STAG3 is a meiosis-specific component of the cohesin complex. Cohesin is required for the cohesion of sister chromatids after DNA replication, and it apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The meiosis-specific cohesin complex, which includes cohesin subunit SA-3, probably replaces the mitosis-specific cohesin complex when that complex dissociates from chromatin during prophase I.

The human STAG3 gene encodes a nuclear protein that localises to chromosomes, including the centromere. UniProt places it in the SCC3 family, and HGNC classifies it within the cohesin complex, armadillo-like helical domain containing and STAG gene groups. The gene has mouse and rat orthologs, both named Stag3. Alternative splicing gives multiple transcript variants that encode distinct isoforms, and the gene has multiple pseudogenes, which is worth bearing in mind when designing nucleic acid assays.

The protein was previously known as stromal antigen 3, and SA3 remains a common alias. A mutation in this gene is associated with premature ovarian failure, which links meiotic chromosome cohesion to reproductive biology. Researchers studying STAG3 often compare it with the mitotic cohesin subunit STAG2 to understand how meiotic and mitotic cohesin complexes differ.