ATG16L1

autophagy related 16 like 1, the group of WD repeat domain containing|Autophagy related

Basic information

Region (hg38): 2:233210050-233295674

Previous symbols: [ "APG16L", "ATG16L" ]

Links

ENSG00000085978 ∙ NCBI:55054 ∙ OMIM:610767 ∙ HGNC:21498 ∙ Uniprot:Q676U5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATG16L1 gene.

• Inborn genetic diseases (17 variants)
• not provided (2 variants)
• not specified (1 variants)
• Inflammatory bowel disease 10, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG16L1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	2

Variants in ATG16L1

This is a list of pathogenic ClinVar variants found in the ATG16L1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-233251887-A-G		ATG16L1-related disorder	Likely benign (Feb 26, 2019)
2-233256112-G-T		not specified	Uncertain significance (Mar 07, 2024)
2-233256125-G-C		not specified	Uncertain significance (May 25, 2022)
2-233256143-G-T		not specified	Uncertain significance (Aug 28, 2023)
2-233256173-G-A		not specified	Likely benign (Jan 26, 2022)
2-233263140-G-A			Uncertain significance (Feb 24, 2015)
2-233264911-A-T		not specified	Uncertain significance (Aug 14, 2023)
2-233264930-C-T		not specified	Uncertain significance (Jun 29, 2022)
2-233265016-A-G		not specified	Uncertain significance (Jun 30, 2022)
2-233265054-G-A		ATG16L1-related disorder	Likely benign (Jun 17, 2019)
2-233265130-GAA-G		Inflammatory bowel disease 10	Uncertain significance (Apr 04, 2024)
2-233270016-G-A		ATG16L1-related disorder	Likely benign (Aug 20, 2019)
2-233274710-G-A		not specified	Uncertain significance (May 23, 2023)
2-233274722-A-G		Inflammatory bowel disease 10, susceptibility to • not specified • ATG16L1-related disorder	Benign (Oct 17, 2019)
2-233281118-C-G		not specified	Uncertain significance (Sep 29, 2022)
2-233281126-C-T		not specified	Uncertain significance (Dec 21, 2022)
2-233281146-G-A		not specified	Uncertain significance (Mar 13, 2023)
2-233282700-G-A		not specified	Uncertain significance (Jan 26, 2023)
2-233289912-C-T		not specified	Uncertain significance (Jun 11, 2021)
2-233289934-C-T		ATG16L1-related disorder	Likely benign (Feb 19, 2019)
2-233292244-A-G		not specified	Uncertain significance (Aug 21, 2023)
2-233292246-C-T		not specified	Uncertain significance (Sep 26, 2022)
2-233292258-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-233292261-A-G		not specified	Likely benign (Jan 02, 2024)
2-233292406-G-A		not specified	Uncertain significance (Aug 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATG16L1	protein_coding	protein_coding	ENST00000392017	18	85624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.965	0.0355	125737	0	9	125746	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.63	207	345	0.601	0.0000192	3957
Missense in Polyphen		63	133.95	0.47031		1629
Synonymous	0.322	128	133	0.964	0.00000745	1173
Loss of Function	4.94	7	41.2	0.170	0.00000249	419

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in autophagy: interacts with ATG12-ATG5 to mediate the conjugation of phosphatidylethanolamine (PE) to LC3 (MAP1LC3A, MAP1LC3B or MAP1LC3C), to produce a membrane-bound activated form of LC3 named LC3-II. Thereby, controls the elongation of the nascent autophagosomal membrane (PubMed:24553140, PubMed:23376921, PubMed:24954904, PubMed:27273576, PubMed:23392225). Regulates mitochondrial antiviral signaling (MAVS)-dependent type I interferon (IFN-I) production (PubMed:25645662). Negatively regulates NOD1- and NOD2- driven inflammatory cytokine response (PubMed:24238340). Instead, promotes with NOD2 an autophagy-dependent antibacterial pathway (PubMed:20637199). Plays a role in regulating morphology and function of Paneth cell (PubMed:18849966). {ECO:0000269|PubMed:18849966, ECO:0000269|PubMed:22749352, ECO:0000269|PubMed:23376921, ECO:0000269|PubMed:23392225, ECO:0000269|PubMed:24238340, ECO:0000269|PubMed:24553140, ECO:0000269|PubMed:24954904, ECO:0000269|PubMed:25645662, ECO:0000269|PubMed:27273576}.
• Disease: DISEASE: Inflammatory bowel disease 10 (IBD10) [MIM:611081]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. {ECO:0000269|PubMed:17200669, ECO:0000269|PubMed:17435756, ECO:0000269|PubMed:17484864, ECO:0000269|PubMed:18047540, ECO:0000269|PubMed:18499543, ECO:0000269|PubMed:18985712, ECO:0000269|PubMed:19659808, ECO:0000269|PubMed:24553140, ECO:0000269|PubMed:24656308, ECO:0000269|PubMed:25645662, ECO:0000269|PubMed:27273576}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Nanoparticle triggered autophagic cell death;Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.296
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.246
• hipred: Y
• hipred_score: 0.775
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Atg16l1
• Phenotype: immune system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: autophagosome assembly;protein transport;macroautophagy;protein localization to phagophore assembly site;negative stranded viral RNA replication;protein homooligomerization;protein lipidation involved in autophagosome assembly;xenophagy
• Cellular component: autophagosome membrane;autophagosome;cytosol;axoneme;phagophore assembly site membrane
• Molecular function: protein binding;ubiquitin-like protein transferase activity;identical protein binding;GTPase binding