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Aliases for PLOD3 Gene

Aliases for PLOD3 Gene

  • Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 2 3
  • Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3 3 5
  • Lysyl Hydroxylase 3 3 4
  • Lysyl Hydroxlase 3 2 3
  • EC 4 63
  • LH3 3 4
  • Lysine Hydroxylase 3 3

External Ids for PLOD3 Gene

Previous GeneCards Identifiers for PLOD3 Gene

  • GC07M099332
  • GC07M100395
  • GC07M100409
  • GC07M100442
  • GC07M100635
  • GC07M100849
  • GC07M095442

Summaries for PLOD3 Gene

Entrez Gene Summary for PLOD3 Gene

  • The protein encoded by this gene is a membrane-bound homodimeric enzyme that is localized to the cisternae of the rough endoplasmic reticulum. The enzyme (cofactors iron and ascorbate) catalyzes the hydroxylation of lysyl residues in collagen-like peptides. The resultant hydroxylysyl groups are attachment sites for carbohydrates in collagen and thus are critical for the stability of intermolecular crosslinks. Some patients with Ehlers-Danlos syndrome type VIB have deficiencies in lysyl hydroxylase activity. [provided by RefSeq, Jul 2008]

GeneCards Summary for PLOD3 Gene

PLOD3 (Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3) is a Protein Coding gene. Diseases associated with PLOD3 include Lysyl Hydroxylase 3 Deficiency and Connective Tissue Disorder Due To Lysyl Hydroxylase-3 Deficiency. Among its related pathways are Lysine degradation and Other types of O-glycan biosynthesis. GO annotations related to this gene include oxidoreductase activity and oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen. An important paralog of this gene is COLGALT1.

UniProtKB/Swiss-Prot for PLOD3 Gene

  • Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links.

Gene Wiki entry for PLOD3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLOD3 Gene

Genomics for PLOD3 Gene

Regulatory Elements for PLOD3 Gene

Enhancers for PLOD3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PLOD3 on UCSC Golden Path with GeneCards custom track

Promoters for PLOD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PLOD3 on UCSC Golden Path with GeneCards custom track

Genomic Location for PLOD3 Gene

101,205,977 bp from pter
101,218,420 bp from pter
12,444 bases
Minus strand

Genomic View for PLOD3 Gene

Genes around PLOD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLOD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLOD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLOD3 Gene

Proteins for PLOD3 Gene

  • Protein details for PLOD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
    Protein Accession:
    Secondary Accessions:
    • B2R6W6
    • Q540C3

    Protein attributes for PLOD3 Gene

    738 amino acids
    Molecular mass:
    84785 Da
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Homodimer.

neXtProt entry for PLOD3 Gene

Proteomics data for PLOD3 Gene at MOPED

Post-translational modifications for PLOD3 Gene

  • Glycosylation at Asn 63 and Asn 548
  • Modification sites at PhosphoSitePlus

Other Protein References for PLOD3 Gene

Domains & Families for PLOD3 Gene

Suggested Antigen Peptide Sequences for PLOD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 Fe2OG dioxygenase domain.
  • Contains 1 Fe2OG dioxygenase domain.
genes like me logo Genes that share domains with PLOD3: view

No data available for Gene Families for PLOD3 Gene

Function for PLOD3 Gene

Molecular function for PLOD3 Gene

GENATLAS Biochemistry:
procollagen-lysine,2-oxoglutarate 5 dioxygenase 3,highly expressed in heart,placenta,pancreas
UniProtKB/Swiss-Prot CatalyticActivity:
L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO(2).
UniProtKB/Swiss-Prot Function:
Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links.

Enzyme Numbers (IUBMB) for PLOD3 Gene

genes like me logo Genes that share phenotypes with PLOD3: view

Human Phenotype Ontology for PLOD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PLOD3 Gene

MGI Knock Outs for PLOD3:

Animal Model Products

  • Taconic Biosciences Mouse Models for PLOD3

CRISPR Products

miRNA for PLOD3 Gene

miRTarBase miRNAs that target PLOD3

No data available for Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for PLOD3 Gene

Localization for PLOD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLOD3 Gene

Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side.

