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LDLR Gene

protein-coding   GIFtS: 72
GCID: GC19P011200

Low Density Lipoprotein Receptor

  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)
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Aliases
Low Density Lipoprotein Receptor1 2     LDLCQ22 5
LDL Receptor2 3     Familial Hypercholesterolemia1
FH2 5     Low-Density Lipoprotein Receptor2
FHC2 5     Low-Density Lipoprotein Receptor Class A Domain-Containing Protein 32

External Ids:    HGNC: 65471   Entrez Gene: 39492   Ensembl: ENSG000001301647   OMIM: 6069455   UniProtKB: P011303   

Export aliases for LDLR gene to outside databases

Previous GC identifers: GC19P011331 GC19P011045 GC19P011061 GC19P010777


(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 LDLR Gene:
The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in
receptor-mediated endocytosis of specific ligands. Low density lipoprotein (LDL) is normally bound at the cell
membrane and taken into the cell ending up in lysosomes where the protein is degraded and the cholesterol is made
available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the
rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester
synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial
hypercholesterolemia. Alternate splicing results in multiple transcript variants.(provided by RefSeq, Sep 2010)

GeneCards Summary for LDLR Gene:
LDLR (low density lipoprotein receptor) is a protein-coding gene. Diseases associated with LDLR include familial hypercholesterolemia, and ldlr-related familial hypercholesterolemia, autosomal dominant. GO annotations related to this gene include low-density lipoprotein particle binding and calcium ion binding. An important paralog of this gene is LRP6.

UniProtKB/Swiss-Prot: LDLR_HUMAN, P01130
Function: Binds LDL, the major cholesterol-carrying lipoprotein of plasma, and transports it into cells by
endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated
pits. In case of HIV-1 infection, functions as a receptor for extracellular Tat in neurons, mediating its
internalization in uninfected cells

Gene Wiki entry for LDLR (LDL receptor) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NT_011295.12  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the LDLR gene promoter:
         C/EBPbeta   AP-2alpha isoform 3   AP-1   AP-2alpha isoform 2   PPAR-gamma1   PPAR-gamma2   AP-2alpha isoform 4   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): LDLR promoter sequence
   Search Chromatin IP Primers for LDLR

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


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

Entrez Gene cytogenetic band: 19p13.2   Ensembl cytogenetic band:  19p13.2   HGNC cytogenetic band: 19p13.2

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

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P011200:  view genomic region     (about GC identifiers)

Start:
11,200,038 bp from pter      End:
11,244,506 bp from pter
Size:
44,469 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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: LDLR_HUMAN, P01130 (See protein sequence)
Recommended Name: Low-density lipoprotein receptor precursor  
Size: 860 amino acids; 95376 Da
Subunit: Interacts with LDLRAP1, ARRB1, SNX17. Interacts (via NPXY motif) with DAB2 (via PID domain); the
interaction is impaired by tyrosine phosphorylation of the NPXY motif. Interacts with the full length immature
form of PCSK9 (via C-terminus). Interacts with HCV E1/E2 heterodimer. Interacts with HIV-1 Tat
Sequence caution: Sequence=BAD92646.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Selected PDB 3D structures from and Proteopedia for LDLR (see all 29):
1AJJ (3D)        1D2J (3D)        1F5Y (3D)        1F8Z (3D)        1HJ7 (3D)        1HZ8 (3D)    
Secondary accessions: B4DII3 B4DJZ8 B4DR00 B4DTQ3 C0JYY8 H0YLU8 H0YNT7 Q53ZD9 Q59FQ1 Q9UDH7
Alternative splicing: 6 isoforms:  P01130-1   P01130-2   P01130-3   P01130-4   P01130-5   P01130-6   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for LDLR: NX_P01130

Explore proteomics data for LDLR at MOPED

Post-translational modifications: 

  • N- and O-glycosylated1
  • Ubiquitinated by MYLIP leading to degradation1
  • Glycosylation2 at Asn97, Asn156, Asn272, Asn515, Asn657, Thr721, Thr724, Ser725, Thr726, Ser732,
                                 Ser733, Thr734, Thr738, Thr741, Thr742, Thr743, Ser750
  • Modification sites at PhosphoSitePlus

