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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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ACER3
alkaline ceramidase 3
Chromosome 11 Β· 11q13.5
NCBI Gene: 55331Ensembl: ENSG00000078124.13HGNC: HGNC:16066UniProt: A0A7P0T8K3
27PubMed Papers
21Diseases
0Drugs
6Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
calcium ion bindingzinc ion bindingN-acylsphingosine amidohydrolase activityphytosphingosine biosynthetic processalkaline ceramidase 3 deficiencyleukodystrophysubarachnoid hemorrhageplacenta praevia
✦AI Summary

ACER3 is an endoplasmic reticulum and Golgi-localized alkaline ceramidase that catalyzes hydrolysis of unsaturated long-chain ceramides (C18:1, C20:1, C20:4) into sphingosine and free fatty acids at alkaline pH 1. The enzyme functions as a zinc-dependent amidase with conserved catalytic residues forming its active site 1. ACER3 regulates sphingoid base generation, particularly controlling sphingosine-1-phosphate levels in plasma and erythrocytes, which mediate cell proliferation, apoptosis, and differentiation signaling 2. In hepatocellular carcinoma, ACER3 promotes cell growth via S1P/S1PR2/PI3K/AKT signaling; ACER3 knockdown decreases proliferation and increases apoptosis 2. ACER3 expression is dysregulated in multiple diseases: elevated in cholestatic liver injury where ACER3 ablation attenuates hepatic necrosis and inflammation 3; upregulated during liver ischemia/reperfusion injury where it increases oxidative stress via respiratory complex I activation 4; and associated with poor glioma prognosis through LINC01087/miR-1277-5p regulatory networks 5. In asthma, ACER3 acts as a hub lipid metabolism gene inversely correlating with CD8+ T cell and NK cell infiltration 6. Dysregulation of ACER3 expression and ceramide metabolism contributes to inflammatory and neoplastic diseases, suggesting therapeutic potential for ACER3 targeting.

Sources cited
1
ACER3 is a zinc-dependent amidase with conserved catalytic residues (histidine, aspartate, serine) that catalyze ceramide hydrolysis at alkaline pH
PMID: 36048828
2
ACER3 promotes HCC cell growth through S1P/S1PR2/PI3K/AKT signaling; ACER3 knockdown reduces cell proliferation and increases apoptosis
PMID: 30097213
3
ACER3 is upregulated in cholestatic liver injury and ACER3 ablation attenuates bile duct ligation-induced liver injury with reduced necrosis and inflammation
PMID: 40025008
4
ACER3 is upregulated during liver ischemia/reperfusion injury and promotes oxidative stress via respiratory complex I; ACER3 ablation and ceramide treatment reduce injury
PMID: 40244698
5
ACER3 is regulated by LINC01087/miR-1277-5p axis in glioma; high ACER3 expression associates with poor glioma prognosis
PMID: 34817752
6
ACER3 is a hub lipid metabolism gene in asthma inversely correlated with CD8+ T cells and activated NK cells but positively correlated with M0 macrophages
PMID: 38297226
7
ACER3 is an integral membrane protein with seven transmembrane segments in the Golgi and ER with unique substrate specificity for unsaturated ceramides
PMID: 33271224
Disease Associationsβ“˜21
alkaline ceramidase 3 deficiencyOpen Targets
0.76Strong
leukodystrophyOpen Targets
0.37Weak
