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Aliases for P3H3 Gene

Aliases for P3H3 Gene

  • Prolyl 3-Hydroxylase 3 2 3 3 5
  • Procollagen-Proline 3-Dioxygenase 2 3
  • Leprecan-Like 2 2 3
  • Protein B 3 4
  • LEPREL2 3 4
  • Leprecan-Like Protein 2 4
  • Gene Rich Cluster, B 3
  • EC 1.14.11.7 4
  • HSU47926 3
  • GRCB 3

External Ids for P3H3 Gene

Previous HGNC Symbols for P3H3 Gene

  • LEPREL2

Summaries for P3H3 Gene

Entrez Gene Summary for P3H3 Gene

  • The protein encoded by this gene belongs to the leprecan family of proteoglycans, which function as collagen prolyl hydroxylases that are required for proper collagen biosynthesis, folding and assembly. This protein, like other family members, is thought to reside in the endoplasmic reticulum. Epigenetic inactivation of this gene is associated with breast and other cancers, suggesting that it may function as a tumor suppressor. [provided by RefSeq, Aug 2013]

GeneCards Summary for P3H3 Gene

P3H3 (Prolyl 3-Hydroxylase 3) is a Protein Coding gene. Diseases associated with P3H3 include Xanthogranulomatous Cholecystitis. Among its related pathways are Collagen chain trimerization and Degradation of the extracellular matrix. Gene Ontology (GO) annotations related to this gene include iron ion binding and L-ascorbic acid binding. An important paralog of this gene is P3H1.

UniProtKB/Swiss-Prot for P3H3 Gene

  • Part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils. Required for normal hydroxylation of lysine residues in type I collagen chains in skin, bone, tendon, aorta and cornea. Required for normal skin stability via its role in hydroxylation of lysine residues in collagen alpha chains and in collagen fibril assembly. Apparently not required for normal prolyl 3-hydroxylation on collagen chains, possibly because it functions redundantly with other prolyl 3-hydroxylases.

Gene Wiki entry for P3H3 Gene

Additional gene information for P3H3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for P3H3 Gene

Genomics for P3H3 Gene

GeneHancer (GH) Regulatory Elements for P3H3 Gene

Promoters and enhancers for P3H3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J006826 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 677.3 +0.3 325 3.7 HDGF ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 ZNF143 P3H3 ZNF384 ENSG00000219410 CHD4 ENSG00000247853 NCAPD2 ENSG00000256967 SPSB2 C1RL-AS1 NOP2
GH12J006530 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 23.3 -291.3 -291277 12.8 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 GAPDH ENSG00000269968 GPR162 ZNF384 ENSG00000219410 CHD4 ENSG00000247853 NCAPD2 NOP2 SPSB2
GH12J006602 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 18.5 -222.6 -222645 7.4 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 CHD4 ZNF384 ENSG00000219410 ENSG00000247853 NOP2 NCAPD2 ING4 SPSB2 ENSG00000126749 SCARNA12
GH12J006751 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.5 -75.2 -75218 3 HDGF FOXA2 PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 MLF2 CHD4 ZNF384 ATN1 ENSG00000247853 ENSG00000219410 P3H3 NOP2 GNB3 ENSG00000126749
GH12J006940 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.1 +125.3 125285 25.9 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 PTPN6 C12orf57 EMG1 ZNF384 ENSG00000219410 ENSG00000247853 SPSB2 SCARNA12 NCAPD2 ENSG00000256967
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around P3H3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for P3H3 Gene

Genomic Locations for P3H3 Gene
chr12:6,828,373-6,839,854
(GRCh38/hg38)
Size:
11,482 bases
Orientation:
Plus strand
chr12:6,937,572-6,949,018
(GRCh37/hg19)
Size:
11,447 bases
Orientation:
Plus strand

Genomic View for P3H3 Gene

Genes around P3H3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
P3H3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for P3H3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for P3H3 Gene

Proteins for P3H3 Gene

  • Protein details for P3H3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IVL6-P3H3_HUMAN
    Recommended name:
    Prolyl 3-hydroxylase 3
    Protein Accession:
    Q8IVL6
    Secondary Accessions:
    • Q13512
    • Q15740
    • Q66K32
    • Q6NX61
    • Q7L2T1

    Protein attributes for P3H3 Gene

    Size:
    736 amino acids
    Molecular mass:
    81837 Da
    Cofactor:
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Identified in a complex with PLOD1 and P3H4.

