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PLOD1 Gene

protein-coding   GIFtS: 66
GCID: GC01P011994

Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 1

(Previous names: procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine...)
(Previous symbols: LLH, PLOD)
  See PLOD1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 11 2     Procollagen-Lysine 1, 2-Oxoglutarate 5-Dioxygenase (Lysine Hydroxylase,
Ehlers-Danlos Syndrome Type VI)1
LLH1 2 3 5     LH2
PLOD1 2 3     Lysine Hydroxylase2
LH12 3 5     Procollagen-Lysine 1, 2-Oxoglutarate 5-Dioxygenase 12
Lysyl Hydroxlase 11 2     Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 12
EC 1.14.11.43 8     Lysyl Hydroxylase 13
EDS62 5     

External Ids:    HGNC: 90811   Entrez Gene: 53512   Ensembl: ENSG000000834447   OMIM: 1534545   UniProtKB: Q028093   

Export aliases for PLOD1 gene to outside databases

Previous GC identifers: GC01P011930 GC01P011149


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. (provided by RefSeq, Jul 2008)

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, kyphoscoliotic form, and ehlers-danlos syndrome kyphoscoliotic type. GO annotations related to this gene include L-ascorbic acid binding and protein homodimerization activity. An important paralog of this gene is COLGALT2.

UniProtKB/Swiss-Prot: PLOD1_HUMAN, Q02809
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




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the PLOD1 gene promoter:
         STAT5B   TBP   Sp1   FOXO1a   GR-alpha   Nkx2-5   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPLOD1 promoter sequence
   Search Chromatin IP Primers for PLOD1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PLOD1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p36.22   Ensembl cytogenetic band:  1p36.22   HGNC cytogenetic band: 1p36.22

PLOD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PLOD1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P011994:  view genomic region     (about GC identifiers)

Start:
11,994,262 bp from pter      End:
12,035,599 bp from pter
Size:
41,338 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: PLOD1_HUMAN, Q02809 (See protein sequence)
Recommended Name: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor  
Size: 727 amino acids; 83550 Da
Cofactor: Iron
Cofactor: Ascorbate
Subunit: Homodimer
Secondary accessions: Q96AV9 Q9H132

Explore the universe of human proteins at neXtProt for PLOD1: NX_Q02809

Explore proteomics data for PLOD1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn163, Asn197, Asn538, Asn686
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for PLOD1 (Q02809) (see all 25)
     FVVRYKP  AYDTLPV  DWKEKYI  EDLVILF 


    See PLOD1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000293.2  
    ENSEMBL proteins: 
     ENSP00000414443   ENSP00000405372   ENSP00000196061   ENSP00000365548  
    Reactome Protein details: Q02809

    PLOD1 Human Recombinant Protein Products:

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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PLOD1

     
    Search eBioscience for Proteins for PLOD1 

     
    antibodies-online proteins for PLOD1 (5 products) 

     
    antibodies-online peptides for PLOD1

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    antibodies-online antibodies for PLOD1 (11 products) 

    PLOD1 Assay Products:

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    antibodies-online kits for PLOD1 (23 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR006620 Pro_4_hyd_alph
     IPR001006 Procol_lys_dOase
     IPR005123 Oxoglu/Fe-dep_dioxygenase

    Graphical View of Domain Structure for InterPro Entry Q02809

    ProtoNet protein and cluster: Q02809

    2 Blocks protein domains:
    IPB001006 Procollagen-lysine 5-dioxygenase
    IPB006620 Prolyl 4-hydroxylase


    UniProtKB/Swiss-Prot: PLOD1_HUMAN, Q02809
    Similarity: Contains 1 Fe2OG dioxygenase domain


    Find genes that share domains with PLOD1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PLOD1_HUMAN, Q02809
    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
    Catalytic activity: L-lysine-[procollagen] + 2-oxoglutarate + O(2) = (2S,5R)-5-hydroxy-L-lysine-[procollagen] +
    succinate + CO(2)

         Enzyme Number (IUBMB): EC 1.14.11.41 2

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005506iron ion binding IEA--
    GO:0008475procollagen-lysine 5-dioxygenase activity IEA--
    GO:0016491oxidoreductase activity ----
    GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ----
    GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors ----
         