subarachnoid hemorrhageOpen Targets
0.23Weak
placenta praeviaOpen Targets
0.18Weak
cervical carcinomaOpen Targets
0.16Weak
neuromuscular diseaseOpen Targets
0.15Weak
non-alcoholic steatohepatitisOpen Targets
0.08Suggestive
colitisOpen Targets
0.07Suggestive
hepatocellular carcinomaOpen Targets
0.06Suggestive
gliomaOpen Targets
0.05Suggestive
asthmaOpen Targets
0.03Suggestive
Platelet-activating factor acetylhydrolase deficiencyOpen Targets
0.03Suggestive
cholestasisOpen Targets
0.03Suggestive
SepsisOpen Targets
0.03Suggestive
acute myeloid leukemiaOpen Targets
0.03Suggestive
steatosisOpen Targets
0.02Suggestive
neoplasmOpen Targets
0.02Suggestive
infectionOpen Targets
0.02Suggestive
corneal edemaOpen Targets
0.02Suggestive
osteoarthritisOpen Targets
0.02Suggestive
Leukodystrophy, progressive, early childhood-onsetUniProt
Pathogenic Variants6
NM_018367.7(ACER3):c.703A>C (p.Ser235Arg)Pathogenic
Alkaline ceramidase 3 deficiency
β˜…β˜†β˜†β˜†2024β†’ Residue 235
NM_018367.7(ACER3):c.631G>T (p.Gly211Cys)Pathogenic
Alkaline ceramidase 3 deficiency
β˜…β˜†β˜†β˜†2023β†’ Residue 211
NM_018367.7(ACER3):c.436C>T (p.Gln146Ter)Pathogenic
ACER3-related disorder|Familial cancer of breast
β˜…β˜†β˜†β˜†2022β†’ Residue 146
NM_018367.7(ACER3):c.475C>T (p.Arg159Ter)Likely pathogenic
Alkaline ceramidase 3 deficiency
β˜…β˜†β˜†β˜†2019β†’ Residue 159
NM_018367.7(ACER3):c.607C>T (p.Arg203Ter)Pathogenic
Alkaline ceramidase 3 deficiency
β˜…β˜†β˜†β˜†2019β†’ Residue 203
NM_018367.7(ACER3):c.566G>A (p.Trp189Ter)Pathogenic
Alkaline ceramidase 3 deficiency
β˜†β˜†β˜†β˜†β†’ Residue 189
View on ClinVar β†—
Related Genes
SPHK2Protein interaction99%ATP5F1BProtein interaction96%CERS4Protein interaction96%CERS6Protein interaction95%KDSRProtein interaction95%DEGS1Protein interaction95%
Tissue Expression6 tissues
Brain
100%
Lung
53%
Bone Marrow
50%
Heart
25%
Ovary
17%
Liver
17%
Gene Interaction Network
Click a node to explore
ACER3SPHK2ATP5F1BCERS4CERS6KDSRDEGS1
PROTEIN STRUCTURE
Preparing viewer…
PDB6YXH Β· 2.60 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.81LoF Tolerant
pLIβ“˜
0.30Tolerant
Observed/Expected LoF0.41 [0.23–0.81]
RankingsWhere ACER3 stands among ~20K protein-coding genes
  • #12,497of 20,598
    Most Researched27
  • #3,431of 5,498
    Most Pathogenic Variants6
  • #6,882of 17,882
    Most Constrained (LOEUF)0.81
Genes detectedACER3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Lipid metabolism-related genes are involved in the occurrence of asthma and regulate the immune microenvironment.
PMID: 38297226
BMC Genomics Β· 2024
1.00
2
Targeting the ceramidase ACER3 attenuates cholestasis in mice by mitigating bile acid overload via unsaturated ceramide-mediated LXRΞ² signaling transduction.
PMID: 40025008
Nat Commun Β· 2025
0.90
3
Ceramide(d18:1/18:1)-NDUFA6 interaction inactivates respiratory complex I to attenuate oxidative-stress-driven pathogenesis in liver ischemia/reperfusion injury.
PMID: 40244698
JCI Insight Β· 2025
0.80
4
Alkaline ceramidase 3 promotes growth of hepatocellular carcinoma cells via regulating S1P/S1PR2/PI3K/AKT signaling.
PMID: 30097213
Pathol Res Pract Β· 2018
0.70
5
LINC01087 indicates a poor prognosis of glioma patients with preoperative MRI.
PMID: 34817752
Funct Integr Genomics Β· 2022
0.60