MAP1LC3A
Basic information
Region (hg38): 20:34546854-34560345
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP1LC3A 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in MAP1LC3A
This is a list of pathogenic ClinVar variants found in the MAP1LC3A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-34559225-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
| 20-34559759-C-T | not specified | Uncertain significance (Nov 09, 2021) | ||
| 20-34559835-G-C | not specified | Uncertain significance (Sep 27, 2024) | ||
| 20-34559894-T-G | not specified | Uncertain significance (Feb 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MAP1LC3A | protein_coding | protein_coding | ENST00000374837 | 4 | 13492 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0279 | 0.811 | 125722 | 0 | 8 | 125730 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.46 | 45 | 82.4 | 0.546 | 0.00000511 | 831 |
| Missense in Polyphen | 6 | 21.799 | 0.27525 | 217 | ||
| Synonymous | 0.0596 | 34 | 34.4 | 0.987 | 0.00000251 | 214 |
| Loss of Function | 1.07 | 3 | 5.77 | 0.520 | 2.45e-7 | 69 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000627 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000354 | 0.0000352 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes) (PubMed:20713600, PubMed:24290141). Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (PubMed:20713600). {ECO:0000269|PubMed:20713600, ECO:0000269|PubMed:24290141}.;
- Pathway
- Ferroptosis - Homo sapiens (human);Nanoparticle triggered autophagic cell death;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;Senescence and Autophagy in Cancer;Pink/Parkin Mediated Mitophagy;Receptor Mediated Mitophagy;Mitophagy;Macroautophagy;Cellular responses to external stimuli
(Consensus)
Recessive Scores
- pRec
- 0.0962
Intolerance Scores
- loftool
- 0.580
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- 0.0984
- hipred
- Y
- hipred_score
- 0.633
- ghis
- 0.610
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Map1lc3a
- Phenotype
Gene ontology
- Biological process
- autophagosome assembly;autophagy of mitochondrion;cellular response to nitrogen starvation;cellular response to starvation;response to iron(II) ion;response to lead ion;macroautophagy;cellular response to amino acid starvation;response to morphine;cellular response to hydrogen peroxide;cellular response to copper ion;autophagosome maturation
- Cellular component
- autophagosome membrane;late endosome;autophagosome;cytosol;microtubule;organelle membrane;autolysosome;synapse
- Molecular function
- protein binding;phospholipid binding;microtubule binding;phosphatidylethanolamine binding;ubiquitin protein ligase binding