    Find genes that share ontologies with PLOD1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for PLOD1:
     Increased gamma-H2AX phosphory 

         6 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Plod1):
     behavior/neurological  cardiovascular system  integument  mortality/aging  muscle 
     no phenotypic analysis 

    Find genes that share phenotypes with PLOD1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Plod1tm1Soin for PLOD1

       genOway: Develop your customized and physiologically relevant rodent model for PLOD1

    miRNA
    Products:
        
    miRTarBase miRNAs that target PLOD1:
    hsa-mir-215-5p (MIRT024504), hsa-mir-149-5p (MIRT045528), hsa-mir-484 (MIRT041701), hsa-mir-124-3p (MIRT022239), hsa-mir-23b-3p (MIRT046301), hsa-let-7a-5p (MIRT052618), hsa-mir-192-5p (MIRT026202)

    Block miRNA regulation of human, mouse, rat PLOD1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PLOD1 (see all 10):
    hsa-miR-140-5p hsa-miR-34c-5p hsa-miR-449b hsa-miR-449a hsa-miR-323b-5p hsa-miR-3922-3p hsa-miR-633 hsa-miR-34a
    SwitchGear 3'UTR luciferase reporter plasmidPLOD1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for PLOD1
    Predesigned siRNA for gene silencing in human, mouse, rat PLOD1

    Gene Editing
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    OriGene ORF clones in mouse, rat for PLOD1
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    GenScript: all cDNA clones in your preferred vector: PLOD1 (NM_000302)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PLOD1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PLOD1

    Cell Line
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PLOD1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PLOD1_HUMAN, Q02809: Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum5
    extracellular2
    golgi apparatus1
    lysosome1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005581collagen ----
    GO:0005783endoplasmic reticulum ----
    GO:0005789endoplasmic reticulum membrane TAS--
    GO:0030867rough endoplasmic reticulum membrane IEA--
    GO:0070062extracellular vesicular exosome IDA19056867

    Find genes that share ontologies with PLOD1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for PLOD1 About    
    See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.75
    Collagen formation0.75
    2Degradation of the extracellular matrix
    Extracellular matrix organization0.34
    3Lysine degradation
    Lysine degradation


    Find genes that share SuperPaths with PLOD1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for PLOD1
        Collagen biosynthesis and modifying enzymes


    1 Kegg Pathway  (Kegg details for PLOD1):
        Lysine degradation

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PLOD1
    Interactions:

        GeneGlobe Interaction Network for PLOD1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for PLOD1 (Q028092, 3 ENSP000001960614) via UniProtKB, MINT, STRING, and/or I2D (see all 111)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MAP3K3Q997592, 3MINT-48443 I2D: score=2 
    PDIA3P301012, 3MINT-4301261 I2D: score=1 
    H2AFXP161043, ENSP000003643104I2D: score=2 STRING: ENSP00000364310
    TERF1P542743, ENSP000002766034I2D: score=1 STRING: ENSP00000276603
    TERF2Q155543, ENSP000002549424I2D: score=1 STRING: ENSP00000254942
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001666response to hypoxia IEP15174142
    GO:0006464cellular protein modification process NAS1577494
    GO:0008544epidermis development TAS1577494
    GO:0030198extracellular matrix organization TAS--
    GO:0046947hydroxylysine biosynthetic process TAS1577494

    Find genes that share ontologies with PLOD1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PLOD1

    9 HMDB Compounds for PLOD1    About this table
    CompoundSynonyms CAS #PubMed Ids
    Ascorbic acid(+)-ascorbate (see all 140)50-81-76325436
    5-Hydroxylysine(2S,5R)-2,6-diamino-5-hydroxyhexanoic acid (see all 21)1190-94-9--
    Carbon dioxideCarbon oxide (see all 5)124-38-9--
    IronArmco iron (see all 19)7439-89-6--
    L-Lysine(+)-S-Lysine (see all 25)56-87-1--
    Oxoglutaric acid2-Ketoglutarate (see all 9)328-50-7--
    OxygenOxygen (see all 5)7782-44-7--
    Succinic acid1,2-Ethanedicarboxylate (see all 11)110-15-6--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    2 DrugBank Compounds for PLOD1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Vitamin CAscorbate (see all 6)50-81-7targetactivator11752352 17100196
    Succinic acid1,2-Ethanedicarboxylic acid (see all 8)110-15-6target--17610258

