MAP1LC3A

protein-coding

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

Gene summary

MAP1A and MAP1B are microtubule-associated proteins which mediate the physical interactions between microtubules and components of the cytoskeleton. MAP1A and MAP1B each consist of a heavy chain subunit and multiple light chain subunits. The protein encoded by this gene is one of the light chain subunits and can associate with either MAP1A or MAP1B. Two transcript variants encoding different isoforms have been found for this gene. The expression of variant 1 is suppressed in many tumor cell lines, suggesting that may be involved in carcinogenesis. [provided by RefSeq, Feb 2012]

MANE transcript

NM_032514.4

Inheritance

—

ClinVar variants

U:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr20:34,546,854-34,560,345

External References & Databases

Ensembl (ENSG00000101460)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAP1LC3A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032514.4. 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						0
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	10	0	0	10

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032514.4	RefSeq	NP_115903.1	4	MANE Select
ENST00000360668.8	Ensembl	ENSP00000353886.3	4	MANE Select
NM_181509.3	RefSeq	NP_852610.1	4	Standard
ENST00000374837.7	Ensembl	ENSP00000363970.3	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ferroptosis - Homo sapiens (human)
Nanoparticle triggered autophagic cell death
Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling
Senescence and Autophagy in Cancer
Pink/Parkin Mediated Mitophagy

Biological Process

autophagosome assembly
autophagy of mitochondrion
cellular response to nitrogen starvation
cellular response to starvation
response to iron(II) ion

Molecular Function

protein binding
phospholipid binding
microtubule binding
phosphatidylethanolamine binding
ubiquitin protein ligase binding

Cellular Component

autophagosome membrane
late endosome
autophagosome
cytosol
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374837
Coding exons: 4
Length: 13492
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125730
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.46	45	82.4	0.546	0.00000511	831
Missense (PolyPhen)		6	21.799	0.27525		217
Synonymous	0.0596	34	34.4	0.987	0.00000251	214
Loss of Function	1.07	3	5.77	0.520	2.45e-7	69

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes) (PubMed:20713600, PubMed:24290141). Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (PubMed:20713600). {ECO:0000269|PubMed:20713600, ECO:0000269|PubMed:24290141}.;

Recessive Scores

pRec: 0.0962

Intolerance Scores

LoFtool: 0.580
RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low