MAP1LC3C

Summary

MAP1LC3C (microtubule associated protein 1 light chain 3 gamma, HGNC:13353) is a protein-coding gene on chromosome 1q43, encoding Microtubule-associated protein 1 light chain 3 gamma (Q9BXW4). Ubiquitin-like modifier that plays a crucial role in antibacterial autophagy (xenophagy) through the selective binding of CALCOCO2.

Autophagy is a highly regulated bulk degradation process that plays an important role in cellular maintenance and development. MAP1LC3C is an ortholog of the yeast autophagosome protein Atg8 (He et al., 2003 [PubMed 12740394]).

Source: NCBI Gene 440738 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 25 total
• Druggable target: yes
• MANE Select transcript: NM_001004343

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13353
Approved symbol	MAP1LC3C
Name	microtubule associated protein 1 light chain 3 gamma
Location	1q43
Locus type	gene with protein product
Status	Approved
Aliases	ATG8J
Ensembl gene	ENSG00000197769
Ensembl biotype	protein_coding
OMIM	609605
Entrez	440738

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000357246, ENST00000943070

RefSeq mRNA: 1 — MANE Select: NM_001004343 NM_001004343

CCDS: CCDS31074

Canonical transcript exons

ENST00000357246 — 4 exons

Exon	Start	End
ENSE00001410833	241998951	241999098
ENSE00001411268	241998776	241998831
ENSE00001411828	241998514	241998620
ENSE00001413311	241995490	241996385

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 82.03.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2489 / max 215.0814, expressed in 227 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
18307	1.2489	227

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.03	gold quality
diaphragm	UBERON:0001103	80.93	gold quality
secondary oocyte	CL:0000655	79.94	silver quality
buccal mucosa cell	CL:0002336	79.88	silver quality
cervix squamous epithelium	UBERON:0006922	79.76	gold quality
mucosa of stomach	UBERON:0001199	79.30	gold quality
body of tongue	UBERON:0011876	78.64	silver quality
right lung	UBERON:0002167	77.81	gold quality
oocyte	CL:0000023	77.12	silver quality
cerebellar vermis	UBERON:0004720	76.44	gold quality
tongue	UBERON:0001723	75.82	silver quality
subcutaneous adipose tissue	UBERON:0002190	75.81	gold quality
minor salivary gland	UBERON:0001830	75.02	gold quality
cartilage tissue	UBERON:0002418	74.97	silver quality
adipose tissue	UBERON:0001013	74.86	gold quality
omental fat pad	UBERON:0010414	74.84	gold quality
peritoneum	UBERON:0002358	74.82	gold quality
superior surface of tongue	UBERON:0007371	74.56	silver quality
adipose tissue of abdominal region	UBERON:0007808	74.40	gold quality
connective tissue	UBERON:0002384	74.25	gold quality
nipple	UBERON:0002030	73.48	silver quality
tibial nerve	UBERON:0001323	73.10	gold quality
fundus of stomach	UBERON:0001160	72.96	gold quality
trachea	UBERON:0003126	72.81	gold quality
mouth mucosa	UBERON:0003729	72.79	gold quality
thymus	UBERON:0002370	72.75	silver quality
vena cava	UBERON:0004087	72.68	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	72.52	gold quality
lymph node	UBERON:0000029	72.44	gold quality
upper arm skin	UBERON:0004263	71.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting MAP1LC3C, 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-3613-3P	100.00	76.36	7965
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-410-3P	99.27	69.98	2457
HSA-MIR-140-3P	99.04	67.69	1324
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-4731-3P	98.56	68.60	1860
HSA-MIR-4252	98.45	66.37	987
HSA-MIR-6842-3P	98.07	66.33	1325
HSA-MIR-6884-3P	98.05	65.32	750
HSA-MIR-5189-3P	97.52	66.33	487
HSA-MIR-6849-3P	97.25	64.57	1371
HSA-MIR-6730-3P	97.03	67.54	889
HSA-MIR-101-2-5P	95.96	68.62	55
HSA-MIR-1251-5P	95.78	64.10	374
HSA-MIR-6874-5P	95.73	64.94	545