    Selected Novoseek inferred chemical compound relationships for PLOD1 gene (see all 22)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hydroxylysine 95.1 33 17610258 (2), 1704364 (1), 9617436 (1), 9724729 (1) (see all 20)
    hydroxylysinonorleucine 86.9 4 15589118 (1)
    dhlnl 86.8 3 2301849 (1), 15589118 (1)
    minoxidil 79.1 25 8311472 (5), 15908192 (4), 1309293 (3), 8112995 (3) (see all 8)
    deoxyhypusine 73.5 1 16452303 (1)
    pyridinoline 72.6 5 16758144 (2), 14679583 (1), 15955452 (1), 15908192 (1)
    lysine 71.4 25 1314568 (2), 15908192 (2), 15589118 (2), 1704364 (1) (see all 14)
    alpha-ketoglutarate 70.2 11 17610258 (3), 9738467 (2), 15480877 (1), 8592059 (1) (see all 5)
    procollagen 62.8 1 8112995 (1)
    deoxypyridinoline 55.9 2 16758144 (2)



    Find genes that share compounds with PLOD1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PLOD1 gene: 
    NM_000302.3  

    Unigene Cluster for PLOD1:

    Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1
    Hs.75093  [show with all ESTs]
    Unigene Representative Sequence: NM_000302
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000485046 ENST00000449038 ENST00000358133 ENST00000429000 ENST00000196061(uc001atm.3 uc010obb.2)
    ENST00000465920 ENST00000491536 ENST00000470133 ENST00000481933 ENST00000376369

    miRNA
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    hsa-miR-140-5p hsa-miR-34c-5p hsa-miR-449b hsa-miR-449a hsa-miR-323b-5p hsa-miR-3922-3p hsa-miR-633 hsa-miR-34a
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      QuantiTect SYBR Green Assays in human, mouse, rat PLOD1
      QuantiFast Probe-based Assays in human, mouse, rat PLOD1

    Additional mRNA sequence: 

    AK294688.1 AK295254.1 AK299150.1 AK312243.1 AK316285.1 BC016657.2 M98252.1 

    24 DOTS entries:

    DT.95305653  DT.95305664  DT.453446  DT.100838133  DT.100838139  DT.100838127  DT.102833086  DT.121453393 
    DT.100838125  DT.102833089  DT.102833090  DT.100765825  DT.100838121  DT.100838123  DT.95228734  DT.121453334 
    DT.121453349  DT.121453375  DT.121453376  DT.91792222  DT.91917019  DT.91957826  DT.92388979  DT.91719554 

    Selected AceView cDNA sequences (see all 553):

    BF195173 BU616887 CB529653 CA454729 AK124035 AI658630 AU076468 CA425349 
    BQ891616 CD671728 AL134886 AA827564 BG056841 AI669714 CD672601 BQ182542 
    CB150060 CA952566 BQ024318 AL572625 F09209 AW166339 BE904953 BQ447373 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PLOD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGAGCAAACC
    PLOD1 Expression
    About this image


    PLOD1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 10) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Myelinating Oligodendrocyte Cells Forebrain White Matter
             Thalamus
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Osteochondro Mesenchymal Cells Vertebrae
             Membranous Facial Bones
     