Subcellular locations from

Jensen Localization Image for PLOD3 Gene COMPARTMENTS Subcellular localization image for PLOD3 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
cytosol 1
golgi apparatus 1
lysosome 1
mitochondrion 1
nucleus 1
peroxisome 1
plasma membrane 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components for PLOD3 Gene

Pathways & Interactions for PLOD3 Gene

genes like me logo Genes that share pathways with PLOD3: view

Pathways by source for PLOD3 Gene

Gene Ontology (GO) - Biological Process for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0042311 vasodilation IEA --
genes like me logo Genes that share ontologies with PLOD3: view

No data available for SIGNOR curated interactions for PLOD3 Gene

Drugs & Compounds for PLOD3 Gene

(6) Drugs for PLOD3 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Succinic acid Approved Nutra Full agonist, Agonist, Target 0
Vitamin C Approved Nutra Target 471,471
L-Lysine Approved Nutra Full agonist, Agonist 0
Uridine diphosphategalactose Experimental Pharma 0
Uridine-5'-Diphosphate Experimental Pharma 0

(8) Additional Compounds for PLOD3 Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (2S,5R)-2,6-diamino-5-hydroxyhexanoate
  • (2S,5R)-2,6-diamino-5-hydroxyhexanoic acid
  • (2S,5R)-5-hydroxylysine
  • (5R)-5-hydroxy-L-lysine
  • 5-Hydroxy-L-lysine
carbon dioxide
  • Carbon oxide
  • Carbon-12 dioxide
  • Carbonic acid anhydride
  • Carbonic acid gas
  • Carbonic anhydride
  • Armco iron
  • Carbonyl iron
  • FE
  • Ferrovac e
  • Hematite
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
  • Dioxygen
  • Molecular oxygen
  • O2
  • Oxygen
  • Oxygen molecule
genes like me logo Genes that share compounds with PLOD3: view

Transcripts for PLOD3 Gene

Unigene Clusters for PLOD3 Gene

Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PLOD3 Gene

No ASD Table

Relevant External Links for PLOD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PLOD3 Gene

mRNA expression in normal human tissues for PLOD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLOD3 Gene

This gene is overexpressed in Bone marrow stromal cell (32.2) and Testis (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PLOD3 Gene

SOURCE GeneReport for Unigene cluster for PLOD3 Gene Hs.153357

genes like me logo Genes that share expression patterns with PLOD3: view

Protein tissue co-expression partners for PLOD3 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PLOD3 Gene

Orthologs for PLOD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLOD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PLOD3 35
  • 89.86 (n)
  • 94.67 (a)
PLOD3 36
  • 92 (a)
(Canis familiaris)
Mammalia PLOD3 35
  • 89.51 (n)
  • 95.13 (a)
PLOD3 36
  • 94 (a)
(Mus musculus)
Mammalia Plod3 35
  • 85.77 (n)
  • 91.6 (a)
Plod3 16
Plod3 36
  • 91 (a)
(Pan troglodytes)
Mammalia PLOD3 35
  • 99.55 (n)
  • 99.59 (a)
PLOD3 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Plod3 35
  • 85.55 (n)
  • 91.33 (a)
(Monodelphis domestica)
Mammalia PLOD3 36
  • 86 (a)
(Ornithorhynchus anatinus)
Mammalia PLOD3 36
  • 77 (a)
(Anolis carolinensis)
Reptilia PLOD3 36
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia plod3 35
  • 69.04 (n)
  • 69.6 (a)
Str.1520 35
African clawed frog
(Xenopus laevis)
Amphibia plod-prov 35
(Danio rerio)
Actinopterygii wu:fb72h05 35
  • 67.28 (n)
  • 66.34 (a)
wufa10a05 35
plod3 36
  • 65 (a)
PLOD3 (2 of 2) 36
  • 65 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6199 37
  • 46 (a)
Plod 35
  • 55.14 (n)
  • 47.03 (a)
Plod 36
  • 45 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001507 35
  • 57.83 (n)
  • 47.58 (a)
(Caenorhabditis elegans)
Secernentea let-268 37
  • 46 (a)
let-268 35
  • 51.63 (n)
  • 47.69 (a)
let-268 36
  • 46 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 36
  • 50 (a)
Species with no ortholog for PLOD3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for PLOD3 Gene

