Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PLOD3 Gene

Aliases for PLOD3 Gene

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

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 Bone Fragility With Contractures, Arterial Rupture, And Deafness and Recessive Dystrophic Epidermolysis Bullosa. Among its related pathways are Collagen chain trimerization and Degradation of the extracellular matrix. Gene Ontology (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 PLOD2.

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

Additional gene information for PLOD3 Gene

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

Genomics for PLOD3 Gene

GeneHancer (GH) Regulatory Elements for PLOD3 Gene

Promoters and enhancers for PLOD3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J101215 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.2 237 4.7 FOXA2 PKNOX1 CLOCK ARNT ARID4B SIN3A ZNF2 YY1 POLR2B ZNF213 ZNHIT1 PLOD3 FIS1 GIGYF1 SRRT STAG3L5P PILRB PPP1R35 NAT16 EPHB4
GH07J101192 Enhancer 1.4 Ensembl ENCODE dbSUPER 13.7 +25.8 25833 1.2 HDGF ATF1 ARNT ARID4B IRF4 ZNF48 YY1 ARID2 ZNF143 ATF7 AP1S1 PLOD3 ZNHIT1 VGF NAT16
GH07J101283 Enhancer 0.8 ENCODE 12.2 -64.7 -64735 0.2 RB1 ARID4B SIN3A ZNF2 RAD21 RFX5 ZNF335 ZNF121 ARID2 ZNF143 PLOD3 ZNHIT1 VGF AP1S1 NAT16 FIS1 LOC101927746 AZGP1P2 ENSG00000278683
GH07J101185 Enhancer 0.7 ENCODE 13.7 +33.0 33025 0.2 FOXA2 TEAD4 JUN FOSL1 ZNF335 TCF12 EGR1 CBFA2T2 TRIM24 FOS ZNHIT1 PLOD3 AP1S1 NAT16 VGF
GH07J101116 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 1.9 +94.7 94677 15.1 CLOCK MLX DMAP1 IRF4 YY1 ZNF143 MEF2D SSRP1 ZNF610 GLIS1 SERPINE1 SRRT GIGYF1 ENSG00000242798 PPP1R35 STAG3L5P MEPCE PCOLCE-AS1 PILRB LRCH4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLOD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PLOD3 gene promoter:
  • HTF
  • Pax-4a
  • YY1
  • p53
  • FOXL1
  • NRSF form 2
  • NRSF form 1
  • deltaCREB
  • p300
  • CREB

Genomic Locations for PLOD3 Gene

Genomic Locations for PLOD3 Gene
12,444 bases
Minus strand
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(2+); Xref=ChEBI:CHEBI:29033;
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Homodimer.

neXtProt entry for PLOD3 Gene

Post-translational modifications for PLOD3 Gene

  • Glycosylation at Asn548 and isoforms=63
  • Modification sites at PhosphoSitePlus

Other Protein References for PLOD3 Gene

No data available for DME Specific Peptides for PLOD3 Gene

Domains & Families for PLOD3 Gene

Gene Families for PLOD3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for PLOD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for PLOD3 Gene

Function for PLOD3 Gene

Molecular function for PLOD3 Gene

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.
UniProtKB/Swiss-Prot CatalyticActivity:
L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] + succinate + CO(2).
GENATLAS Biochemistry:
procollagen-lysine,2-oxoglutarate 5 dioxygenase 3,highly expressed in heart,placenta,pancreas

Enzyme Numbers (IUBMB) for PLOD3 Gene

Phenotypes From GWAS Catalog for PLOD3 Gene

Gene Ontology (GO) - Molecular Function for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0008475 procollagen-lysine 5-dioxygenase activity TAS --
GO:0016491 oxidoreductase activity IEA --
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen IEA --
genes like me logo Genes that share ontologies with PLOD3: view
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

miRNA for PLOD3 Gene

Clone Products

No data available for 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

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 PLOD3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
golgi apparatus 5
plasma membrane 1
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum TAS 9724729
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005794 Golgi apparatus IDA 10934207
GO:0005802 trans-Golgi network IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PLOD3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) 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:0001886 endothelial cell morphogenesis IEA --
GO:0006493 protein O-linked glycosylation IMP 10934207
GO:0008104 protein localization IEA --
GO:0017185 peptidyl-lysine hydroxylation IMP,IEA 10934207
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

(11) 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 581,581
Carbon dioxide Approved, Investigational, Vet_approved Pharma 0
Oxygen Approved, Vet_approved Pharma 0
Water Approved Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (2S,5R)-5-Hydroxylysine
  • (5R)-5-Hydroxy-L-lysine
  • alpha,epsilon-diamino-delta-Hydroxycaproic acid
  • L-erythro-5-Hydroxylysine
  • L-Normal-5-hydroxylysine
  • FE (II) ion
  • Fe(II)
  • Fe(2+)
  • Ferrous ion
  • Iron ion(2+)
genes like me logo Genes that share compounds with PLOD3: view

Transcripts for PLOD3 Gene

mRNA/cDNA for PLOD3 Gene

Unigene Clusters for PLOD3 Gene

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

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for PLOD3 Gene

Protein tissue co-expression partners for PLOD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PLOD3 Gene:


SOURCE GeneReport for Unigene cluster for PLOD3 Gene:


