Background and AimsAutism spectrum disorder (ASD) is influenced by genetic and environmental factors. This study investigates genetic mutations and prenatal factors associated with ASD, including their interplay, in a multicenter case-control study.MethodsThe study included 297 participants (149 ASD cases, 148 controls). Genetic data were analyzed using Multiplex Ligation-dependent Probe Amplification (MLPA) for ASD-associated chromosomal regions. Environmental data covered prenatal, perinatal, and neonatal factors. Logistic regression and stratified analyses were performed.ResultsSignificant associations were found between ASD and mutations in 15q11-15q13, 16p11, and 11q13 regions, particularly in SHANK2 and SHANK3. Females with ASD showed higher mutation rates than males. Prenatal factors (e.g., MgB6 use, labor-inducing drugs, maternal stress, pregnancy complications, shorter interpregnancy intervals) exacerbated ASD risk when combined with specific genetic variations. Duphaston use during pregnancy, alongside certain mutations, may influence ASD risk, potentially offering protective effects.ConclusionThis study highlights the importance of integrating genetic and environmental factors in ASD research. Findings underscore the need for tailored early interventions, prenatal care advice, and genetic counseling for at-risk families. Future studies should validate these findings in larger, diverse populations and explore underlying mechanisms.