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Aliases for ACER3 Gene

Aliases for ACER3 Gene

  • Alkaline Ceramidase 3 2 3 3 5
  • Alkaline Phytoceramidase 2 3 4
  • APHC 3 4 4
  • Alkaline Dihydroceramidase SB89 3 4
  • Phytoceramidase, Alkaline 2 3
  • Alkaline CDase 3 3 4
  • AlkCDase 3 3 4
  • PHCA 3 4
  • EC 3.5.1.- 4
  • PLDECO 3

External Ids for ACER3 Gene

Previous HGNC Symbols for ACER3 Gene

  • PHCA

Previous GeneCards Identifiers for ACER3 Gene

  • GC11P076250
  • GC11P076571
  • GC11P072869

Summaries for ACER3 Gene

GeneCards Summary for ACER3 Gene

ACER3 (Alkaline Ceramidase 3) is a Protein Coding gene. Diseases associated with ACER3 include Leukodystrophy, Progressive, Early Childhood-Onset and Farber Lipogranulomatosis. Among its related pathways are Metabolism and Sphingolipid metabolism. Gene Ontology (GO) annotations related to this gene include hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides and phytoceramidase activity.

UniProtKB/Swiss-Prot for ACER3 Gene

  • Hydrolyzes only phytoceramide into phytosphingosine and free fatty acid. Does not have reverse activity.

Gene Wiki entry for ACER3 Gene

Additional gene information for ACER3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ACER3 Gene

Genomics for ACER3 Gene

GeneHancer (GH) Regulatory Elements for ACER3 Gene

Promoters and enhancers for ACER3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J076860 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 665.2 +0.5 452 2.5 HDGF PKNOX1 SIN3A ZNF2 YY1 ZNF213 ZNF207 ZNF143 SP3 SP5 ACER3 EMSY ENSG00000271757 ENSG00000255135 ENSG00000272301 GVQW3 ENSG00000254988
GH11J076859 Enhancer 0.2 Ensembl 656.9 -1.8 -1766 0.2 ACER3 ENSG00000254988 ENSG00000261578
GH11J076823 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 17.9 -36.1 -36077 3.1 HDGF PKNOX1 ATF1 ARNT TCF12 ZNF766 GATA2 ZFP91 ZNF548 FOS EMSY ACER3 B3GNT6 GDPD4 ENSG00000261578
GH11J076919 Enhancer 1 Ensembl ENCODE 27 +59.4 59440 1.7 ELF3 RB1 SIN3A RAD21 RFX5 NCOA2 ARID2 ZNF143 ATF7 DEK ACER3 ENSG00000254988
GH11J076806 Enhancer 1.2 Ensembl ENCODE dbSUPER 17.9 -53.3 -53315 1.1 HDGF YBX3 ATF1 RB1 NFRKB SIN3A YBX1 NFXL1 ZNF48 RAD21 ACER3 LOC101928837 TSKU ENSG00000255363 EMSY B3GNT6 ENSG00000261578
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ACER3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ACER3 gene promoter:
  • C/EBPalpha
  • Pax-3
  • RORalpha1
  • Evi-1
  • STAT1
  • ZIC2
  • Pax-6
  • c-Myb
  • YY1

Genomic Locations for ACER3 Gene

Genomic Locations for ACER3 Gene
165,931 bases
Plus strand
165,931 bases
Plus strand

Genomic View for ACER3 Gene

Genes around ACER3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ACER3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ACER3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ACER3 Gene

Proteins for ACER3 Gene

  • Protein details for ACER3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Alkaline ceramidase 3
    Protein Accession:
    Secondary Accessions:
    • B2RC99

    Protein attributes for ACER3 Gene

    267 amino acids
    Molecular mass:
    31552 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for ACER3 Gene


neXtProt entry for ACER3 Gene

Post-translational modifications for ACER3 Gene

  • Glycosylation at Asn24
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for ACER3 Gene

Domains & Families for ACER3 Gene

Gene Families for ACER3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for ACER3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the alkaline ceramidase family.
  • Belongs to the alkaline ceramidase family.
genes like me logo Genes that share domains with ACER3: view

Function for ACER3 Gene

Molecular function for ACER3 Gene

UniProtKB/Swiss-Prot Function:
Hydrolyzes only phytoceramide into phytosphingosine and free fatty acid. Does not have reverse activity.
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by Ca(2+) and inhibited by Zn(2+).