  • See LDLR Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_000518.1  NP_001182727.1  NP_001182728.1  NP_001182729.1  NP_001182732.1  

    ENSEMBL proteins: 
     ENSP00000454071   ENSP00000453557   ENSP00000397829   ENSP00000440520   ENSP00000437639  
     ENSP00000453346   ENSP00000252444   ENSP00000453513   ENSP00000453696  
    Reactome Protein details: P01130

    LDLR Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
    R&D Systems Recombinant & Natural Proteins for LDLR (LDL R)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Proteins for LDLR
    OriGene Protein Over-expression Lysate for LDLR
    OriGene MassSpec for LDLR
    OriGene Custom Protein Services for LDLR
    GenScript Custom Purified and Recombinant Proteins Services for LDLR
    Novus Biologicals LDLR Proteins
    Novus Biologicals LDLR Lysates
    Sino Biological Recombinant Protein for LDLR
    Sino Biological Cell Lysate for LDLR
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for LDLR

    LDLR Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    R&D Systems Antibodies for LDLR (LDL R)
    OriGene Antibodies for LDLR
    OriGene Custom Antibody Services for LDLR
    Novus Biologicals LDLR Antibodies
    Abcam antibodies for LDLR
    Cloud-Clone Corp. Antibodies for LDLR
    ThermoFisher Antibodies for LDLR
    LSBio Antibodies in human, mouse, rat for LDLR

    LDLR Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for LDLR
    R&D Systems ELISAs for LDLR (LDL R)
    GenScript Custom Assay Services for LDLR
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for LDLR
    Cloud-Clone Corp. CLIAs for LDLR


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    LDLR: Low density lipoprotein receptors

    Selected InterPro protein domains (see all 11):
     IPR002172 LDrepeatLR_classA_rpt
     IPR000033 LDLR_classB_rpt
     IPR001881 EGF-like_Ca-bd_dom
     IPR023415 LDLR_class-A_CS
     IPR000742 EG-like_dom

    Graphical View of Domain Structure for InterPro Entry P01130

    ProtoNet protein and cluster: P01130

    4 Blocks protein domains:
    IPB000033 Low-density lipoprotein receptor
    IPB000152 Aspartic acid and asparagine hydroxylation site
    IPB001881 EGF-like calcium-binding
    IPB002172 Low density lipoprotein-receptor


    UniProtKB/Swiss-Prot: LDLR_HUMAN, P01130
    Domain: The NPXY motif mediates the interaction with the clathrin adaptor DAB2 involved in receptor
    internalization (By similarity)
    Similarity: Belongs to the LDLR family
    Similarity: Contains 3 EGF-like domains
    Similarity: Contains 7 LDL-receptor class A domains
    Similarity: Contains 6 LDL-receptor class B repeats


    LDLR 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,
    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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: LDLR_HUMAN, P01130
    Function: Binds LDL, the major cholesterol-carrying lipoprotein of plasma, and transports it into cells by
    endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated
    pits. In case of HIV-1 infection, functions as a receptor for extracellular Tat in neurons, mediating its
    internalization in uninfected cells

         Genatlas biochemistry entry for LDLR:
    lipoprotein,low density,receptor

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001948glycoprotein binding IPI10571240
    GO:0005041low-density lipoprotein receptor activity IDA6091915
    GO:0005509calcium ion binding IEA--
    GO:0005515protein binding IPI12221107
    GO:0030169low-density lipoprotein particle binding IEA--
         
    LDLR for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for LDLR:
     Increased viability after born 

         Selected MGI mutant phenotypes (inferred from 6 alleles(MGI details for Ldlr) (see all 19):
     adipose tissue  behavior/neurological  cardiovascular system  cellular  endocrine/exocrine gland 
     growth/size/body  hematopoietic system  homeostasis/metabolism  immune system  integument 
     liver/biliary system  mortality/aging  muscle  nervous system  no phenotypic analysis 

    LDLR for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Ldlrtm1Her for LDLR

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for LDLR
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for LDLR