Literature-anchored findings (GeneRIF, showing 18)

• ccytoplasm against Salmonella. (PMID:23022382)
• both autophagy-related 5 and microtubule-associated protein 1 light chain 3B levels are decreased in patients with melanomas as compared with those with benign nevi (PMID:24300435)
• Results indicate that TECPR2 Binds LC3and the complex is required for autophagosome formation, possibly through regulation of functional ER exit sites (PMID:26431026)
• a non-canonical autophagy pathway reminiscent of LC3-associated phagocytosis contributes to Vpu counteraction of BST2 restriction. (PMID:27880899)
• The WDR81 interacts with LC3C through canonical LC3-interacting regions in the BEACH domain, promoting LC3C recruitment to ubiquitinated proteins. (PMID:28404643)
• a basal, housekeeping mitophagy pathway that involves piecemeal degradation of mitochondrial proteins in a LC3C- and p62-dependent manner and contributes to mitochondrial homeostasis maintenance when cells rely on oxidative phosphorylation. (PMID:29149599)
• Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site. (PMID:31578424)
• LC3C-Mediated Autophagy Selectively Regulates the Met RTK and HGF-Stimulated Migration and Invasion. (PMID:31851933)
• LC3C mediates selective autophagy of the MET RTK, inhibiting cancer cell invasion. (PMID:32065021)
• TECPR1 promotes aggrephagy by direct recruitment of LC3C autophagosomes to lysosomes. (PMID:32532970)
• Novel Insights into the Cellular Localization and Regulation of the Autophagosomal Proteins LC3A, LC3B and LC3C. (PMID:33081014)
• Autophagy-Related Protein MAP1LC3C Plays a Crucial Role in Odontogenic Differentiation of Human Dental Pulp Cells. (PMID:33230801)
• TFG binds LC3C to regulate ULK1 localization and autophagosome formation. (PMID:33932238)
• Selective MAP1LC3C (LC3C) autophagy requires noncanonical regulators and the C-terminal peptide. (PMID:33988680)
• PGM5P3-AS1 regulates MAP1LC3C to promote cell ferroptosis and thus inhibiting the malignant progression of triple-negative breast cancer. (PMID:35325342)
• Microtubule-associated protein MAP1LC3C regulates lysosomal exocytosis and induces zinc reprogramming in renal cancer cells. (PMID:37003503)
• ATG5 selectively engages virus-tethered BST2/tetherin in an LC3C-associated pathway. (PMID:37155854)
• Reticulophagy mediated by the V-ATPase-ATG16L1-LC3C axis. (PMID:38348842)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	map1lc3cl	ENSDARG00000075727
caenorhabditis_elegans		WBGENE00002981

Paralogs (6): GABARAPL2 (ENSG00000034713), MAP1LC3A (ENSG00000101460), GABARAPL1 (ENSG00000139112), MAP1LC3B (ENSG00000140941), GABARAP (ENSG00000170296), MAP1LC3B2 (ENSG00000258102)

Protein

Protein identifiers

Microtubule-associated protein 1 light chain 3 gamma — Q9BXW4 (reviewed: Q9BXW4)

Alternative names: Autophagy-related protein LC3 C, Autophagy-related ubiquitin-like modifier LC3 C, MAP1 light chain 3-like protein 3, Microtubule-associated proteins 1A/1B light chain 3C

All UniProt accessions (1): Q9BXW4

UniProt curated annotations — full annotation on UniProt →

Function. Ubiquitin-like modifier that plays a crucial role in antibacterial autophagy (xenophagy) through the selective binding of CALCOCO2. Recruits all ATG8 family members to infecting bacteria such as S.typhimurium. May also play a role in aggrephagy, the macroautophagic degradation of ubiquitinated and aggregated proteins.

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. Interacts with TP53INP1 and TP53INP2. Interacts with CALCOCO2. Interacts with TECPR2. Interacts with TBC1D5. Found in a complex with UBQLN1 and UBQLN2. Interacts with UBQLN4 (via STI1 1 and 2 domains). Interacts with UBQLN1 in the presence of UBQLN4. Interacts with TRIM5. Interacts with ATG13. Interacts with MEFV and TRIM21. Interacts with WDR81; recruits MAP1LC3C to ubiquitinated protein aggregates in the aggrephagy process. Interacts with MOAP1 (via LIR motif). Interacts with reticulophagy regulators RETREG1, RETREG2 and RETREG3. Interacts with TAX1BP1. Interacts with IRGM. Interacts with SPART.

