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    PHOSPHO1 phosphoethanolamine/phosphocholine phosphatase 1 [ Homo sapiens (human) ]

    Gene ID: 162466, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PHOSPHO1provided by HGNC
    Official Full Name
    phosphoethanolamine/phosphocholine phosphatase 1provided by HGNC
    Primary source
    HGNC:HGNC:16815
    See related
    Ensembl:ENSG00000173868 AllianceGenome:HGNC:16815
    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
    Summary
    Enables pyrophosphatase activity. Predicted to be involved in bone mineralization involved in bone maturation. Predicted to act upstream of or within endochondral ossification. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in testis (RPKM 17.3), bone marrow (RPKM 8.3) and 3 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17q21.32
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (49223366..49230787, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (50086450..50093871, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (47300728..47308149, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:47287312-47287988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12354 Neighboring gene G protein subunit gamma transducin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12357 Neighboring gene ABI family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:47300636-47301544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:47301545-47302452 Neighboring gene uncharacterized LOC124904022 Neighboring gene uncharacterized FLJ40194

    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. PHOSPHO1 Serves as a Key Metabolism-Related Biomarker in the Tumorigenesis of Diffuse Large B-cell Lymphoma. Chen TR, et al. Curr Med Sci, 2022 Aug. PMID 35943680, Free PMC Article
    2. Identification of a novel splice variant of the haloacid dehalogenase: PHOSPHO1. Roberts SJ, et al. Biochem Biophys Res Commun, 2008 Jul 11. PMID 18471996
    3. Comparative modelling of human PHOSPHO1 reveals a new group of phosphatases within the haloacid dehalogenase superfamily. Stewart AJ, et al. Protein Eng, 2003 Dec. PMID 14983068
    4. DNA methylation of loci within ABCG1 and PHOSPHO1 in blood DNA is associated with future type 2 diabetes risk. Dayeh T, et al. Epigenetics, 2016 Jul 2. PMID 27148772, Free PMC Article
    5. Role of bone-type tissue-nonspecific alkaline phosphatase and PHOSPO1 in vascular calcification. Bobryshev YV, et al. Curr Pharm Des, 2014. PMID 24533943

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHOSPHO1 Serves as a Key Metabolism-Related Biomarker in the Tumorigenesis of Diffuse Large B-cell Lymphoma.
      Title: PHOSPHO1 Serves as a Key Metabolism-Related Biomarker in the Tumorigenesis of Diffuse Large B-cell Lymphoma.
    2. CpG sites located in PHOSPHO1 gene showed differential methylation in association with lipid traits. Genetic variants in PHOSPHO1 gene were also associated with lipid profile.
      Title: Identification and validation of seven new loci showing differential DNA methylation related to serum lipid profile: an epigenome-wide approach. The REGICOR study.
    3. DNA methylation at the PHOSPHO1 locus cg02650017 in blood DNA was associated with a decreased risk for future type 2 diabetes.
      Title: DNA methylation of loci within ABCG1 and PHOSPHO1 in blood DNA is associated with future type 2 diabetes risk.
    4. REVIEW: role of bone-type tissue-nonspecific alkaline phosphatase and PHOSPO1 in vascular calcification
      Title: Role of bone-type tissue-nonspecific alkaline phosphatase and PHOSPO1 in vascular calcification.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
    6. The identification of a novel, alternatively spliced PHOSPHO1 transcript (PHOSPHO1-3a), was described.
      Title: Identification of a novel splice variant of the haloacid dehalogenase: PHOSPHO1.
    7. Models of PHOSPHO2 and PHOSPHO1 suggest subtle differences in the charge distributions around the putative substrate entry site and in the location of potential H-bond donors.
      Title: Probing the substrate specificities of human PHOSPHO1 and PHOSPHO2.
    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
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphocholine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphoethanolamine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables pyrophosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in bone mineralization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in bone mineralization involved in bone maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endochondral ossification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of bone mineralization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular membrane-bounded organelle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    phosphoethanolamine/phosphocholine phosphatase
    Names
    phosphatase, orphan 1
    NP_001137276.1
    NP_848595.1
    XP_047291460.1
    XP_047291461.1
    XP_047291462.1
    XP_054171246.1
    XP_054171247.1
    XP_054171248.1

    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_001143804.2 → NP_001137276.1  phosphoethanolamine/phosphocholine phosphatase isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).
      Source sequence(s)
      AC004797, AJ457189, BC029931
      Consensus CDS
      CCDS45726.1
      UniProtKB/Swiss-Prot
      Q8TCT1
      Related
      ENSP00000406909.1, ENST00000413580.5
      Conserved Domains (2) summary
      pfam00702
      Location:53 → 241
      Hydrolase; haloacid dehalogenase-like hydrolase
      pfam06888
      Location:52 → 289
      Put_Phosphatase; Putative Phosphatase

    2. NM_178500.4 → NP_848595.1  phosphoethanolamine/phosphocholine phosphatase isoform 2

      See identical proteins and their annotated locations for NP_848595.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses a different splice site, compared to variant 1, that results in the use of an upstream start codon. The resulting protein (isoform 2) has a shorter and distinct N-terminus when it is compared to isoform 1.
      Source sequence(s)
      AC004797, AJ457189
      Consensus CDS
      CCDS11547.1
      UniProtKB/Swiss-Prot
      E9PAM0, Q17RU6, Q8TCT1
      Related
      ENSP00000311925.4, ENST00000310544.9
      Conserved Domains (1) summary
      pfam06888
      Location:27 → 264
      Put_Phosphatase; Putative Phosphatase

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      49223366..49230787 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435506.1 → XP_047291462.1  phosphoethanolamine/phosphocholine phosphatase isoform X2

      UniProtKB/Swiss-Prot
      E9PAM0, Q17RU6, Q8TCT1

    2. XM_047435505.1 → XP_047291461.1  phosphoethanolamine/phosphocholine phosphatase isoform X1

    3. XM_047435504.1 → XP_047291460.1  phosphoethanolamine/phosphocholine phosphatase isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      50086450..50093871 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315273.1 → XP_054171248.1  phosphoethanolamine/phosphocholine phosphatase isoform X2

      UniProtKB/Swiss-Prot
      E9PAM0, Q17RU6, Q8TCT1

    2. XM_054315271.1 → XP_054171246.1  phosphoethanolamine/phosphocholine phosphatase isoform X1

    3. XM_054315272.1 → XP_054171247.1  phosphoethanolamine/phosphocholine phosphatase isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TCT1.1 GenPept UniProtKB/Swiss-Prot:Q8TCT1

    Gene LinkOut

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