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for LDLR
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for LDLR

    miRNA
    Products:
        
    miRTarBase miRNAs that target LDLR:
    hsa-mir-92a-3p (MIRT049680), hsa-mir-30a-5p (MIRT028459), hsa-mir-149-5p (MIRT045415), hsa-mir-26b-3p (MIRT038952), hsa-mir-19b-3p (MIRT031195), hsa-mir-93-5p (MIRT027940), hsa-mir-130b-3p (MIRT020235), hsa-mir-130a-3p (MIRT007140), hsa-let-7b-5p (MIRT032197), hsa-mir-128-3p (MIRT021895), hsa-mir-335-5p (MIRT017122), hsa-mir-124-3p (MIRT022254), hsa-mir-744-5p (MIRT037702), hsa-mir-92b-3p (MIRT040715)

    Block miRNA regulation of human, mouse, rat LDLR using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LDLR (see all 51):
    hsa-miR-140-5p hsa-miR-106a hsa-miR-128 hsa-miR-301a hsa-miR-30d hsa-miR-519a hsa-miR-30a hsa-miR-3658
    SwitchGear 3'UTR luciferase reporter plasmidLDLR 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for LDLR
    Predesigned siRNA for gene silencing in human, mouse, rat LDLR

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

    Clone
    Products:
         
    OriGene clones in human, mouse for LDLR (see all 25)
    OriGene ORF clones in mouse, rat for LDLR
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 6): LDLR (NM_000527)
    Sino Biological Human cDNA Clone for LDLR
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LDLR
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LDLR

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for LDLR
    Browse ESI BIO Cell Lines and PureStem Progenitors for LDLR 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LDLR


    (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
    LDLR_HUMAN, P01130: Cell membrane; Single-pass type I membrane protein. Endomembrane system; Single-pass type I
    membrane protein. Membrane, clathrin-coated pit; Single-pass type I membrane protein. Golgi apparatus. Early
    endosome. Late endosome. Cell surface. Lysosome. Note=Found distributed from the plasma membrane to intracellular
    compartments. Localizes to the Golgi apparatus, early and late endosomes/lysosomes and cell surface in the
    presence of PCSK9
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endosome5
    golgi apparatus5
    lysosome5
    plasma membrane5
    vacuole5
    extracellular3
    endoplasmic reticulum2
    nucleus2
    peroxisome2
    cytoskeleton1
    cytosol1
    mitochondrion1

    Gene Ontology (GO): Selected cellular component terms (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005764lysosome IDA15166224
    GO:0005768endosome ----
    GO:0005769early endosome IDA15166224
    GO:0005770late endosome IDA17461796
    GO:0005794Golgi apparatus IDA17461796

    LDLR for ontologies           About GeneDecksing


    (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 LDLR About   (see all 20)  
    See pathways by source

    SuperPathContained pathways About
    1Statin Pathway
    Statin Pathway0.73
    Statin Pathway, Pharmacodynamics0.73
    2G protein signaling Ras family GTPases in kinase cascades scheme
    Immune response Oncostatin M signaling via MAPK in human cells0.39
    Oncostatin M Signaling Pathway0.37
    3Lipoprotein metabolism
    Lipoprotein metabolism0.59
    LDL-mediated lipid transport0.00
    Lipid digestion, mobilization, and transport0.59
    Chylomicron-mediated lipid transport0.00
    4Wnt Signaling Pathway (WikiPathways)
    Wnt Signaling Pathway0.55
    DNA damage response (only ATM dependent)0.32
    Wnt Signaling Pathway and Pluripotency0.55
    5Diseases associated with visual transduction
    Visual phototransduction0.44
    Diseases associated with visual transduction0.43
    Retinoid metabolism and transport0.44

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 R&D Systems Pathway for LDLR
        A-beta Uptake & Degradation

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for LDLR
        SREBP Proteolysis

    3 GeneGo (Thomson Reuters) Pathways for LDLR
        Transcription Ligand-dependent activation of the ESR1/SP pathway
    Cholesterol and Sphingolipids transport / Influx to the early endosome in lung (normal and CF)
    Immune response Oncostatin M signaling via MAPK in human cells

    Selected BioSystems Pathways for LDLR (see all 8)
        Wnt Signaling Pathway
    Wnt Signaling Pathway and Pluripotency
    DNA damage response (only ATM dependent)
    Statin Pathway
    SREBP signalling


