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Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®


Reviewed August 2007

What is the official name of the ATG16L1 gene?

The official name of this gene is “autophagy related 16 like 1.”

ATG16L1 is the gene's official symbol. The ATG16L1 gene is also known by other names, listed below.

What is the normal function of the ATG16L1 gene?

The ATG16L1 gene provides instructions for making a protein called autophagy related 16-like 1. This protein is part of a larger family of proteins that are 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.

Does the ATG16L1 gene share characteristics with other genes?

The ATG16L1 gene belongs to a family of genes called WDR (WD repeat domain containing).

A gene family is a group of genes that share important characteristics. Classifying individual genes into families helps researchers describe how genes are related to each other. For more information, see What are gene families? ( in the Handbook.

How are changes in the ATG16L1 gene related to health conditions?

Crohn disease - increased risk from variations of the ATG16L1 gene

At least one variation in the ATG16L1 gene is associated with an increased risk of Crohn disease, particularly a form of the disorder that affects the lower part of the small intestine (the ileum). This increased risk has been found primarily in white populations. The identified ATG16L1 variation changes a single protein building block (amino acid) in a critical region of the autophagy related 16-like 1 protein. Specifically, it replaces the amino acid threonine with the amino acid alanine at protein position 300 (written as Thr300Ala or T300A).

The effects of variations in the ATG16L1 gene on Crohn disease risk are unclear. Changes in this gene may affect 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 disease. Researchers continue to study the relationship between changes in the ATG16L1 gene and a person's risk of developing this disorder.

Where is the ATG16L1 gene located?

Cytogenetic Location: 2q37.1

Molecular Location on chromosome 2: base pairs 233,251,571 to 233,295,674

(Homo sapiens Annotation Release 107, GRCh38.p2) (NCBI (

The ATG16L1 gene is located on the long (q) arm of chromosome 2 at position 37.1.

The ATG16L1 gene is located on the long (q) arm of chromosome 2 at position 37.1.

More precisely, the ATG16L1 gene is located from base pair 233,251,571 to base pair 233,295,674 on chromosome 2.

See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about ATG16L1?

You and your healthcare professional may find the following resources about ATG16L1 helpful.

You may also be interested in these resources, which are designed for genetics professionals and researchers.

What other names do people use for the ATG16L1 gene or gene products?

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

See How are genetic conditions and genes named? ( in the Handbook.

What glossary definitions help with understanding ATG16L1?

alanine ; amino acid ; apoptosis ; autophagy ; bacteria ; cell ; chronic ; critical region ; digestive ; domain ; gene ; ileum ; immune system ; inflammation ; intestine ; nucleotide ; polymorphism ; protein ; single nucleotide polymorphism ; threonine

You may find definitions for these and many other terms in the Genetics Home Reference Glossary.


  • Cummings JR, Cooney R, Pathan S, Anderson CA, Barrett JC, Beckly J, Geremia A, Hancock L, Guo C, Ahmad T, Cardon LR, Jewell DP. Confirmation of the role of ATG16L1 as a Crohn's disease susceptibility gene. Inflamm Bowel Dis. 2007 Aug;13(8):941-6. (
  • Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Günther S, Prescott NJ, Onnie CM, Häsler R, Sipos B, Fölsch 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. Epub 2006 Dec 31. (
  • NCBI Gene (
  • Prescott NJ, Fisher SA, Franke A, Hampe J, Onnie CM, Soars D, Bagnall R, Mirza MM, Sanderson J, Forbes A, Mansfield JC, Lewis CM, Schreiber S, Mathew CG. A nonsynonymous SNP in ATG16L1 predisposes to ileal Crohn's disease and is independent of CARD15 and IBD5. Gastroenterology. 2007 May;132(5):1665-71. Epub 2007 Mar 24. (
  • 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. Epub 2007 Apr 15. (
  • Yamazaki K, Onouchi Y, Takazoe M, Kubo M, Nakamura Y, Hata A. Association analysis of genetic variants in IL23R, ATG16L1 and 5p13.1 loci with Crohn's disease in Japanese patients. J Hum Genet. 2007;52(7):575-83. Epub 2007 May 30. (
  • 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. (


The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? ( in the Handbook.

Reviewed: August 2007
Published: February 1, 2016