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    VLDLR very low density lipoprotein receptor [ Homo sapiens (human) ]

    Gene ID: 7436, updated on 2-Nov-2024

    Summary

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    Official Symbol
    VLDLRprovided by HGNC
    Official Full Name
    very low density lipoprotein receptorprovided by HGNC
    Primary source
    HGNC:HGNC:12698
    See related
    Ensembl:ENSG00000147852 MIM:192977; AllianceGenome:HGNC:12698
    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
    CAMRQ1; CARMQ1; CHRMQ1; VLDL-R; VLDLRCH
    Summary
    The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. This gene encodes a lipoprotein receptor that is a member of the LDLR family and plays important roles in VLDL-triglyceride metabolism and the reelin signaling pathway. Mutations in this gene cause VLDLR-associated cerebellar hypoplasia. Alternative splicing generates multiple transcript variants encoding distinct isoforms for this gene. [provided by RefSeq, Aug 2009]
    Expression
    Broad expression in ovary (RPKM 37.5), heart (RPKM 20.5) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VLDLR in Genome Data Viewer
    Location:
    9p24.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (2621787..2660056)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (2624554..2662816)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (2621787..2660056)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375955 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:2361801-2363000 Neighboring gene uncharacterized LOC101930053 Neighboring gene uncharacterized LOC105375956 Neighboring gene Sharpr-MPRA regulatory region 8982 Neighboring gene NANOG hESC enhancer GRCh37_chr9:2548993-2549494 Neighboring gene VLDLR antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28137 Neighboring gene Sharpr-MPRA regulatory region 6053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19734 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19737 Neighboring gene uncharacterized LOC105375957 Neighboring gene NANOG hESC enhancer GRCh37_chr9:2677398-2677906 Neighboring gene Sharpr-MPRA regulatory region 5035 Neighboring gene potassium voltage-gated channel modifier subfamily V member 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:2808488-2809363 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:2811115-2811988 Neighboring gene Sharpr-MPRA regulatory region 9529 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:2843124-2843685 Neighboring gene Sharpr-MPRA regulatory region 29 Neighboring gene pumilio RNA binding family member 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Interaction of Fibrin with the Very Low Density Lipoprotein Receptor: Further Characterization and Localization of the Fibrin-Binding Site. Yakovlev S, et al. Biochemistry, 2015 Aug 4. PMID 26153297, Free PMC Article
    2. Homozygous deletion of the very low density lipoprotein receptor gene causes autosomal recessive cerebellar hypoplasia with cerebral gyral simplification. Boycott KM, et al. Am J Hum Genet, 2005 Sep. PMID 16080122, Free PMC Article
    3. Low Very low-Density Lipoprotein Cholesterol but High Very low-Density Lipoprotein Receptor mRNA Expression in Peripheral White Blood Cells: An Atherogenic Phenotype for Atherosclerosis in a Community-Based Population. Zhao F, et al. EBioMedicine, 2017 Nov. PMID 29042132, Free PMC Article
    4. Decreased expression of reelin receptor VLDLR in peripheral lymphocytes of drug-naive schizophrenic patients. Suzuki K, et al. Schizophr Res, 2008 Jan. PMID 17936586
    5. Identification of a nonsense mutation in the very low-density lipoprotein receptor gene (VLDLR) in an Iranian family with dysequilibrium syndrome. Moheb LA, et al. Eur J Hum Genet, 2008 Feb. PMID 18043714

    See all (130) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes.
      Title: The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes.
    2. Identification of the miR-423-3p/VLDLR Regulatory Network for Glioma Using Transcriptome Analysis.
      Title: Identification of the miR-423-3p/VLDLR Regulatory Network for Glioma Using Transcriptome Analysis.
    3. ADAM17 mediates ectodomain shedding of the soluble VLDL receptor fragment in the retinal epithelium.
      Title: ADAM17 mediates ectodomain shedding of the soluble VLDL receptor fragment in the retinal epithelium.
    4. Expression level of VLDL receptor and VLDL-c levels in the malignant and benign breast tumors: The correlation with miRNA-4465 and miRNA-1297.
      Title: Expression level of VLDL receptor and VLDL-c levels in the malignant and benign breast tumors: The correlation with miRNA-4465 and miRNA-1297.
    5. Four single nucleotide polymorphisms (SNPs); rs6921438 and rs4416670 in LOC100132354-C6orf223, rs6993770 in ZFPM2, and rs10738760 in VLDLR-KCNV2 were reported to explain up to 50% of the heritability of vascular endothelial growth factor circulating levels. These SNPs were also studied for possible associations with circulating lipid levels in supposedly healthy European individuals and in a limited number of Iranian indi
      Title: Association between SNPs of Circulating Vascular Endothelial Growth Factor Levels, Hypercholesterolemia and Metabolic Syndrome.
    6. Postprandial VLDL particles are strongly bound and internalized into cells expressing the VLDL receptor. The presence of various specific ligands in VLDL remnants may enhance the capacity for binding to the VLDL receptor, which play the role primarily for energy delivery to the peripheral tissues, but is also a causal factor in atherogenic diseases when excessively and/or continuously remained in plasma.
      Title: The VLDL receptor plays a key role in the metabolism of postprandial remnant lipoproteins.
    7. This study presents the nuclear magnetic resonance solution structure of the recombinant VLDLR(2-4) fragment containing all three fibrin-binding cysteine-rich (CR) domains of this receptor.
      Title: Nuclear Magnetic Resonance Solution Structure of the Recombinant Fragment Containing Three Fibrin-Binding Cysteine-Rich Domains of the Very Low Density Lipoprotein Receptor.
    8. In summary, ER retention of pathogenic VLDLR mutants involves binding to calnexin, elevated endoplasmic reticulum stress, and delayed degradation which is dependent on SEL1L.
      Title: Degradation routes of trafficking-defective VLDLR mutants associated with Dysequilibrium syndrome.
    9. Our findings described an atherogenic phenotype characterized by low VLDL-C but high VLDLR mRNA expression in peripheral WBCs, which suggested that VLDLR in all types of peripheral WBCs may be involved in lipid deposition, and VLDL-C and VLDLR may co-determine the development of atherosclerosis.
      Title: Low Very low-Density Lipoprotein Cholesterol but High Very low-Density Lipoprotein Receptor mRNA Expression in Peripheral White Blood Cells: An Atherogenic Phenotype for Atherosclerosis in a Community-Based Population.
    10. In the second family, we identified a previously unreported homozygous missense change, c.154T > C (p.Cys52Arg) in the VLDLR gene
      Title: Whole exome sequencing is necessary to clarify ID/DD cases with de novo copy number variants of uncertain significance: Two proof-of-concept examples.
    Submit: New GeneRIF Correction See all GeneRIFs (64)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genome-wide association analysis of age-at-onset in Alzheimer's disease.
    EBI GWAS Catalog
    Genome-wide association study of a quantitative disordered gambling trait.
    EBI GWAS Catalog
    Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of VLDLR PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ35024

