MAP1LC3C
Basic information
Region (hg38): 1:241995490-241999098
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 MAP1LC3C 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 0 |
Variants in MAP1LC3C
This is a list of pathogenic ClinVar variants found in the MAP1LC3C region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-241996168-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 1-241996248-G-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 1-241996249-C-T | not specified | Uncertain significance (Dec 25, 2024) | ||
| 1-241996293-T-C | not specified | Uncertain significance (Oct 13, 2023) | ||
| 1-241996294-A-C | not specified | Uncertain significance (Oct 13, 2023) | ||
| 1-241996305-A-G | not specified | Uncertain significance (Dec 25, 2024) | ||
| 1-241996317-A-G | not specified | Likely benign (Dec 22, 2023) | ||
| 1-241996317-A-T | not specified | Uncertain significance (Feb 27, 2025) | ||
| 1-241996345-G-T | not specified | Uncertain significance (Mar 15, 2024) | ||
| 1-241998526-A-G | not specified | Uncertain significance (Jun 03, 2024) | ||
| 1-241998541-G-T | not specified | Uncertain significance (Sep 26, 2023) | ||
| 1-241998564-C-G | not specified | Uncertain significance (Jan 19, 2025) | ||
| 1-241998789-G-C | not specified | Uncertain significance (Aug 14, 2024) | ||
| 1-241998988-G-C | not specified | Uncertain significance (Feb 26, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MAP1LC3C | protein_coding | protein_coding | ENST00000357246 | 4 | 3584 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000581 | 0.149 | 125706 | 0 | 36 | 125742 | 0.000143 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.496 | 73 | 85.9 | 0.849 | 0.00000429 | 967 |
| Missense in Polyphen | 21 | 23.988 | 0.87545 | 305 | ||
| Synonymous | -0.725 | 39 | 33.6 | 1.16 | 0.00000183 | 275 |
| Loss of Function | -0.701 | 7 | 5.27 | 1.33 | 2.23e-7 | 64 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000827 | 0.000826 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000169 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000150 | 0.000149 |
| Middle Eastern | 0.000169 | 0.000163 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-like modifier that plays a crucial role in antibacterial autophagy (xenophagy) through the selective binding of CALCOCO2. Recruits all ATG8 family members to infecting bacteria such as S.Typhimurium (PubMed:23022382). May also play a role in aggrephagy, the macroautophagic degradation of ubiquitinated and aggregated proteins (PubMed:28404643). {ECO:0000269|PubMed:23022382, ECO:0000269|PubMed:28404643}.;
- Pathway
- Ferroptosis - Homo sapiens (human);Senescence and Autophagy in Cancer;Macroautophagy;Cellular responses to external stimuli
(Consensus)
Recessive Scores
- pRec
- 0.0871
Intolerance Scores
- loftool
- 0.623
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.26
Haploinsufficiency Scores
- pHI
- 0.123
- hipred
- N
- hipred_score
- 0.492
- ghis
- 0.404
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.716
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- autophagosome assembly;autophagy of mitochondrion;cellular response to nitrogen starvation;cellular response to starvation;macroautophagy;aggrephagy;autophagosome maturation
- Cellular component
- autophagosome membrane;autophagosome;cytosol;microtubule;endomembrane system;organelle membrane;cytoplasmic vesicle;cytoplasmic ribonucleoprotein granule
- Molecular function
- protein binding;microtubule binding;ubiquitin protein ligase binding