The culprit gene is part of what has been called junk DNA, regions whose function, if any, is largely unknown. In this case, the dead genes had seemed permanently disabled. But, said Dr. Collins, “the first law of the genome is that anything that can go wrong, will.” David Housman, a geneticist at M.I.T., said scientists will now be looking for other diseases with similar causes, and they expect to find them.

“As soon as you understand something that was staring you in the face and leaving you clueless, the first thing you ask is, ‘Where else is this happening?’ ” Dr. Housman said.

But, he added, in a way FSHD was the easy case — it is a disease that affects every single person who inherits the genetic defect. Other diseases are more subtle, affecting some people more than others, causing a range of symptoms. The trick, he said, is to be “astute enough to pick out the patterns that connect you to the DNA.”

FSHD affects about 1 in 20,000 people, causing a progressive weakening of muscles in the upper arms, around the shoulder blades and in the face — people who have the disease cannot smile. It is a dominant genetic disease. If a parent has the gene mutation that causes it, each child has a 50 percent chance of getting it too. And anyone who inherits the gene is absolutely certain to get the disease.

About two decades ago, geneticists zeroed in on the region of the genome that seemed to be the culprit: the tip of the longer arm of chromosome 4, which was made up of a long chain of repeated copies of a dead gene. The dead gene was also repeated on chromosome 10, but that area of repeats seemed innocuous, unrelated to the disease. Only chromosome 4 was a problem.