I. G. Koh, E. Chang, Y. S. Choi, S.-W. Kim, Y. Kim, H. Lee, G. Byeon, Y. Ryu, S. Kim, J. Lee, H. Park, H. Sim, Y. Ryu, W. Shim, J. Lee, N. B. Salazar, M. M. de Aquino, W. Engchuan, X. Zhou, J. H. Son, J. Lee, G. Bong, I. B. Kim, J. H. Han, D. M. Werling, S. H. Kim, M. Oh, M.-S. Kim, D. Lee, J. Kim, Y.-S. Lee, W. Sun, E. Kim, S. W. Scherer, M. Jeon, H. J. Yoo, J.-Y. An
Autism gene discovery is constrained by the rarity and heterogeneity of damaging variants, requiring large cohorts to identify susceptibility genes. Neural organoids and single-cell foundation models enable perturbation modeling in neurodevelopmental contexts. Here, we show that perturbation-informed foundation modeling of neural organoids can provide functional context for prioritizing candidate genes with genomic and clinical support. We constructed a 3.6-million-cell organoid atlas and trained models to predict genome-wide perturbation responses. Benchmarking 17 models identified a telencephalic neuron-specific model best preserving autism-relevant perturbation structure. Genome-wide profiling revealed two clusters associated with mid-fetal synaptic neuronal processes and early radial glia ubiquitin signaling. These clusters were supported by damaging-variant enrichment and clinical phenotypes across 89,916 family-based samples. Logistic-regression prioritization identified 343 candidates, including 167 in the key clusters, with convergence across TADA signals and recurrent evidence for NBEA and KLHDC10. This framework integrates predicted perturbation effects with genomic evidence to support autism candidate prioritization.