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

    Gene ID: 7436, updated on 3-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    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

    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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    Preferred Names
    very low-density lipoprotein receptor
    Names
    VLDL receptor

    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_012741.2 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001018056.3NP_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:71103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:505547
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:396426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3367
      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:237273
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:568608
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:360394
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    2. NM_001322225.2NP_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:71103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:464506
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:355385
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3367
      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:710772
      Mucin; Mucin-like glycoprotein
      pfam00057
      Location:196232
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:527567
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:319353
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    3. NM_001322226.2NP_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:71103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:464506
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:355385
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3367
      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:196232
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:527567
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:319353
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    4. NM_003383.5NP_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:71103
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:505547
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:396426
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3367
      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:751813
      Mucin; Mucin-like glycoprotein
      pfam00057
      Location:237273
      Ldl_recept_a; Low-density lipoprotein receptor domain class A
      pfam00058
      Location:568608
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam14670
      Location:360394
      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_047423848.1XP_047279804.1  very low-density lipoprotein receptor isoform X1

      UniProtKB/TrEMBL
      A0A7P0T8N9, Q59HD7
      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_054363754.1XP_054219729.1  very low-density lipoprotein receptor isoform X1

      UniProtKB/TrEMBL
      A0A7P0T8N9, Q59HD7