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

Tissue specificity. Most abundant in placenta, lung and ovary.

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. (Microbial infection) The Legionella effector RavZ is a deconjugating enzyme that hydrolyzes the amide bond between the C-terminal glycine residue and an adjacent aromatic residue in ATG8 proteins conjugated to phosphatidylethanolamine (PE), producing an ATG8 protein that is resistant to reconjugation by the host machinery due to the cleavage of the reactive C-terminal glycine. RavZ is also able to mediate delipidation of ATG8 proteins conjugated to phosphatidylserine (PS). Phosphorylation at Ser-96 and Ser-98 by TBK1 prevents interaction with ATG4 (ATG4A, ATG4B, ATG4C or ATG4D). Phosphorylation by TBK1 on autophagosomes prevents their delipidation by ATG4 and premature removal from nascent autophagosomes.

Similarity. Belongs to the ATG8 family.

RefSeq proteins (1): NP_001004343* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004241	Atg8-like	Family
IPR027731	MAP1A/MAP1B_LC3C	Family
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily

Pfam: PF02991

UniProt features (23 total): strand 8, helix 4, mutagenesis site 3, modified residue 2, lipid moiety-binding region 2, chain 1, propeptide 1, turn 1, site 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
3WAM	X-RAY DIFFRACTION	1.75
5DPW	X-RAY DIFFRACTION	2.19
3VVW	X-RAY DIFFRACTION	2.5
3WAP	X-RAY DIFFRACTION	3.1
2NCN	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BXW4-F1	80.53	0.40

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): 126–127 (cleavage; by atg4b)

Post-translational modifications (4): 93, 96, 126, 126

Mutagenesis-validated functional residues (3):

Position	Phenotype
93–96	impaired phosphorylation by tbk1.
93–96	phospho-mimetic mutant; impaired interaction with atg4 proteins, preventing cleavage at the c-terminus, conjugation to p
126	no processing of precursor.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1632852	Macroautophagy
R-HSA-9612973	Autophagy

MSigDB gene sets: 72 (showing top): GOBP_VACUOLE_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOCC_VACUOLAR_MEMBRANE, GOBP_MACROAUTOPHAGY, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_RESPONSE_TO_STARVATION, chr1q43, GOBP_PROTEIN_EXIT_FROM_ENDOPLASMIC_RETICULUM, GOBP_AUTOPHAGOSOME_ORGANIZATION, GOBP_RESPONSE_TO_STARVATION, GOCC_AUTOPHAGOSOME, GOCC_RIBONUCLEOPROTEIN_GRANULE, GOCC_AUTOPHAGOSOME_MEMBRANE, GOMF_UBIQUITIN_LIKE_PROTEIN_LIGASE_BINDING

GO Biological Process (10): autophagosome assembly (GO:0000045), mitophagy (GO:0000423), cellular response to nitrogen starvation (GO:0006995), cellular response to starvation (GO:0009267), macroautophagy (GO:0016236), protein exit from endoplasmic reticulum (GO:0032527), aggrephagy (GO:0035973), autophagosome maturation (GO:0097352), autophagy (GO:0006914), response to stress (GO:0006950)

GO Molecular Function (4): phosphatidylethanolamine binding (GO:0008429), ubiquitin protein ligase binding (GO:0031625), protein binding (GO:0005515), phospholipid binding (GO:0005543)

