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Aliases for PLOD2 Gene

Aliases for PLOD2 Gene

  • Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 2 2 3 5
  • Procollagen-Lysine 5-Dioxygenase 2 3
  • Lysyl Hydroxylase 2 3 4
  • Lysyl Hydroxlase 2 2 3
  • EC 4 56
  • LH2 3 4
  • Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase (Lysine Hydroxylase) 2 2
  • Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 2 2
  • Telopeptide Lysyl Hydroxylase 3
  • Lysine Hydroxylase 2 3
  • BRKS2 3
  • TLH 3

External Ids for PLOD2 Gene

Previous GeneCards Identifiers for PLOD2 Gene

  • GC03M142579
  • GC03M146646
  • GC03M147068
  • GC03M147109
  • GC03M147110
  • GC03M147269
  • GC03M145787
  • GC03M143165

Summaries for PLOD2 Gene

Entrez Gene Summary for PLOD2 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. Mutations in the coding region of this gene are associated with Bruck syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for PLOD2 Gene

PLOD2 (Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 2) is a Protein Coding gene. Diseases associated with PLOD2 include Bruck Syndrome 2 and Bruck Syndrome. Among its related pathways are Collagen chain trimerization and Lysine degradation. 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 PLOD1.

UniProtKB/Swiss-Prot for PLOD2 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.

Additional gene information for PLOD2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLOD2 Gene

Genomics for PLOD2 Gene

GeneHancer (GH) Regulatory Elements for PLOD2 Gene

Promoters and enhancers for PLOD2 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
GH03I146151 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 574.7 +4.1 4055 15.9 FOXA2 MLX ARNT ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ZBTB7B YY1 PLOD2 LNCSRLR PLSCR4 ENSG00000243415 ENSG00000261051 GC03M146166 LOC105374145 GC03P146077
GH03I146125 Enhancer 1.1 Ensembl ENCODE dbSUPER 31.5 +37.6 37570 1.4 GATAD2A FOXA2 JUN CEBPB REST CEBPG EP300 RFX5 SP1 JUND PLOD2 LNCSRLR ENSG00000243415 PLSCR5 ENSG00000261051 GC03P146077
GH03I146115 Enhancer 1.1 ENCODE dbSUPER 31.2 +47.9 47914 1.2 PKNOX1 CLOCK FOXA2 MLX ARID4B DMAP1 YY1 RXRA REST PPARG LNCSRLR PLOD2 ENSG00000243415 PLSCR4 GC03P146077
GH03I146130 Enhancer 0.9 Ensembl ENCODE dbSUPER 31.5 +31.9 31876 2.3 RFX1 REST FOSL2 FOS PLOD2 ENSG00000261051 LNCSRLR ENSG00000243415 GC03P146077
GH03I146142 Enhancer 0.7 ENCODE dbSUPER 31.7 +20.4 20436 1.7 MAFF BACH1 PRDM10 MAFK YY1 ZBTB17 PLOD2 LNCSRLR ENSG00000243415 PLSCR4 GC03P146077
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PLOD2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PLOD2 gene promoter:

Genomic Locations for PLOD2 Gene

Genomic Locations for PLOD2 Gene
94,218 bases
Minus strand

Genomic View for PLOD2 Gene

Genes around PLOD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLOD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLOD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLOD2 Gene

Proteins for PLOD2 Gene

  • Protein details for PLOD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
    Protein Accession:
    Secondary Accessions:
    • B3KWS3
    • Q59ED2
    • Q8N170

    Protein attributes for PLOD2 Gene

    737 amino acids
    Molecular mass:
    84686 Da
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Homodimer.
    • Sequence=BAD93116.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for PLOD2 Gene


neXtProt entry for PLOD2 Gene

Selected DME Specific Peptides for PLOD2 Gene


Post-translational modifications for PLOD2 Gene

  • Ubiquitination at isoforms=2344
  • Glycosylation at isoforms=263, isoforms=2209, Asn297, Asn365, isoforms=2, 3522, isoforms=2, 3696, and isoforms=2, 3725

Domains & Families for PLOD2 Gene

Gene Families for PLOD2 Gene

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

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PLOD2: view

No data available for UniProtKB/Swiss-Prot for PLOD2 Gene

Function for PLOD2 Gene

Molecular function for PLOD2 Gene

GENATLAS Biochemistry:
procollagen-lysine,2-oxoglutarate 5 dioxygenase 2
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 PLOD2 Gene

