Today's reproductive tests can't spot the problem, said study co-author Dr. Theodore Tollner of the University of California, Davis.
"You would have no reason to think many of these men with the genetic mutation would have reduced sperm function," he said.
Anywhere from 10 percent to 15 percent of couples experience infertility, and doctors can't always find the cause. A lack of sperm or problems with their shape or ability to move explains only a fraction of infertility.
The California-led team found a new reason, a protein that's part of a family of germ-killing molecules found on the surfaces of a variety of tissues. It's secreted as sperm journey into the female reproductive tract, helping the sperm to penetrate the mucus in a woman's cervix and to avoid being tagged as an invader by her immune system.
Having two copies of a particular gene mutation means sperm cannot produce that coating. Lab tests show those sperm have a hard time making it through the mucus.
But how much does that affect fertility?
The researchers tracked 500 newly married Chinese couples attempting to conceive. The birth rate was 30 percent lower among couples with a husband who harbored that double mutation, scientists reported in the journal Science Translational Medicine.
Having just one copy of the mutated gene doesn't seem to hinder conception.
The coatless sperm don't always fail, so it's not clear just how much this issue contributes to male infertility overall.
But creating a test to diagnose these men would be easy, the researchers said. Such a test potentially would lessen the time that a couple having problems conceiving spends in limbo before trying treatments such as having sperm placed directly into the woman's uterus.
One day, a vaginal gel might even let sperm pick up the protein coating as it travels into the cervix. The California researchers say they're already trying that with animals.