Evidence on tissue expression from TISSUES for PLOD3 Gene

  • Nervous system(4.6)
  • Intestine(4.5)
  • Pancreas(4.4)
  • Skin(4)
  • Kidney(3)
  • Lung(2.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PLOD3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • skull
  • chest wall
  • clavicle
  • diaphragm
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • intestine
  • large intestine
  • liver
  • small intestine
  • stomach
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with PLOD3: view

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
(Pan troglodytes)
Mammalia PLOD3 34 33
  • 99.55 (n)
(Bos Taurus)
Mammalia PLOD3 34 33
  • 89.86 (n)
(Canis familiaris)
Mammalia PLOD3 34 33
  • 89.51 (n)
(Monodelphis domestica)
Mammalia PLOD3 34
  • 86 (a)
(Mus musculus)
Mammalia Plod3 16 34 33
  • 85.77 (n)
(Rattus norvegicus)
Mammalia Plod3 33
  • 85.55 (n)
(Ornithorhynchus anatinus)
Mammalia PLOD3 34
  • 77 (a)
(Anolis carolinensis)
Reptilia PLOD3 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia plod3 33
  • 69.04 (n)
Str.1520 33
African clawed frog
(Xenopus laevis)
Amphibia plod-prov 33
(Danio rerio)
Actinopterygii wu:fb72h05 33
  • 67.28 (n)
PLOD3 (2 of 2) 34
  • 65 (a)
plod3 34
  • 65 (a)
wufa10a05 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001507 33
  • 57.83 (n)
fruit fly
(Drosophila melanogaster)
Insecta Plod 34 33
  • 55.14 (n)
CG6199 35
  • 46 (a)
(Caenorhabditis elegans)
Secernentea let-268 34 35 33
  • 51.63 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 34
  • 50 (a)
Species where no ortholog for PLOD3 was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for PLOD3: view image

Paralogs for PLOD3 Gene

Paralogs for PLOD3 Gene

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

  • C9JU11_HUMAN
  • H7C0B8_HUMAN
  • H7C2A8_HUMAN
  • H7C2S8_HUMAN
  • H7C2V1_HUMAN
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 Variation AA Info Type
rs121434414 pathogenic, Bone fragility with contractures, arterial rupture, and deafness, Lysyl hydroxylase 3 deficiency (LH3 deficiency) [MIM:612394] 101,215,100(-) T/C coding_sequence_variant, missense_variant
rs41281013 benign, likely-benign, not specified, not provided 101,211,934(-) C/G coding_sequence_variant, missense_variant
rs748105435 likely-pathogenic, Bone fragility with contractures, arterial rupture, and deafness 101,207,623(-) A/C coding_sequence_variant, stop_gained
rs786205872 pathogenic, Bone fragility with contractures, arterial rupture, and deafness 101,206,427(-) A/ coding_sequence_variant, frameshift
rs138623639 likely-benign, not specified 101,216,767(-) A/G coding_sequence_variant, synonymous_variant

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

Variant ID Type Subtype PubMed ID
dgv11534n54 CNV loss 21841781
esv2422326 CNV duplication 17116639
esv2422376 CNV duplication 17116639
esv2734888 CNV deletion 23290073
esv2752134 CNV gain 17911159
esv3614318 CNV loss 21293372
esv3614319 CNV gain 21293372
esv3614321 CNV gain 21293372
nsv1018841 CNV gain 25217958
nsv1030604 CNV gain 25217958
nsv607973 CNV loss 21841781
nsv607974 CNV loss 21841781
nsv831075 CNV loss 17160897
nsv831076 CNV loss 17160897
nsv970915 CNV duplication 23825009

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)

Additional Variant Information for PLOD3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for PLOD3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PLOD3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bone fragility with contractures, arterial rupture, and deafness
  • lysyl hydroxylase 3 deficiency
recessive dystrophic epidermolysis bullosa
  • autosomal recessive dystrophic epidermolysis bullosa generalisata gravis
ehlers-danlos syndrome
  • cutis hyperelastica
ullrich congenital muscular dystrophy 1
  • ucmd1
- 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.

Additional Disease Information for PLOD3

Genetic Association Database
Human Genome Epidemiology 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 … Myllylä R (The Journal of biological chemistry 1998) 2 3 4 22 58
  2. Cloning and characterization of a third human lysyl hydroxylase isoform. (PMID: 9724729) Passoja K … Kivirikko KI (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 4 22 58
  3. A connective tissue disorder caused by mutations of the lysyl hydroxylase 3 gene. (PMID: 18834968) Salo AM … Myllylä R (American journal of human genetics 2008) 3 4 22 58
  4. Complete exon-intron organization of the gene for human lysyl hydroxylase 3 (LH3). (PMID: 10686427) Rautavuoma K … Kivirikko KI (Matrix biology : journal of the International Society for Matrix Biology 2000) 3 4 22 58
  5. The glycosyltransferase activities of lysyl hydroxylase 3 (LH3) in the extracellular space are important for cell growth and viability. (PMID: 18298658) Wang C … Myllylä R (Journal of cellular and molecular medicine 2009) 3 22 58

Products for PLOD3 Gene

Sources for PLOD3 Gene

Loading form....