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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 1.14.11.4 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 Lysine degradation and Collagen biosynthesis and modifying enzymes. 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
- Elite enhancer/Elite enhancer-gene association

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

ENSRs around PLOD1 on UCSC Golden Path with GeneCards custom track

Genomic Location for PLOD1 Gene

Chromosome:
1
Start:
11,934,205 bp from pter
End:
11,975,542 bp from pter
Size:
41,338 bases
Orientation:
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:
    Q02809-PLOD1_HUMAN
    Recommended name:
    Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
    Protein Accession:
    Q02809
    Secondary Accessions:
    • B4DR87
    • Q96AV9
    • Q9H132

    Protein attributes for PLOD1 Gene

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

    Alternative splice isoforms for PLOD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry 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

Domains & Families for PLOD1 Gene

Suggested Antigen Peptide Sequences for PLOD1 Gene

Graphical View of Domain Structure for InterPro Entry

Q02809

UniProtKB/Swiss-Prot:

PLOD1_HUMAN :
  • Contains 1 Fe2OG dioxygenase domain.
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:0008198 ferrous iron binding IEA --
GO:0008475 procollagen-lysine 5-dioxygenase activity TAS --
GO:0031418 L-ascorbic acid binding IEA --
GO:0042277 peptide binding IEA --
GO:0042803 protein homodimerization activity TAS 1577494
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

CRISPR Products

Inhibitory RNA Products

Clone 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

COMPARTMENTS
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:0005789 endoplasmic reticulum membrane TAS --
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:0017185 peptidyl-lysine hydroxylation IEA --
GO:0032870 cellular response to hormone stimulus IEA --
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 488,488
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: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-Hydroxylysine
  • (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
1190-94-9
Fe2+
  • Armco iron
  • Carbonyl iron
  • FE
  • Ferrovac e
  • Hematite
15438-31-0
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
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:

CRISPR Products

Inhibitory RNA Products

Clone 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
PLOD1
ECgene alternative splicing isoforms for
PLOD1

Expression for PLOD1 Gene

mRNA expression in normal human tissues 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:

PLOD1

SOURCE GeneReport for Unigene cluster for PLOD1 Gene:

Hs.75093
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
cow
(Bos Taurus)
Mammalia PLOD1 34
  • 90.72 (n)
  • 92.97 (a)
PLOD1 35
  • 88 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PLOD1 34
  • 90.53 (n)
  • 93.95 (a)
PLOD1 35
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Plod1 34
  • 86.32 (n)
  • 91.96 (a)
Plod1 16
Plod1 35
  • 91 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PLOD1 34
  • 99.04 (n)
  • 99.04 (a)
PLOD1 35
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Plod1 34
  • 86.46 (n)
  • 91.82 (a)
oppossum
(Monodelphis domestica)
Mammalia PLOD1 35
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 82 (a)
OneToMany
-- 35
  • 76 (a)
OneToMany
chicken
(Gallus gallus)
Aves PLOD1 34
  • 72.95 (n)
  • 77.9 (a)
PLOD1 35
  • 76 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLOD1 35
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plod1 34
  • 66.52 (n)
  • 72.23 (a)
zebrafish
(Danio rerio)
Actinopterygii plod1a 34
  • 66.71 (n)
  • 68.56 (a)
wufc29c10 34
plod1a 35
  • 66 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8691 34
fruit fly
(Drosophila melanogaster)
Insecta Plod 35
  • 44 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea let-268 35
  • 43 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 35
  • 49 (a)
OneToMany
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

ENSEMBL:
Gene Tree for PLOD1 (if available)
TreeFam:
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
rs121913553 Ehlers-Danlos syndrome 6 (EDS6) 11,970,750(+) GAGTG(C/G)CACAA reference, missense
rs121913551 Ehlers-Danlos syndrome 6 (EDS6) 11,974,656(+) AGGGC(A/G)GGGGC reference, missense
rs7551175 - 11,949,899(+) TCTTC(A/G)CAGAC reference, missense
VAR_023466 Ehlers-Danlos syndrome 6 (EDS6)
rs199730384 Ehlers-Danlos syndrome 6 (EDS6) 11,972,968(+) ACATC(A/G)CCCTG reference, missense

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)
PLOD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLOD1

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

Disorders for PLOD1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
ehlers-danlos syndrome, type vi
  • eds vi
ehlers-danlos syndrome, kyphoscoliotic form
  • eds, kyphoscoliotic form
ehlers-danlos syndrome type via
  • eds via
ehlers-danlos syndrome
  • cutis hyperelastica
brittle cornea syndrome
  • brittle cornea syndrome 2
- elite association - COSMIC cancer census association via MalaCards
Search PLOD1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PLOD1_HUMAN
  • 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)
PLOD1
Human Genome Epidemiology (HuGE) Navigator
PLOD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PLOD1
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 65
  2. Multiple osteoporosis susceptibility genes on chromosome 1p36 in Chinese. (PMID: 19442614) Huang Q.Y. … Kung A.W. (Bone 2009) 3 22 46 65
  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 65
  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 65
  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 65

Products for PLOD1 Gene

Sources for PLOD1 Gene

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