MAP1LC3C

Chr 1

microtubule associated protein 1 light chain 3 gamma

ENSG00000197769UniProt: Q9BXW4OMIM: 609605

MAP1LC3C encodes a ubiquitin-like modifier that plays a crucial role in antibacterial autophagy (xenophagy) by selectively recruiting autophagy machinery to eliminate intracellular bacteria and may also function in the degradation of aggregated proteins. The gene shows low constraint against loss-of-function variants (pLI near 0, LOEUF 1.9), and no definitive human disease associations have been established from mutations in this gene. Clinical phenotypes resulting from MAP1LC3C variants remain to be characterized.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.91
Clinical Summary— MAP1LC3C
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.91LOEUF
pLI 0.000
Z-score -0.70
OE 1.33 (0.72–1.91)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.50Z-score
OE missense 0.85 (0.70–1.03)
73 obs / 85.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE1.33 (0.72–1.91)
0≤0.351.4
Missense OE0.85 (0.70–1.03)
0≤0.61.4
Synonymous OE1.16
0≤1.21.6
LoF obs/exp: 7 / 5.3Missense obs/exp: 73 / 85.9Syn Z: -0.72
DN
0.6258th %ile
GOF
0.5955th %ile
LOF
0.3355th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

MAP1LC3C · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
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Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
MAP1LC3C repression reduces CIITA- and HLA class II expression in non-small cell lung cancer.
Barbeau LMO et al.·PLoS One
2025Open Access
Microtubule-associated protein MAP1LC3C regulates lysosomal exocytosis and induces zinc reprogramming in renal cancer cells.
Verma R et al.·J Biol Chem
2023Open Access
PGM5P3-AS1 regulates MAP1LC3C to promote cell ferroptosis and thus inhibiting the malignant progression of triple-negative breast cancer.
Qi L et al.·Breast Cancer Res Treat
2022
Immunotherapeutic Value of MAP1LC3C and Its Candidate FDA-Approved Drugs Identified by Pan-Cancer Analysis, Virtual Screening and Sensitivity Analysis.
Zhang X et al.·Front Pharmacol
2022Open Access
Selective MAP1LC3C (LC3C) autophagy requires noncanonical regulators and the C-terminal peptide.
Bischoff ME et al.·J Cell Biol
2021Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients