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Aliases for PLOD1 Gene

Aliases for PLOD1 Gene

  • Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 1 2 3 5
  • Lysyl Hydroxlase 1 2 3
  • EC 4 61
  • PLOD 3 4
  • LLH 3 4
  • LH1 3 4
  • Procollagen-Lysine 1, 2-Oxoglutarate 5-Dioxygenase (Lysine Hydroxylase, Ehlers-Danlos Syndrome Type VI) 2
  • Procollagen-Lysine 1, 2-Oxoglutarate 5-Dioxygenase 1 3
  • Lysyl Hydroxylase 1 4
  • Lysine Hydroxylase 3
  • EDS6 3
  • LH 3

External Ids for PLOD1 Gene

Previous HGNC Symbols for PLOD1 Gene

  • LLH
  • PLOD

Previous GeneCards Identifiers for PLOD1 Gene

  • GC01P011930
  • GC01P011994
  • GC01P011149

Summaries for PLOD1 Gene

Entrez Gene Summary for PLOD1 Gene

  • Lysyl hydroxylase is a membrane-bound homodimeric protein localized to the cisternae of the 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 VI have deficiencies in lysyl hydroxylase activity. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

GeneCards Summary for PLOD1 Gene

PLOD1 (Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 1) is a Protein Coding gene. Diseases associated with PLOD1 include Ehlers-Danlos Syndrome, Type Vi and Ehlers-Danlos Syndrome, Kyphoscoliotic Form. Among its related pathways are Collagen biosynthesis and modifying enzymes and Lysine degradation. GO annotations related to this gene include protein homodimerization activity and iron ion binding. An important paralog of this gene is PLOD3.

UniProtKB/Swiss-Prot for PLOD1 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.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLOD1 Gene

Genomics for PLOD1 Gene

Regulatory Elements for PLOD1 Gene

Enhancers for PLOD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F011885 0.5 VISTA 23.6 -46.8 -46753 4.0 BCOR CTCF USF1 CBX3 ZMYM3 NFXL1 ZNF316 GLIS2 ZNF766 ZBTB48 PLOD1 MFN2 MIIP NPPB KIAA2013 NPPA-AS1 LOC390997 RNU5E-1
GH01F011952 0.2 ENCODE 19 +18.7 18674 0.2 ZNF121 EMSY PLOD1 MFN2
GH01F011879 1.7 VISTA FANTOM5 Ensembl ENCODE 18.3 -52.2 -52195 4.1 HDGF PKNOX1 ZFP64 ARID4B YY1 KLF13 SP5 REST MEF2D SMARCA4 PLOD1 KIAA2013 NPPB RNU5E-1 RNU5E-4P NPPA-AS1 LOC102724659 C1orf167 LOC390997 ENSG00000226849
GH01F011989 0.8 FANTOM5 ENCODE 11.4 +56.3 56305 2.2 BCOR CTCF SAP130 KLF17 ZIC2 TEAD3 YY1 ZNF316 GATA3 EED MFN2 MIIP PLOD1 KIAA2013 RNU5E-1 RNU5E-4P NPPB NPPA ENSG00000270914
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PLOD1 on UCSC Golden Path with GeneCards custom track

Promoters for PLOD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000074809 695 1801 CREB3L1 MLX ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF143 SP3 SP5

Genomic Location for PLOD1 Gene

11,934,205 bp from pter
11,975,542 bp from pter
41,338 bases
Plus strand

Genomic View for PLOD1 Gene

Genes around PLOD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLOD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLOD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLOD1 Gene

Proteins for PLOD1 Gene

  • Protein details for PLOD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
    Protein Accession:
    Secondary Accessions:
    • B4DR87
    • Q96AV9
    • Q9H132

    Protein attributes for PLOD1 Gene

    727 amino acids
    Molecular mass:
    83550 Da
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Homodimer.

