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ACER3 alkaline ceramidase 3 [ Homo sapiens (human) ]

Gene ID: 55331, updated on 11-Apr-2024

Summary

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Official Symbol
ACER3provided by HGNC
Official Full Name
alkaline ceramidase 3provided by HGNC
Primary source
HGNC:HGNC:16066
See related
Ensembl:ENSG00000078124 MIM:617036; AllianceGenome:HGNC:16066
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
APHC; PHCA; PLDECO
Summary
Enables N-acylsphingosine amidohydrolase activity and metal ion binding activity. Involved in several processes, including myelination; positive regulation of cell population proliferation; and sphingolipid metabolic process. Is integral component of Golgi membrane and integral component of endoplasmic reticulum membrane. Biomarker of hepatocellular carcinoma and non-alcoholic steatohepatitis. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 8.3), brain (RPKM 5.5) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
11q13.5
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (76860918..77026797)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (76791211..76957150)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (76571962..76737841)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5299 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:76494061-76494705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76497093-76498015 Neighboring gene Sharpr-MPRA regulatory region 10511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76505429-76506334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76506335-76507240 Neighboring gene TSKU antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5302 Neighboring gene tsukushi, small leucine rich proteoglycan Neighboring gene uncharacterized LOC124902720 Neighboring gene CRISPRi-validated cis-regulatory element chr11.4478 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:76550011-76551210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3792 Neighboring gene Sharpr-MPRA regulatory region 1403 Neighboring gene NANOG hESC enhancer GRCh37_chr11:76653242-76653743 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:76656496-76657284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:76657285-76658073 Neighboring gene uncharacterized LOC124902721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3793 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:76674446-76675645 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3795 Neighboring gene uncharacterized LOC105369399 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Alkaline ceramidase catalyzes the hydrolysis of ceramides via a catalytic mechanism shared by Zn2+-dependent amidases. Yi JK, et al. PLoS One, 2022. PMID 36048828, Free PMC Article
  2. ACER3-related leukoencephalopathy: expanding the clinical and imaging findings spectrum due to novel variants. Dehnavi AZ, et al. Hum Genomics, 2021 Jul 19. PMID 34281620, Free PMC Article
  3. ACER3 supports development of acute myeloid leukemia. Chen C, et al. Biochem Biophys Res Commun, 2016 Sep 9. PMID 27470583
  4. Ceramidases: regulators of cellular responses mediated by ceramide, sphingosine, and sphingosine-1-phosphate. Mao C, et al. Biochim Biophys Acta, 2008 Sep. PMID 18619555, Free PMC Article
  5. Circular RNA circ_0001955 promotes hepatocellular carcinoma tumorigenesis by up-regulating alkaline ceramidase 3 expression through microRNA-655-3p. Bai K, et al. Bioengineered, 2022 Feb. PMID 35034572, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Alkaline ceramidase catalyzes the hydrolysis of ceramides via a catalytic mechanism shared by Zn2+-dependent amidases.
    Title: Alkaline ceramidase catalyzes the hydrolysis of ceramides via a catalytic mechanism shared by Zn2+-dependent amidases.
  2. LINC01087 indicates a poor prognosis of glioma patients with preoperative MRI.
    Title: LINC01087 indicates a poor prognosis of glioma patients with preoperative MRI.
  3. Circular RNA circ_0001955 promotes hepatocellular carcinoma tumorigenesis by up-regulating alkaline ceramidase 3 expression through microRNA-655-3p.
    Title: Circular RNA circ_0001955 promotes hepatocellular carcinoma tumorigenesis by up-regulating alkaline ceramidase 3 expression through microRNA-655-3p.
  4. ACER3-related leukoencephalopathy: expanding the clinical and imaging findings spectrum due to novel variants.
    Title: ACER3-related leukoencephalopathy: expanding the clinical and imaging findings spectrum due to novel variants.
  5. Our study suggests that Acer3 contributes to hepatocellular carcinoma propagation
    Title: Alkaline ceramidase 3 promotes growth of hepatocellular carcinoma cells via regulating S1P/S1PR2/PI3K/AKT signaling.
  6. Homozygosity for the p.E33G mutation in the ACER3 gene results in inactivation of ACER3.
    Title: Deficiency of the alkaline ceramidase ACER3 manifests in early childhood by progressive leukodystrophy.
  7. The ACER3 deficiency resulted in decreased cell growth and colony formation, elevated apoptosis, and lower AKT signaling of leukemia cells. This study indicates that ACER3 contributes to AML pathogenesis, and suggests that alkaline ceramidase inhibition is an option to treat acute myeloid leukemia.
    Title: ACER3 supports development of acute myeloid leukemia.
  8. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  10. ACER3 catalyzes the hydrolysis of unsaturated long chain ceramides and dihydroceramides and coordinates with ACER2 to regulate cell proliferation and survival
    Title: Alkaline ceramidase 3 (ACER3) hydrolyzes unsaturated long-chain ceramides, and its down-regulation inhibits both cell proliferation and apoptosis.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Alkaline ceramidase 3 deficiency
MedGen: C4540358 OMIM: 617762 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11238

