MAP1LC3B2

Summary

MAP1LC3B2 (microtubule associated protein 1 light chain 3 beta 2, HGNC:34390) is a protein-coding gene on chromosome 12q24.22, encoding Microtubule-associated protein 1 light chain 3 beta 2 (A6NCE7). Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes).

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 cytoplasmic vesicle; endomembrane system; and microtubule. Predicted to be active in autophagosome membrane.

Source: NCBI Gene 643246 — RefSeq curated summary.

At a glance

• Gene–disease (curated): hereditary predisposition to infections (Limited, GenCC)
• GWAS associations: 2
• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_001085481

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34390
Approved symbol	MAP1LC3B2
Name	microtubule associated protein 1 light chain 3 beta 2
Location	12q24.22
Locus type	gene with protein product
Status	Approved
Aliases	ATG8G
Ensembl gene	ENSG00000258102
Ensembl biotype	protein_coding
OMIM	620673
Entrez	643246

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding_CDS_not_defined, 1 protein_coding, 1 retained_intron

ENST00000547114, ENST00000556529, ENST00000625301, ENST00000630062

RefSeq mRNA: 1 — MANE Select: NM_001085481 NM_001085481

CCDS: CCDS41841

Canonical transcript exons

ENST00000556529 — 2 exons

Exon	Start	End
ENSE00002522833	116575842	116576606
ENSE00003771783	116559381	116559433

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 87.93.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4365 / max 163.3760, expressed in 76 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128230	0.1427	31
128231	0.0918	20
128237	0.0788	31
206916	0.0637	15
128229	0.0595	17

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	87.93	gold quality
cerebellar cortex	UBERON:0002129	87.82	gold quality
cerebellum	UBERON:0002037	87.76	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.71	gold quality
blood	UBERON:0000178	85.85	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.39	gold quality
left ovary	UBERON:0002119	81.02	gold quality
gastrocnemius	UBERON:0001388	80.69	gold quality
tibial nerve	UBERON:0001323	80.64	gold quality
prefrontal cortex	UBERON:0000451	80.54	gold quality
stromal cell of endometrium	CL:0002255	79.53	gold quality
ovary	UBERON:0000992	79.32	gold quality
right ovary	UBERON:0002118	79.20	gold quality
muscle of leg	UBERON:0001383	78.68	gold quality
sural nerve	UBERON:0015488	78.59	gold quality
cortical plate	UBERON:0005343	78.42	gold quality
skin of abdomen	UBERON:0001416	77.81	gold quality
frontal cortex	UBERON:0001870	77.70	gold quality
hindlimb stylopod muscle	UBERON:0004252	77.43	gold quality
zone of skin	UBERON:0000014	77.01	gold quality
primary visual cortex	UBERON:0002436	76.91	gold quality
skin of leg	UBERON:0001511	76.70	gold quality
omental fat pad	UBERON:0010414	76.64	gold quality
superior frontal gyrus	UBERON:0002661	76.59	gold quality
granulocyte	CL:0000094	75.98	gold quality
mucosa of stomach	UBERON:0001199	75.91	gold quality
brain	UBERON:0000955	75.89	gold quality
left uterine tube	UBERON:0001303	75.78	gold quality
heart left ventricle	UBERON:0002084	75.77	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	16.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting MAP1LC3B2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-452-5P	99.65	69.63	1762
HSA-MIR-4676-3P	99.65	69.31	1733
HSA-MIR-892C-3P	99.65	69.38	1745
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-629-5P	98.78	68.72	1032
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-432-5P	98.00	68.13	989
HSA-MIR-188-5P	97.89	67.01	756
HSA-MIR-203B-3P	97.82	66.27	979
HSA-MIR-483-3P	97.77	64.95	731
HSA-MIR-4708-5P	97.77	67.82	831
HSA-MIR-6866-3P	97.38	66.94	748
HSA-MIR-6874-5P	95.73	64.94	545

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	map1lc3b	ENSDARG00000101127
caenorhabditis_elegans		WBGENE00002981

Paralogs (6): GABARAPL2 (ENSG00000034713), MAP1LC3A (ENSG00000101460), GABARAPL1 (ENSG00000139112), MAP1LC3B (ENSG00000140941), GABARAP (ENSG00000170296), MAP1LC3C (ENSG00000197769)

