Human articular chondrocytes secrete several proteins involved in cartilage biogenesis. Hu et al. (1996) identified YKL39 as a protein in conditioned medium from human articular cartilage chondrocytes in primary culture that copurified with YKL40 (HC gp39).

The name 'YKL' refers to the N-terminal amino acid sequence of the protein. Hu et al. (1996) found that YKL39 is most closely related by sequence analysis to YKL40. Unlike YKL40, the YKL39 protein is not glycosylated; like YKL40, it is related to bacterial chitinases but does not have chitinase activity because it lacks the active site glutamate. The authors found the highest level of YKL39 mRNA expression in chondrocytes, followed by synoviocytes, lung, and heart. No YKL39 mRNA was detected in brain, spleen, pancreas, or liver.