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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PLOD3 Gene

protein-coding   GIFtS: 68
GCID: GC07M100849

Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 3

  See 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)
About This Section

Aliases
Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 31 2     EC 1.14.11.43 8
Lysyl Hydroxlase 31 2     Lysine Hydroxylase 32
Lysyl Hydroxylase 32 3     Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 32
LH32 3     

External Ids:    HGNC: 90831   Entrez Gene: 89852   Ensembl: ENSG000001063977   OMIM: 6030665   UniProtKB: O605683   

Export aliases for PLOD3 gene to outside databases

Previous GC identifers: GC07M099332 GC07M100395 GC07M100409 GC07M100442 GC07M100635 GC07M095442


(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 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 lysyl hydroxylase 3 deficiency, and ullrich congenital muscular dystrophy, and among its related super-pathways are Collagen formation. GO annotations related to this gene include L-ascorbic acid binding and iron ion binding. An important paralog of this gene is COLGALT2.

UniProtKB/Swiss-Prot: PLOD3_HUMAN, O60568
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

Gene Wiki entry for PLOD3 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.2  NT_007933.15  NT_079596.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PLOD3 gene promoter:
         p53   p300   NRSF form 1   HTF   NRSF form 2   FOXL1   YY1   CREB   deltaCREB   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 3): PLOD3 promoter sequence
   Search SABiosciences Chromatin IP Primers for PLOD3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PLOD3


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

Entrez Gene cytogenetic band: 7q22   Ensembl cytogenetic band:  7q22.1   HGNC cytogenetic band: 7q22.1

PLOD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PLOD3 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M100849:  view genomic region     (about GC identifiers)

Start:
100,849,258 bp from pter      End:
100,861,701 bp from pter
Size:
12,444 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 100,207,645-100,219,398     

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PLOD3_HUMAN, O60568 (See protein sequence)
Recommended Name: Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 precursor  
Size: 738 amino acids; 84785 Da
Cofactor: Iron
Cofactor: Ascorbate
Subunit: Homodimer
Subcellular location: Rough endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side
Secondary accessions: B2R6W6 Q540C3

Explore the universe of human proteins at neXtProt for PLOD3: NX_O60568

Explore proteomics data for PLOD3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O60568

  • 4/14 DME Specific Peptides for PLOD3 (O60568) (see all 14)
     PHHDSST  IFQNLNG  LWSNFWG  WNVPYIS 

    PLOD3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PLOD3 Protein Expression
    REFSEQ proteins: NP_001075.1  
    ENSEMBL proteins: 
     ENSP00000407555   ENSP00000223127   ENSP00000394045   ENSP00000407908   ENSP00000404799  
     ENSP00000407551   ENSP00000416070  
    Reactome Protein details: O60568
    Human Recombinant Protein Products for PLOD3: 
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    Novus Biologicals PLOD3 Protein
    Novus Biologicals PLOD3 Lysate
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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PLOD3 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005783endoplasmic reticulum TAS9724729
    GO:0005789endoplasmic reticulum membrane TAS--
    GO:0030867rough endoplasmic reticulum membrane IEA--

    PLOD3 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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 O60568

    ProtoNet protein and cluster: O60568

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


    UniProtKB/Swiss-Prot: PLOD3_HUMAN, O60568
    Similarity: Contains 1 Fe2OG dioxygenase domain


    PLOD3 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PLOD3_HUMAN, O60568
    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)

         Genatlas biochemistry entry for PLOD3:
    procollagen-lysine,2-oxoglutarate 5 dioxygenase 3,highly expressed in heart,placenta,pancreas

         Enzyme Number (IUBMB): EC 1.14.11.41 2

         Gene Ontology (GO): 5/10 molecular function terms (GO ID links to tree view) (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005506iron ion binding IEA--
    GO:0005515protein binding IPI16189514
    GO:0008475procollagen-lysine 5-dioxygenase activity IEA--
    GO:0016491oxidoreductase activity ----
    GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen ----
         
    PLOD3 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for PLOD3:
     Decreased p24 protein expressi  Upregulation of Wnt/beta-caten 