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N-acylsphingosine amidohydrolase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables N-acylsphingosine amidohydrolase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables calcium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ceramidase activity IEA
Inferred from Electronic Annotation
more info
  
enables dihydroceramidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables dihydroceramidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables phytoceramidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phytoceramidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phytoceramidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in ceramide catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in ceramide catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in myelination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in phytosphingosine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phytosphingosine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of programmed cell death IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sphingosine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sphingosine biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
alkaline ceramidase 3
Names
alkCDase 3
alkaline CDase 3
alkaline dihydroceramidase SB89
alkaline phytoceramidase
phytoceramidase, alkaline
NP_001287882.1
NP_001287883.1
NP_001287884.1
NP_060837.3
XP_011543453.1
XP_011543454.1
XP_016873476.1
XP_047283191.1
XP_054225268.1
XP_054225269.1
XP_054225270.1
XP_054225271.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001300953.2 → NP_001287882.1  alkaline ceramidase 3 isoform b

    See identical proteins and their annotated locations for NP_001287882.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AI885537, AK294978, AP000752, AP002498, BG702017
    Consensus CDS
    CCDS76454.1
    UniProtKB/TrEMBL
    A0A7P0T912, B7Z2Q2
    Related
    ENSP00000436252.1, ENST00000533873.1
    Conserved Domains (1) summary
    pfam05875
    Location:9 → 222
    Ceramidase; Ceramidase

  2. NM_001300954.2 → NP_001287883.1  alkaline ceramidase 3 isoform c

    See identical proteins and their annotated locations for NP_001287883.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an internal exon and has another exon in its place compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
    Source sequence(s)
    AI885537, AP000752, BC049837, BG702017
    Consensus CDS
    CCDS73352.1
    UniProtKB/TrEMBL
    B7Z2V2
    Related
    ENSP00000431149.1, ENST00000526597.5
    Conserved Domains (1) summary
    pfam05875
    Location:1 → 164
    Ceramidase

  3. NM_001300955.2 → NP_001287884.1  alkaline ceramidase 3 isoform c

    See identical proteins and their annotated locations for NP_001287884.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon and uses a downstream translation start codon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
    Source sequence(s)
    AI885537, AK316120, AP000752, BG702017
    Consensus CDS
    CCDS73352.1
    UniProtKB/TrEMBL
    B7Z2V2
    Related
    ENSP00000505842.1, ENST00000680583.1
    Conserved Domains (1) summary
    pfam05875
    Location:1 → 164
    Ceramidase

  4. NM_018367.7 → NP_060837.3  alkaline ceramidase 3 isoform a

    See identical proteins and their annotated locations for NP_060837.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AI885537, AK315000, AP000752, AP002498, DB461413
    Consensus CDS
    CCDS8247.1
    UniProtKB/Swiss-Prot
    B2RC99, Q9NUN7
    UniProtKB/TrEMBL
    A0A7P0T912
    Related
    ENSP00000434480.1, ENST00000532485.6
    Conserved Domains (1) summary
    pfam05875
    Location:9 → 259
    Ceramidase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    76860918..77026797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545151.3 → XP_011543453.1  alkaline ceramidase 3 isoform X1

    UniProtKB/TrEMBL
    A0A7P0T912
    Conserved Domains (1) summary
    pfam05875
    Location:9 → 225
    Ceramidase; Ceramidase

  2. XM_047427235.1 → XP_047283191.1  alkaline ceramidase 3 isoform X4

    UniProtKB/TrEMBL
    A0A7P0T8K3
    Related
    ENSP00000505175.1, ENST00000679866.1

  3. XM_017017987.2 → XP_016873476.1  alkaline ceramidase 3 isoform X3

    UniProtKB/TrEMBL
    A0A7P0TAD8
    Related
    ENSP00000506160.1, ENST00000681257.1

  4. XM_011545152.3 → XP_011543454.1  alkaline ceramidase 3 isoform X2

    See identical proteins and their annotated locations for XP_011543454.1

    UniProtKB/TrEMBL
    E9PIN9
    Related
    ENSP00000435733.1, ENST00000534206.5
    Conserved Domains (1) summary
    pfam05875
    Location:1 → 217
    Ceramidase; Ceramidase

RNA

  1. XR_007062489.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    76791211..76957150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369293.1 → XP_054225268.1  alkaline ceramidase 3 isoform X1

  2. XM_054369296.1 → XP_054225271.1  alkaline ceramidase 3 isoform X4

  3. XM_054369295.1 → XP_054225270.1  alkaline ceramidase 3 isoform X3

  4. XM_054369294.1 → XP_054225269.1  alkaline ceramidase 3 isoform X2

    UniProtKB/TrEMBL
    B7Z1R2

RNA

  1. XR_008488417.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NUN7.3 GenPept UniProtKB/Swiss-Prot:Q9NUN7

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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