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    ACER3 alkaline ceramidase 3 [ Homo sapiens (human) ]

    Gene ID: 55331, updated on 2-Nov-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; calcium ion binding activity; and zinc ion binding activity. Involved in several processes, including myelination; positive regulation of cell population proliferation; and sphingolipid metabolic process. Located in Golgi membrane and endoplasmic reticulum membrane. Biomarker of hepatocellular carcinoma and metabolic dysfunction-associated steatohepatitis. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in fat (RPKM 8.3), brain (RPKM 5.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ACER3 in Genome Data Viewer
    Location:
    11q13.5
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (76860918..77026797)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (76791211..76957150)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid silent region 3793 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:76674446-76675645 Neighboring gene ACER antisense RNA 1 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 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. 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
    4. ACER3 supports development of acute myeloid leukemia. Chen C, et al. Biochem Biophys Res Commun, 2016 Sep 9. PMID 27470583
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 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_2024_08

    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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