MAP1LC3B

Chr 16

microtubule associated protein 1 light chain 3 beta

Also known as: ATG8F, LC3B, MAP1A/1BLC3, MAP1LC3B-a

NCBI Gene: 81631 ENSG00000140941 UniProt: Q9GZQ8 OMIM: 609604

The protein is an ubiquitin-like modifier essential for autophagosome formation and plays critical roles in mitophagy, primary ciliogenesis, and endoplasmic reticulum turnover. Mutations cause autosomal recessive autism spectrum disorder with epilepsy and intellectual disability. The gene is not highly constrained against loss-of-function variants, suggesting tolerance to haploinsufficiency.

OMIM ResearchSummary from RefSeq, UniProt

The product of this gene is a subunit of neuronal microtubule-associated MAP1A and MAP1B proteins, which are involved in microtubule assembly and important for neurogenesis. Studies on the rat homolog implicate a role for this gene in autophagy, a process that involves the bulk degradation of cytoplasmic component. [provided by RefSeq, Jul 2008]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.37

Clinical Summary— MAP1LC3B

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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

21 VUS of 28 total submissions

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Clinical Trials

1 active or recruiting trial — potential therapeutic options may be available

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?

1.37LOEUF

pLI 0.002

Z-score 0.89

OE 0.65 (0.34–1.37)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.29Z-score

OE missense 0.90 (0.73–1.11)

61 obs / 67.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.65 (0.34–1.37)

0≤0.351.4

Missense OE?0.90 (0.73–1.11)

0≤0.61.4

Synonymous OE?1.16

0≤1.21.6

LoF obs/exp: 5 / 7.6Missense obs/exp: 61 / 67.8Syn Z: -0.63

This gene — mechanism propensity

0.6356th %ile

GOF

0.4973th %ile

LOF

0.3844th %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

28 submitted variants in ClinVar

ClinVar

Classification Summary

VUS21

Likely Benign2

Benign1

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	21	0	21
Likely Benign	0	2	2
Benign	1	0	1
Total	22	2	24

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

View in ClinVar →

53 pathogenic / likely-pathogenic (of 72) ClinVar copy-number / structural variants overlap MAP1LC3B — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →