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GIFtS

PLOD1 Gene

protein-coding   GIFtS: 64
GCID: GC01P011994

procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1

(Previous names: procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine...)
(Previous symbols: LLH, PLOD)
 Explore 29 diseases affiliated with
PLOD1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for PLOD1    

Aliases
for PLOD1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 11 2     LH2
PLOD1 2 3 5     Lysine Hydroxylase2
LH11 2 3     Lysyl Hydroxlase 12
LLH1 2 3     Procollagen-Lysine 1, 2-Oxoglutarate 5-Dioxygenase 12
EC 1.14.11.43 8     Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 12
Procollagen-Lysine 1, 2-Oxoglutarate 5-Dioxygenase (Lysine Hydroxylase,
Ehlers-Danlos Syndrome Type VI)1
     Lysyl Hydroxylase 13
EDS62     

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


Summaries
for PLOD1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for PLOD1:
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)

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




Genomic Views
for PLOD1 gene

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_021937.19  
Regulatory elements:
   SABiosciences 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 plasmid: PLOD1 promoter sequence
   Search SABiosciences Chromatin IP Primers for PLOD1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for PLOD1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
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
Subcellular location: Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side
Secondary accessions: Q96AV9 Q9H132

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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q02809

    • 4/25 DME Specific Peptides for PLOD1 (Q02809) (see all 25)
     FVVRYKP  AYDTLPV  DWKEKYI  EDLVILF 

    PLOD1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_000293.2  
    ENSEMBL proteins: 
     ENSP00000414443   ENSP00000350851   ENSP00000405372   ENSP00000196061   ENSP00000365548  
    Reactome Protein details: Q02809
    Human Recombinant Protein Products: 
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    Uscn Proteins for PLOD1

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005581collagen ----
    GO:0005783endoplasmic reticulum ----
    GO:0005789endoplasmic reticulum membrane TAS--
    GO:0030867rough endoplasmic reticulum membrane IEA--


    PLOD1 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for PLOD1

    Protein Domains /
    Families
    for PLOD1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    PLOD1 for domains           About GeneDecksing

    3 InterPro domains/families:
     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 families:
    IPB001006 Procollagen-lysine 5-dioxygenase
    IPB006620 Prolyl 4-hydroxylase


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


    Function
    for PLOD1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         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
    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

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat PLOD1
    8/10 QIAGEN miScript miRNA 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 plasmid: PLOD1 3' UTR sequence
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PLOD1 (see all 7)
    OriGene shRNA RFP: PLOD1
    OriGene siRNA: PLOD1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PLOD1

    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for PLOD1

    Clone
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    Cell Line
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    In Situ Assay
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    Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005506iron ion binding IEA--
    GO:0008475procollagen-lysine 5-dioxygenase activity IEA--
    GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen IEA--
    GO:0031418L-ascorbic acid binding IEA--
    GO:0042803protein homodimerization activity TAS1577494


    PLOD1 for ontologies           About GeneDecksing


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

    Animal Models:
         Mouse knock-out Plod1tm1Soin for PLOD1
         6 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Plod1):
     behavior/neurological  cardiovascular system  integument  mortality/aging  muscle 
     no phenotypic analysis 

    PLOD1 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for PLOD1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Collagen formation
    		Collagen formation1.00
    		Extracellular matrix organization0.54
    		Collagen biosynthesis and modifying enzymes0.74
    2Lysine degradation
    		Lysine degradation1.00

    Pathway sources
    See GeneCards unified pathways
    Show all pathways


    3        Reactome Pathways for PLOD1
        Extracellular matrix organization
    Collagen biosynthesis and modifying enzymes
    Collagen formation


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


    PLOD1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for PLOD1

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

    5/99 Interacting proteins for PLOD1 (Q028092, 3 ENSP000001960614) via UniProtKB, MINT, STRING, and/or I2D (see all 99)
    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): 5/6 biological process terms (GO ID links to tree view) (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


    PLOD1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for PLOD1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    PLOD1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    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

    10/22 Novoseek 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)

    Search CenterWatch for drugs/clinical trials and news about PLOD1 

    Transcripts
    for PLOD1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    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
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000485046 ENST00000449038 ENST00000358133 ENST00000429000 ENST00000196061(uc001atm.3 uc010obb.2)
    ENST00000465920 ENST00000491536 ENST00000470133 ENST00000496354 ENST00000481933
    ENST00000376369

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    8/10 QIAGEN miScript miRNA 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 plasmid: PLOD1 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PLOD1 (see all 7)
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    Clone
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    Additional cDNA 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 

    24/553 AceView cDNA sequences (see all 553):

    CK904391 CA454111 F05949 CO248614 BG054535 CF125177 AA903123 AI347587 
    CF265123 BQ682575 CA413697 CR610822 CA952781 AL556481 CF121239 AA331148 
    BQ959275 BQ447373 BQ717325 BQ064845 BI767395 CA454729 CD672601 BU172029 

