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    LDLR low density lipoprotein receptor [ Homo sapiens (human) ]

    Gene ID: 3949, updated on 8-Nov-2017
    Official Symbol
    LDLRprovided by HGNC
    Official Full Name
    low density lipoprotein receptorprovided by HGNC
    Primary source
    HGNC:HGNC:6547
    See related
    Ensembl:ENSG00000130164 MIM:606945; Vega:OTTHUMG00000171935
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FH; FHC; LDLCQ2
    Summary
    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]
    Orthologs
    Location:
    19p13.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 19 NC_000019.10 (11089362..11133830)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (11200037..11244506)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene Yip1 domain family member 2 Neighboring gene translocase of inner mitochondrial membrane 29 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 Neighboring gene RNA, 7SL, cytoplasmic 192, pseudogene Neighboring gene microRNA 6886 Neighboring gene SPC24, NDC80 kinetochore complex component Neighboring gene KN motif and ankyrin repeat domains 2

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Professional guidelines

    Description
    Professional guideline
    ACMG 2013

    The ACMG recommends that laboratories performing clinical sequencing seek and report mutations in LDLR that are pathogenic or expected to be pathogenic.

    GuidelinePubMed

    Associated conditions

    Description Tests
    Familial hypercholesterolemia
    MedGen: C0020445 OMIM: 143890 GeneReviews: Familial Hypercholesterolemia
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2015-11-16)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2015-11-16)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    A variant in LDLR is associated with abdominal aortic aneurysm.
    NHGRI GWA Catalog
    Biological, clinical and population relevance of 95 loci for blood lipids.
    NHGRI GWA Catalog
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    NHGRI GWA Catalog
    Discovery and refinement of loci associated with lipid levels.
    NHGRI GWA Catalog
    Eight genetic loci associated with variation in lipoprotein-associated phospholipase A2 mass and activity and coronary heart disease: meta-analysis of genome-wide association studies from five community-based studies.
    NHGRI GWA Catalog
    Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.
    NHGRI GWA Catalog
    Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.
    NHGRI GWA Catalog
    Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
    NHGRI GWA Catalog
    Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
    NHGRI GWA Catalog
    Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
    NHGRI GWA Catalog
    Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
    NHGRI GWA Catalog
    Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
    NHGRI GWA Catalog
    Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations.
    NHGRI GWA Catalog
    Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
    NHGRI GWA Catalog
    Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
    NHGRI GWA Catalog
    Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
    NHGRI GWA Catalog
    Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque.
    NHGRI GWA Catalog
    Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
    NHGRI GWA Catalog
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    NHGRI GWA Catalog
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    NHGRI GWA Catalog
    Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
    NHGRI GWA Catalog

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with low density lipoprotein receptor (LDLR) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with low density lipoprotein receptor (LDLR) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Nef nef HIV-1 Nef expression in Jurkat cells upregulates LDLR, which is involved in cholesterol uptake PubMed
    Vif vif HIV-1 Vif upregulates the expression of low density lipoprotein receptor (LDLR) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

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    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    amyloid-beta binding IEA
    Inferred from Electronic Annotation
    more info
     
    calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    clathrin heavy chain binding TAS
    Traceable Author Statement
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    low-density lipoprotein particle binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    low-density lipoprotein receptor activity IC
    Inferred by Curator
    more info
    PubMed 
    low-density lipoprotein receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    low-density lipoprotein receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    low-density lipoprotein receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    protease binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    very-low-density lipoprotein particle receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    virus receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    amyloid-beta clearance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cellular response to fatty acid IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to low-density lipoprotein particle stimulus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cholesterol homeostasis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    cholesterol homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cholesterol homeostasis TAS
    Traceable Author Statement
    more info
    PubMed 
    cholesterol import IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cholesterol import ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cholesterol transport TAS
    Traceable Author Statement
    more info
    PubMed 
    chylomicron remnant clearance TAS
    Traceable Author Statement
    more info
     
    endocytosis TAS
    Traceable Author Statement
    more info
    PubMed 
    intestinal cholesterol absorption IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lipid metabolic process TAS
    Traceable Author Statement
    more info
    PubMed 
    lipoprotein catabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    long-term memory IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    low-density lipoprotein particle clearance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    low-density lipoprotein particle clearance TAS
    Traceable Author Statement
    more info
     
    membrane organization TAS
    Traceable Author Statement
    more info
     
    negative regulation of amyloid fibril formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of astrocyte activation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of microglial cell activation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    negative regulation of protein metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phospholipid transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    plasma lipoprotein particle clearance TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of amyloid-beta clearance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of lipoprotein particle clearance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of lysosomal protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of triglyceride biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    receptor-mediated endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    receptor-mediated endocytosis involved in cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cholesterol homeostasis IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of phosphatidylcholine catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of protein metabolic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    response to caloric restriction IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    viral entry into host cell IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    PCSK9-LDLR complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    apical part of cell ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    basolateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    clathrin-coated pit IDA
    Inferred from Direct Assay
    more info
    PubMed 
    early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endolysosome membrane TAS
    Traceable Author Statement
    more info
     
    endosome membrane TAS
    Traceable Author Statement
    more info
     
    external side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    intracellular ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    low-density lipoprotein particle IEA
    Inferred from Electronic Annotation
    more info
     
    lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    receptor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    somatodendritic compartment IEA
    Inferred from Electronic Annotation
    more info
     
    sorting endosome IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    low-density lipoprotein receptor
    Names
    LDL receptor
    low-density lipoprotein receptor class A domain-containing protein 3