     Cartilage (Muscoskeletal System)    fully expand to see all 2 entries
             Osteochondro Mesenchymal Cells Vertebrae
             Intervertebral Disc
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Metencephalon
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
    PLOD1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PLOD1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.75093
        Custom PCR Arrays for PLOD1
    Primer
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    OriGene qPCR primer pairs and template standards for PLOD1
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    QuantiFast Probe-based Assays in human, mouse, rat PLOD1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PLOD1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for PLOD1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Plod11 , 5 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 11, 5 86.32(n)1
    91.96(a)1
      4 (78.57 cM)5
    188221  NM_011122.31  NP_035252.11 
     1479097535 
    chicken
    (Gallus gallus)
    Aves PLOD11 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 72.95(n)
    77.9(a)
      419485  NM_001005618.1  NP_001005618.1 
    lizard
    (Anolis carolinensis)
    Reptilia PLOD16
    procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1...
    70(a)
    1 ↔ 1
    GL345002.1(1765-10699)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia plod11 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 66.52(n)
    72.23(a)
      779793  NM_001078872.1  NP_001072340.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufc29c102 Transcribed sequence with moderate similarity to protein more 77.63(n)    CK236154.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Plod6
    procollagen lysyl hydroxylase
    44(a)
    1 → many
    3L(11191266-11199116)
    worm
    (Caenorhabditis elegans)
    Secernentea let-2686
    Protein LET-268 (let-268) mRNA, complete cds
    43(a)
    1 → many
    II(10033307-10039940) WBGene00002497


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PLOD1 gene
    COLGALT22  COLGALT12  PLOD22  PLOD32  CERCAM2  
    3 SIMAP similar genes for PLOD1 using alignment to 5 protein entries:     PLOD1_HUMAN (see all proteins):
    DKFZp564O1822    PLOD2    PLOD3

    Find genes that share paralogs with PLOD1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PLOD1 (see all 1219)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1997303841,2,,4
    Ehlers-Danlos syndrome 6 (EDS6)4 --12051298(+) ACATCA/GCCCTG 2 T A mis10--------
    VAR_0354794
    A breast cancer sample4--see VAR_0354792 Q H mis40--------
    VAR_0234664
    Ehlers-Danlos syndrome 6 (EDS6)4--see VAR_0234662 W G mis40--------
    VAR_0063564
    Ehlers-Danlos syndrome 6 (EDS6)4--see VAR_0063562 G R mis40--------
    VAR_0063554
    Ehlers-Danlos syndrome 6 (EDS6)4--see VAR_0063552 W C mis40--------
    VAR_0234684
    Ehlers-Danlos syndrome 6 (EDS6)4--see VAR_0234682 H R mis40--------
    rs1219135521,2
    Cpathogenic112043862(+) AGCTAC/GCGCAC 2 Y * stg10--------
    rs1219135541,2
    Cpathogenic112051307(+) TGAACC/TGAGTC 2 R * stg10--------
    rs351252621,2
    C--11993167(+) TTTTC-/TTTTTT 1 -- us2k11Minor allele frequency- T:0.00CSA 2
    rs1135321871,2
    C,F--11993853(+) GGAGGC/TGGAGG 1 -- us2k12Minor allele frequency- T:0.50WA CSA 4

    HapMap Linkage Disequilibrium report for PLOD1 (11994262 - 12035599 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for PLOD1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2674148CNV Deletion23128226
    esv2743774CNV Deletion23290073
    nsv870926CNV Loss21882294
    dgv142n71CNV Loss21882294
    nsv870723CNV Loss21882294
    esv27905CNV Gain19812545

    Human Gene Mutation Database (HGMD): PLOD1
    Locus Specific Mutation Databases (LSDB): PLOD1

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PLOD1
    DNA2.0 Custom Variant and Variant Library Synthesis for PLOD1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 153454   
    OMIM disorders: 225400  
    UniProtKB/Swiss-Prot: PLOD1_HUMAN, Q02809
  • 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. Note=The disease is caused by mutations affecting the gene
    represented in this entry

  • 8 diseases for PLOD1:    
    About MalaCards
    ehlers-danlos syndrome, kyphoscoliotic form    ehlers-danlos syndrome kyphoscoliotic type    nevo syndrome    ehlers-danlos syndrome type via
    type vi ehlers-danlos syndrome    ehlers-danlos syndrome    congenital contractures    alzheimer's disease

    1 disease from the University of Copenhagen DISEASES database for PLOD1:
    Ehlers-Danlos syndrome