    GeneLoc Exon Structure


    Expression
    for PLOD1 gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PLOD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AGAGCAAACC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    PLOD1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    7 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BoneSacral VertebraeOsteochondro Mesenchymal CellsBone, Cartilage
    CartilageCervical Intervertebral DiscIntervertebral Disc Annulus Fibrosus CellsCartilage
    CartilageCervical Intervertebral DiscIntervertebral Disc Nucleus Pulposus CellsCartilage
    CartilageCervical Intervertebral DiscCartilage
    CartilageLumbar Intervertebral DiscCartilage
    CartilageThoracic Intervertebral DiscCartilage
    SomiteSacral Mesencymal SclerotomeSomite
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See PLOD1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PLOD1

    SOURCE GeneReport for Unigene cluster: Hs.75093
        SABiosciences Custom PCR Arrays for PLOD1
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    In Situ
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    Orthologs
    for PLOD1 gene

    (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)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for PLOD1 gene from 5/20 species (see all 20)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves PLOD11 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1 72.58(n)
    76.98(a)    		   419485  NM_001005618.1  NP_001005618.1 
    lizard
    (Anolis carolinensis)    		 Reptilia PLOD16
    		 --
    		 68(a)
    		 1 ↔ 1
    		 GL345002.1(1765-8202)
    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
    		 Procollagen-lysine,2-oxoglutarate 5-dioxygenase
    		 44(a)
    		 1 → many
    		 II(10033248-10039881)


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

    Paralogs
    for PLOD1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PLOD1 gene
    GLT25D12  GLT25D22  PLOD22  PLOD32  CERCAM2  
    3 SIMAP similar genes for PLOD1 using alignment to 5 protein entries:     PLOD1_HUMAN (see all proteins):
    DKFZp564O1822    PLOD2    PLOD3

    PLOD1 for paralogs           About GeneDecksing



    Genomic Variants
    for PLOD1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/943 NCBI SNPs in PLOD1 are shown (see all 943)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 1 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1219135521,2
    		Cprobable-pathogenic12025599(+) AGCTAC/GCGCAC 2 Y * stg10--------
    rs1219135541,2
    		C,probable-pathogenic12033034(+) TGAACC/TGAGTC 2 R * stg10--------
    rs600790801,2
    		--11992918(+) GTACTA/GGGATT 1 -- us2k10--------
    rs605852461,2
    		F,--11992995(+) CAGACG/TCATAG 1 -- us2k11Minor allele frequency- T:0.11WA 118
    rs1911715121,2
    		--11993001(+) CATAGC/TCTGCT 1 -- us2k10--------
    rs1821638951,2
    		--11993040(+) TCCTTC/TTCTCC 1 -- us2k10--------
    rs351252621,2
    		C--11993167(+) TTTTC-/TTTTTT 1 -- us2k11Minor allele frequency- T:0.00CSA 2
    rs1464736081,2
    		--11993198(+) TCGCTC/TTGTCG 1 -- us2k10--------
    rs1391604451,2
    		--11993214(+) GCTGGA/GGTGCA 1 -- us2k10--------
    rs1489221991,2
    		--11993215(+) CTGGAA/GTGCAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for PLOD1 (11994262 - 12035599 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for PLOD1
         1 Indel: 72932
    Human Gene Mutation Database (HGMD): PLOD1

    Locus Specific Mutation Databases (LSDB): PLOD1

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PLOD1
    DNA2.0 Custom Variant and Variant Library Synthesis for PLOD1

    Disorders / Diseases
    for PLOD1 gene

    (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.)
    About This Section
    PLOD1 for disorders           About GeneDecksing

    OMIM gene information: 153454   
    OMIM disorders: 225400  601451  
    UniProtKB/Swiss-Prot: PLOD1_HUMAN, Q02809
  • Defects in PLOD1 are the cause of Ehlers-Danlos syndrome type 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

    20/29 diseases for PLOD1 (see all 29):    About MalaCards
    ehlers-danlos syndrome    ehlers-danlos syndrome type via    type vi ehlers-danlos syndrome    open-angle glaucoma
    dandy-walker malformation    primary open angle glaucoma    connective tissue disease    nevo syndrome
    bruck syndrome    congenital contractures    retinal detachment    glaucoma
    osteoporosis    amenorrhea    diabetes mellitus    myopia
    hypotonia    meningitis    choriocarcinoma    homocysteine

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

    7 Novoseek 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
    Ehlers-Danlos Syndrome, Kyphoscoliotic Form

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

    Export disorders for PLOD1 gene to outside databases

    Publications
    for PLOD1 gene

    (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)
    About This Section

    PubMed articles for PLOD1 gene, integrated from 9 sources (see all 146):
    (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. (1992)
    2. 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. (2005)
    3. 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. (2003)
    4. 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. (1998)
    5. 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. (2000)
    6. 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. (1994)
    7. 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. (1994)
    8. 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. (2005)
    9. 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. (1996)
    10. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)

    External Searches for PLOD1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing PLOD1 gene

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

    Other Databases showing PLOD1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing PLOD1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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/sites/GeneTests/lab/gene/PLOD1

    Intellectual Property
    for PLOD1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		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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    About This Section

     
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