    3 Reactome Pathways for LDLR
        Retinoid metabolism and transport
    Chylomicron-mediated lipid transport
    LDL-mediated lipid transport

    1 PharmGKB Pathway for LDLR
        Statin Pathway, Pharmacodynamics

    5 Kegg Pathways  (Kegg details for LDLR):
        Endocytosis
    Ovarian steroidogenesis
    Bile secretion
    Toxoplasmosis
    Hepatitis C


    LDLR for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including LDLR: 
              Insulin Signaling Pathway in human mouse rat
              Atherosclerosis in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat
              Fatty Liver in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for LDLR

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    Selected Interacting proteins for LDLR (P011301, 2, 3 ENSP000002524444) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FLT1P179482, 3, ENSP000002823974MINT-6177193 MINT-6177086 I2D: score=3 STRING: ENSP00000282397
    CREBBPQ927932, 3, ENSP000002623674MINT-6804492 I2D: score=1 STRING: ENSP00000262367
    PDIA3P301012, 3MINT-4301346 I2D: score=1 
    PCSK9Q8NBP71, 3, ENSP000003032084EBI-988319,EBI-7539251 I2D: score=1 STRING: ENSP00000303208
    SNX17Q150363, ENSP000002335754I2D: score=5 STRING: ENSP00000233575
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 19):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001523retinoid metabolic process TAS--
    GO:0006629lipid metabolic process TAS10827173
    GO:0006897endocytosis TAS12671190
    GO:0006898receptor-mediated endocytosis TAS--
    GO:0007603phototransduction, visible light TAS--

    LDLR for ontologies           About GeneDecksing



    (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 LDLR

    2 DrugBank Compounds for LDLR    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    PorfimerDHP ether (see all 3)87806-31-3targetother/unknown7994588 2945739 1531856 1450993 7661580
    Alpha-D-Mannose-- 3458-28-4target--17139284 17016423

    Selected Novoseek inferred chemical compound relationships for LDLR gene (see all 123)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hbgg 95.1 107 12960666 (3), 10582364 (3), 11005173 (3), 7595304 (2) (see all 71)
    cholesterol 89.3 865 11369802 (7), 11387232 (5), 1318843 (5), 8820113 (5) (see all 99)
    sterol 83.7 132 18704882 (3), 11058701 (3), 18852694 (3), 11997513 (2) (see all 86)
    3-hydroxy-3-methylglutaryl-coa 76.6 45 15736419 (3), 2176080 (2), 9096609 (2), 9405278 (2) (see all 26)
    25-hydroxycholesterol 75.6 27 14704295 (3), 17156886 (2), 2007178 (1), 7510705 (1) (see all 19)
    lipid 75.3 225 16099208 (4), 17258176 (3), 14744149 (3), 7861934 (3) (see all 99)
    cholesterol ester 74.9 14 1998641 (1), 2007178 (1), 1310398 (1), 10843165 (1) (see all 12)
    lovastatin 68.3 51 9196047 (4), 8800498 (3), 18266936 (3), 8765518 (2) (see all 30)
    lifibrol 61.8 8 11058701 (3), 10447220 (2), 15989622 (1)
    pravastatin 60.2 24 7695485 (4), 9409246 (4), 1658544 (2), 2118022 (2) (see all 15)

    2 PharmGKB related drug/compound annotations for LDLR gene    About this table
    Drug/compound PharmGKB Annotation
    atenololCA  
    atorvastatin



    LDLR for compounds           About GeneDecksing



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for LDLR gene (6 alternative transcripts): 
    NM_000527.4  NM_001195798.1  NM_001195799.1  NM_001195800.1  NM_001195803.1  NM_001195802.1  

    Unigene Cluster for LDLR:

