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ENPP3 ectonucleotide pyrophosphatase/phosphodiesterase 3 [ Homo sapiens (human) ]

Gene ID: 5169, updated on 3-Apr-2024

Summary

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Official Symbol
ENPP3provided by HGNC
Official Full Name
ectonucleotide pyrophosphatase/phosphodiesterase 3provided by HGNC
Primary source
HGNC:HGNC:3358
See related
Ensembl:ENSG00000154269 MIM:602182; AllianceGenome:HGNC:3358
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
B10; NPP3; PDNP3; CD203c; PD-IBETA
Summary
The protein encoded by this gene belongs to a series of ectoenzymes that are involved in hydrolysis of extracellular nucleotides. These ectoenzymes possess ATPase and ATP pyrophosphatase activities and are type II transmembrane proteins. Expression of the related rat mRNA has been found in a subset of immature glial cells and in the alimentary tract. The corresponding rat protein has been detected in the pancreas, small intestine, colon, and liver. The human mRNA is expressed in glioma cells, prostate, and uterus. Expression of the human protein has been detected in uterus, basophils, and mast cells. Two transcript variants, one protein coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Oct 2015]
Expression
Biased expression in small intestine (RPKM 19.6), duodenum (RPKM 6.7) and 6 other tissues See more
Orthologs
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Genomic context

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See ENPP3 in Genome Data Viewer
Location:
6q23.2
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (131637302..131747410)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (132822841..132942332)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (131958442..132068550)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21 pseudogene 67 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:131825416-131826081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:131852503-131853004 Neighboring gene NANOG hESC enhancer GRCh37_chr6:131893832-131894333 Neighboring gene mediator complex subunit 23 Neighboring gene arginase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17546 Neighboring gene RNA, U4 small nuclear 18, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:132021641-132022226 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:132022227-132022812 Neighboring gene olfactory receptor family 2 subfamily A member 4 Neighboring gene CTAGE family member 9 Neighboring gene ribosomal protein L15 pseudogene 9 Neighboring gene microRNA 548h-5

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. Identification of CD203c as a New Basophil-Specific Flow-Marker in Ph(+) Chronic Myeloid Leukemia. Sadovnik I, et al. Cells, 2022 Dec 20. PMID 36611797, Free PMC Article
  2. Serum CD203c+ Extracellular Vesicle Serves as a Novel Diagnostic and Prognostic Biomarker for Succinylated Gelatin Induced Perioperative Hypersensitive Reaction. Qi Z, et al. Front Immunol, 2021. PMID 34650557, Free PMC Article
  3. Phase I Trials of Anti-ENPP3 Antibody-Drug Conjugates in Advanced Refractory Renal Cell Carcinomas. Thompson JA, et al. Clin Cancer Res, 2018 Sep 15. PMID 29848572, Free PMC Article
  4. Basophil biomarkers as useful predictors for sublingual immunotherapy in allergic rhinitis. Caruso M, et al. Int Immunopharmacol, 2018 Jul. PMID 29702283
  5. Expression of ENPP3 in human cyclic endometrium: a novel molecule involved in embryo implantation. Chen Q, et al. Reprod Fertil Dev, 2018 Oct. PMID 29614240

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of CD203c as a New Basophil-Specific Flow-Marker in Ph[+] Chronic Myeloid Leukemia.
    Title: Identification of CD203c as a New Basophil-Specific Flow-Marker in Ph(+) Chronic Myeloid Leukemia.
  2. Activated steady status and distinctive FcepsilonRI-mediated responsiveness in basophils of atopic dermatitis.
    Title: Activated steady status and distinctive FcεRI-mediated responsiveness in basophils of atopic dermatitis.
  3. Serum CD203c+ Extracellular Vesicle Serves as a Novel Diagnostic and Prognostic Biomarker for Succinylated Gelatin Induced Perioperative Hypersensitive Reaction.
    Title: Serum CD203c+ Extracellular Vesicle Serves as a Novel Diagnostic and Prognostic Biomarker for Succinylated Gelatin Induced Perioperative Hypersensitive Reaction.
  4. Updates on the surface antigens of basophils: CD16 on basophils of patients with respiratory or insect venom allergy and the rejection of CD203c and CD63 externalization decoupling by bisindolylmaleimides.
    Title: Updates on the surface antigens of basophils: CD16 on basophils of patients with respiratory or insect venom allergy and the rejection of CD203c and CD63 externalization decoupling by bisindolylmaleimides.
  5. ENPP3 was detected at high levels in archived tumor samples in agreement with preclinical data
    Title: Phase I Trials of Anti-ENPP3 Antibody-Drug Conjugates in Advanced Refractory Renal Cell Carcinomas.
  6. ENPP3 was expressed in endometrial epithelial cells and its expression levels changed during the menstrual cycle, peaking in the mid-secretory phase, corresponding to the time of embryo implantation. ENPP3 may play an important role in embryo implantation and may be a unique biomarker of endometrial receptivity.
    Title: Expression of ENPP3 in human cyclic endometrium: a novel molecule involved in embryo implantation.
  7. Studies determined the crystal structure of ectonucleotide pyrophosphatase/phosphodiesterase 3 (NPP3) as well as its complex with an ATP analog.
    Title: Structural basis for nucleotide recognition by the ectoenzyme CD203c.
  8. We showed the ability of the immunological marker CD203c to predict the clinical efficacy of sublingual immunotherapy on rhinitis subjects allergic to Parietaria.
    Title: Basophil biomarkers as useful predictors for sublingual immunotherapy in allergic rhinitis.
  9. Basophil CD203c surface expression reliably discriminated cystic fibrosis with allergic bronchopulmonary aspergillosis from cystic fibrosis with Aspergillus colonization and cystic fibrosis over time.
    Title: Blood basophil activation is a reliable biomarker of allergic bronchopulmonary aspergillosis in cystic fibrosis.
  10. Both NPP1 and NPP3 ectoenzymes are expressed in N2a cells, their levels dramatically changing when cells differentiate into a neuronal-like phenotype
    Title: Ectonucleotide pyrophosphatase/phosphodiesterase activity in Neuro-2a neuroblastoma cells: changes in expression associated with neuronal differentiation.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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