Protein

Protein identifiers

Microtubule-associated protein 1 light chain 3 beta 2 — A6NCE7 (reviewed: A6NCE7)

Alternative names: Microtubule-associated proteins 1A/1B light chain 3 beta 2, Microtubule-associated proteins 1A/1B light chain 3B-like

All UniProt accessions (1): A6NCE7

UniProt curated annotations — full annotation on UniProt →

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. In response to cellular stress and upon mitochondria fission, binds C-18 ceramides and anchors autophagolysosomes to outer mitochondrial membranes to eliminate damaged mitochondria. While LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation.

Subunit / interactions. 3 different light chains, LC1 (a cleavage product of MAP1B), LC2 (a cleavage product of MAP1A) and LC3 (produced by one of the MAP1LC3 genes), can associate with the MAP1A or MAP1B heavy chains.

Subcellular location. Cytoplasmic vesicle. Autophagosome membrane. Endomembrane system. Cytoplasm. Cytoskeleton.

Post-translational modifications. The precursor molecule is cleaved by ATG4 (ATG4A, ATG4B, ATG4C or ATG4D) to expose the glycine at the C-terminus and form the cytosolic form, LC3-I. The processed form is then activated by APG7L/ATG7, transferred to ATG3 and conjugated to phosphatidylethanolamine (PE) phospholipid to form the membrane-bound form, LC3-II. During non-canonical autophagy, the processed form is conjugated to phosphatidylserine (PS) phospholipid. ATG4 proteins also mediate the delipidation of PE-conjugated forms. In addition, ATG4B and ATG4D mediate delipidation of ATG8 proteins conjugated to PS during non-canonical autophagy.

Similarity. Belongs to the ATG8 family.

RefSeq proteins (1): NP_001078950* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004241	Atg8-like	Family
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily

Pfam: PF02991

UniProt features (5 total): lipid moiety-binding region 2, chain 1, propeptide 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NCE7-F1	92.12	0.80

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 120–121 (cleavage; by atg4b)

Post-translational modifications (2): 120, 120

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): GOBP_VACUOLE_ORGANIZATION, GOCC_VACUOLAR_MEMBRANE, GOBP_MACROAUTOPHAGY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_RESPONSE_TO_STARVATION, GOBP_AUTOPHAGOSOME_ORGANIZATION, GOBP_RESPONSE_TO_STARVATION, SASSON_RESPONSE_TO_GONADOTROPHINS_UP, GOCC_AUTOPHAGOSOME, GOCC_AUTOPHAGOSOME_MEMBRANE, chr12q24, GOMF_CYTOSKELETAL_PROTEIN_BINDING, GOMF_UBIQUITIN_LIKE_PROTEIN_LIGASE_BINDING, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING

GO Biological Process (6): autophagosome assembly (GO:0000045), mitophagy (GO:0000423), cellular response to nitrogen starvation (GO:0006995), autophagosome maturation (GO:0097352), autophagy of mitochondrion (GO:0000422), autophagy (GO:0006914)

GO Molecular Function (4): microtubule binding (GO:0008017), phosphatidylethanolamine binding (GO:0008429), ubiquitin protein ligase binding (GO:0031625), phospholipid binding (GO:0005543)

