MAP1LC3C

Chr 1

microtubule associated protein 1 light chain 3 gamma

Also known as: ATG8J, LC3C

NCBI Gene: 440738 ENSG00000197769 UniProt: Q9BXW4 OMIM: 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.

OMIM ResearchSummary from RefSeq, UniProt

Autophagy is a highly regulated bulk degradation process that plays an important role in cellular maintenance and development. MAP1LC3C is an ortholog of the yeast autophagosome protein Atg8 (He et al., 2003 [PubMed 12740394]).[supplied by OMIM, Nov 2010]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.91

Clinical Summary— MAP1LC3C

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

22 VUS of 25 total submissions

Explore recent and relevant literature in Research Assistant →

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 OE?1.33 (0.72–1.91)

0≤0.351.4

Missense OE?0.85 (0.70–1.03)

0≤0.61.4

Synonymous OE?1.16

0≤1.21.6

LoF obs/exp: 7 / 5.3Missense obs/exp: 73 / 85.9Syn Z: -0.72

This gene — mechanism propensity

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

25 submitted variants in ClinVar

ClinVar

Classification Summary

VUS22

Likely Benign1

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	22	22
Likely Benign	1	1
Benign	0	0
Total	23	23

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

69 pathogenic / likely-pathogenic (of 89) ClinVar copy-number / structural variants overlap MAP1LC3C — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →