Loss-of-function of FOXP1 can be caused by a (partial) deletion of the gene (either interstitial 3p deletions or intragenic deletions) or by mutations in the gene. Most pathogenic FOXP1 variants result in premature truncation, however missense and splice site variants are present in a minority of patients. Frameshift and spice site mutations may occur throughout the gene, whereas missense mutations are located in or close to the DNA-binding FOX-domain.
All pathogenic variants that have been reported to date were de novo.
All variants identified so far have been detected through CNV analysis, direct sanger sequencing of FOXP1 or exome sequencing.