The MKRN3 gene provides instructions for making a protein called makorin ring finger protein 3 (MKRN3). This protein plays a role in directing the onset of puberty, which describes the changes in the body related to sexual development that normally occur in adolescence. Puberty begins when a gland in the brain called the hypothalamus is stimulated to release bursts of a hormone called gonadotropin releasing hormone (GnRH). This hormone triggers the release of other hormones that direct sexual development. Research suggests that the MKRN3 protein blocks (inhibits) the release of GnRH from the hypothalamus, thus holding off the onset of puberty.

The exact function of the MKRN3 protein is unknown. Based on its structure, the protein is thought to play a role in the cell machinery that breaks down (degrades) unwanted proteins, called the ubiquitin-proteasome system, by helping attach a molecule called ubiquitin to unwanted proteins. Ubiquitin acts as a signal to the ubiquitin-proteasome system to break the protein down. Researchers speculate that MKRN3 adds ubiquitin to proteins that would otherwise stimulate GnRH release. The breakdown of such proteins ensures that puberty does not begin until the right time.

For most genes, both copies of the gene (one copy inherited from each parent) are active in all cells. However, the activity of the MKRN3 gene depends on which parent it was inherited from. Only the copy inherited from a person's father is active; the copy inherited from the mother is not active. This sort of parent-specific difference in gene activation is caused by a phenomenon called genomic imprinting.