MAP1LC3B

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

Basic information

Region (hg38): 16:87383952-87404779

Links

ENSG00000140941 ∙ NCBI:81631 ∙ OMIM:609604 ∙ HGNC:13352 ∙ Uniprot:Q9GZQ8 ∙ 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 MAP1LC3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAP1LC3B 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				2		2
missense			9		1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	1

Variants in MAP1LC3B

This is a list of pathogenic ClinVar variants found in the MAP1LC3B region.

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

Position	Type	Phenotype	Significance	ClinVar
16-87392432-C-G		not specified	Uncertain significance (Aug 17, 2022)
16-87392459-G-T		not specified	Uncertain significance (Aug 12, 2021)
16-87398846-A-T			Likely benign (Aug 16, 2018)
16-87398847-G-C			Benign (Jun 22, 2018)
16-87398860-C-T		not specified	Uncertain significance (Mar 02, 2023)
16-87402208-C-T		not specified	Uncertain significance (Jun 29, 2022)
16-87402209-T-C		not specified	Uncertain significance (Jun 29, 2022)
16-87402245-A-G		not specified	Uncertain significance (May 27, 2022)
16-87402949-A-G		not specified	Uncertain significance (Jun 16, 2024)
16-87402975-C-G		not specified	Uncertain significance (May 31, 2023)
16-87402990-G-A		not specified	Uncertain significance (Jun 22, 2021)
16-87403023-G-A		not specified	Uncertain significance (Jan 19, 2024)
16-87403064-C-T			Likely benign (May 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAP1LC3B	protein_coding	protein_coding	ENST00000268607	4	20785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00191	0.745	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.293	61	67.8	0.900	0.00000371	801
Missense in Polyphen		18	19.791	0.9095		267
Synonymous	-0.631	29	25.0	1.16	0.00000143	222
Loss of Function	0.886	5	7.64	0.654	5.76e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

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. Promotes primary ciliogenesis by removing OFD1 from centriolar satellites via the autophagic pathway. {ECO:0000269|PubMed:20418806, ECO:0000269|PubMed:23209295, ECO:0000269|PubMed:24089205}.
• Pathway: Ferroptosis - Homo sapiens (human);Senescence and Autophagy in Cancer;Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Pink/Parkin Mediated Mitophagy;Receptor Mediated Mitophagy;Mitophagy;Macroautophagy;Cellular responses to external stimuli;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.721
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.207
• hipred: Y
• hipred_score: 0.502
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Map1lc3b
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype

Gene ontology

• Biological process: autophagosome assembly;autophagy of mitochondrion;autophagy;cellular response to nitrogen starvation;cellular response to starvation;macroautophagy;autophagosome maturation
• Cellular component: autophagosome membrane;mitochondrion;autophagosome;cytosol;microtubule;axoneme;endomembrane system;organelle membrane;cytoplasmic vesicle
• Molecular function: protein binding;microtubule binding;ubiquitin protein ligase binding