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ATG16L1 gene

autophagy related 16 like 1

Normal Function

The ATG16L1 gene provides instructions for making a protein that is required for a process called autophagy. Cells use this process to recycle worn-out cell parts and break down certain proteins when they are no longer needed. Autophagy also plays an important role in controlled cell death (apoptosis). Additionally, autophagy is involved in the body's inflammatory response and helps the immune system destroy some types of harmful bacteria and viruses.

Health Conditions Related to Genetic Changes

Crohn's disease

At least one variation in the ATG16L1 gene is associated with an increased risk of Crohn's disease, particularly a form of the disorder that affects the lower part of the small intestine (the ileum) and the colon. This increased risk has been found primarily in people of northern European ancestry. The identified ATG16L1 variation changes a single protein building block (amino acid) in a critical region of the ATG16L1 protein. Specifically, it replaces the amino acid threonine with the amino acid alanine at protein position 300 (written as Thr300Ala or T300A).

This change in the ATG16L1 gene impairs the autophagy process, allowing worn-out cell parts and harmful bacteria to persist when they would otherwise be destroyed. These cell components and bacteria may trigger an inappropriate immune system response, leading to chronic inflammation in the intestinal walls and the digestive problems characteristic of Crohn's disease. Researchers continue to study the relationship between changes in the ATG16L1 gene and a person's risk of developing this disorder.

More About This Health Condition

Other Names for This Gene

  • APG16 autophagy 16-like
  • APG16L
  • ATG16 autophagy related 16-like 1 (S. cerevisiae)
  • ATG16 autophagy related 16-like protein 1
  • ATG16A
  • ATG16L
  • Autophagy 16-like 1
  • autophagy related 16-like 1
  • autophagy related 16-like 1 (S. cerevisiae)
  • WD repeat domain 30
  • WDR30

Additional Information & Resources

Tests Listed in the Genetic Testing Registry

Scientific Articles on PubMed

Catalog of Genes and Diseases from OMIM

Gene and Variant Databases


  • Boada-Romero E, Serramito-Gomez I, Sacristan MP, Boone DL, Xavier RJ, Pimentel-Muinos FX. The T300A Crohn's disease risk polymorphism impairs function of the WD40 domain of ATG16L1. Nat Commun. 2016 Jun 8;7:11821. doi: 10.1038/ncomms11821. Citation on PubMed or Free article on PubMed Central
  • Cadwell K, Liu JY, Brown SL, Miyoshi H, Loh J, Lennerz JK, Kishi C, Kc W, Carrero JA, Hunt S, Stone CD, Brunt EM, Xavier RJ, Sleckman BP, Li E, Mizushima N, Stappenbeck TS, Virgin HW 4th. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature. 2008 Nov 13;456(7219):259-63. doi: 10.1038/nature07416. Epub 2008 Oct 5. Citation on PubMed or Free article on PubMed Central
  • Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Gunther S, Prescott NJ, Onnie CM, Hasler R, Sipos B, Folsch UR, Lengauer T, Platzer M, Mathew CG, Krawczak M, Schreiber S. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet. 2007 Feb;39(2):207-11. doi: 10.1038/ng1954. Epub 2006 Dec 31. Citation on PubMed
  • Kuballa P, Huett A, Rioux JD, Daly MJ, Xavier RJ. Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant. PLoS One. 2008;3(10):e3391. doi: 10.1371/journal.pone.0003391. Epub 2008 Oct 13. Citation on PubMed or Free article on PubMed Central
  • Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A, Green T, Kuballa P, Barmada MM, Datta LW, Shugart YY, Griffiths AM, Targan SR, Ippoliti AF, Bernard EJ, Mei L, Nicolae DL, Regueiro M, Schumm LP, Steinhart AH, Rotter JI, Duerr RH, Cho JH, Daly MJ, Brant SR. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet. 2007 May;39(5):596-604. doi: 10.1038/ng2032. Epub 2007 Apr 15. Citation on PubMed or Free article on PubMed Central
  • Salem M, Ammitzboell M, Nys K, Seidelin JB, Nielsen OH. ATG16L1: A multifunctional susceptibility factor in Crohn disease. Autophagy. 2015 Apr 3;11(4):585-94. doi: 10.1080/15548627.2015.1017187. Citation on PubMed or Free article on PubMed Central
  • Zhang HF, Qiu LX, Chen Y, Zhu WL, Mao C, Zhu LG, Zheng MH, Wang Y, Lei L, Shi J. ATG16L1 T300A polymorphism and Crohn's disease susceptibility: evidence from 13,022 cases and 17,532 controls. Hum Genet. 2009 Jun;125(5-6):627-31. doi: 10.1007/s00439-009-0660-7. Epub 2009 Apr 1. Citation on PubMed
  • Zheng H, Ji C, Li J, Jiang H, Ren M, Lu Q, Gu S, Mao Y, Xie Y. Cloning and analysis of human Apg16L. DNA Seq. 2004 Aug;15(4):303-5. doi: 10.1080/10425170400004104. Citation on PubMed

The information on this site should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health.