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In the first genome-wide association study of foveal hypoplasia, we identified 42 sentinel variants mapping to 54 effector genes supported by \u2265 2 criteria from a variant-to-gene framework incorporating developmental multi-omics. Disruption of six effector genes using mutant lines and CRISPR knockouts in the zebrafish high acuity zone recapitulates structural, functional, and ultrastructural hallmarks of foveal hypoplasia, establishing the first vertebrate disease model. Integration with human foetal single-cell and spatial transcriptomics reveals two temporal waves of effector gene expression and identifies M\u00fcller glia as critical mediators of foveal patterning. Phenome-wide analyses reveal foveal variants are pleiotropic with refractive, lenticular, and metabolic traits, connecting foveal development to anterior segment and systemic disease biology. These findings should inform mechanistic studies of macular disease.<\/jats:p>","DOI":"10.64898\/2026.06.11.26355452","type":"posted-content","created":{"date-parts":[[2026,6,13]],"date-time":"2026-06-13T00:35:17Z","timestamp":1781310917000},"source":"Crossref","is-referenced-by-count":1,"title":["Genome-wide association and multi-omics functional screens reveal the genetic architecture of foveal development"],"prefix":"10.64898","author":[{"given":"Callum","family":"Hunt","sequence":"first","affiliation":[{"name":"Ulverscroft Eye Unit, School of Psychology and Vision Sciences, University of Leicester, Leicester, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manjiri","family":"Patil","sequence":"additional","affiliation":[{"name":"Ulverscroft Eye Unit, School of Psychology and Vision Sciences, University of Leicester, Leicester, 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