         10 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Plod3):
     cardiovascular system  cellular  embryogenesis  growth/size  integument 
     mortality/aging  muscle  nervous system  other  respiratory system 

    PLOD3 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Plod3tm1Rmyl for PLOD3

       inGenious Targeting Laboratory - Custom generated mouse model solutions for PLOD3 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PLOD3 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PLOD3 

    miRNA
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    miRTarBase miRNAs that target PLOD3:
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    6 QIAGEN miScript miRNA Assays for microRNAs that regulate PLOD3:
    hsa-miR-4324 hsa-miR-140-5p hsa-miR-124 hsa-miR-520d-5p hsa-miR-524-5p hsa-miR-506
    SwitchGear 3'UTR luciferase reporter plasmidPLOD3 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for PLOD3 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.74
    Extracellular matrix organization0.39
    Collagen formation0.74
    2Other types of O-glycan biosynthesis
    Other types of O-glycan biosynthesis
    3Lysine degradation
    Lysine degradation

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    3        Reactome Pathways for PLOD3
        Extracellular matrix organization
    Collagen biosynthesis and modifying enzymes
    Collagen formation


    2         Kegg Pathways  (Kegg details for PLOD3):
        Lysine degradation
    Other types of O-glycan biosynthesis


    PLOD3 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PLOD3

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

    5/115 Interacting proteins for PLOD3 (O605681, 2, 3 ENSP000002231274) via UniProtKB, MINT, STRING, and/or I2D (see all 115)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RHOXF2Q9BQY41, 2, 3, ENSP000003604414EBI-741582,EBI-372094 MINT-66268 I2D: score=6 STRING: ENSP00000360441
    ENSG00000206376Q96KQ72, 3MINT-67128 I2D: score=5 
    ENSG00000232045Q96KQ72, 3MINT-67128 I2D: score=5 
    ENSG00000236759Q96KQ72, 3MINT-67128 I2D: score=5 
    CCDC85BQ158342, 3, ENSP000003116954MINT-66181 I2D: score=5 STRING: ENSP00000311695
    About this table

    Gene Ontology (GO): 5/13 biological process terms (GO ID links to tree view) (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001701in utero embryonic development IEA--
    GO:0001886endothelial cell morphogenesis IEA--
    GO:0006464cellular protein modification process TAS9724729
    GO:0008104protein localization IEA--
    GO:0021915neural tube development IEA--

    PLOD3 for ontologies           About GeneDecksing



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

    PLOD3 for compounds           About GeneDecksing

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

    Browse Tocris compounds for PLOD3

    9 HMDB Compounds for PLOD3    About this table
    CompoundSynonyms CAS #PubMed Ids
    5-Hydroxylysine(2S,5R)-2,6-diamino-5-hydroxyhexanoic acid (see all 21)1190-94-9--
    Ascorbic acid(+)-ascorbate (see all 140)50-81-7--
    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 PLOD3    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Succinic acid1,2-Ethanedicarboxylic acid (see all 8)110-15-6target--17139284 17016423
    Vitamin CAscorbate (see all 6)50-81-7target--17139284 17016423

    2 Novoseek inferred chemical compound relationships for PLOD3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    pyridinoline 59.9 1 15908192 (1)
    lysine 58.8 5 10457259 (1), 15523625 (1), 20470363 (1)

    Search CenterWatch for drugs/clinical trials and news about PLOD3

    (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,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PLOD3 gene: 
    NM_001084.4  

    Unigene Cluster for PLOD3:

    Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3
    Hs.153357  [show with all ESTs]
    Unigene Representative Sequence: NM_001084
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000454310 ENST00000223127(uc003uyd.3) ENST00000487563 ENST00000460132
    ENST00000440925 ENST00000466881 ENST00000421736 ENST00000463479 ENST00000478082
    ENST00000460475 ENST00000478264 ENST00000424135 ENST00000489927 ENST00000414785
    ENST00000456079 ENST00000481461
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    SwitchGear 3'UTR luciferase reporter plasmidPLOD3 3' UTR sequence
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    Additional mRNA sequence: 