    Alternative splice isoforms for PLOD1 Gene


neXtProt entry for PLOD1 Gene

Selected DME Specific Peptides for PLOD1 Gene


Post-translational modifications for PLOD1 Gene

  • Glycosylation at Asn 163, Asn 197, Asn 538, and Asn 686
  • Modification sites at PhosphoSitePlus

Other Protein References for PLOD1 Gene

Antibody Products

  • Cloud-Clone Corp. Antibodies for PLOD1
  • Santa Cruz Biotechnology (SCBT) Antibodies for PLOD1

Domains & Families for PLOD1 Gene

Suggested Antigen Peptide Sequences for PLOD1 Gene

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 PLOD1: view

No data available for Gene Families for PLOD1 Gene

Function for PLOD1 Gene

Molecular function for PLOD1 Gene

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 PLOD1 Gene

Gene Ontology (GO) - Molecular Function for PLOD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
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 --
GO:0031418 L-ascorbic acid binding IEA --
genes like me logo Genes that share ontologies with PLOD1: view
genes like me logo Genes that share phenotypes with PLOD1: view

Human Phenotype Ontology for PLOD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PLOD1 Gene

MGI Knock Outs for PLOD1:

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for PLOD1 Gene

Localization for PLOD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLOD1 Gene

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

Subcellular locations from

Jensen Localization Image for PLOD1 Gene COMPARTMENTS Subcellular localization image for PLOD1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
nucleus 2
golgi apparatus 1
lysosome 1
mitochondrion 1
peroxisome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for PLOD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0030867 rough endoplasmic reticulum membrane IEA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PLOD1: view

Pathways & Interactions for PLOD1 Gene

genes like me logo Genes that share pathways with PLOD1: view

Pathways by source for PLOD1 Gene

Gene Ontology (GO) - Biological Process for PLOD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEP 15174142
GO:0006464 cellular protein modification process NAS 1577494
GO:0008544 epidermis development TAS 1577494
GO:0046947 hydroxylysine biosynthetic process TAS 1577494
GO:0055114 oxidation-reduction process TAS 1577494
genes like me logo Genes that share ontologies with PLOD1: view

No data available for SIGNOR curated interactions for PLOD1 Gene

Drugs & Compounds for PLOD1 Gene

(15) Drugs for PLOD1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin C Approved Nutra Target, activator 514,514
Succinic acid Approved Nutra Full agonist, Agonist, Target 0
Carbon dioxide Approved, Vet_approved Pharma 0
Oxygen Approved, Vet_approved Pharma 0
Water Approved Pharma 0

(15) Additional Compounds for PLOD1 Gene - From: Novoseek and HMDB

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
  • 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
genes like me logo Genes that share compounds with PLOD1: view

Transcripts for PLOD1 Gene

Unigene Clusters for PLOD1 Gene

Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLOD1 Gene

No ASD Table

Relevant External Links for PLOD1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PLOD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PLOD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLOD1 Gene

This gene is overexpressed in Bone marrow stromal cell (13.3) and Fetal ovary (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PLOD1 Gene

Protein tissue co-expression partners for PLOD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PLOD1 Gene:


SOURCE GeneReport for Unigene cluster for PLOD1 Gene:

genes like me logo Genes that share expression patterns with PLOD1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PLOD1 Gene

Orthologs for PLOD1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLOD1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PLOD1 34 35
  • 99.04 (n)
(Bos Taurus)
Mammalia PLOD1 34 35
  • 90.72 (n)
(Canis familiaris)
Mammalia PLOD1 34 35
  • 90.53 (n)
(Rattus norvegicus)
Mammalia Plod1 34
  • 86.46 (n)
(Mus musculus)
Mammalia Plod1 34 16 35
  • 86.32 (n)
(Monodelphis domestica)
Mammalia PLOD1 35
  • 85 (a)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 82 (a)
-- 35
  • 76 (a)
(Gallus gallus)
Aves PLOD1 34 35
  • 72.95 (n)
(Anolis carolinensis)
Reptilia PLOD1 35
  • 70 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia plod1 34
  • 66.52 (n)
(Danio rerio)
Actinopterygii plod1a 34 35
  • 66.71 (n)
wufc29c10 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8691 34
fruit fly
(Drosophila melanogaster)
Insecta Plod 35
  • 44 (a)
(Caenorhabditis elegans)
Secernentea let-268 35
  • 43 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 35
  • 49 (a)
Species where no ortholog for PLOD1 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)
  • 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)
  • 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 PLOD1 Gene

