats (STRs), mitochondrial variants, and polygenic risk score (PRS).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Potentially pathogenic variants that could explain observed phenotypes were identified in 18 patients (31.6%) overall and in 10 of 23 patients (43.5%) with comorbid intellectual developmental disorder (IDD). De novo variants in <jats:italic>PTEN<\/jats:italic>, <jats:italic>CHD7<\/jats:italic>, and <jats:italic>HNRNPH2<\/jats:italic> were identified in patients referred for genetic counseling who exhibited previously reported phenotypes, including one patient with ASD who had profound IDD and macrocephaly with <jats:italic>PTEN<\/jats:italic> L320S. Analysis of the AlphaFold3 protein structure indicated potential inhibition of intramolecular interactions within PTEN. SV analysis identified deletions in <jats:italic>ARHGAP11B<\/jats:italic> and <jats:italic>TMLHE.<\/jats:italic> A pathogenic de novo mitochondrial variant was identified in a patient with ASD who had a history of encephalitis and cognitive decline. GO enrichment analysis of genes with nonsense variants and missense variants (Missense badness, PolyPhen\u20102, and Constraint &gt;1) showed associations with regulation of growth and ATP\u2010dependent chromatin remodeler activity. 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