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The least active group would be comparable to Americans who get little exercise beyond normal activities of daily living, Snitker said.
The authors said it is not clear how the FTO gene influences excess weight, but it is believed to be involved in the function of a protein that may affect how the body regulates food intake.
"It's only if you're not active that the gene hurts," Snitker said. "If you are active, then either way, it doesn't matter whether you have the gene or not."
So far, blood tests identifying the gene variant are only available for research. Experts say there are likely many other genetic differences that also influence obesity, so it is too soon to recommend routine testing for the general public.
Dr. Joel Hirschhorn, a genetics and obesity researcher at Children's Hospital Boston, said people should not interpret the study to mean, "I don't have this gene variant so I don't need to be physically active."
He noted that other obesity gene variants might also be affected by physical activity, which has benefits beyond helping people stay trim.
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