Several scientific papers were published in the 1980s and early 1990s about a n orthopedic disease specific to Australian Shepherds involving multiple skeletal anomalies, including cleft palate. In Europe it has been referred to as “skeletal lethal.” This disease was due to an X-linked mutation that arose in a single female dog. All male offspring that inherited the mutation had severely deformed skeletons and cleft palate; all but one died shortly after birth. Females with a copy of the mutation had crooked long bones in the legs and polydactyly and/or fused toes. Presumably, if a female were to inherit two copies of the mutation she would be as severely affected as the males.
This is not a breed health problem. It was confined to one family of dogs. Very few if any of them remain today.