Some children with autism carry rare mutations in DNA segments that flank genes and control their expression—and they tend to inherit these mutations from their unaffected fathers, according to a study published today in Science1.

The finding is unexpected because most studies implicate mutations inherited from mothers in autism risk. For this reason, some experts are skeptical of the results.

The study is the largest yet to explore how mutations outside of genes contribute to autism: It is based on an analysis of 9,274 whole genomes. And it focuses on ‘structural variants’—deletions or duplications in DNA—in these noncoding regions. Once dismissed as ‘junk DNA,’ some of these regions are now known to control the expression of genes.

“These are the types of variants which, before, if you did clinical genetic testing, you would ignore,” says lead investigator Jonathan Sebat, chief of the Beyster Center for Genomics and Neuropyschiatric Diseases at the University of California, San Diego.

The variants overall account for only a small proportion of individuals with autism, however: an estimated 0.39 to 1.13 percent.

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