    Alternative splice isoforms for P3H3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for P3H3 Gene

Post-translational modifications for P3H3 Gene

  • Glycosylation at Asn462 and Asn331
  • Ubiquitination at isoforms=2517
  • Modification sites at PhosphoSitePlus

Other Protein References for P3H3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for P3H3 Gene

Domains & Families for P3H3 Gene

Gene Families for P3H3 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted secreted proteins

Protein Domains for P3H3 Gene

Suggested Antigen Peptide Sequences for P3H3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8IVL6

UniProtKB/Swiss-Prot:

P3H3_HUMAN :
  • Belongs to the leprecan family.
Family:
  • Belongs to the leprecan family.
genes like me logo Genes that share domains with P3H3: view

Function for P3H3 Gene

Molecular function for P3H3 Gene

UniProtKB/Swiss-Prot Function:
Part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils. Required for normal hydroxylation of lysine residues in type I collagen chains in skin, bone, tendon, aorta and cornea. Required for normal skin stability via its role in hydroxylation of lysine residues in collagen alpha chains and in collagen fibril assembly. Apparently not required for normal prolyl 3-hydroxylation on collagen chains, possibly because it functions redundantly with other prolyl 3-hydroxylases.
UniProtKB/Swiss-Prot CatalyticActivity:
L-proline-[procollagen] + 2-oxoglutarate + O(2) = trans-3-hydroxy-L-proline-[procollagen] + succinate + CO(2).

Enzyme Numbers (IUBMB) for P3H3 Gene

Phenotypes From GWAS Catalog for P3H3 Gene

Gene Ontology (GO) - Molecular Function for P3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
GO:0005515 protein binding IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen IEA --
GO:0019797 procollagen-proline 3-dioxygenase activity IBA --
genes like me logo Genes that share ontologies with P3H3: view
genes like me logo Genes that share phenotypes with P3H3: view

Animal Models for P3H3 Gene

MGI Knock Outs for P3H3:
  • P3h3 P3h3<tm1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for P3H3

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for P3H3 Gene

Localization for P3H3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for P3H3 Gene

Endoplasmic reticulum.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for P3H3 gene
Compartment Confidence
plasma membrane 3
endoplasmic reticulum 3
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoli (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for P3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IBA --
GO:1902494 catalytic complex ISS,IEA --
genes like me logo Genes that share ontologies with P3H3: view

Pathways & Interactions for P3H3 Gene

genes like me logo Genes that share pathways with P3H3: view

Pathways by source for P3H3 Gene

Interacting Proteins for P3H3 Gene

Gene Ontology (GO) - Biological Process for P3H3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008285 negative regulation of cell proliferation IDA 19436308
GO:0017185 peptidyl-lysine hydroxylation ISS,IEA --
GO:0019511 peptidyl-proline hydroxylation IEA --
GO:0032963 collagen metabolic process IBA --
GO:0032964 collagen biosynthetic process ISS,IEA --
genes like me logo Genes that share ontologies with P3H3: view

No data available for SIGNOR curated interactions for P3H3 Gene

Drugs & Compounds for P3H3 Gene

(5) Drugs for P3H3 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Proline Approved Nutra Target 0
Succinic acid Approved Nutra Full agonist, Agonist, Target 0
Vitamin C Approved Nutra Target 581,581
Oxygen Approved, Vet_approved Pharma 0
Oxogluric acid Experimental, Investigational Nutra 0

(2) Additional Compounds for P3H3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
3-Hydroxy-L-proline
  • cis-3-Hydroxy-D-proline
  • Procollagen trans-3-hydroxy-L-proline
4298-08-2
Fe2+
  • FE (II) ion
  • Fe(II)
  • Fe(2+)
  • Ferrous ion
  • Iron ion(2+)
15438-31-0
genes like me logo Genes that share compounds with P3H3: view

Transcripts for P3H3 Gene

mRNA/cDNA for P3H3 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for P3H3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for P3H3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c · 9d · 9e ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ·
SP1: - - - - -
SP2: - - -
SP3: - -
SP4: - - -
SP5:
SP6:
SP7: - - -
SP8: - - - -
SP9: -
SP10:
SP11: - - - -
SP12: - - - - - - -
SP13:
SP14:
SP15:

