A genome-wide association analysis conducted in 2007 identified Atg16L1 as a Crohn’s disease (CD) susceptibility gene [95], and the relationship between IBD and genes associated with autophagy, such as nucleotide-binding oligomerization domain-containing protein (NOD)2, immunity-related GTPase family M protein (IRGM), leucine-rich repeat kinase (LRRK)2, and ULK1, has also been examined [96,97,98,99,100]. Here, IRGM is linked to Cowden disease.