SMC6 is a core component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. It is also required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines, where it mediates sumoylation of shelterin complex (telosome) components. This is proposed to lead to shelterin disassembly in ALT-associated PML bodies (APBs), and the complex is required for recruitment of telomeres to PML nuclear bodies.

The SMC5-SMC6 complex may also prevent transcription of episomal DNA, such as circular viral DNA genomes. Consistent with this, NCBI Gene annotation links the SMC6 gene to host-mediated suppression of viral genome replication, as well as to cellular senescence and telomere maintenance via recombination. The protein is reported to enable DNA secondary structure binding and ubiquitin protein ligase binding. Researchers studying SMC6 protein may therefore work across genome stability, telomere biology and host-virus interactions.

In UniProt, SMC6 is localised to the nucleus, including nuclear speckles, chromosomes, PML bodies and telomeres. HGNC places the gene in the structural maintenance of chromosomes proteins group and the SMC5/6 complex group. The gene was previously named SMC6 structural maintenance of chromosomes 6-like 1 (yeast), with the symbol SMC6L1, reflecting its yeast homologue origin. The mouse ortholog is Smc6.