Basilicata–Akhtar syndrome is caused by de novo variants in the X-linked gene MSL3. Inherited pathogenic variants have not been described to date. Variants are typically loss-of-function-variants therefore suggesting haploinsufficency as pathophysiologic mechanism. All variants reported to date are located in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Variants were identified by genome or exome sequencing.