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009060.1 RefSeqGene

      Range
      4982..49450
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_274

    mRNA and Protein(s)

    1. NM_000527.4NP_000518.1  low-density lipoprotein receptor isoform 1 precursor

      See identical proteins and their annotated locations for NP_000518.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC011485, AY114155, BM785950, DC306821
      Consensus CDS
      CCDS12254.1
      UniProtKB/Swiss-Prot
      P01130
      UniProtKB/TrEMBL
      A0A024R7D5
      Related
      ENSP00000454071.1, OTTHUMP00000247210, ENST00000558518.5, OTTHUMT00000415973
      Conserved Domains (6) summary
      smart00135
      Location:553595
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:354388
      EGF_CA; Calcium-binding EGF-like domain
      pfam00057
      Location:195231
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:529569
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:318346
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl00104
      Location:278308
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
    2. NM_001195798.1NP_001182727.1  low-density lipoprotein receptor isoform 2 precursor

      See identical proteins and their annotated locations for NP_001182727.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AB209409, AC011485, BM785950, DC306821
      Consensus CDS
      CCDS58651.1
      UniProtKB/Swiss-Prot
      P01130
      Related
      ENSP00000453346.1, OTTHUMP00000247209, ENST00000558013.5, OTTHUMT00000415972
      Conserved Domains (6) summary
      smart00135
      Location:553595
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:354388
      EGF_CA; Calcium-binding EGF-like domain
      pfam00057
      Location:195231
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:529569
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:318346
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl00104
      Location:278308
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
    3. NM_001195799.1NP_001182728.1  low-density lipoprotein receptor isoform 3 precursor

      See identical proteins and their annotated locations for NP_001182728.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AC011485, AK300313, BM785950, DC306821
      Consensus CDS
      CCDS56085.1
      UniProtKB/Swiss-Prot
      P01130
      Related
      ENSP00000440520.1, OTTHUMP00000247206, ENST00000535915.5, OTTHUMT00000415969
      Conserved Domains (5) summary
      smart00135
      Location:512554
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:313347
      EGF_CA; Calcium-binding EGF-like domain
      pfam00057
      Location:154190
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:488528
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:277305
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    4. NM_001195800.1NP_001182729.1  low-density lipoprotein receptor isoform 4 precursor

      See identical proteins and their annotated locations for NP_001182729.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AC011485, AK299038, BM785950, DC306821
      Consensus CDS
      CCDS56084.1
      UniProtKB/Swiss-Prot
      P01130
      Related
      ENSP00000397829.2, OTTHUMP00000247212, ENST00000455727.6, OTTHUMT00000415976
      Conserved Domains (5) summary
      smart00135
      Location:385427
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:186220
      EGF_CA; Calcium-binding EGF-like domain
      pfam00057
      Location:2558
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:361401
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:150178
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    5. NM_001195803.1NP_001182732.1  low-density lipoprotein receptor isoform 6 precursor

      See identical proteins and their annotated locations for NP_001182732.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks an alternate in-frame exon in both the 5' and 3' coding regions, compared to variant 1. The encoded isoform (6) is shorter than isoform 1.
      Source sequence(s)
      AC011485, AK296312, BM785950, DC306821
      Consensus CDS
      CCDS56083.1
      UniProtKB/Swiss-Prot
      P01130
      Related
      ENSP00000437639.1, OTTHUMP00000247207, ENST00000545707.5, OTTHUMT00000415970
      Conserved Domains (5) summary
      smart00135
      Location:426468
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:227261
      EGF_CA; Calcium-binding EGF-like domain
      pfam00057
      Location:2558
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:402442
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:191219
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p7 Primary Assembly

      Range
      11089362..11133830
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528010.1XP_011526312.1  low-density lipoprotein receptor isoform X1

      Conserved Domains (6) summary
      smart00135
      Location:553595
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:354388
      EGF_CA; Calcium-binding EGF-like domain
      pfam00057
      Location:195231
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:529569
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:318346
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl00104
      Location:278308
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...

    RNA

    1. XR_001753685.1 RNA Sequence

    2. XR_001753686.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018930.2 Alternate CHM1_1.1

      Range
      11201264..11245760
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001195802.1: Suppressed sequence

      Description
      NM_001195802.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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