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

Gene ID: 3949, updated on 6-Sep-2021

Summary

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
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; FHCL1; 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]
Expression
Ubiquitous expression in adrenal (RPKM 29.0), lung (RPKM 28.5) and 25 other tissues See more
Orthologs
NEW
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Genomic context

See LDLR in Genome Data Viewer
Location:
19p13.2
Exon count:
18
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (11089432..11133820)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (11200139..11244496)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes 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 LDLR antisense RNA 1 Neighboring gene microRNA 6886 Neighboring gene VISTA enhancer hs1754 Neighboring gene SPC24 component of NDC80 kinetochore complex

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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
A variant in LDLR is associated with abdominal aortic aneurysm.
GeneReviews: Not available
Biological, clinical and population relevance of 95 loci for blood lipids.
GeneReviews: Not available
Common variants at 30 loci contribute to polygenic dyslipidemia.
GeneReviews: Not available
Discovery and refinement of loci associated with lipid levels.
GeneReviews: Not available
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.
GeneReviews: Not available
Familial hypercholesterolemia Compare labs
Familial hypercholesterolemia 1
MedGen: C0745103 OMIM: 143890 GeneReviews: Familial Hypercholesterolemia
Compare labs
Forty-three loci associated with plasma lipoprotein size, concentration, and cholesterol content in genome-wide analysis.
GeneReviews: Not available
Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.
GeneReviews: Not available
Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
GeneReviews: Not available
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
GeneReviews: Not available
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants.
GeneReviews: Not available
Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
GeneReviews: Not available
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
GeneReviews: Not available
Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations.
GeneReviews: Not available
Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease.
GeneReviews: Not available
Large-scale genome-wide association studies in East Asians identify new genetic loci influencing metabolic traits.
GeneReviews: Not available
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
GeneReviews: Not available
Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque.
GeneReviews: Not available
Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
GeneReviews: Not available
Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
GeneReviews: Not available
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
GeneReviews: Not available
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
GeneReviews: Not available

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in amyloid-beta clearance ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in amyloid-beta clearance by cellular catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in artery morphogenesis IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to fatty acid IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to low-density lipoprotein particle stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cholesterol homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cholesterol homeostasis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in cholesterol homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cholesterol homeostasis TAS
Traceable Author Statement
more info
PubMed 
involved_in cholesterol import IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cholesterol import ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cholesterol metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in cholesterol transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cholesterol transport TAS
Traceable Author Statement
more info
PubMed 
involved_in endocytosis TAS
Traceable Author Statement
more info
PubMed 
involved_in high-density lipoprotein particle clearance IEA
Inferred from Electronic Annotation
more info
 
involved_in intestinal cholesterol absorption IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in lipid metabolic process TAS
Traceable Author Statement
more info
PubMed 
involved_in lipoprotein catabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in long-term memory IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in low-density lipoprotein particle clearance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of amyloid fibril formation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of astrocyte activation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of microglial cell activation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in negative regulation of protein metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in phagocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in phospholipid transport ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in plasma lipoprotein particle clearance ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in plasma lipoprotein particle clearance TAS
Traceable Author Statement
more info
PubMed 
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of lysosomal protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of triglyceride biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in receptor-mediated endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in receptor-mediated endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in receptor-mediated endocytosis TAS
Traceable Author Statement
more info
PubMed 
involved_in receptor-mediated endocytosis involved in cholesterol transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in receptor-mediated endocytosis involved in cholesterol transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of cholesterol metabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of phosphatidylcholine catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of protein metabolic process IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in response to caloric restriction IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in viral entry into host cell IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
part_of PCSK9-LDLR complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in apical part of cell ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in basolateral plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cell surface IDA
Inferred from Direct Assay
more info
PubMed 
located_in cell surface ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in clathrin-coated endocytic vesicle membrane TAS
Traceable Author Statement
more info
 
located_in clathrin-coated pit IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in early endosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in endolysosome membrane TAS
Traceable Author Statement
more info
 
located_in endosome membrane TAS
Traceable Author Statement
more info
 
located_in external side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
located_in late endosome IDA
Inferred from Direct Assay
more info
PubMed 
part_of low-density lipoprotein particle IEA
Inferred from Electronic Annotation
more info
 
located_in lysosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane HDA PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
part_of receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in somatodendritic compartment IEA
Inferred from Electronic Annotation
more info
 
located_in sorting endosome IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
low-density lipoprotein receptor
Names
LDL receptor
low-density lipoprotein receptor class A domain-containing protein 3

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_000527.5NP_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, ENST00000558518.6
    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_001195798.2NP_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, ENST00000558013.5
    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_001195799.2NP_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
    Consensus CDS
    CCDS56085.1
    UniProtKB/Swiss-Prot
    P01130
    Related
    ENSP00000440520.1, ENST00000535915.5
    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_001195800.2NP_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
    Consensus CDS
    CCDS56084.1
    UniProtKB/Swiss-Prot
    P01130
    Related
    ENSP00000397829.2, ENST00000455727.6
    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_001195803.2NP_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
    Consensus CDS
    CCDS56083.1
    UniProtKB/Swiss-Prot
    P01130
    Related
    ENSP00000437639.1, ENST00000545707.5
    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 Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    11089432..11133820
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011528010.2XP_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_001753685.2 RNA Sequence

  2. XR_001753686.2 RNA Sequence

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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