May play a role in regulating epithelial homeostasis in an ATG16L1-dependent manner. Homooligomer. Heterooligomer with ATG16L1. Interacts with ATG5. Self-oligomerizes to form a 800-kDa complex composed of ATG12-ATG5 and ATG16L2. Interacts with RAB33B. Localizes also to discrete punctae along the ciliary axoneme. Although ATG16L2 is structurally similar to ATG16L1 and is likewise able to form a complex with the autophagy proteins ATG5 and ATG12, overexpression and knockdown studies in mouse suggest that ATG16L2 is not essential for canonical autophagy. Belongs to the WD repeat ATG16 family.