    Low density lipoprotein receptor
    Hs.213289
    Unigene Representative Sequence: AA069104
    14 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000558518 ENST00000557933 ENST00000560502 ENST00000557958 ENST00000455727
    ENST00000535915 ENST00000545707 ENST00000558013 ENST00000252444(uc010xlk.2 uc002mqk.4 uc010xll.2 uc021upc.1 uc010xln.2 uc010xlo.2 uc010xlm.2 uc021upd.1 uc010dxu.3)
    ENST00000560467 ENST00000558528 ENST00000560173 ENST00000559340 ENST00000560628

    miRNA
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    Block miRNA regulation of human, mouse, rat LDLR using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate LDLR (see all 51):
    hsa-miR-140-5p hsa-miR-106a hsa-miR-128 hsa-miR-301a hsa-miR-30d hsa-miR-519a hsa-miR-30a hsa-miR-3658
    SwitchGear 3'UTR luciferase reporter plasmidLDLR 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for LDLR
    Predesigned siRNA for gene silencing in human, mouse, rat LDLR
    Clone
    Products:
         
    OriGene clones in human, mouse for LDLR (see all 25)
    OriGene ORF clones in mouse, rat for LDLR
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 6): LDLR (NM_000527)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for LDLR
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat LDLR
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for LDLR
    OriGene qSTAR qPCR primer pairs in human, mouse for LDLR
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat LDLR
      QuantiTect SYBR Green Assays in human, mouse, rat LDLR
      QuantiFast Probe-based Assays in human, mouse, rat LDLR

    Additional mRNA sequence: M28219.1 

    1 DOTS entry:

    DT.452779 

    6 AceView cDNA sequences:

    AY114155 NM_000527 S70123 BC014514 BT007361 BX648281 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for LDLR (see all 8)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^
    SP1:                          -           -                                                           -                                               -         
    SP2:                          -           -                                                           -                                               -         
    SP3:                                                                          -     -                                                                           
    SP4:                                                                                                                                                            
    SP5:                          -                                                                                                                                 

    ExUns: 18a · 18b · 18c
    SP1:                  
    SP2:                  
    SP3:                  
    SP4:                  
    SP5:                  


    ECgene alternative splicing isoforms for LDLR

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


    LDLR expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Liver (Hepatobiliary System)    fully expand to see all 2 entries
             Immature hepatocytes
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Myelinating Oligodendrocyte Cells Forebrain White Matter
             Mature brain microvascular endothelial cells
     
     Endothelium (Cardiovascular System)
             Mature brain microvascular endothelial cells
     
     Spinal Cord (Nervous System)
             Myelinating Oligodendrocyte Cells Spinal Cord White Matter
     
     Lung (Respiratory System)
    LDLR Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    LDLR Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.213289
        Pathway & Disease-focused RT2 Profiler PCR Arrays including LDLR: 
              Insulin Signaling Pathway in human mouse rat
              Atherosclerosis in human mouse rat
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat
              Fatty Liver in human mouse rat

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for LDLR

    (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 LDLR gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ldlr1 , 5 low density lipoprotein receptor1, 5 79.75(n)1
    78.97(a)1
      9 (7.87 cM)5
    168351  NM_010700.31  NP_034830.21 
     217235765 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    13(a)
    many ↔ many
    4(48984184-48996527)
    lizard
    (Anolis carolinensis)
    Reptilia LDLR6
    low density lipoprotein receptor
    66(a)
    1 ↔ 1
    2(79626653-79656843)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3977572 low density lipoprotein receptor-1 77.32(n)    M62976.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ldlra1 low density lipoprotein receptor a 63(n)
    60.95(a)
      387529  NM_001030283.1  NP_001025454.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG48613 low-density lipoprotein receptor 39(a)     --
    worm
    (Caenorhabditis elegans)
    Secernentea T13C2.66
    Protein T13C2.6, isoform b (T13C2.6) mRNA, complet...
    32(a)
    1 → many
    II(6783427-6788459) WBGene00020481


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for LDLR gene
    LRP62  LRP52  LRP22  LRP1B2  EGF2  LRP5L2  LRP42  VLDLR2  
    NID12  NID22  LRP82  LRP12  
    Selected SIMAP similar genes for LDLR using alignment to 10 protein entries:     LDLR_HUMAN (see all proteins) (see all similar genes):
    ldlr    EFEMP2    LRP5    LRP8    VLDLR    FBLN2
    PROS1    SCUBE2    LRP6    LTBP1    LRP5L    NID2
    LRP4    MEGF6    MATN2    LTBP4    LTBP3    C1R