    AF046889.1 AF068229.1 AK075338.1 AK297559.1 AK298537.1 AK312743.1 AL049952.1 AY220458.1 
    BC011674.2 BC018946.2 

    24 DOTS entries:

    DT.446678  DT.97860330  DT.95282626  DT.91761063  DT.121126449  DT.100038114  DT.100788312  DT.121126473 
    DT.121126568  DT.97842928  DT.100038113  DT.95260306  DT.100791405  DT.317183  DT.91764386  DT.95252861 
    DT.121126511  DT.91764384  DT.91764387  DT.95161326  DT.100788310  DT.100841654  DT.121126500  DT.91649100 

    24/432 AceView cDNA sequences (see all 432):

    BM762534 AA443910 NM_001084 BM818654 CF131926 BM796391 CA489345 CR592883 
    BU156072 BM827792 BQ019087 BM743116 BU950438 BU732023 CA308748 CB111086 
    BQ448627 AA313622 BU838743 BM829528 BF941815 BU502459 BM772935 BU178362 

    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™, 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

    PLOD3 expression in normal human tissues (normalized intensities)      PLOD3 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTCCGCGTGC
    PLOD3 Expression
    About this image


    PLOD3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/11 selected tissues (see all 11) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 4 entries
             Mandibular Condyle
             sensory organ/ear/inner ear   
     
     Neural Crest (Gastrulation Derivatives)
             skeleton/cranium   
     
     Mesoderm (Gastrulation Derivatives)
             skeleton/axial skeleton   
     
     Cartilage (Muscoskeletal System)
             skeleton/cranium   
     
     Somite (Muscoskeletal System)
             skeleton/axial skeleton   

    See PLOD3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PLOD3

    SOURCE GeneReport for Unigene cluster: Hs.153357
        SABiosciences Expression via Pathway-Focused PCR Array including PLOD3: 
              Amino Acid Metabolism II in human mouse rat

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PLOD3

    (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 PLOD3 gene from 6/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Plod31 , 5 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 31, 5 85.77(n)1
    91.6(a)1
      5 (76.09 cM)5
    264331  NM_011962.31  NP_036092.11 
     1369870195 
    lizard
    (Anolis carolinensis)
    Reptilia PLOD36
    procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3...
    72(a)
    1 ↔ 1
    GL343466.1(525-33938)
    African clawed frog
    (Xenopus laevis)
    Amphibia plod-prov2 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 75.26(n)    BC043893.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufa10a052 wufa10a05 77.49(n)   334935  BU808678.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG61993
    Plod1
    procollagen-lysine 5-dioxygenase3
    procollagen lysyl hydroxylase1
    46(a)3
    55.14(n)1
    47.03(a)1
      68B13
    392651  NM_140194.11  NP_648451.11 
    worm
    (Caenorhabditis elegans)
    Secernentea let-2681 , 3 procollagen-lysine,2-oxoglutarate
    5-dioxygenase more3
    Protein LET-2681
    46(a)3
    51.66(n)1
    47.69(a)1
      II(10033358-10038027)3
    1745641  NM_063769.21  NP_496170.11 


    ENSEMBL Gene Tree for PLOD3 (if available)
    TreeFam Gene Tree for PLOD3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PLOD3 gene
    COLGALT22  COLGALT12  PLOD22  CERCAM2  PLOD12  
    5 SIMAP similar genes for PLOD3 using alignment to 7 protein entries:     PLOD3_HUMAN (see all proteins):
    DKFZp564O1822    PLOD2    PLOD1    COLGALT2    COLGALT1

    PLOD3 for paralogs           About GeneDecksing



    (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) 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

    10/542 SNPs in PLOD3 are shown (see all 542)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0549134
    Lysyl hydroxylase 3 deficiency (LH3 deficiency)4--see VAR_0549132 N S mis40--------
    rs3690910541,2
    C--100848944(+) TTTGT-/TTTTTA 1 -- ds50010--------
    rs39882391,2
    C--100856788(+) CCTTG-/TTTT  
            