GO Cellular Component (11): autophagosome membrane (GO:0000421), autophagosome (GO:0005776), cytosol (GO:0005829), microtubule (GO:0005874), endomembrane system (GO:0012505), organelle membrane (GO:0031090), cytoplasmic vesicle (GO:0031410), cytoplasmic ribonucleoprotein granule (GO:0036464), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Autophagy	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
cellular anatomical structure	4
macroautophagy	3
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
cellular response to nutrient levels	1
cellular response to stress	1
response to starvation	1
autophagosome assembly	1
autophagy	1
intracellular protein transport	1
protein-containing complex disassembly	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
response to stimulus	1
phospholipid binding	1
ubiquitin-like protein ligase binding	1
binding	1
lipid binding	1
vacuolar membrane	1
autophagosome	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
plasma membrane	1
membrane	1
membrane-bounded organelle	1
intracellular vesicle	1
ribonucleoprotein granule	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1406 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAP1LC3C	CALCOCO2	Q13137	994
MAP1LC3C	ATG4B	Q9Y4P1	923
MAP1LC3C	WDFY3	Q8IZQ1	899
MAP1LC3C	ATG3	Q9NT62	847
MAP1LC3C	MAP1A	P78559	839
MAP1LC3C	CD300C	Q08708	836
MAP1LC3C	MAP1S	Q66K74	819
MAP1LC3C	TECPR2	O15040	796
MAP1LC3C	MAP1B	P46821	783
MAP1LC3C	ATG7	O95352	780
MAP1LC3C	SQSTM1	Q13501	771
MAP1LC3C	OPN3	Q9H1Y3	757
MAP1LC3C	WDR81	Q562E7	728
MAP1LC3C	NBR1	Q14596	704
MAP1LC3C	ATG12	O94817	694

IntAct

151 interactions, top by confidence:

A	B	Type	Score
MAP1LC3C	SQSTM1	psi-mi:“MI:0914”(association)	0.900
MAP1LC3C	SQSTM1	psi-mi:“MI:0915”(physical association)	0.900
SQSTM1	MAP1LC3C	psi-mi:“MI:0407”(direct interaction)	0.900
MAP1LC3C	SQSTM1	psi-mi:“MI:0407”(direct interaction)	0.900
ATG13	MAP1LC3C	psi-mi:“MI:0915”(physical association)	0.750
MAP1LC3C	ATG13	psi-mi:“MI:0914”(association)	0.750
ATG13	MAP1LC3C	psi-mi:“MI:0407”(direct interaction)	0.750
MAP1LC3C	ATG13	psi-mi:“MI:0407”(direct interaction)	0.750
ATG101	MAP1LC3C	psi-mi:“MI:0407”(direct interaction)	0.730
MAP1LC3C	ULK1	psi-mi:“MI:0407”(direct interaction)	0.730
ATG101	MAP1LC3C	psi-mi:“MI:0915”(physical association)	0.730
ULK1	MAP1LC3C	psi-mi:“MI:0915”(physical association)	0.730
KBTBD6	MAP1LC3C	psi-mi:“MI:0407”(direct interaction)	0.700
KBTBD7	MAP1LC3C	psi-mi:“MI:0407”(direct interaction)	0.700
KBTBD6	MAP1LC3C	psi-mi:“MI:0915”(physical association)	0.700
MAP1LC3C	KBTBD7	psi-mi:“MI:0915”(physical association)	0.700
MAP1LC3C	ATG4B	psi-mi:“MI:0915”(physical association)	0.680
MAP1LC3C	NBR1	psi-mi:“MI:0915”(physical association)	0.680
NBR1	MAP1LC3C	psi-mi:“MI:0407”(direct interaction)	0.680
MAP1LC3C	ATG4B	psi-mi:“MI:0407”(direct interaction)	0.680
MAP1LC3C	NBR1	psi-mi:“MI:0407”(direct interaction)	0.680
ATG7	GABARAP	psi-mi:“MI:0914”(association)	0.670

BioGRID (130): ACTA2 (Affinity Capture-MS), WDFY3 (Affinity Capture-Western), WDFY3 (Reconstituted Complex), KBTBD7 (Reconstituted Complex), KBTBD6 (Reconstituted Complex), CUL3 (Reconstituted Complex), MAP1LC3C (Reconstituted Complex), TRIM21 (Reconstituted Complex), MAP1LC3C (Two-hybrid), MAP1LC3C (Two-hybrid), MAP1LC3C (Two-hybrid), CALCOCO2 (Affinity Capture-Western), ACTA2 (Affinity Capture-MS), MAP1LC3C (Affinity Capture-Western), WDR81 (Affinity Capture-Western)