    LDLR 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), 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 LDLR (see all 1509)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1378539601,2,,4
    C,FFamilial hypercholesterolemia (FH)4 untested111147914(+) GCAGCG/TCTGAG 11 A S mis1 int12Minor allele frequency- A:0.00NA EU 5873
    rs1486986501,2,,4
    CFamilial hypercholesterolemia (FH)4 --11155013(+) TCTGCG/AAGGGA 12 /K /E mis11Minor allele frequency- A:0.00NA 4552
    rs1393616351,2,,4
    C,FFamilial hypercholesterolemia (FH)4 --11158347(+) GCCCCG/AACGGC 12 /N /D mis11Minor allele frequency- A:0.00NA 4552
    rs289420781,2,,4
    CFamilial hypercholesterolemia (FH)4 other111161089(+) GGAACA/GTGGTC 12 M V mis10--------
    rs289420791,2,,4
    CFamilial hypercholesterolemia (FH)4 probable-pathogenic111161095(+) TGGTCA/C/GCTCTG 18 T P A mis1 ese30--------
    rs289420831,2,,4
    CFamilial hypercholesterolemia (FH)4 other111168095(+) CTGGTA/GTGAGA 11 Y C mis1 int10--------
    rs289420841,2,,4
    C,FFamilial hypercholesterolemia (FH)4 other111168149(+) TGCCCC/TGCAGA 11 P L mis1 int1 ese32Minor allele frequency- T:0.00NA EU 5863
    VAR_0053274
    Familial hypercholesterolemia (FH)4--see VAR_0053272 S L mis40--------
    VAR_0054154
    Familial hypercholesterolemia (FH)4--see VAR_0054152 V M mis40--------
    VAR_0623774
    Familial hypercholesterolemia (FH)4--see VAR_0623772 C Y mis40--------

    HapMap Linkage Disequilibrium report for LDLR (11200038 - 11244506 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for LDLR:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv833751CNV Loss17160897
    nsv470126CNV Loss18288195

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

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

    (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

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    OMIM gene information: 606945   
    OMIM disorders: 143890  
    UniProtKB/Swiss-Prot: LDLR_HUMAN, P01130
  • Familial hypercholesterolemia (FH) [MIM:143890]: Common autosomal semi-dominant disease that affects
    about 1 in 500 individuals. The receptor defect impairs the catabolism of LDL, and the resultant elevation in
    plasma LDL-cholesterol promotes deposition of cholesterol in the skin (xanthelasma), tendons (xanthomas), and
    coronary arteries (atherosclerosis). Note=The disease is caused by mutations affecting the gene represented in
    this entry

  • Selected diseases for LDLR (see all 120):    
    About MalaCards
    familial hypercholesterolemia    ldlr-related familial hypercholesterolemia, autosomal dominant    ldl cholesterol level qtl2    hypercholesterolemia
    pinguecula    defective apolipoprotein b-100    myeloperoxidase deficiency    lipoprotein glomerulopathy
    suppression amblyopia    amblyopia    cholesteryl ester storage disease    nephrotic syndrome, type 2
    arcus senilis    hypobetalipoproteinemia    hyperlipoproteinemia type iii    hypoalphalipoproteinemia
    hyperalphalipoproteinemia    aortic disease    primary angle-closure glaucoma    chronic progressive external ophthalmoplegia

    6 diseases from the University of Copenhagen DISEASES database for LDLR:
    Atherosclerosis     Familial hyperlipidemia     Alzheimer's disease     Coronary heart disease
    Aortic disease     Xanthomatosis

    LDLR for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for LDLR gene (see all 92)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hypercholesterolemia familial 96.7 320 19319977 (3), 1677927 (2), 9889019 (2), 17625505 (2) (see all 99)
    apolipoprotein b-100, familial defective 91.3 24 2313203 (1), 1453124 (1), 1347103 (1), 1600334 (1) (see all 23)
    hypercholesterolemia, autosomal dominant 89.5 20 17964958 (2), 15767856 (2), 20144596 (1), 17566095 (1) (see all 14)
    hypercholesterolemia 88.7 240 18726262 (3), 17784865 (3), 10064736 (3), 19538517 (3) (see all 99)
    hypercholesterolemia, autosomal recessive 88.4 13 12464675 (1), 18417616 (1), 15327785 (1), 20356098 (1) (see all 8)
    atherosclerosis 79.4 126 11369802 (5), 18198584 (4), 12208466 (3), 17234631 (3) (see all 89)
    xanthoma 79 9 8551675 (1), 10208489 (1), 20428891 (1), 19439299 (1) (see all 7)
    hyperlipoproteinemia type iii 74.1 4 9777289 (1), 19106071 (1), 11076954 (1), 15863833 (1)
    hypocholesterolemia 73 3 7829645 (2), 8625123 (1)
    hyperlipoproteinemia 68.7 5 10525128 (2), 15450205 (1), 16207455 (1)