    TTTTT
    1 -- int11Minor allele frequency- TTTT:0.50CSA 2
    rs58861711,2
    C,H--100856797(+) tttttA/Tttatt 1 -- int10--------
    rs1888012671,2
    C--104214334(+) AGTGCA/CGGGGC 1 -- ds50010--------
    rs1905217041,2
    C--104214348(+) ATCTCA/GGCTCA 1 -- ds50010--------
    rs1833762961,2
    C--104214364(+) AGCTCC/TGCCTC 1 -- ds50010--------
    rs1877204721,2
    C--104214371(+) CCTCCA/CGGGTT 1 -- ds50010--------
    rs1122967461,2
    C--104214422(+) TACAGA/GTGCCC 1 -- ds50010--------
    rs1924888891,2
    C--104214425(+) AGATGC/GCCGCC 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for PLOD3 (100849258 - 100861701 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for PLOD3:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2734888CNV Deletion23290073
    esv2422376CNV Duplication17116639
    esv2422326CNV Duplication17116639
    nsv831075CNV Loss17160897
    nsv831076CNV Loss17160897
    dgv7409n71CNV Loss21882294
    dgv7410n71CNV Loss21882294
    esv2752134CNV Gain17911159


    Human Gene Mutation Database (HGMD): PLOD3

    Locus Specific Mutation Databases (LSDB): PLOD3
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing PLOD3
    DNA2.0 Custom Variant and Variant Library Synthesis for PLOD3

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 603066   
    OMIM disorders: 612394  
    UniProtKB/Swiss-Prot: PLOD3_HUMAN, O60568
  • 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. Note=The disease is caused by mutations affecting the gene represented in this
    entry

  • 6 diseases for PLOD3:    About MalaCards
    lysyl hydroxylase 3 deficiency    ullrich congenital muscular dystrophy    ehlers-danlos syndrome    congenital muscular dystrophy
    muscular dystrophy    endotheliitis

    2 diseases from the University of Copenhagen DISEASES database for PLOD3:
    Ehlers-Danlos syndrome     Ullrich congenital muscular dystrophy

    PLOD3 for disorders           About GeneDecksing

    1 Novoseek inferred disease relationship for PLOD3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ehlers-danlos syndrome 70.4 1 9724729 (1)

    Genetic Association Database (GAD): PLOD3
    Human Genome Epidemiology (HuGE) Navigator: PLOD3 (1 document)

    Export disorders for PLOD3 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)
    About This Section

    PubMed articles for PLOD3 gene, integrated from 9 sources (see all 49):
    (articles sorted by number of sources associating them with PLOD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Primary structure, tissue distribution, and chromosomal localization of a novel isoform of lysyl hydroxylase (lysyl hydroxylase 3). (PubMed id 9582318)1, 2, 3, 9 Valtavaara M.... Myllylae R. (1998)
    2. Cloning and characterization of a third human lysyl hydroxylase isoform. (PubMed id 9724729)1, 2, 3, 9 Passoja K.... Kivirikko K.I. (1998)
    3. Complete exon-intron organization of the gene for human lysyl hydroxylase 3 (LH3). (PubMed id 10686427)1, 2, 9 Rautavuoma K.... Kivirikko K.I. (2000)
    4. A connective tissue disorder caused by mutations of the lysyl hydroxylase 3 gene. (PubMed id 18834968)1, 2, 9 Salo A.M.... Myllylae R. (2008)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    6. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (2003)
    7. The glycosyltransferase activities of lysyl hydroxylase 3 (LH3) in the extracellular space are important for cell growth and viability. (PubMed id 18298658)1, 9 Wang C....MyllylAo R. (2009)
    8. Lysyl hydroxylase 3 is a multifunctional protein possessing collagen glucosyltransferase activity. (PubMed id 10934207)1, 9 Heikkinen J....Myllyla R. (2000)
    9. The third activity for lysyl hydroxylase 3: galactosylation of hydroxylysyl residues in collagens in vitro. (PubMed id 12475640)1, 9 Wang C....Myllyla R. (2002)
    10. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)

    (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)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 8985 HGNC: 9083 AceView: PLOD3 Ensembl:ENSG00000106397 euGenes: HUgn8985
    ECgene: PLOD3 Kegg: 8985 H-InvDB: PLOD3

    (According to HUGE)
    About This Section
      --

    (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 PLOD3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PLOD3 gene:
    Search GeneIP for patents involving PLOD3

    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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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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