MAP1LC3B

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

Basic information

Region (hg38): 16:87383953-87404779

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.

not_specified (19 variants)
not_provided (3 variants)

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. These statistics are base on transcript: NM_000022818.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			19 clinvar		1 clinvar	20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	19	2	1

Loading clinvar variants...

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