    Genatlas disease: LDLR
    familial hypercholesterolemia,hyperlipoproteinemia,type IIa,characterized by a selective increase of LDL
    particles in plasma giving rise to tendon and skin xanthomas,arcus corneae and premature mortality from
    cardiovascular complications,autosomal dominant with a gene dosage effect and a more severe phenotype in
    homozygotes

    Genetic Association Database (GAD): LDLR
    Human Genome Epidemiology (HuGE) Navigator: LDLR (447 documents)

    Export disorders for LDLR 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 LDLR gene, integrated from 10 sources (see all 1868):
    (articles sorted by number of sources associating them with LDLR)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The molecular basis of familial hypercholesterolemia in Lebanon: spectrum of LDLR mutations and role of PCSK9 as a modifier gene. (PubMed id 19319977)1, 2, 4, 9 Abifadel M.... Boileau C. (Hum. Mutat. 2009)
    2. Genetic causes of familial hypercholesterolaemia in patients in the UK: relation to plasma lipid levels and coronary heart disease risk. (PubMed id 17142622)1, 2, 4, 9 Humphries S.E.... Neil H.A.W. (J. Med. Genet. 2006)
    3. Molecular characterization of Polish patients with familial hypercholesterolemia: novel and recurrent LDLR mutations. (PubMed id 20145306)1, 4, 9 Chmara M....Limon J. (J. Appl. Genet. 2010)
    4. The cellular trafficking of the secretory proprotein convertase PCSK9 and its dependence on the LDLR. (PubMed id 17461796)1, 2, 9 Nassoury N.... Seidah N.G. (Traffic 2007)
    5. Mutational analysis in UK patients with a clinical diagnosis of familial hypercholesterolaemia: relationship with plasma lipid traits, heart disease risk and utility in relative tracing. (PubMed id 16389549)1, 4, 9 Humphries S.E....Wierzbicki A.S. (J. Mol. Med. 2006)
    6. Identification of a common low density lipoprotein receptor mutation (C163Y) in the west of Scotland. (PubMed id 9678702)1, 2, 9 Lee W.K....Dominiczak A.F. (J. Med. Genet. 1998)
    7. Aortic calcifications in familial hypercholesterolemia: potential role of the low-density lipoprotein receptor gene. (PubMed id 19081415)1, 4, 9 Alrasadi K....Genest J. (Am. Heart J. 2009)
    8. Multiplex ligation-dependent probe amplification analysis to screen for deletions and duplications of the LDLR gene in patients with familial hypercholesterolaemia. (PubMed id 19538517)1, 4, 9 Taylor A....Norbury G. (Clin. Genet. 2009)
    9. Frequency of low-density lipoprotein receptor gene mutations in patients with a clinical diagnosis of familial combined hyperlipidemia in a clinical setting. (PubMed id 19007590)1, 4, 9 Civeira F....PocovA- M. (J. Am. Coll. Cardiol. 2008)
    10. Diagnosis of families with familial hypercholesterolaemia and/or Apo B-100 defect by means of DNA analysis of LDL-receptor gene mutations. (PubMed id 17347910)1, 4, 9 Widhalm K....Kostner G. (J. Inherit. Metab. Dis. 2007)

    (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: 3949 HGNC: 6547 AceView: LDLR Ensembl:ENSG00000130164 euGenes: HUgn3949
    ECgene: LDLR Kegg: 3949 H-InvDB: LDLR

    (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 LDLR Pharmacogenomics, SNPs, Pathways
    LDLRhttp://www.ucl.ac.uk/fh/
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=LDLR[genesymbol]
    SHMPDhttp://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=LDLR

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

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



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