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 stabili... See more...

Aliases for PLOD3 Gene

Aliases for PLOD3 Gene

  • Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 3 2 3 5
  • Multifunctional Procollagen Lysine Hydroxylase And Glycosyltransferase LH3 3 4
  • Lysyl Hydroxlase 3 2 3
  • LH3 2 3
  • Lysine Hydroxylase 3 3
  • Lysyl Hydroxylase 3 3
  • EC 1.14.11.4 50
  • PLOD3 5

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 Ehlers-Danlos Syndrome. Among its related pathways are Degradation of the extracellular matrix and Collagen chain trimerization. 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 Summary for PLOD3 Gene

  • Multifunctional enzyme that catalyzes a series of essential post-translational modifications on Lys residues in procollagen (PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Plays a redundant role in catalyzing the formation of hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens (PubMed:9582318, PubMed:9724729, PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Plays a redundant role in catalyzing the transfer of galactose onto hydroxylysine groups, giving rise to galactosyl 5-hydroxylysine (PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Has an essential role by catalyzing the subsequent transfer of glucose moieties, giving rise to 1,2-glucosylgalactosyl-5-hydroxylysine residues (PubMed:10934207, PubMed:11896059, PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Catalyzes hydroxylation and glycosylation of Lys residues in the MBL1 collagen-like domain, giving rise to hydroxylysine and 1,2-glucosylgalactosyl-5-hydroxylysine residues (PubMed:25419660). Essential for normal biosynthesis and secretion of type IV collagens (PubMed:18834968) (Probable). Essential for normal formation of basement membranes (By similarity).

Gene Wiki entry for PLOD3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PLOD3 Gene

Genomics for PLOD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PLOD3 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PLOD3

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

Genomic Locations for PLOD3 Gene

Latest Assembly
chr7:101,205,977-101,218,420
(GRCh38/hg38)
Size:
12,444 bases
Orientation:
Minus strand

Previous Assembly
chr7:100,849,265-100,860,862
(GRCh37/hg19 by Entrez Gene)
Size:
11,598 bases
Orientation:
Minus strand

chr7:100,849,258-100,861,701
(GRCh37/hg19 by Ensembl)
Size:
12,444 bases
Orientation:
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:
    O60568-PLOD3_HUMAN
    Recommended name:
    Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
    Protein Accession:
    O60568
    Secondary Accessions:
    • B2R6W6
    • Q540C3

    Protein attributes for PLOD3 Gene

    Size:
    738 amino acids
    Molecular mass:
    84785 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PLOD3 Gene

neXtProt entry for PLOD3 Gene

Selected DME Specific Peptides for PLOD3 Gene

O60568:
  • HPGRLTHYHEGLPTT
  • DYEGGGCRFLRY
  • PCPDVYWFP
  • PHHDSST
  • LWSNFWG
  • GKRFLNSG
  • PTELLKKF
  • RVGVWNVPY
  • PRKGWAL
  • GTRYIMVSF
  • WGLAEQYPEVG
  • HGNGPTKLQ
  • IFQNLNG
  • WNVPYIS

Post-translational modifications for PLOD3 Gene

  • Glycosylation at Asn63 and Asn548
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PLOD3_HUMAN (1635)

Other Protein References for PLOD3 Gene

Antibodies for research

  • Abcam antibodies for PLOD3
  • Boster Bio Antibodies for PLOD3

Domains & Families for PLOD3 Gene

Gene Families for PLOD3 Gene

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

Protein Domains for PLOD3 Gene

InterPro:
Blocks:
  • Procollagen-lysine 5-dioxygenase
  • Prolyl 4-hydroxylase, alpha subunit

Suggested Antigen Peptide Sequences for PLOD3 Gene

GenScript: Design optimal peptide antigens:
  • Lysyl hydroxylase 3 (PLOD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O60568

UniProtKB/Swiss-Prot:

PLOD3_HUMAN :
  • The N-terminal domain mediates glycosyltransferase activity.
Domain:
  • The N-terminal domain mediates glycosyltransferase activity.
  • The C-terminal domain that mediates lysyl hydroxylase activity is also important for homodimerization.
genes like me logo Genes that share domains with PLOD3: view

