MAP1LC3B2

protein-coding

microtubule associated protein 1 light chain 3 beta 2, the group of Autophagy related

Gene summary

Predicted to enable microtubule binding activity; phosphatidylethanolamine binding activity; and ubiquitin protein ligase binding activity. Predicted to be involved in cellular response to nitrogen starvation and macroautophagy. Predicted to be located in several cellular components, including autophagosome; cytoplasmic vesicle; and microtubule. Predicted to be active in autophagosome membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001085481.3

Inheritance

ClinVar variants

U:16B:1

Top phenotype

Primary ciliary dyskinesia

Max pathogenic AF

—

Genomic locus

chr12:116,548,105-116,576,606

External References & Databases

Ensembl (ENSG00000258102)

Transcript & Mutation Effects

hg38 • Region Span ~28.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hereditary predisposition to infectionsLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0015979

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP1LC3B2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 15

not providedTotal: 1

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001085481.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			15 clinvar			15
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	0	1	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001085481.3	RefSeq	NP_001078950.1	1	MANE Select
ENST00000556529.4	Ensembl	ENSP00000450524.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

autophagosome assembly
autophagy of mitochondrion
cellular response to nitrogen starvation

Molecular Function

microtubule binding

Cellular Component

autophagosome membrane
cytosol
microtubule
endomembrane system
cytoplasmic vesicle

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes). Plays a role in mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (By similarity). {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.712
RVIS EVS: 0.57
RVIS percentile EVS: 81.99

Essentials

Essential (CRISPR): N
Indispensability pred.: E
Indispensability score: 0.798

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium