Basilicata–Akhtar syndrome is caused by variants (also known as mutations) in a single gene, the MSL3 gene. As the MSL3 gene is located on the X chromosome, Basilicata-Akhtar syndrome is a X-linked condition. In males (who have only one X chromosome), a variant in the only copy of the gene causes the disorder. In females (who have two X chromosomes), a variant in one of the two copies of the is sufficient to cause the condition. Variants in MSL3 are typically not inherited from the parents and occur in the affected family member for the first time (a so called de novo variant). Variants in MSL3 are suspected to lead to a disrupted MSL3 protein.