ESM2 similar proteins: A0A1B7XV12, A3GFU8, A5DK05, A5DWI6, A5PF44, A7KAJ7, A7TJM4, A8PJX4, A8WXX7, B3MZY6, F4HVA6, H2KZB2, O59800, O94817, P0C075, P87068, Q10931, Q18691, Q2TBJ5, Q3T0W7, Q3V0G7, Q3V2K1, Q5QFG1, Q5R7W1, Q5RAV3, Q5VVW2, Q62625, Q6BT31, Q6BZZ1, Q6C4Q6, Q6CUD5, Q6DTM3, Q6FMM7, Q6PB19, Q6PBN2, Q6XL73, Q75EB4, Q7LKZ5, Q8C4Q6, Q8CDA1

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

7 interactions.

A	Effect	B	Mechanism
ATG4B	“up-regulates activity”	MAP1LC3C	cleavage
MAP1LC3C	down-regulates	NBR1	binding
TP53INP1	up-regulates	MAP1LC3C	binding
MAP1LC3C	up-regulates	Autophagosome_formation
MAP1LC3C	“up-regulates activity”	WDFY3	binding
ATG7	“up-regulates activity”	MAP1LC3C	binding
MAP1LC3C	“up-regulates activity”	ATG3	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 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.

Reactome pathways:

Pathway	Partners	Fold	FDR
TBC/RABGAPs	6	31.1×	4e-06
Autophagy	8	23.7×	2e-07
Macroautophagy	10	23.1×	4e-09

GO biological processes:

GO term	Partners	Fold	FDR
piecemeal microautophagy of the nucleus	5	68.8×	1e-06
mitophagy	8	37.4×	1e-08
autophagosome assembly	11	36.4×	5e-12
macroautophagy	7	24.8×	1e-06
positive regulation of autophagy	8	24.5×	2e-07
autophagy	8	13.0×	2e-05
protein import into nucleus	5	10.6×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

462 predictions. Top by Δscore:

Variant	Effect	Δscore
1:241998512:A:AC	donor_gain	1.0000
1:241998513:C:CC	donor_gain	1.0000
1:241998617:CCAC:C	acceptor_gain	1.0000
1:241998618:CACC:C	acceptor_gain	1.0000
1:241998619:ACC:A	acceptor_loss	1.0000
1:241998621:CT:C	acceptor_loss	1.0000
1:241998622:T:G	acceptor_loss	1.0000
1:241998770:TCTTA:T	donor_loss	1.0000
1:241998771:CTTA:C	donor_loss	1.0000
1:241998772:TTA:T	donor_loss	1.0000
1:241998773:TA:T	donor_loss	1.0000
1:241998774:A:AC	donor_gain	1.0000
1:241998775:C:CA	donor_loss	1.0000
1:241998775:C:CC	donor_gain	1.0000
1:241998960:T:A	donor_gain	1.0000
1:241996344:A:T	acceptor_gain	0.9900
1:241996383:CTC:C	acceptor_gain	0.9900
1:241996384:TCC:T	acceptor_loss	0.9900
1:241996386:C:CC	acceptor_gain	0.9900
1:241996387:T:G	acceptor_loss	0.9900
1:241998512:A:T	donor_loss	0.9900
1:241998621:C:CC	acceptor_gain	0.9900
1:241998775:CCG:C	donor_gain	0.9900
1:241998775:CCGGG:C	donor_gain	0.9900
1:241998829:TTG:T	acceptor_gain	0.9900
1:241998844:C:CT	acceptor_gain	0.9900
1:241998845:A:T	acceptor_gain	0.9900
1:241998848:C:CT	acceptor_gain	0.9900
1:241998851:A:T	acceptor_gain	0.9900
1:241998944:AATTT:A	donor_loss	0.9900

