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    P3H1 prolyl 3-hydroxylase 1 [ Homo sapiens (human) ]

    Gene ID: 64175, updated on 27-Nov-2024

    Summary

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    Official Symbol
    P3H1provided by HGNC
    Official Full Name
    prolyl 3-hydroxylase 1provided by HGNC
    Primary source
    HGNC:HGNC:19316
    See related
    Ensembl:ENSG00000117385 MIM:610339; AllianceGenome:HGNC:19316
    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
    OI8; GROS1; LEPRE1
    Summary
    This gene encodes an enzyme that is a member of the collagen prolyl hydroxylase family. These enzymes are localized to the endoplasmic reticulum and their activity is required for proper collagen synthesis and assembly. Mutations in this gene are associated with osteogenesis imperfecta type VIII. Three alternatively spliced transcript variants encoding different isoforms have been described. Other variants may exist, but their biological validity has not been determined. [provided by RefSeq, Aug 2011]
    Expression
    Ubiquitous expression in placenta (RPKM 18.9), testis (RPKM 10.8) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See P3H1 in Genome Data Viewer
    Location:
    1p34.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (42746374..42767028, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (42616864..42637518, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (43212045..43232699, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 763 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 765 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 766 Neighboring gene Y-box binding protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43207264-43207866 Neighboring gene claudin 19 Neighboring gene MPRA-validated peak195 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:43216651-43217315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 767 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 768 Neighboring gene chromosome 1 open reading frame 50 Neighboring gene TMEM269 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43250662-43251403 Neighboring gene uncharacterized LOC107984946 Neighboring gene transmembrane protein 269

    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. A Founder Intronic Variant in P3H1 Likely Results in Aberrant Splicing and Protein Truncation in Patients of Karen Descent with Osteogenesis Imperfecta Type VIII. Kantaputra PN, et al. Genes (Basel), 2023 Jan 26. PMID 36833249, Free PMC Article
    2. Recessive osteogenesis imperfecta caused by LEPRE1 mutations: clinical documentation and identification of the splice form responsible for prolyl 3-hydroxylation. Willaert A, et al. J Med Genet, 2009 Apr. PMID 19088120
    3. Lethal/severe osteogenesis imperfecta in a large family: a novel homozygous LEPRE1 mutation and bone histological findings. van Dijk FS, et al. Pediatr Dev Pathol, 2011 May-Jun. PMID 20946018
    4. Cell Surface Accumulation of Intracellular Leucine Proline-Enriched Proteoglycan 1 Enhances Odontogenic Potential of Human Dental Pulp Stem Cells. Kang KJ, et al. Stem Cells Dev, 2022 Nov. PMID 35859453
    5. A founder mutation in LEPRE1 carried by 1.5% of West Africans and 0.4% of African Americans causes lethal recessive osteogenesis imperfecta. Cabral WA, et al. Genet Med, 2012 May. PMID 22281939, Free PMC Article

    See all (95) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A Founder Intronic Variant in P3H1 Likely Results in Aberrant Splicing and Protein Truncation in Patients of Karen Descent with Osteogenesis Imperfecta Type VIII.
      Title: A Founder Intronic Variant in P3H1 Likely Results in Aberrant Splicing and Protein Truncation in Patients of Karen Descent with Osteogenesis Imperfecta Type VIII.
    2. Cell Surface Accumulation of Intracellular Leucine Proline-Enriched Proteoglycan 1 Enhances Odontogenic Potential of Human Dental Pulp Stem Cells.
      Title: Cell Surface Accumulation of Intracellular Leucine Proline-Enriched Proteoglycan 1 Enhances Odontogenic Potential of Human Dental Pulp Stem Cells.
    3. Phenotypic Variation in Vietnamese Osteogenesis Imperfecta Patients Sharing a Recessive P3H1 Pathogenic Variant.
      Title: Phenotypic Variation in Vietnamese Osteogenesis Imperfecta Patients Sharing a Recessive P3H1 Pathogenic Variant.
    4. Biomarker LEPRE1 induces pelitinib-specific drug responsiveness by regulating ABCG2 expression and tumor transition states in human leukemia and lung cancer.
      Title: Biomarker LEPRE1 induces pelitinib-specific drug responsiveness by regulating ABCG2 expression and tumor transition states in human leukemia and lung cancer.
    5. A novel P3H1 mutation is associated with osteogenesis imperfecta type VIII and dental anomalies.
      Title: A novel P3H1 mutation is associated with osteogenesis imperfecta type VIII and dental anomalies.
    6. Osteogenesis Imperfecta: Search for Mutations in Patients from the Republic of Bashkortostan (Russia).
      Title: Osteogenesis Imperfecta: Search for Mutations in Patients from the Republic of Bashkortostan (Russia).
    7. A new case of osteogenesis imperfecta type VIII and retinal detachment.
      Title: A new case of osteogenesis imperfecta type VIII and retinal detachment.
    8. Upregulated LEPRE1 correlates with poor outcome and its knockdown attenuates cells proliferation, migration and invasion in osteosarcoma.
      Title: Upregulated LEPRE1 correlates with poor outcome and its knockdown attenuates cells proliferation, migration and invasion in osteosarcoma.
    9. Osteogenesis imperfecta caused by COL1A1, CRTAP and LEPRE1 mutations. Report of 2cases.", trans "Osteogenesis imperfecta causada por mutacion en los genes COL1A1, CRTAP y LEPRE1. Estudio de 2casos.
      Title: Osteogenesis imperfecta caused by COL1A1, CRTAP and LEPRE1 mutations. Report of 2cases.
    10. P3H1 mutation is associated with Non-Lethal Type VIII Osteogenesis Imperfecta.
      Title: Non-Lethal Type VIII Osteogenesis Imperfecta Has Elevated Bone Matrix Mineralization.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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
    Osteogenesis imperfecta type 8
    MedGen: C1970458 OMIM: 610915 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)