Gene Tree for PLOD1 (if available)
Gene Tree for PLOD1 (if available)

Paralogs for PLOD1 Gene

Paralogs for PLOD1 Gene

(3) SIMAP similar genes for PLOD1 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with PLOD1: view

Variants for PLOD1 Gene

Sequence variations from dbSNP and Humsavar for PLOD1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs121913551 Ehlers-Danlos syndrome 6 (EDS6) [MIM:225400], Pathogenic 11,974,656(+) AGGGC(A/G)GGGGC reference, missense
rs121913553 Ehlers-Danlos syndrome 6 (EDS6) [MIM:225400], Pathogenic 11,970,750(+) GAGTG(C/G)CACAA reference, missense
rs199730384 Ehlers-Danlos syndrome 6 (EDS6) [MIM:225400] 11,972,968(+) ACATC(A/G)CCCTG reference, missense
VAR_023466 Ehlers-Danlos syndrome 6 (EDS6) [MIM:225400]
VAR_023468 Ehlers-Danlos syndrome 6 (EDS6) [MIM:225400]

Structural Variations from Database of Genomic Variants (DGV) for PLOD1 Gene

Variant ID Type Subtype PubMed ID
dgv110n54 CNV loss 21841781
dgv111n54 CNV loss 21841781
esv2674148 CNV deletion 23128226
esv2743774 CNV deletion 23290073
esv27905 CNV gain 19812545
nsv1075165 CNV deletion 25765185
nsv1126178 CNV deletion 24896259
nsv545427 CNV loss 21841781
nsv545430 CNV gain 21841781
nsv545433 CNV gain 21841781
nsv545434 CNV gain+loss 21841781
nsv545435 CNV gain 21841781
nsv955252 CNV deletion 24416366

Variation tolerance for PLOD1 Gene

Residual Variation Intolerance Score: 82.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.30; 92.59% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PLOD1 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLOD1 Gene

Disorders for PLOD1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for PLOD1 Gene - From: OMIM, ClinVar, GeneTests, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PLOD1 in MalaCards View complete list of genes associated with diseases


  • Ehlers-Danlos syndrome 6 (EDS6) [MIM:225400]: A connective tissue disorder characterized by generalized joint hypermobility, hyperextensible skin, atrophic cutaneous scars due to tissue fragility, progressive kyphoscoliosis already present at birth, ocular manifestations, arterial rupture, easy bruising, severe neonatal muscle hypotonia and delayed motor development. {ECO:0000269 PubMed:10686424, ECO:0000269 PubMed:15666309, ECO:0000269 PubMed:15854030, ECO:0000269 PubMed:15979919, ECO:0000269 PubMed:8163671, ECO:0000269 PubMed:9617436}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PLOD1

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 PLOD1: view

No data available for Genatlas for PLOD1 Gene

Publications for PLOD1 Gene

  1. Cloning of human lysyl hydroxylase: complete cDNA-derived amino acid sequence and assignment of the gene (PLOD) to chromosome 1p36.3- p36.2. (PMID: 1577494) Hautala T. … Myllylae R. (Genomics 1992) 2 3 4 22 64
  2. Multiple osteoporosis susceptibility genes on chromosome 1p36 in Chinese. (PMID: 19442614) Huang Q.Y. … Kung A.W. (Bone 2009) 3 22 46 64
  3. Association of PLOD1 polymorphisms with bone mineral density in a population-based study of women from the UK. (PMID: 16758144) Tasker P.N. … Albagha O.M. (Osteoporos Int 2006) 3 22 46 64
  4. A novel mutation in the lysyl hydroxylase 1 gene causes decreased lysyl hydroxylase activity in an Ehlers-Danlos VIA patient. (PMID: 15854030) Walker L.C. … Yeowell H.N. (J. Invest. Dermatol. 2005) 3 4 22 64
  5. Mutation analysis of the PLOD1 gene: an efficient multistep approach to the molecular diagnosis of the kyphoscoliotic type of Ehlers-Danlos syndrome (EDS VIA). (PMID: 15979919) Giunta C. … Steinmann B. (Mol. Genet. Metab. 2005) 3 4 22 64

Products for PLOD1 Gene

Sources for PLOD1 Gene

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