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…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.91

LOEUF

Mechanism· predicted

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

Background carrier burden — how many people carry a rare variant somewhere in MAP1LC3C?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 670

185 rare PASS variants

Rare truncating (LoF)

1 in 8,500

24 rare PASS variants

Rare synonymous (reference)

1 in 900

71 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MAP1LC3C. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 820	1 in 11,000
South Asian	~43k	1 in 470	≈ 1 in 14,000
Remaining (unassigned)	~30k	1 in 250	≈ 1 in 7,500
European (Finnish)	~27k	1 in 3,000	≈ 1 in 27,000
Admixed American	~22k	1 in 240	≈ 1 in 5,600
African / African American	~21k	1 in 320	1 in 1,000
East Asian	~20k	1 in 330	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 770	none seen
Middle Eastern	~2,884	≈ 1 in 720	≈ 1 in 960

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