Autism spectrum disorder (ASD) is a neurodevelopmental disorder with prenatal and early postnatal biological onset. Genetic factors contribute to the predisposition and development of ASD with estimated heritability rates of 50-83%. Large-scale genetic studies have implicated several hundred risk (rASD) genes that appear to be associated with many different pathways, cell processes, and neurodevelopmental stages. This highly heterogeneous genetic landscape has raised challenges in elucidating the biological mechanisms involved in the disorder. While rigorous proof remains lacking, current evidence suggests that rASD genes fall into networks and biological processes that modulate one or more critical stages of prenatal and early postnatal brain development, including neuronal proliferation, migration, neurite growth, synapse formation and function. However, these insights are mostly gained from focused studies on single rASD genes or based on transcriptome data of non-ASD brains, leaving an incomplete picture of rASD-induced molecular changes at the individual level and relationships with early-age clinical heterogeneity.