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SMPDL3A sphingomyelin phosphodiesterase acid like 3A [ Homo sapiens (human) ]

Gene ID: 10924, updated on 27-Nov-2024

Summary

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Official Symbol
SMPDL3Aprovided by HGNC
Official Full Name
sphingomyelin phosphodiesterase acid like 3Aprovided by HGNC
Primary source
HGNC:HGNC:17389
See related
Ensembl:ENSG00000172594 MIM:610728; AllianceGenome:HGNC:17389
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
ASM3A; ASML3a; yR36GH4.1
Summary
Enables phosphoric diester hydrolase activity and zinc ion binding activity. Involved in negative regulation of cGAS/STING signaling pathway and nucleoside triphosphate catabolic process. Located in extracellular exosome. Is active in extracellular space. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in colon (RPKM 18.5), small intestine (RPKM 18.4) and 25 other tissues See more
Orthologs
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Genomic context

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See SMPDL3A in Genome Data Viewer
Location:
6q22.31
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (122789258..122809720)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (123977551..123998013)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (123110403..123130865)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:123076853-123077432 Neighboring gene RNA, 7SL, cytoplasmic 564, pseudogene Neighboring gene fatty acid binding protein 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:123110213-123110714 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:123110715-123111214 Neighboring gene Sharpr-MPRA regulatory region 4155 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89596 Neighboring gene Sharpr-MPRA regulatory region 10347 Neighboring gene MPRA-validated peak6080 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:123141927-123142470 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:123142471-123143014 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:123165703-123166295 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:123166296-123166889 Neighboring gene ATP synthase membrane subunit g pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25022 Neighboring gene uncharacterized LOC124901392

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. N-glycosylation of human sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is essential for stability, secretion and activity. Traini M, et al. Biochem J, 2017 Mar 8. PMID 28104755
  2. Regulation of sphingomyelin phosphodiesterase acid-like 3A gene (SMPDL3A) by liver X receptors. Noto PB, et al. Mol Pharmacol, 2012 Oct. PMID 22810003
  3. SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing. Hou Y, et al. Immunity, 2023 Nov 14. PMID 37890481
  4. Ligand-dependent and -independent regulation of human hepatic sphingomyelin phosphodiesterase acid-like 3A expression by pregnane X receptor and crosstalk with liver X receptor. Jeske J, et al. Biochem Pharmacol, 2017 Jul 15. PMID 28414139
  5. The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a--an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity. Lim SM, et al. FEBS J, 2016 Mar. PMID 26783088

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Activation of pregnane X receptor induces SMPDL3A expression in primary hepatocytes.
    Title: Ligand-dependent and -independent regulation of human hepatic sphingomyelin phosphodiesterase acid-like 3A expression by pregnane X receptor and crosstalk with liver X receptor.
  2. Site-specific N-glycosylation is essential for the intracellular stability, secretion and activity of human SMPDL3A.
    Title: N-glycosylation of human sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is essential for stability, secretion and activity.
  3. Solved the structure of SMPDL3a revealing a calcineurin-like fold. A dimetal site, glycosylation pattern and a disulfide bond network are likely to be conserved also in aSMase. We show that the binuclear site of SMPDL3a is occupied by two Zn(2+) ions.
    Title: The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a--an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.
  4. Data indicate that sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a nucleotide phosphodiesterase secreted from cholesterol-loaded macrophages.
    Title: Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a novel nucleotide phosphodiesterase regulated by cholesterol in human macrophages.
  5. the induction of SMPDL3A is liver X receptor-dependent and is restricted to human blood cells with no induction observed in mouse cellular systems.
    Title: Regulation of sphingomyelin phosphodiesterase acid-like 3A gene (SMPDL3A) by liver X receptors.
  6. ASML3a is involved in the process of bladder tumorigenesis
    Title: Increased expression of the acid sphingomyelinase-like protein ASML3a in bladder tumors.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20177

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent H2AZ histone chaperone activity IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent H3-H4 histone complex chaperone activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA clamp loader activity IEA
Inferred from Electronic Annotation
more info
  
enables chromatin extrusion motor activity IEA
Inferred from Electronic Annotation
more info
  
enables cohesin loader activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphoric diester hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphoric diester hydrolase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphoric diester hydrolase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
NOT enables sphingomyelin phosphodiesterase activity 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 chromatin looping IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of cGAS/STING signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nucleoside triphosphate catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
NOT involved_in sphingomyelin catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in extracellular space IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in extracellular space IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
cyclic GMP-AMP phosphodiesterase SMPDL3A
Names
0610010C24Rik
2',3'-cGAMP phosphodiesterase SMPDL3A
ASM-like phosphodiesterase 3a
acid sphingomyelinase-like phosphodiesterase 3a
NP_001273067.1
NP_006705.1

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_001286138.2 → NP_001273067.1  cyclic GMP-AMP phosphodiesterase SMPDL3A isoform b

    See identical proteins and their annotated locations for NP_001273067.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AK301365, DA510600, Y08136
    Consensus CDS
    CCDS69190.1
    UniProtKB/Swiss-Prot
    Q92484
    Related
    ENSP00000442152.1, ENST00000539041.5
    Conserved Domains (2) summary
    COG1409
    Location:13 → 206
    CpdA; 3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms]
    cd00842
    Location:1 → 205
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain

  2. NM_006714.5 → NP_006705.1  cyclic GMP-AMP phosphodiesterase SMPDL3A isoform a precursor

    See identical proteins and their annotated locations for NP_006705.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    BC018999, DA510600, Y08136
    Consensus CDS
    CCDS5128.1
    UniProtKB/Swiss-Prot
    B7Z729, Q8WV13, Q92484
    Related
    ENSP00000357425.4, ENST00000368440.5
    Conserved Domains (1) summary
    cd00842
    Location:40 → 336
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    122789258..122809720
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    123977551..123998013
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92484.2 GenPept UniProtKB/Swiss-Prot:Q92484

Gene LinkOut

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