[5] This protein is characterized as a subunit of the autophagy-related ATG12-ATG5/ATG16 complex and is essentially important for the LC3 (ATG8) lipidation and autophagosome formation.

[6] Autophagy in general plays a crucial role in pathways leading to innate and adaptive immunity activation.

[7] That is why many autophagy-related proteins, including ATG16L1, their gene expression and its role in autoimmune diseases are studied in-depth nowadays.[when?]

Cytoplasmic constituents, including organelles, are sequestered into double-membraned autophagosomes, which subsequently fuse with lysosomes.

It appears that ATGL16L has an important role not only in autophagy but also in xenophagy for example during a bacterial infection, in antigen presentation in human B cells, plasma membrane repair in mouse embryonic fibroblasts, hormone secretion and in alcohol-induced sedation response in Drosophila.

It has been shown that changes in ATG16L2 expression are correlated with Multiple Sclerosis (MS) and can be used as a serum biomarker of the disease and specifically for the prediction of relapse rates.

Interestingly ATG16L2 mRNA expression was significantly reduced (~4-fold lower) in T cells isolated from the peripheral blood of MS patients in comparison to healthy age-matched controls, which may reflect their abnormal activation.