Patients with the congenital variant of Rett syndrome have features similar to classic Rett syndrome, but hypotonia and severe developmental delay starts in the first months of life. Abnormalities of the FOXG1 [OMIM #164874] gene, or forkhead box G1, have been identified in patients with the congenital variant of Rett syndrome. Ariani F, et al  studied 53 patients with classic Rett syndrome and the variant forms of Rett syndrome. In their study, 2/2 patients with the congenital variant of Rett syndrome had truncating mutations in FOXG1. None of the other patients were found to have mutations or deletions in FOXG1.
Deletions and/or duplications of the FOXG1 gene as causative of Rett syndrome have been reported.