AlphaMissense

970 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:241998561:G:C	F58L	0.998
1:241998561:G:T	F58L	0.998
1:241998563:A:G	F58L	0.998
1:241996265:G:C	F114L	0.997
1:241996265:G:T	F114L	0.997
1:241996267:A:G	F114L	0.997
1:241998791:G:C	F33L	0.997
1:241998791:G:T	F33L	0.997
1:241998793:A:G	F33L	0.997
1:241998562:A:G	F58S	0.996
1:241998556:A:T	V60D	0.994
1:241998564:C:A	K57N	0.993
1:241998564:C:G	K57N	0.993
1:241996273:C:G	D112H	0.990
1:241998529:A:G	F69S	0.990
1:241998562:A:C	F58C	0.990
1:241998782:T:A	K36N	0.990
1:241998782:T:G	K36N	0.990
1:241998824:T:A	R22S	0.990
1:241998824:T:G	R22S	0.990
1:241998825:C:G	R22T	0.989
1:241998619:A:T	V39E	0.988
1:241998514:C:G	R74P	0.987
1:241996232:A:C	F125L	0.986
1:241996232:A:T	F125L	0.986
1:241996234:A:G	F125L	0.986
1:241996266:A:G	F114S	0.986
1:241996347:A:G	L87S	0.986
1:241998777:G:T	P38Q	0.986
1:241998970:G:C	F13L	0.986

dbSNP variants (sampled 300 via entrez): RS1000237875 (1:242002893 G>A), RS1000324821 (1:242003152 C>T), RS1000486300 (1:241997849 T>C), RS1000793861 (1:241996457 C>A,T), RS1001278802 (1:242002151 G>C), RS1001372413 (1:241996637 A>C), RS1001766483 (1:241995989 A>G), RS1002069056 (1:242003365 C>T), RS1002231343 (1:241997687 T>C), RS1002373207 (1:241995420 A>C,T), RS1002489373 (1:241995156 G>A), RS1002501797 (1:241997441 G>A), RS1002688525 (1:242000883 A>C,G), RS1003219032 (1:241999864 G>A), RS1003743076 (1:241999646 T>C)

Disease associations

OMIM: gene MIM:609605 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST008156_59	Hip circumference adjusted for BMI	4.000000e-06
GCST009391_1427	Metabolite levels	5.000000e-06
GCST009391_1838	Metabolite levels	8.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference
EFO:0010407	triacylglycerol 48:4 measurement
EFO:0010412	triacylglycerol 50:5 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (6): CHEMBL4879505 (SINGLE PROTEIN), CHEMBL6066859 (PROTEIN-PROTEIN INTERACTION), CHEMBL6193844 (PROTEIN-PROTEIN INTERACTION), CHEMBL6193845 (PROTEIN-PROTEIN INTERACTION), CHEMBL6195681 (PROTEIN-PROTEIN INTERACTION), CHEMBL6195682 (PROTEIN-PROTEIN INTERACTION)

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

ChEMBL bioactivities

1 potent at pChembl≥5 of 1 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.34	IC50	4520	nM	CHEMBL5556385

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
5-(5,6-dichloro-1H-indol-4-yl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086251: Inhibition of LC3C (unknown origin) by Alphascreen assay	ic50	4.5200	uM

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases expression, increases methylation	3
methylmercuric chloride	decreases expression	2
trichostatin A	decreases expression, increases expression	2
Vorinostat	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
bisphenol A	affects cotreatment, increases expression	1
trovafloxacin	decreases reaction, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	1
clothianidin	increases expression	1
belinostat	increases expression	1
dorsomorphin	affects cotreatment, increases expression, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Decitabine	affects expression	1
Cisplatin	affects expression	1
Dexamethasone	affects cotreatment, increases expression	1
Endosulfan	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Phenylmercuric Acetate	increases expression, affects cotreatment	1
Plant Extracts	affects cotreatment, decreases expression	1
Thimerosal	affects cotreatment, decreases expression	1
Thiram	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	increases methylation	1

ChEMBL screening assays

30 unique, capped per target: 30 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4835343	Binding	Binding affinity to human LC3C expressed in Escherichia coli BL21-(DE3) by single site binding model based isothermal titration calorimetry	Demonstrating Ligandability of the LC3A and LC3B Adapter Interface. — J Med Chem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SW34	HAP1 MAP1LC3C (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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