GeneBe

ATG12

autophagy related 12, the group of Autophagy related

Basic information

Region (hg38): 5:115828200-115841837

Previous symbols: [ "APG12L" ]

Links

ENSG00000145782 ∙ NCBI:9140 ∙ OMIM:609608 ∙ HGNC:588 ∙ Uniprot:O94817 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • colorectal cancer (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATG12 gene.

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.

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
0
missense
10
clinvar
 10
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 10 0 0

Variants in ATG12

This is a list of pathogenic ClinVar variants found in the ATG12 region.

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

Position Type Phenotype Significance ClinVar
5-115832606-T-G not specified Uncertain significance (Dec 04, 2024)3442832
5-115832624-T-C not specified Uncertain significance (Sep 10, 2024)3442821
5-115832661-T-C not specified Uncertain significance (Jul 13, 2022)2214605
5-115837759-T-C not specified Uncertain significance (Dec 21, 2023)3130860
5-115841414-G-A not specified Uncertain significance (Nov 14, 2024)3442810
5-115841488-A-C not specified Uncertain significance (Aug 20, 2024)3442791
5-115841522-G-C not specified Uncertain significance (Oct 20, 2024)3442802
5-115841531-C-G not specified Uncertain significance (Sep 28, 2022)2230856
5-115841536-T-G not specified Uncertain significance (Mar 25, 2024)3320700
5-115841539-G-A not specified Uncertain significance (Aug 10, 2024)3442780

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATG12protein_codingprotein_codingENST00000509910 413663
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000004690.2421257210201257410.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.3710673.11.450.00000334885
Missense in Polyphen1619.6310.81502260
Synonymous-1.974228.61.470.00000135290
Loss of Function-0.062287.811.025.13e-781

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005900.0000590
Ashkenazi Jewish0.000.00
East Asian0.00005460.0000544
Finnish0.000.00
European (Non-Finnish)0.0001230.000123
Middle Eastern0.00005460.0000544
South Asian0.00009840.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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