Function for PLOD3 Gene

Molecular function for PLOD3 Gene

UniProtKB/Swiss-Prot Function:
Multifunctional enzyme that catalyzes a series of essential post-translational modifications on Lys residues in procollagen (PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Plays a redundant role in catalyzing the formation of hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens (PubMed:9582318, PubMed:9724729, PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Plays a redundant role in catalyzing the transfer of galactose onto hydroxylysine groups, giving rise to galactosyl 5-hydroxylysine (PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Has an essential role by catalyzing the subsequent transfer of glucose moieties, giving rise to 1,2-glucosylgalactosyl-5-hydroxylysine residues (PubMed:10934207, PubMed:11896059, PubMed:11956192, PubMed:12475640, PubMed:18298658, PubMed:30089812, PubMed:18834968). Catalyzes hydroxylation and glycosylation of Lys residues in the MBL1 collagen-like domain, giving rise to hydroxylysine and 1,2-glucosylgalactosyl-5-hydroxylysine residues (PubMed:25419660). Essential for normal biosynthesis and secretion of type IV collagens (PubMed:18834968) (Probable). Essential for normal formation of basement membranes (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2-oxoglutarate + L-lysyl-[procollagen] + O2 = (5R)-5-hydroxy-L-lysyl-[procollagen] + CO2 + succinate; Xref=Rhea:RHEA:16569, Rhea:RHEA-COMP:12751, Rhea:RHEA-COMP:12752, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:29969, ChEBI:CHEBI:30031, ChEBI:CHEBI:133442; EC=1.14.11.4; Evidence={ECO:0000269|PubMed:10934207, ECO:0000269|PubMed:11956192, ECO:0000269|PubMed:12475640, ECO:0000269|PubMed:18298658, ECO:0000269|PubMed:18834968, ECO:0000269|PubMed:30089812, ECO:0000269|PubMed:9582318, ECO:0000269|PubMed:9724729};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(5R)-5-hydroxy-L-lysyl-[procollagen] + UDP-alpha-D-galactose = (5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysyl-[procollagen] + H(+) + UDP; Xref=Rhea:RHEA:12637, Rhea:RHEA-COMP:12752, Rhea:RHEA-COMP:12753, ChEBI:CHEBI:15378, ChEBI:CHEBI:58223, ChEBI:CHEBI:66914, ChEBI:CHEBI:133442, ChEBI:CHEBI:133443; EC=2.4.1.50; Evidence={ECO:0000269|PubMed:12475640, ECO:0000269|PubMed:18298658, ECO:0000269|PubMed:18834968, ECO:0000269|PubMed:30089812};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysyl-[procollagen] + UDP-alpha-D-glucose = (5R)-5-O-[alpha-D-glucosyl-(1->2)-beta-D-galactosyl]-5-hydroxy-L-lysyl-[procollagen] + H(+) + UDP; Xref=Rhea:RHEA:12576, Rhea:RHEA-COMP:12753, Rhea:RHEA-COMP:12754, ChEBI:CHEBI:15378, ChEBI:CHEBI:58223, ChEBI:CHEBI:58885, ChEBI:CHEBI:133443, ChEBI:CHEBI:133452; EC=2.4.1.66; Evidence={ECO:0000269|PubMed:10934207, ECO:0000269|PubMed:11896059, ECO:0000269|PubMed:11956192, ECO:0000269|PubMed:12475640, ECO:0000269|PubMed:18298658, ECO:0000269|PubMed:18834968, ECO:0000269|PubMed:30089812};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=35 uM for UDP-galactose {ECO:0000269|PubMed:12475640}; KM=17 uM for UDP-glucose {ECO:0000269|PubMed:12475640}; KM=100 uM for 2-oxoglutarate {ECO:0000269|PubMed:11956192, ECO:0000269|PubMed:9724729}; KM=300 uM for ascorbate {ECO:0000269|PubMed:9724729}; KM=350 uM for ascorbate {ECO:0000269|PubMed:11956192};
UniProtKB/Swiss-Prot EnzymeRegulation:
Lysyl hydroxylase activity is strongly inhibited by imidazole.
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:0003824 catalytic activity IEA --
GO:0005506 iron ion binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0008475 procollagen-lysine 5-dioxygenase activity IBA,IMP 10934207
GO:0016491 oxidoreductase activity 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 Models for research

  • Taconic Biosciences Mouse Models for PLOD3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLOD3

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. Endoplasmic reticulum lumen. Endoplasmic reticulum membrane. Peripheral membrane protein. Lumenal side. Secreted. Secreted, extracellular space. Note=The majority of the secreted protein is associated with the extracellular matrix. {ECO:0000250 UniProtKB:Q9R0E1}.

Subcellular locations from

COMPARTMENTS
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 4
golgi apparatus 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
endosome 1
cytosol 1
lysosome 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for PLOD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space ISS --
GO:0005783 endoplasmic reticulum TAS 9724729
GO:0005788 endoplasmic reticulum lumen IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
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

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:0008152 metabolic process 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

(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 Enzyme, product of 0
Vitamin C Approved Nutra Target, cofactor 836,836
Lysine Approved Nutra 187
Carbon dioxide Approved, Investigational, Vet_approved Pharma 0
Oxygen Approved, Vet_approved Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
5-Hydroxylysine
  • (2S,5R)-5-Hydroxylysine
  • (5R)-5-Hydroxy-L-lysine
  • alpha,epsilon-Diamino-delta-hydroxycaproic acid
  • L-Erythro-5-hydroxylysine
  • L-Normal-5-hydroxylysine
1190-94-9
genes like me logo Genes that share compounds with PLOD3: view

Transcripts for PLOD3 Gene

mRNA/cDNA for PLOD3 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLOD3

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

No ASD Table

Relevant External Links for PLOD3 Gene

GeneLoc Exon Structure for
PLOD3

Expression for PLOD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PLOD3

SOURCE GeneReport for Unigene cluster for PLOD3 Gene:

Hs.153357

mRNA Expression by UniProt/SwissProt for PLOD3 Gene:

O60568-PLOD3_HUMAN
Tissue specificity: Ubiquitous (PubMed:9724729). Detected in heart, placenta and pancreas and at lower levels in lung, liver and skeletal muscle (PubMed:9582318, PubMed:9724729).

