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Here we systematically contextualize genes associated with ASD across neurodevelopment and cortical areas, integrating developmental single-cell and spatial atlases with gene- and isoform co-expression, regulatory, proteomic, and synaptic networks. Genetic burden concentrates within temporally-resolved neuronal subclasses: newborn excitatory neurons, immature interneurons, and maturing intratelencephalic lineages. Genes associated with ASD converge on three functional programs\u2014gene regulation, neuronal morphogenesis, and synaptic transmembrane signaling machinery\u2014resolved from 28 ASD-associated networks, several of which are directly regulated by ASD genes including\n                  <jats:bold>\n                    <jats:italic>MEF2C<\/jats:italic>\n                    ,\n                    <jats:italic>SOX11<\/jats:italic>\n                  <\/jats:bold>\n                  , and\n                  <jats:bold>\n                    <jats:italic>FOXP2<\/jats:italic>\n                  <\/jats:bold>\n                  . These programs are spatially patterned, with risk genes exhibiting an increasing anterior-to-posterior cortical expression gradient, anchored in the primary visual cortex and driven by excitatory neuron gene-regulatory programs. Finally, ASD risk genes associated with more severe developmental phenotypes show broader excitatory neuron enrichment and less interneuron involvement. Together, these findings anchor ASD genetic vulnerability to specific neurodevelopmental lineages, epochs, and molecular substrates, and delineate the features that distinguish ASD from comorbidities with broader developmental impacts.\n                <\/jats:p>","DOI":"10.64898\/2026.09.22.753508","type":"posted-content","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T16:05:14Z","timestamp":1790179514000},"source":"Crossref","is-referenced-by-count":4,"title":["Autism genes converge on three functional programs organized by neuronal subclass, developmental timing, and cortical patterning"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-5318-219X","authenticated-orcid":false,"given":"Rachel L.","family":"Smith","sequence":"first","affiliation":[{"name":"Departments of Psychiatry, Genetics, and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"The Lurie Autism Institute at Penn Medicine and the Children\u2019s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"The Lifespan Brain Institute at Penn Medicine and the Children\u2019s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0969-6927","authenticated-orcid":false,"given":"Yundan","family":"Liao","sequence":"additional","affiliation":[{"name":"Departments of Psychiatry, Genetics, and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"The Lurie Autism Institute at Penn Medicine and the Children\u2019s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"The Lifespan Brain Institute at Penn Medicine and the Children\u2019s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lambertus","family":"Klei","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lujing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunlong","family":"Ma","sequence":"additional","affiliation":[{"name":"Departments of Psychiatry, Genetics, and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"The Lurie Autism Institute at Penn Medicine and the Children\u2019s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"The Lifespan Brain Institute at Penn Medicine and the Children\u2019s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miao","family":"Tang","sequence":"additional","affiliation":[{"name":"Departments of Psychiatry, Genetics, and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"The Lurie Autism Institute at Penn Medicine and the Children\u2019s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA"},{"name":"The Lifespan Brain Institute at Penn Medicine and the Children\u2019s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"F. 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