ATG16L1
autophagy related 16 like 1, the group of WD repeat domain containing|Autophagy related
Basic information
Region (hg38): 2:233210051-233295674
Previous symbols: [ "APG16L", "ATG16L" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (44 variants)
- ATG16L1-related_disorder (5 variants)
- not_provided (3 variants)
- Inflammatory_bowel_disease_10 (2 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. These statistics are base on transcript: NM_000030803.7. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | |||||
| missense | 42 | 46 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 43 | 10 | 1 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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