EBI GWAS Catalog

Description
Genome-Wide Association Study of L-Arginine and Dimethylarginines Reveals Novel Metabolic Pathway for Symmetric Dimethylarginine.
EBI GWAS Catalog
Preliminary evidence of genetic determinants of adiponectin response to fenofibrate in the Genetics of Lipid Lowering Drugs and Diet Network.
EBI GWAS Catalog

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleoside triphosphate diphosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nucleoside triphosphate diphosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphodiesterase I 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 ATP metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in basophil activation involved in immune response ISS
Inferred from Sequence or Structural Similarity
more info
  
NOT involved_in inorganic diphosphate transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of mast cell activation involved in immune response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of mast cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in nucleoside triphosphate catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nucleoside triphosphate catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in phosphate ion homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in phosphate-containing compound metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in pyrimidine nucleotide metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in apical plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ectonucleotide pyrophosphatase/phosphodiesterase family member 3
Names
dJ1005H11.3 (phosphodiesterase I/nucleotide pyrophosphatase 3)
dJ914N13.3 (phosphodiesterase I/nucleotide pyrophosphatase 3)
gp130RB13-6
phosphodiesterase I/nucleotide pyrophosphatase 3
phosphodiesterase-I beta
NP_005012.2
XP_011534199.1
XP_016866421.1
XP_054211567.1
XP_054211568.1
XP_054211569.1
XP_054211570.1
XP_054211571.1

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.

Genomic

  1. NG_033982.1 RefSeqGene

    Range
    5001..115109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005021.5 → NP_005012.2  ectonucleotide pyrophosphatase/phosphodiesterase family member 3

    See identical proteins and their annotated locations for NP_005012.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer, protein-coding transcript.
    Source sequence(s)
    AK024899, AL121575, EF560735, HY106781
    Consensus CDS
    CCDS5148.1
    UniProtKB/Swiss-Prot
    O14638, Q5JTL3
    UniProtKB/TrEMBL
    A8KA38
    Related
    ENSP00000350265.3, ENST00000357639.8
    Conserved Domains (3) summary
    smart00201
    Location:94 → 137
    SO; Somatomedin B -like domains
    smart00477
    Location:627 → 857
    NUC; DNA/RNA non-specific endonuclease
    cd16018
    Location:159 → 525
    Enpp; Ectonucleotide pyrophosphatase/phosphodiesterase, also called autotaxin

RNA

  1. NR_133007.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate 3' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK024899, AL121575, EF560735, HY106781
    Related
    ENST00000358229.6

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    131637302..131747410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010932.2 → XP_016866421.1  ectonucleotide pyrophosphatase/phosphodiesterase family member 3 isoform X1

    UniProtKB/TrEMBL
    A8KA38

  2. XM_011535897.2 → XP_011534199.1  ectonucleotide pyrophosphatase/phosphodiesterase family member 3 isoform X2

    Conserved Domains (3) summary
    smart00477
    Location:373 → 603
    NUC; DNA/RNA non-specific endonuclease
    pfam01663
    Location:2 → 232
    Phosphodiest; Type I phosphodiesterase / nucleotide pyrophosphatase
    cd16018
    Location:2 → 271
    Enpp; Ectonucleotide pyrophosphatase/phosphodiesterase, also called autotaxin

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    132822841..132942332
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355593.1 → XP_054211568.1  ectonucleotide pyrophosphatase/phosphodiesterase family member 3 isoform X3

    UniProtKB/Swiss-Prot
    O14638, Q5JTL3

  2. XM_054355592.1 → XP_054211567.1  ectonucleotide pyrophosphatase/phosphodiesterase family member 3 isoform X3

    UniProtKB/Swiss-Prot
    O14638, Q5JTL3

  3. XM_054355595.1 → XP_054211570.1  ectonucleotide pyrophosphatase/phosphodiesterase family member 3 isoform X4

    UniProtKB/TrEMBL
    F8W6H5

  4. XM_054355594.1 → XP_054211569.1  ectonucleotide pyrophosphatase/phosphodiesterase family member 3 isoform X1

  5. XM_054355596.1 → XP_054211571.1  ectonucleotide pyrophosphatase/phosphodiesterase family member 3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14638.2 GenPept UniProtKB/Swiss-Prot:O14638

Gene LinkOut

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