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

Gene ID: 64175, updated on 2-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
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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 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
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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

  • 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 molecular_function ND
No biological Data available
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

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