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Features include always present findings: Sloping forehead, Dystonia, Short stature, and Relative macrocephaly and others.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 6 | Dystonia, Severe intellectual disability, Brain shrinkage (cerebral atrophy) |
ACER3 encodes alkaline ceramidase 3 (267 aa). Endoplasmic reticulum and Golgi ceramidase that catalyzes the hydrolysis of unsaturated long-chain C18:1-, C20:1- and C20:4-ceramides, dihydroceramides and phytoceramides into sphingoid bases like sphingosine and free fatty acids at alkaline pH. Highest expression in Brain Spinal cord cervical c-1 (20.2 TPM) and Nerve Tibial (19.1 TPM).
Alkaline ceramidase 3 deficiency is associated with mutations in the ACER3 gene on chromosome 11.
ACER3 is classified as a druggable target (Enzyme category) with score 0.0.
6 pathogenic variants reported in ACER3 in ClinVar.
Genetic testing for ACER3 is available. Testing is considered confirmatory for diagnosis.
Phenotype severity distribution: 23 always present features.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for alkaline ceramidase 3 deficiency.
8 publications have been identified in PubMed for alkaline ceramidase 3 deficiency. Research spans Basic Science / Preclinical (50%), Case Report / Case Series (25%), and Review / Meta-Analysis (13%).
Nobumoto W (2026). [PMID: 41570988](https://pubmed.ncbi.nlm.nih.gov/41570988/). *The Journal of biological chemistry*. [Basic Science / Preclinical]
Yamada C (2025). [PMID: 40266422](https://pubmed.ncbi.nlm.nih.gov/40266422/). *Current osteoporosis reports*. [Review / Meta-Analysis]
Smółka KA (2025). [PMID: 41303265](https://pubmed.ncbi.nlm.nih.gov/41303265/). *Journal of clinical medicine*. [Case Report / Case Series]
Wang K (2025). [PMID: 40244698](https://pubmed.ncbi.nlm.nih.gov/40244698/). *JCI insight*. [Basic Science / Preclinical]
Liao L (2025). [PMID: 40025008](https://pubmed.ncbi.nlm.nih.gov/40025008/). *Nature communications*. [Basic Science / Preclinical]
Data assembled from 7 of 12 sources · Last updated Sep 20, 2026, 5:28 AM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
Common questions about alkaline ceramidase 3 deficiency
3 |
Relative macrocephaly, Coarse facial features, Thick lower lip vermilion |
Muscles | 3 | Axial hypotonia, Brain shrinkage (cerebral atrophy), Joint contracture |
Growth and development | 1 | Short stature |
Bones and joints | 1 | Joint contracture |
Eyes | 1 | Optic disc pallor |
Age of onset: infancy.
Menicucci L (2025). [PMID: 40753802](https://pubmed.ncbi.nlm.nih.gov/40753802/). *European journal of paediatric neurology : EJPN : official journal of the European Paediatric Neurology Society*. [Epidemiology / Natural History]
Eskin-Schwartz M (2024). [PMID: 39500555](https://pubmed.ncbi.nlm.nih.gov/39500555/). *Journal of medical genetics*. [Case Report / Case Series]
Choi EK (2024). [PMID: 38839750](https://pubmed.ncbi.nlm.nih.gov/38839750/). *Nature communications*. [Basic Science / Preclinical]