The BBC notes:
The fault is in a gene receptor present in healthy people without inflammatory bowel disease but rare in those with the condition.
Further background is provided by the Baltimore Sun:
In 2001, scientists identified the first major gene underlying Crohn's disease. Called Nod2, the gene regulates the immune system's response to bacteria in the gut. People with one flawed copy have twice the normal risk of developing the disease, researchers found. Two flawed copies and the risk jumps 20- to 40-fold.
Researchers have since uncovered a handful of other suspicious gene mutations thought to play a role in inflammatory bowel disease. But the new finding marks the first time researchers have identified a mutation that may actually help protect against Crohn's.
The potential result of this finding is better drug therapies, eventually.