ATG12
Basic information
Region (hg38): 5:115828200-115841837
Previous symbols: [ "APG12L" ]
Links
Phenotypes
GenCC
Source:
- colorectal cancer (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATG12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004707.4. 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 | 0 | |||||
| missense | 22 | 22 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATG12 | protein_coding | protein_coding | ENST00000509910 | 4 | 13663 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000469 | 0.242 | 125721 | 0 | 20 | 125741 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.37 | 106 | 73.1 | 1.45 | 0.00000334 | 885 |
| Missense in Polyphen | 16 | 19.631 | 0.81502 | 260 | ||
| Synonymous | -1.97 | 42 | 28.6 | 1.47 | 0.00000135 | 290 |
| Loss of Function | -0.0622 | 8 | 7.81 | 1.02 | 5.13e-7 | 81 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000590 | 0.0000590 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000546 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000123 | 0.000123 |
| Middle Eastern | 0.0000546 | 0.0000544 |
| South Asian | 0.0000984 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-like protein involved in autophagy vesicles formation. Conjugation with ATG5 through a ubiquitin-like conjugating system involving also ATG7 as an E1-like activating enzyme and ATG10 as an E2-like conjugating enzyme, is essential for its function. The ATG12-ATG5 conjugate acts as an E3-like enzyme which is required for lipidation of ATG8 family proteins and their association to the vesicle membranes. {ECO:0000269|PubMed:12207896, ECO:0000269|PubMed:17999726, ECO:0000269|PubMed:19074260, ECO:0000269|PubMed:19164948, ECO:0000269|PubMed:23202584}.;
- Pathway
- Autophagy - animal - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Autophagy - other - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);RIG-I-like receptor signaling pathway - Homo sapiens (human);Nanoparticle triggered autophagic cell death;RIG-I-like Receptor Signaling;Senescence and Autophagy in Cancer;DDX58/IFIH1-mediated induction of interferon-alpha/beta;Innate Immune System;Immune System;Pink/Parkin Mediated Mitophagy;Receptor Mediated Mitophagy;Mitophagy;Macroautophagy;Cellular responses to external stimuli;Negative regulators of DDX58/IFIH1 signaling
(Consensus)
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- 0.436
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.11
Haploinsufficiency Scores
- pHI
- 0.103
- hipred
- N
- hipred_score
- 0.170
- ghis
- 0.437
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.491
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atg12
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- autophagosome assembly;autophagy of mitochondrion;C-terminal protein lipidation;macroautophagy
- Cellular component
- autophagosome;cytosol;phagocytic vesicle membrane;phagophore assembly site membrane;Atg12-Atg5-Atg16 complex
- Molecular function
- protein binding;Atg8 ligase activity