Due to the suspicious findings of both antibody‐positive diabetes mellitus and autoimmune thyroiditis in this young infant, rapid trio, whole‐genome sequencing (WGS) was performed at 5.5 months of age which identified a maternally inherited, hemizygous, pathogenic canonical splice site variant (c.−23 + 1G > T) in FOXP3, which was clinically confirmed by Sanger sequencing. The gene discussed is FOXP3; the disease is diabetes mellitus.