AIM: To identify the genetic factors underlying anophthalmia and microphthalmia (A/M), and to perform computational analysis to verify the pathophysiological mechanisms of the disease.​ METHODS: This study investigated a consanguineous Pakistani family with multiple affected individuals. Clinical evaluations were conducted using A-Scan and ophthalmic B-Scan ultrasonography (B-Scan). To identify the disease-causing variant, whole exome sequencing (WES) and Sanger sequencing were performed. In silico functional analyses were carried out using AlphaFold (for protein modeling) and ClusPro (for protein docking analysis) tools, and the hydrodynamic properties of the protein were determined via molecular dynamics simulations.​ RESULTS: Clinical analysis of the five patients revealed severe phenotypes of bilateral anophthalmia. Ocular B-Scan did not detect ocular tissue or intraocular fluid, thus confirming the diagnosis of anophthalmia in all patients. Due to these structural defects, all patients exhibited complete blindness and absence of light perception; additionally, two patients had mild to moderate intellectual disability. Genetic analysis identified a splice site variant [NM_000693.2: c.884-2_885dup; p.(Asp296SerfsTer35)] in the 9th exon of the ALDH1A3 gene.​ CONCLUSION: The present study expands the genetic spectrum of ALDH1A3 and contributes to establishing the genotype-phenotype correlation for this gene.​