    Find genes that share disorders with PLOD1           About GenesLikeMe

    7 Novoseek inferred disease relationships for PLOD1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    eds vi 98.1 89 7646078 (5), 9344473 (5), 15979919 (3), 9220536 (2) (see all 23)
    ehlers-danlos syndrome 86.3 11 15979919 (2), 8449506 (2), 9724729 (1), 8981946 (1) (see all 8)
    heritable connective tissue disorder 78.9 2 9724729 (1), 9502428 (1)
    connective tissue diseases 72.2 6 15979919 (1), 1345174 (1), 7646078 (1), 8981946 (1) (see all 5)
    osteoporosis 22.4 2 16758144 (1)
    tumors 2.05 3 14565595 (1), 15480877 (1)
    necrosis 0 3 14565595 (1), 15480877 (1)

    GeneTests: PLOD1
    GeneReviews: PLOD1
    Genetic Association Database (GAD): PLOD1
    Human Genome Epidemiology (HuGE) Navigator: PLOD1 (5 documents)

    Export disorders for PLOD1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PLOD1 gene, integrated from 10 sources (see all 149):
    (articles sorted by number of sources associating them with PLOD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning of human lysyl hydroxylase: complete cDNA-derived amino acid sequence and assignment of the gene (PLOD) to chromosome 1p36.3- p36.2. (PubMed id 1577494)1, 2, 3, 9 Hautala T....Myllylae R. (Genomics 1992)
    2. Association of PLOD1 polymorphisms with bone mineral density in a population-based study of women from the UK. (PubMed id 16758144)1, 4, 9 Tasker P.N....Albagha O.M. (Osteoporos Int 2006)
    3. A novel mutation in the lysyl hydroxylase 1 gene causes decreased lysyl hydroxylase activity in an Ehlers-Danlos VIA patient. (PubMed id 15854030)1, 2, 9 Walker L.C.... Yeowell H.N. (J. Invest. Dermatol. 2005)
    4. Association analysis of bone mineral density and single nucleotide polymorphisms in two candidate genes on chromosome 1p36. (PubMed id 14565595)1, 4, 9 Spotila L.D....Devoto M. (Calcif. Tissue Int. 2003)
    5. Ehlers-Danlos syndrome type VI: lysyl hydroxylase deficiency due to a novel point mutation (W612C). (PubMed id 9617436)1, 2, 9 Brinckmann J.... Kugler S. (Arch. Dermatol. Res. 1998)
    6. Deletion of cysteine 369 in lysyl hydroxylase 1 eliminates enzyme activity and causes Ehlers-Danlos syndrome type VI. (PubMed id 10686424)1, 2, 9 Yeowell H.N....Thai S.F. (Matrix Biol. 2000)
    7. Structure and expression of the human lysyl hydroxylase gene (PLOD): introns 9 and 16 contain Alu sequences at the sites of recombination in Ehlers-Danlos syndrome type VI patients. (PubMed id 7713497)1, 2, 9 Heikkinen J.... Myllylae R. (Genomics 1994)
    8. A patient with Ehlers-Danlos syndrome type VI is a compound heterozygote for mutations in the lysyl hydroxylase gene. (PubMed id 8163671)1, 2, 9 Ha V.T.... Yeowell H.N. (J. Clin. Invest. 1994)
    9. Mutation analysis of the PLOD1 gene: an efficient multistep approach to the molecular diagnosis of the kyphoscoliotic type of Ehlers-Danlos syndrome (EDS VIA). (PubMed id 15979919)1, 2, 9 Giunta C.... Steinmann B. (Mol. Genet. Metab. 2005)
    10. Site-directed mutagenesis of human lysyl hydroxylase expressed in insect cells. Identification of histidine residues and an aspartic acid residue critical for catalytic activity. (PubMed id 8621606)1, 2, 9 Pirskanen A.... Kivirikko K.I. (J. Biol. Chem. 1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5351 HGNC: 9081 AceView: PLOD Ensembl:ENSG00000083444 euGenes: HUgn5351
    ECgene: PLOD1 Kegg: 5351 H-InvDB: PLOD1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PLOD1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for PLOD1 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=PLOD1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PLOD1 gene:
    Search GeneIP for patents involving PLOD1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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