Evidence on tissue expression from TISSUES for PLOD3 Gene

  • Nervous system(4.7)
  • Intestine(4.6)
  • Pancreas(4.4)
  • Skin(4)
  • Kidney(3.2)
  • Lung(3.1)
  • Heart(2.1)
  • Liver(2.1)
  • Muscle(2)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • skull
Thorax:
  • chest wall
  • clavicle
  • diaphragm
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • large intestine
  • liver
  • small intestine
  • stomach
Pelvis:
  • pelvis
Limb:
  • 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
General:
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with PLOD3: view

Primer products for research

No data available for mRNA differential expression in normal tissues 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
Chimpanzee
(Pan troglodytes)
Mammalia PLOD3 29 30
  • 99.55 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PLOD3 29 30
  • 89.86 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PLOD3 29 30
  • 89.51 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PLOD3 30
  • 86 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Plod3 29 16 30
  • 85.77 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Plod3 29
  • 85.55 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia PLOD3 30
  • 77 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PLOD3 30
  • 73 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia plod3 29
  • 69.04 (n)
Str.1520 29
African clawed frog
(Xenopus laevis)
Amphibia plod-prov 29
Zebrafish
(Danio rerio)
Actinopterygii wu:fb72h05 29
  • 67.28 (n)
PLOD3 (2 of 2) 30
  • 65 (a)
OneToMany
plod3 30
  • 65 (a)
OneToMany
wufa10a05 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001507 29
  • 57.83 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Plod 29 30
  • 55.14 (n)
OneToMany
CG6199 31
  • 46 (a)
Worm
(Caenorhabditis elegans)
Secernentea let-268 29 30 31
  • 51.63 (n)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.10744 30
  • 50 (a)
OneToMany
Species where no ortholog for PLOD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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

ENSEMBL:
Gene Tree for PLOD3 (if available)
TreeFam:
Gene Tree for PLOD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLOD3: view image
Alliance of Genome Resources:
Additional Orthologs for PLOD3

Paralogs for PLOD3 Gene

Paralogs for PLOD3 Gene

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

  • PLOD3_HUMAN
  • C9JIX5_HUMAN
  • 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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PLOD3 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
1033683 Pathogenic: Bone fragility with contractures, arterial rupture, and deafness 101,215,907(-) C/T
NM_001084.5(PLOD3):c.615+1G>A
SPLICE_DONOR
1033684 Uncertain Significance: Bone fragility with contractures, arterial rupture, and deafness 101,213,184(-) C/T
NM_001084.5(PLOD3):c.700G>A (p.Asp234Asn)
MISSENSE
915354 Uncertain Significance: Bone fragility with contractures, arterial rupture, and deafness 101,208,957(-) G/A
NM_001084.5(PLOD3):c.1684C>T (p.Pro562Ser)
MISSENSE
973081 Not Provided: PLOD3-Related Disorder 101,215,963(-) T/C
NM_001084.5(PLOD3):c.560A>G (p.Asp187Gly)
MISSENSE
rs112321807 Benign: not provided 101,216,773(-) C/T
NM_001084.5(PLOD3):c.123G>A (p.Val41=)
SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PLOD3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)
PLOD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLOD3
Leiden Open Variation Database (LOVD)
PLOD3

SNP Genotyping and Copy Number Assays for research

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

Disorders for PLOD3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for PLOD3 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
bone fragility with contractures, arterial rupture, and deafness
  • lysyl hydroxylase 3 deficiency
ehlers-danlos syndrome
  • cutis hyperelastica
recessive dystrophic epidermolysis bullosa
  • autosomal recessive dystrophic epidermolysis bullosa generalisata gravis
stickler syndrome
  • arthroophthalmopathy
bruck syndrome
  • osteogenesis imperfecta with congenital joint contractures
- elite association - COSMIC cancer census association via MalaCards
Search PLOD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PLOD3_HUMAN
  • 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, ECO:0000269 PubMed:30089812, ECO:0000269 PubMed:30237576}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for PLOD3

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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No data available for Genatlas for PLOD3 Gene

Publications for PLOD3 Gene

  1. 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 72
  2. 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
  3. 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
  4. 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 4 22
  5. The third activity for lysyl hydroxylase 3: galactosylation of hydroxylysyl residues in collagens in vitro. (PMID: 12475640) Wang C … Myllylä R (Matrix biology : journal of the International Society for Matrix Biology 2002) 3 4 22

Products for PLOD3 Gene

Sources for PLOD3 Gene