GO Cellular Component (8): autophagosome membrane (GO:0000421), microtubule (GO:0005874), endomembrane system (GO:0012505), cytoplasmic vesicle (GO:0031410), cytoplasm (GO:0005737), autophagosome (GO:0005776), cytoskeleton (GO:0005856), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
macroautophagy	2
vacuole	2
Atg12 activating enzyme activity	1
protein-phosphatidylethanolamide deconjugating activity	1
Atg12 conjugating enzyme activity	1
Atg12 ligase activity	1
organelle assembly	1
Atg1/ULK1 kinase complex assembly	1
autophagosome organization	1
autophagy of mitochondrion	1
cellular response to starvation	1
cellular response to nitrogen levels	1
protein-containing complex disassembly	1
autophagy	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
tubulin binding	1
phospholipid binding	1
ubiquitin-like protein ligase binding	1
lipid binding	1
vacuolar membrane	1
autophagosome	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
plasma membrane	1
cytoplasm	1
intracellular vesicle	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1085 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAP1LC3B2	SQSTM1	Q13501	644
MAP1LC3B2	ATG5	Q9H1Y0	611
MAP1LC3B2	ATG3	Q9NT62	591
MAP1LC3B2	ATG12	O94817	577
MAP1LC3B2	ATG7	O95352	541
MAP1LC3B2	NBR1	Q14596	529
MAP1LC3B2	ATG4A	Q8WYN0	487
MAP1LC3B2	CALCOCO2	Q13137	487
MAP1LC3B2	BECN1	Q14457	479
MAP1LC3B2	ATG16L1	Q676U5	452
MAP1LC3B2	ATG9A	Q7Z3C6	450
MAP1LC3B2	ATG10	Q9H0Y0	439
MAP1LC3B2	ATG13	O75143	438
MAP1LC3B2	DIMT1	Q9UNQ2	433
MAP1LC3B2	BNIP3L	O60238	427

IntAct

23 interactions, top by confidence:

A	B	Type	Score
TSPAN3	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.530
SLC9A6	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.530
ATG3	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.530
TNFRSF10A	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
RUSF1	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
RETREG1	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
ATG3	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
NUFIP1	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
KIF3A	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
MAP1LC3B	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
ATG10	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
Npc1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CAV1	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
SNX33	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
TPX2	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350
ATG4B	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.350

BioGRID (26): MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-Western), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS), MAP1LC3B2 (Affinity Capture-MS)

ESM2 similar proteins: A1CQS1, A1D3N4, A2XXR7, A2YAG8, A2YS06, A6NCE7, A6RPU4, A7KAL9, I1S1W5, J4UTT5, M1C146, M2SQA5, N4X184, O41515, P0CM28, P0CM29, P60519, P60520, P60521, P60522, Q0C804, Q0V3Y9, Q1E4K5, Q1SF86, Q2HJ23, Q2RBS4, Q2UBH5, Q2XPP5, Q4P2U6, Q4WJ27, Q69NP0, Q69RC4, Q6XVN8, Q6Z1D5, Q7XPR1, Q86CR8, Q8J282, Q8LEM4, Q8S924, Q8S925

Diamond homologs: A0A1B7XV12, A1CQS1, A1D3N4, A2QPN1, A2XXR7, A2YS06, A3GFU8, A4LA70, A5DWI6, A6NCE7, A6RPU4, A6ZKM4, A7E8H4, A7KAL9, A7TDU7, C4B4E4, I1S1W5, J4UTT5, M1C146, M2SQA5, N4X184, O41515, O94272, O95166, P0C075, P0CO54, P0CO55, P38182, P60517, P60518, P60519, P60520, P60521, P60522, P87068, Q09490, Q0C804, Q0V3Y9, Q0VGK0, Q1E4K5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 16 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
protein transport	5	16.9×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

22 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	0
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

312 predictions. Top by Δscore:

Variant	Effect	Δscore
12:116575834:A:AG	acceptor_gain	0.9900
12:116575835:A:G	acceptor_gain	0.9900
12:116575840:A:AG	acceptor_gain	0.9900
12:116575841:G:GG	acceptor_gain	0.9900
12:116575841:GCCTT:G	acceptor_gain	0.9900
12:116575831:T:TA	acceptor_gain	0.9800
12:116575841:GC:G	acceptor_gain	0.9800
12:116575841:GCC:G	acceptor_gain	0.9800
12:116575838:ATAGC:A	acceptor_loss	0.9700
12:116575840:A:AT	acceptor_loss	0.9700
12:116575828:T:G	acceptor_loss	0.9600
12:116575841:GCCT:G	acceptor_gain	0.9600
12:116560178:C:G	donor_gain	0.9300
12:116559430:GCGG:G	donor_gain	0.8800
12:116559768:TCC:T	donor_gain	0.8800
12:116560177:GC:G	donor_gain	0.8800
12:116575837:A:G	acceptor_gain	0.8800
12:116560178:C:CG	donor_gain	0.8700
12:116559531:C:T	donor_gain	0.8600
12:116575823:T:A	acceptor_loss	0.8600
12:116575829:T:A	acceptor_gain	0.8400
12:116559494:C:T	donor_gain	0.8300
12:116568041:G:GG	donor_gain	0.8200
12:116559610:G:GG	donor_gain	0.8100
12:116559404:G:GT	donor_gain	0.8000
12:116575839:TAGC:T	acceptor_gain	0.7800
12:116576187:T:A	acceptor_gain	0.7800
12:116559525:TG:T	donor_gain	0.7700
12:116568040:A:AG	donor_gain	0.7700
12:116571800:G:T	donor_gain	0.7700

