The gene associated with ATR-X syndrome lies on the X chromosome. Males only have one X chromosome and this is always inherited from their mothers. Females have two X chromosomes and, therefore, two copies of the ATRX gene. If they are carriers and have one damaged copy, the other normal copy fully compensates. This explains why female carriers avoid being affected themselves.

xyWhen carriers have children there is a 50 : 50 chance of passing on the affected gene. If a male inherits the damaged gene he will be affected; if a female inherits the damage gene she will be a carrier like her mother. If a female carrier passes on the normal copy of the gene, a son would be unaffected and a daughter would not be a carrier. The risk of a carrier passing on the gene is the same for each pregnancy and the outcome is as random as tossing a coin.

ATR-X like many genetic conditions can run in a family or arise anew, out of the blue. If a mother has one affected child there are two possibilities: she may be a carrier or else the damage to the gene may have arisen in the egg or developing embryo and in this case the mother would not be a carrier. In the former case other female members of the family may be at risk of carrying the condition; in the latter case, they would not be at risk.