MAP1LC3B2

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

Basic information

Region (hg38): 12:116548104-116576606

Links

ENSG00000258102 ∙ NCBI:643246 ∙ ∙ HGNC:34390 ∙ Uniprot:A6NCE7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAP1LC3B2 gene.

• Inborn genetic diseases (4 variants)
• not specified (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP1LC3B2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	4	1	2

Variants in MAP1LC3B2

This is a list of pathogenic ClinVar variants found in the MAP1LC3B2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-116575925-G-C		not specified	Benign (Jan 24, 2024)
12-116575951-G-A			Likely benign (Jun 01, 2022)
12-116576054-T-C		not specified	Uncertain significance (Sep 25, 2023)
12-116576076-C-T		not specified	Uncertain significance (Jan 24, 2024)
12-116576124-G-C		not specified	Uncertain significance (Jun 27, 2022)
12-116576145-G-C		not specified	Uncertain significance (Apr 13, 2023)
12-116576195-G-C		not specified	Uncertain significance (Jul 16, 2021)
12-116576271-A-G		not specified	Uncertain significance (Dec 14, 2022)
12-116576326-G-GA		not specified	Benign (Jan 24, 2024)

GnomAD

Source: gnomAD

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.164

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.798

Gene Damage Prediction

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

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion;cellular response to nitrogen starvation
• Cellular component: autophagosome membrane;cytosol;microtubule;endomembrane system;cytoplasmic vesicle
• Molecular function: microtubule binding