    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

    • MGC117314

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-ascorbic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    contributes_to collagen binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables procollagen-proline 3-dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables procollagen-proline 3-dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in bone development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chaperone-mediated protein folding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in collagen metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in collagen metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in negative regulation of cell population proliferation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of post-translational protein modification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein folding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein hydroxylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of protein secretion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    colocalizes_with collagen-containing extracellular matrix HDA PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in membrane HDA PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    prolyl 3-hydroxylase 1
    Names
    growth suppressor 1
    leprecan
    leucine proline-enriched proteoglycan (leprecan) 1
    leucine- and proline-enriched proteoglycan 1
    procollagen-proline 3-dioxygenase
    NP_001139761.1
    NP_001230175.1
    NP_071751.3
    XP_047283572.1
    XP_047283577.1
    XP_047283582.1
    XP_047283585.1
    XP_054194132.1
    XP_054194133.1
    XP_054194134.1
    XP_054194135.1

    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_008123.1 RefSeqGene

      Range
      5001..25750
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_5

    mRNA and Protein(s)

    1. NM_001146289.2 → NP_001139761.1  prolyl 3-hydroxylase 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001139761.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 3. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 3, and isoform 2 is a likely cause of a recessive form of osteogenesis imperfecta (OI).
      Source sequence(s)
      BC108311, BE675748, DC404420
      Consensus CDS
      CCDS53307.1
      UniProtKB/Swiss-Prot
      Q32P28
      Related
      ENSP00000380245.3, ENST00000397054.7
      Conserved Domains (1) summary
      smart00702
      Location:479 → 677
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    2. NM_001243246.2 → NP_001230175.1  prolyl 3-hydroxylase 1 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
      Source sequence(s)
      AC098484, AK027648, AK027697, DC404420
      Consensus CDS
      CCDS57986.1
      UniProtKB/Swiss-Prot
      Q32P28
      Related
      ENSP00000236040.4, ENST00000236040.8
      Conserved Domains (1) summary
      smart00702
      Location:479 → 677
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    3. NM_022356.4 → NP_071751.3  prolyl 3-hydroxylase 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_071751.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 3' UTR and coding sequence compared to variant 3. The resulting isoform (1) has a shorter and distinct C-terminus compared to isoform 3.
      Source sequence(s)
      AC098484, AK027697, R67284
      Consensus CDS
      CCDS472.2
      UniProtKB/Swiss-Prot
      Q32P28, Q7KZR4, Q96BR8, Q96SK8, Q96SL5, Q96SN3, Q9H6K3, Q9HC86, Q9HC87
      UniProtKB/TrEMBL
      B4DNM8
      Related
      ENSP00000296388.5, ENST00000296388.10
      Conserved Domains (1) summary
      smart00702
      Location:479 → 677
      P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      42746374..42767028 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427616.1 → XP_047283572.1  prolyl 3-hydroxylase 1 isoform X1

    2. XM_047427626.1 → XP_047283582.1  prolyl 3-hydroxylase 1 isoform X3

    3. XM_047427621.1 → XP_047283577.1  prolyl 3-hydroxylase 1 isoform X2

    4. XM_047427629.1 → XP_047283585.1  prolyl 3-hydroxylase 1 isoform X4

    RNA

    1. XR_946739.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      42616864..42637518 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338157.1 → XP_054194132.1  prolyl 3-hydroxylase 1 isoform X1

    2. XM_054338159.1 → XP_054194134.1  prolyl 3-hydroxylase 1 isoform X3

    3. XM_054338158.1 → XP_054194133.1  prolyl 3-hydroxylase 1 isoform X2

    4. XM_054338160.1 → XP_054194135.1  prolyl 3-hydroxylase 1 isoform X4

    RNA

    1. XR_008486138.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q32P28.2 GenPept UniProtKB/Swiss-Prot:Q32P28

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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