AlphaMissense

823 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:116576096:T:C	F52L	0.993
12:116576098:C:A	F52L	0.993
12:116576098:C:G	F52L	0.993
12:116575990:A:C	R16S	0.985
12:116575990:A:T	R16S	0.985
12:116576264:T:C	F108L	0.984
12:116576266:C:A	F108L	0.984
12:116576266:C:G	F108L	0.984
12:116575961:T:C	F7L	0.982
12:116575963:C:A	F7L	0.982
12:116575963:C:G	F7L	0.982
12:116576095:G:C	K51N	0.982
12:116576095:G:T	K51N	0.982
12:116575989:G:C	R16T	0.978
12:116576097:T:C	F52S	0.978
12:116575966:G:C	K8N	0.974
12:116575966:G:T	K8N	0.974
12:116576032:A:C	K30N	0.973
12:116576032:A:T	K30N	0.973
12:116576043:T:A	I34K	0.973
12:116576013:G:C	R24P	0.972
12:116575989:G:T	R16I	0.967
12:116576100:T:A	L53H	0.966
12:116576130:T:C	L63P	0.965
12:116576210:A:C	S90R	0.965
12:116576212:C:A	S90R	0.965
12:116576212:C:G	S90R	0.965
12:116576297:T:C	F119L	0.965
12:116576299:C:A	F119L	0.965
12:116576299:C:G	F119L	0.965

dbSNP variants (sampled 300 via entrez): RS1000336060 (12:116575037 G>A), RS1000783233 (12:116570481 T>C), RS1000845966 (12:116569230 A>G), RS1000880112 (12:116575337 C>T), RS1000880255 (12:116572735 C>G), RS1001126441 (12:116557769 G>A), RS1001513692 (12:116558059 C>A,T), RS1001611485 (12:116575676 T>A,C), RS1001948422 (12:116576979 A>G), RS1002061746 (12:116564973 T>G), RS1002154336 (12:116571170 C>G), RS1002222283 (12:116570009 G>A,T), RS1002229646 (12:116576041 G>A,T), RS1002398521 (12:116570011 G>A,C), RS1002414506 (12:116558721 C>T)

Disease associations

OMIM: gene MIM:620673 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
hereditary predisposition to infections	Limited	Autosomal dominant

Mondo (1): (MONDO:0015979)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002875_60	Diisocyanate-induced asthma	2.000000e-06
GCST006988_116	Blond vs. brown/black hair color	2.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006995	response to diisocyanate
EFO:0003924	hair color

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases reaction, increases expression, affects expression, decreases expression	4
aristolochic acid I	increases expression	1
ginger extract	decreases expression, increases abundance	1
triphenyl phosphate	affects expression	1
astaxanthine	decreases reaction, increases expression	1
trichostatin A	affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
potassium chromate(VI)	increases expression	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
trovafloxacin	decreases reaction, increases expression	1
2-(2-amino-3-methoxyphenyl)-4H-1-benzopyran-4-one	decreases reaction, increases expression	1
K 7174	increases expression	1
3-(4-methylphenylsulfonyl)-2-propenenitrile	decreases reaction, increases expression	1
abrine	increases expression	1
licochalcone B	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Acetylcysteine	decreases reaction, increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cisplatin	affects cotreatment, decreases expression	1
Diquat	increases expression	1
Oils, Volatile	decreases expression, increases abundance	1
Silver	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E0H0	Ubigene HeLa MAP1LC3B2 KO	Cancer cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.