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables apolipoprotein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables apolipoprotein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables apolipoprotein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables calcium-dependent protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables cargo receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables low-density lipoprotein particle receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables reelin receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables very-low-density lipoprotein particle binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables very-low-density lipoprotein particle receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables very-low-density lipoprotein particle receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cholesterol metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dendrite morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glycoprotein transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in memory TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of dendrite development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in receptor-mediated endocytosis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in reelin-mediated signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in ventral spinal cord development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in very-low-density lipoprotein particle clearance IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in clathrin-coated pit IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of very-low-density lipoprotein particle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    very low-density lipoprotein receptor
    Names
    VLDL receptor

    NCBI Reference Sequences (RefSeq)

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    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_012741.2 RefSeqGene

      Range
      5002..43271
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001018056.3 → NP_001018066.1  very low-density lipoprotein receptor isoform b precursor

      See identical proteins and their annotated locations for NP_001018066.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting protein (isoform b) is shorter than isoform a.
      Source sequence(s)
      AL450467, BC144245, DA386669
      Consensus CDS
      CCDS34979.1
      UniProtKB/TrEMBL
      Q5VVF5, Q8NAN7
      Related
      ENSP00000506072.1, ENST00000681306.1
      Conserved Domains (7) summary
      smart00192
      Location:71 → 103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:505 → 547
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:396 → 426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:33 → 67
      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 ...
      pfam00057
      Location:237 → 273
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:568 → 608
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:360 → 394
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    2. NM_001322225.2 → NP_001309154.1  very low-density lipoprotein receptor isoform c precursor

      Status: REVIEWED

      Source sequence(s)
      AL450467
      Consensus CDS
      CCDS94376.1
      UniProtKB/TrEMBL
      A0A7P0T897, Q8NAN7
      Related
      ENSP00000505030.1, ENST00000680746.1
      Conserved Domains (8) summary
      smart00192
      Location:71 → 103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:464 → 506
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:355 → 385
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:33 → 67
      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 ...
      pfam01456
      Location:710 → 772
      Mucin; Mucin-like glycoprotein
      pfam00057
      Location:196 → 232
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:527 → 567
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:319 → 353
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    3. NM_001322226.2 → NP_001309155.1  very low-density lipoprotein receptor isoform d precursor

      Status: REVIEWED

      Source sequence(s)
      AL450467
      Consensus CDS
      CCDS94377.1
      UniProtKB/TrEMBL
      A0A7P0T9P7, Q8NAN7
      Related
      ENSP00000505773.1, ENST00000681618.1
      Conserved Domains (7) summary
      smart00192
      Location:71 → 103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:464 → 506
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:355 → 385
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:33 → 67
      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 ...
      pfam00057
      Location:196 → 232
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:527 → 567
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:319 → 353
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    4. NM_003383.5 → NP_003374.3  very low-density lipoprotein receptor isoform a precursor

      See identical proteins and their annotated locations for NP_003374.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AL450467, BC136562, DA386669
      Consensus CDS
      CCDS6446.1
      UniProtKB/Swiss-Prot
      B2RMZ7, D3DRH6, P98155, Q5VVF6
      UniProtKB/TrEMBL
      Q8NAN7
      Related
      ENSP00000371532.2, ENST00000382100.8
      Conserved Domains (8) summary
      smart00192
      Location:71 → 103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:505 → 547
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:396 → 426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:33 → 67
      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 ...
      pfam01456
      Location:751 → 813
      Mucin; Mucin-like glycoprotein
      pfam00057
      Location:237 → 273
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:568 → 608
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:360 → 394
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      2621787..2660056
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423848.1 → XP_047279804.1  very low-density lipoprotein receptor isoform X1

      UniProtKB/TrEMBL
      A0A7P0T8N9
      Related
      ENSP00000505282.1, ENST00000681806.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      2624554..2662816
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363754.1 → XP_054219729.1  very low-density lipoprotein receptor isoform X1

      UniProtKB/TrEMBL
      A0A7P0T8N9
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P98155.1 GenPept UniProtKB/Swiss-Prot:P98155

    Gene LinkOut

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