Phenotypes From GWAS Catalog for PLOD2 Gene

Gene Ontology (GO) - Molecular Function for PLOD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005506 iron ion binding IEA --
GO:0008475 procollagen-lysine 5-dioxygenase activity TAS,IEA --
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 PLOD2: view
genes like me logo Genes that share phenotypes with PLOD2: view

Human Phenotype Ontology for PLOD2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Clone Products

  • Addgene plasmids for PLOD2

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PLOD2 Gene

Localization for PLOD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLOD2 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 PLOD2 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nucleoli (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PLOD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum TAS,IEA 9054364
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0030867 rough endoplasmic reticulum membrane IEA --
GO:0070062 extracellular exosome HDA,IDA 19199708
genes like me logo Genes that share ontologies with PLOD2: view

Pathways & Interactions for PLOD2 Gene

genes like me logo Genes that share pathways with PLOD2: view

Pathways by source for PLOD2 Gene

Gene Ontology (GO) - Biological Process for PLOD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEP 15174142
GO:0006464 cellular protein modification process TAS 9054364
GO:0006493 NOT protein O-linked glycosylation IDA 10934207
GO:0017185 peptidyl-lysine hydroxylation ISS 9582318
GO:0046947 hydroxylysine biosynthetic process ISS 9582318
genes like me logo Genes that share ontologies with PLOD2: view

No data available for SIGNOR curated interactions for PLOD2 Gene

Drugs & Compounds for PLOD2 Gene

(7) Drugs for PLOD2 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
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
L-Lysine Approved Nutra Full agonist, Agonist 0

(5) Additional Compounds for PLOD2 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 PLOD2: view

Transcripts for PLOD2 Gene

Unigene Clusters for PLOD2 Gene

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

Clone Products

  • Addgene plasmids for PLOD2

Alternative Splicing Database (ASD) splice patterns (SP) for PLOD2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1: -
SP2: - -

Relevant External Links for PLOD2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PLOD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PLOD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLOD2 Gene

This gene is overexpressed in Bone marrow stromal cell (32.4), Amniocyte (10.9), and Islet of Langerhans (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PLOD2 Gene

Protein tissue co-expression partners for PLOD2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PLOD2 Gene:


SOURCE GeneReport for Unigene cluster for PLOD2 Gene:


mRNA Expression by UniProt/SwissProt for PLOD2 Gene:

Tissue specificity: Highly expressed in pancreas and muscle. Isoform 1 and isoform 2 are expressed in the majority of the examined cell types. Isoform 2 is specifically expressed in skin, lung, dura and aorta.

Evidence on tissue expression from TISSUES for PLOD2 Gene

  • Blood(4.4)
  • Skin(4.4)
  • Kidney(4.3)
  • Liver(4.3)
  • Nervous system(3.6)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PLOD2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • cheek
  • chin
  • eye
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • abdominal wall
  • intestine
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with PLOD2: view

No data available for mRNA differential expression in normal tissues for PLOD2 Gene

Orthologs for PLOD2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLOD2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PLOD2 33 34
  • 99.73 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 94 (a)
-- 34
  • 85 (a)
(Canis familiaris)
Mammalia PLOD2 33 34
  • 93.9 (n)
(Bos Taurus)
Mammalia PLOD2 33 34
  • 93.05 (n)
(Mus musculus)
Mammalia Plod2 16 34 33
  • 87.51 (n)
(Rattus norvegicus)
Mammalia Plod2 33
  • 87.28 (n)
(Monodelphis domestica)
Mammalia PLOD2 34
  • 87 (a)
(Gallus gallus)
Aves PLOD2 33 34
  • 78.94 (n)
(Anolis carolinensis)
Reptilia PLOD2 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia plod2 33
  • 74.78 (n)
(Danio rerio)
Actinopterygii plod2 33 34
  • 68.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6199 35
  • 44 (a)
Plod 34
  • 44 (a)
(Caenorhabditis elegans)
Secernentea let-268 35 34
  • 43 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10744 34
  • 49 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.15539 33
Species where no ortholog for PLOD2 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)
  • 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 PLOD2 Gene

Gene Tree for PLOD2 (if available)
Gene Tree for PLOD2 (if available)

Paralogs for PLOD2 Gene

Paralogs for PLOD2 Gene

(3) SIMAP similar genes for PLOD2 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with PLOD2: view