Enzyme Numbers (IUBMB) for ACER3 Gene

Phenotypes From GWAS Catalog for ACER3 Gene

Gene Ontology (GO) - Molecular Function for ACER3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016787 hydrolase activity IEA --
GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides IEA --
GO:0070774 phytoceramidase activity TAS --
genes like me logo Genes that share ontologies with ACER3: view
genes like me logo Genes that share phenotypes with ACER3: view

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ACER3 Gene

Localization for ACER3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ACER3 Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ACER3 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
plasma membrane 3
lysosome 3
extracellular 1

Gene Ontology (GO) - Cellular Components for ACER3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005794 Golgi apparatus IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with ACER3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ACER3 Gene

Pathways & Interactions for ACER3 Gene

genes like me logo Genes that share pathways with ACER3: view

Pathways by source for ACER3 Gene

Gene Ontology (GO) - Biological Process for ACER3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006672 ceramide metabolic process IEA --
GO:0008284 positive regulation of cell proliferation IMP 20068046
GO:0030148 sphingolipid biosynthetic process TAS --
GO:0046512 sphingosine biosynthetic process IDA 20068046
GO:0071602 phytosphingosine biosynthetic process IDA 11356846
genes like me logo Genes that share ontologies with ACER3: view

No data available for SIGNOR curated interactions for ACER3 Gene

Drugs & Compounds for ACER3 Gene

(2) Drugs for ACER3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
sphinganine Pharma 0

(1) Additional Compounds for ACER3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • N-Acylsphinganine
  • N-[(2S,3R)-1,3-Dihydroxyoctadecan-2-yl]formamide
genes like me logo Genes that share compounds with ACER3: view

Transcripts for ACER3 Gene

Unigene Clusters for ACER3 Gene

Alkaline ceramidase 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ACER3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
SP1: - -
SP2: - - -
SP3: - - - -
SP4: - - - -

Relevant External Links for ACER3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ACER3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ACER3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of ACER3 Gene:


SOURCE GeneReport for Unigene cluster for ACER3 Gene:


mRNA Expression by UniProt/SwissProt for ACER3 Gene:

Tissue specificity: Ubiquitously expressed. Highest expression in placenta.

Evidence on tissue expression from TISSUES for ACER3 Gene

  • Nervous system(4.6)
  • Kidney(4.2)
  • Eye(4)
genes like me logo Genes that share expression patterns with ACER3: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for ACER3 Gene

Orthologs for ACER3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ACER3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ACER3 34 33
  • 99.63 (n)
(Canis familiaris)
Mammalia ACER3 34 33
  • 94.26 (n)
(Bos Taurus)
Mammalia ACER3 34 33
  • 92.88 (n)
(Mus musculus)
Mammalia Acer3 16 34 33
  • 88.51 (n)
(Rattus norvegicus)
Mammalia Acer3 33
  • 87.77 (n)
(Monodelphis domestica)
Mammalia ACER3 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia ACER3 34
  • 69 (a)
(Gallus gallus)
Aves ACER3 34 33
  • 76.94 (n)
(Anolis carolinensis)
Reptilia ACER3 34
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia acer3 33
  • 71.3 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.32071 33
(Danio rerio)
Actinopterygii acer3 34
  • 68 (a)
LOC555411 33
  • 66.42 (n)
Dr.27687 33
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YDC1 36 34 33
  • 49.65 (n)
YPC1 34
  • 28 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E23981g 33
  • 48.72 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons ATCES1 33
  • 45.13 (n)
(Oryza sativa)
Liliopsida Os03g0698900 33
  • 44.81 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02969 33
  • 51.93 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
Species where no ortholog for ACER3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ACER3 Gene

Gene Tree for ACER3 (if available)
Gene Tree for ACER3 (if available)
Evolutionary constrained regions (ECRs) for ACER3: view image

Paralogs for ACER3 Gene

No data available for Paralogs for ACER3 Gene

Variants for ACER3 Gene

Sequence variations from dbSNP and Humsavar for ACER3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000001432 -- 76,891,819(+) A/T genic_upstream_transcript_variant, intron_variant
rs1000010130 -- 76,912,673(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000011843 -- 76,863,736(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000099929 -- 76,921,717(+) T/C intron_variant
rs1000150771 -- 76,872,203(+) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ACER3 Gene

Variant ID Type Subtype PubMed ID
nsv1119894 CNV deletion 24896259
nsv396 CNV deletion 18451855
nsv498761 CNV loss 21111241
nsv507599 OTHER sequence alteration 20534489
nsv518920 CNV loss 19592680
nsv519309 CNV loss 19592680
nsv519700 CNV gain+loss 19592680
nsv555449 CNV loss 21841781
esv3626878 CNV loss 21293372
esv2661671 CNV deletion 23128226
esv23557 CNV loss 19812545
esv1509546 CNV insertion 17803354
dgv1229n100 CNV loss 25217958

Variation tolerance for ACER3 Gene

Residual Variation Intolerance Score: 48.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.15; 3.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ACER3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ACER3 Gene

Disorders for ACER3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for ACER3 Gene - From: HGMD, OMIM, ClinVar, Orphanet, and DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search ACER3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ACER3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ACER3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ACER3 Gene

Publications for ACER3 Gene

  1. Cloning and characterization of a novel human alkaline ceramidase. A mammalian enzyme that hydrolyzes phytoceramide. (PMID: 11356846) Mao C … Obeid LM (The Journal of biological chemistry 2001) 2 3 4 22 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  4. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. (PMID: 19834535) Wheeler HE … Kim SK (PLoS genetics 2009) 3 44 58
  5. Ceramidases: regulators of cellular responses mediated by ceramide, sphingosine, and sphingosine-1-phosphate. (PMID: 18619555) Mao C … Obeid LM (Biochimica et biophysica acta 2008) 2 3 58

Products for ACER3 Gene

Sources for ACER3 Gene

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