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    SGPP2 sphingosine-1-phosphate phosphatase 2 [ Homo sapiens (human) ]

    Gene ID: 130367, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SGPP2provided by HGNC
    Official Full Name
    sphingosine-1-phosphate phosphatase 2provided by HGNC
    Primary source
    HGNC:HGNC:19953
    See related
    Ensembl:ENSG00000163082 MIM:612827; AllianceGenome:HGNC:19953
    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
    SPP2; SPPase2
    Summary
    The protein encoded by this gene is a transmembrane protein that degrades the bioactive signaling molecule sphingosine 1-phosphate. The encoded protein is induced during inflammatory responses and has been shown to be downregulated by the microRNA-31 tumor suppressor. Alternative splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2016]
    Expression
    Broad expression in thyroid (RPKM 13.7), esophagus (RPKM 12.0) and 18 other tissues See more
    Orthologs
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    Genomic context

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    See SGPP2 in Genome Data Viewer
    Location:
    2q36.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (222423988..222562621)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (222909191..223047956)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223288707..223427340)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene paired box 3 Neighboring gene PAX3 promoter region Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171419-223171954 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171955-223172489 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223182883-223183478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12368 Neighboring gene CCDC140 long non-coding RNA Neighboring gene ring finger protein 228 Neighboring gene cancer/testis associated transcript 75 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223258471-223259068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17166 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223335177-223335698 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223335699-223336218 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223342957-223343680 Neighboring gene Nanog homeobox pseudogene 2 Neighboring gene RNA, U6 small nuclear 619, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223383170-223383762 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 49 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:223400343-223400843 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12372 Neighboring gene phenylalanyl-tRNA synthetase subunit beta Neighboring gene ReSE screen-validated silencer GRCh37_chr2:223502966-223503113 Neighboring gene uncharacterized LOC105373902 Neighboring gene tripartite motif containing 60 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17167 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:223521038-223521234 Neighboring gene uncharacterized LOC124907985

    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. Vitamin D-responsive SGPP2 variants associated with lung cell expression and lung function. Reardon BJ, et al. BMC Med Genet, 2013 Nov 25. PMID 24274704, Free PMC Article
    2. Sphingosine pathway deregulation in endometriotic tissues. Santulli P, et al. Fertil Steril, 2012 Apr. PMID 22277765
    3. Sphingosine 1-phosphate phosphatase 2 is induced during inflammatory responses. Mechtcheriakova D, et al. Cell Signal, 2007 Apr. PMID 17113265
    4. Identification and characterization of a novel human sphingosine-1-phosphate phosphohydrolase, hSPP2. Ogawa C, et al. J Biol Chem, 2003 Jan 10. PMID 12411432
    5. Sphingosine-1-phosphate Phosphatase 2 Regulates Pancreatic Islet β-Cell Endoplasmic Reticulum Stress and Proliferation. Taguchi Y, et al. J Biol Chem, 2016 Jun 3. PMID 27059959, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SGPP2, a sphingosine-1-phosphate phosphatase, is a novel vitamin D-responsive gene associated with lung function.
      Title: Vitamin D-responsive SGPP2 variants associated with lung cell expression and lung function.
    2. characterization of SPP2, another member of the SPP family that may play a role in attenuating intracellular S1P signaling.
      Title: Identification and characterization of a novel human sphingosine-1-phosphate phosphohydrolase, hSPP2.
    3. This study provides detailed insights into the regulation of SPP2 gene expression and suggests that SPP2 might be a novel player in pro-inflammatory signalling.
      Title: Sphingosine 1-phosphate phosphatase 2 is induced during inflammatory responses.
    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

    EBI GWAS Catalog

    Description
    Genetic variants associated with disordered eating.
    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

    Clone Names

    • FLJ39004

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables dihydrosphingosine-1-phosphate phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sphingosine-1-phosphate phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables sphingosine-1-phosphate phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sphingosine-1-phosphate phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables sphingosine-1-phosphate phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in phospholipid dephosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of type B pancreatic cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in sphingolipid catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in sphingosine metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sphingosine metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum 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 TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    sphingosine-1-phosphate phosphatase 2
    Names
    sphingosine 1-phosphate phosphohydrolase 2
    sphingosine-1-phosphatase 2
    sphingosine-1-phosphate phosphotase 2

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001320833.2 → NP_001307762.1  sphingosine-1-phosphate phosphatase 2 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' end compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AC097461, AK314322, BC114513, BU676534
      UniProtKB/TrEMBL
      Q4ZFX2
      Conserved Domains (2) summary
      COG0671
      Location:1 → 108
      PgpB; Membrane-associated phospholipid phosphatase [Lipid transport and metabolism]
      cd03388
      Location:1 → 105
      PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...

    2. NM_001320834.2 → NP_001307763.1  sphingosine-1-phosphate phosphatase 2 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b)
      Source sequence(s)
      AC097461, AC112718, AK096323, BU676534
      UniProtKB/TrEMBL
      Q4ZFX2
      Conserved Domains (2) summary
      COG0671
      Location:1 → 108
      PgpB; Membrane-associated phospholipid phosphatase [Lipid transport and metabolism]
      cd03388
      Location:1 → 105
      PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...

    3. NM_152386.4 → NP_689599.2  sphingosine-1-phosphate phosphatase 2 isoform a

      See identical proteins and their annotated locations for NP_689599.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC097461, AF542512, AK314322, BU676534
      Consensus CDS
      CCDS2453.1
      UniProtKB/Swiss-Prot
      A3KPB4, Q8IWX5, Q8N8Q6
      UniProtKB/TrEMBL
      Q3B870
      Related
      ENSP00000315137.7, ENST00000321276.8
      Conserved Domains (1) summary
      cd03388
      Location:84 → 233
      PAP2_SPPase1; PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second ...

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      222423988..222562621
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      222909191..223047956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IWX5.1 GenPept UniProtKB/Swiss-Prot:Q8IWX5

    Gene LinkOut

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