Variants for PLOD2 Gene

Sequence variations from dbSNP and Humsavar for PLOD2 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1055144167 uncertain-significance, Bruck Syndrome 146,161,070(-) G/A 5_prime_UTR_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, upstream_transcript_variant
rs121434459 pathogenic, Bruck syndrome 2, Bruck syndrome 2 (BRKS2) [MIM:609220] 146,071,386(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs121434460 pathogenic, Bruck syndrome 2, Bruck syndrome 2 (BRKS2) [MIM:609220] 146,071,407(-) C/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs121434461 pathogenic, Bruck syndrome 2, Bruck syndrome 2 (BRKS2) [MIM:609220] 146,071,416(-) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs13079521 likely-benign, Bruck Syndrome 146,070,546(-) A/C 3_prime_UTR_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PLOD2 Gene

Variant ID Type Subtype PubMed ID
nsv1011146 CNV loss 25217958
nsv4046 CNV deletion 18451855
nsv525829 CNV loss 19592680

Variation tolerance for PLOD2 Gene

Residual Variation Intolerance Score: 38% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.55; 44.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLOD2 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 PLOD2 Gene

Disorders for PLOD2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PLOD2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bruck syndrome 2
  • brks2
bruck syndrome
  • osteogenesis imperfecta with congenital joint contractures
ehlers-danlos syndrome, kyphoscoliotic type, 1
  • ehlers-danlos syndrome, type vi; eds6
systemic scleroderma
  • scleroderma, familial progressive
arteriovenous malformation
  • arteriovenous hemangioma
- elite association - COSMIC cancer census association via MalaCards
Search PLOD2 in MalaCards View complete list of genes associated with diseases


  • Bruck syndrome 2 (BRKS2) [MIM:609220]: An autosomal recessive disease characterized by generalized osteopenia, congenital joint contractures, fragile bones with onset of fractures in infancy or early childhood, short stature, severe limb deformity, progressive scoliosis, and pterygia. It is distinguished from osteogenesis imperfecta by the absence of hearing loss and dentinogenesis imperfecta, and by the presence of clubfoot and congenital joint limitations. {ECO:0000269 PubMed:12881513, ECO:0000269 PubMed:15523624}. Note=The disease is caused by mutations affecting the gene represented in this entry. The molecular defect leading to Bruck syndrome is an aberrant cross-linking of bone collagen, due to underhydroxylation of lysine residues within the telopeptides of type I collagen, whereas the lysine residues in the triple helix are normal.
  • Note=PLOD2 mutations give rise to a broad variety of phenotypes with variable degrees of severity of bone fragility and joint contractures. Disease-associated mutations have been found in patients with autosomal recessive osteogenesis imperfecta (AR-OI) (PubMed:22689593). {ECO:0000269 PubMed:22689593}.

Additional Disease Information for PLOD2

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 PLOD2: view

No data available for Genatlas for PLOD2 Gene

Publications for PLOD2 Gene

  1. Cloning and characterization of a novel human lysyl hydroxylase isoform highly expressed in pancreas and muscle. (PMID: 9054364) Valtavaara M … Myllylä R (The Journal of biological chemistry 1997) 2 3 4 22 58
  2. Phenotypic and molecular characterization of Bruck syndrome (osteogenesis imperfecta with contractures of the large joints) caused by a recessive mutation in PLOD2. (PMID: 15523624) Ha-Vinh R … Bonafé L (American journal of medical genetics. Part A 2004) 3 4 22 58
  3. Identification of PLOD2 as telopeptide lysyl hydroxylase, an important enzyme in fibrosis. (PMID: 12881513) van der Slot AJ … Bank RA (The Journal of biological chemistry 2003) 3 4 22 58
  4. Tissue specificity of a new splice form of the human lysyl hydroxylase 2 gene. (PMID: 10372558) Yeowell HN … Walker LC (Matrix biology : journal of the International Society for Matrix Biology 1999) 3 4 22 58
  5. Mutations in PLOD2 cause autosomal-recessive connective tissue disorders within the Bruck syndrome--osteogenesis imperfecta phenotypic spectrum. (PMID: 22689593) Puig-Hervás MT … Ruiz-Perez VL (Human mutation 2012) 3 4 58

Products for PLOD2 Gene

  • Addgene plasmids for PLOD2

Sources for PLOD2 Gene

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