Gene Tree for PLOD3 (if available)
Gene Tree for PLOD3 (if available)

Paralogs for PLOD3 Gene

Paralogs for PLOD3 Gene

(5) SIMAP similar genes for PLOD3 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with PLOD3: view

Variants for PLOD3 Gene

Sequence variations from dbSNP and Humsavar for PLOD3 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs1134907 - 101,212,865(-) AGGAC(C/T)GGAGG reference, missense
VAR_051708 -
VAR_054913 Lysyl hydroxylase 3 deficiency (LH3 deficiency)
rs917112 -- 101,213,710(+) TTTTT(C/T)ATGCT intron-variant
rs1468358 -- 101,209,892(+) CAATA(C/T)ACAGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PLOD3 Gene

Variant ID Type Subtype PubMed ID
esv2734888 CNV Deletion 23290073
nsv831075 CNV Loss 17160897
esv2422376 CNV Duplication 17116639
dgv7409n71 CNV Loss 21882294
esv2752134 CNV Gain 17911159
nsv831076 CNV Loss 17160897
dgv7410n71 CNV Loss 21882294
esv2422326 CNV Duplication 17116639

Variation tolerance for PLOD3 Gene

Residual Variation Intolerance Score: 90.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.90; 67.67% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PLOD3 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLOD3 Gene

Disorders for PLOD3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PLOD3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
lysyl hydroxylase 3 deficiency
  • bone fragility with contractures, arterial rupture, and deafness
connective tissue disorder due to lysyl hydroxylase-3 deficiency
  • bone fragility-contractures-arterial rupture-deafness syndrome
ullrich congenital muscular dystrophy 1
  • ullrich congenital muscular dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search PLOD3 in MalaCards View complete list of genes associated with diseases


  • Lysyl hydroxylase 3 deficiency (LH3 deficiency) [MIM:612394]: Connective tissue disorder. The syndrome is characterized by congenital malformations severely affecting many tissues and organs and revealing features of several collagen disorders, most of them involving COL2A1 (type II collagen). The findings suggest that the failure of lysyl hydroxylation and hydroxylysyl carbohydrate addition, which affects many collagens, is the molecular basis of this syndrome. {ECO:0000269 PubMed:18834968}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PLOD3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PLOD3: view

No data available for Genatlas for PLOD3 Gene

Publications for PLOD3 Gene

  1. Primary structure, tissue distribution, and chromosomal localization of a novel isoform of lysyl hydroxylase (lysyl hydroxylase 3). (PMID: 9582318) Valtavaara M. … Myllylae R. (J. Biol. Chem. 1998) 2 3 4 23 67
  2. Cloning and characterization of a third human lysyl hydroxylase isoform. (PMID: 9724729) Passoja K. … Kivirikko K.I. (Proc. Natl. Acad. Sci. U.S.A. 1998) 2 3 23
  3. The glycosyltransferase activities of lysyl hydroxylase 3 (LH3) in the extracellular space are important for cell growth and viability. (PMID: 18298658) Wang C. … MyllylAo R. (J. Cell. Mol. Med. 2009) 3 23
  4. A connective tissue disorder caused by mutations of the lysyl hydroxylase 3 gene. (PMID: 18834968) Salo A.M. … Myllylae R. (Am. J. Hum. Genet. 2008) 3 23
  5. Drugs, their targets and the nature and number of drug targets. (PMID: 17016423) Imming P. … Meyer A. (Nat Rev Drug Discov 2006) 25 26

Products for PLOD3 Gene

Sources for PLOD3 Gene