ExUns: 15c · 15d ^ 16a · 16b ^ 17 ^ 18 ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23
SP1: -
SP2: -
SP3:
SP4: - -
SP5: -
SP6: -
SP7:
SP8:
SP9:
SP10: -
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for P3H3 Gene

GeneLoc Exon Structure for
P3H3
ECgene alternative splicing isoforms for
P3H3

Expression for P3H3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for P3H3 Gene

Protein differential expression in normal tissues from HIPED for P3H3 Gene

This gene is overexpressed in Bone marrow stromal cell (33.8), Bone (13.1), and Breast (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for P3H3 Gene



Protein tissue co-expression partners for P3H3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of P3H3 Gene:

P3H3

mRNA Expression by UniProt/SwissProt for P3H3 Gene:

Q8IVL6-P3H3_HUMAN
Tissue specificity: Detected in fetal cartilage (at protein level) (PubMed:28115524). Weak expression in heart, lung, ovary and skeletal muscle (PubMed:8723724).

Evidence on tissue expression from TISSUES for P3H3 Gene

  • Nervous system(4.5)
  • Eye(4.3)
genes like me logo Genes that share expression patterns with P3H3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for P3H3 Gene

Orthologs for P3H3 Gene

This gene was present in the common ancestor of animals.

Orthologs for P3H3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LEPREL2 34 33
  • 98.72 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LEPREL2 34 33
  • 88.37 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LEPREL2 34 33
  • 87.97 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Leprel2 34 33
  • 85.92 (n)
OneToOne
P3h3 16
rat
(Rattus norvegicus)
Mammalia Leprel2 33
  • 85.41 (n)
oppossum
(Monodelphis domestica)
Mammalia LEPREL2 34
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LEPREL2 34
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves LEPREL2 34 33
  • 62.47 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LEPREL2 34
  • 50 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii leprel2 34 33
  • 52.62 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y73F8A.26 34
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 37 (a)
ManyToMany
Species where no ortholog for P3H3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for P3H3 Gene

ENSEMBL:
Gene Tree for P3H3 (if available)
TreeFam:
Gene Tree for P3H3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for P3H3: view image

Paralogs for P3H3 Gene

Paralogs for P3H3 Gene

genes like me logo Genes that share paralogs with P3H3: view

Variants for P3H3 Gene

Sequence variations from dbSNP and Humsavar for P3H3 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000061715 -- 6,829,050(+) T/A intron_variant
rs1000633921 -- 6,830,301(+) C/T intron_variant
rs1001117334 -- 6,836,634(+) C/T intron_variant
rs1002497738 -- 6,836,769(+) C/T intron_variant
rs1002774305 -- 6,827,749(+) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for P3H3 Gene

Variant ID Type Subtype PubMed ID
esv3580405 CNV gain 25503493
nsv1143556 CNV deletion 24896259
nsv516726 CNV loss 19592680
nsv526312 CNV loss 19592680
nsv557261 CNV loss 21841781
nsv832323 CNV loss 17160897
nsv832324 CNV loss 17160897

Variation tolerance for P3H3 Gene

Residual Variation Intolerance Score: 80.5% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for P3H3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
P3H3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for P3H3 Gene

Disorders for P3H3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for P3H3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
xanthogranulomatous cholecystitis
  • cx
- elite association - COSMIC cancer census association via MalaCards
Search P3H3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for P3H3

genes like me logo Genes that share disorders with P3H3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for P3H3 Gene

Publications for P3H3 Gene

  1. The prolyl 3-hydroxylases P3H2 and P3H3 are novel targets for epigenetic silencing in breast cancer. (PMID: 19436308) Shah R … Crook T (British journal of cancer 2009) 3 22 58
  2. LEPREL1, a novel ER and Golgi resident member of the Leprecan family. (PMID: 15063763) Järnum S … Aman P (Biochemical and biophysical research communications 2004) 2 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination. (PMID: 9074930) Ansari-Lari MA … Gibbs RA (Genome research 1997) 3 4 58
  5. A gene-rich cluster between the CD4 and triosephosphate isomerase genes at human chromosome 12p13. (PMID: 8723724) Ansari-Lari MA … Gibbs RA (Genome research 1996) 3 4 58

Products for P3H3 Gene

Sources for P3H3 Gene

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