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

Gene ID: 7436, updated on 5-Jul-2020

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
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

Genomic context

See VLDLR in Genome Data Viewer
Location:
9p24.2
Exon count:
19
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (2621786..2660056)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (2621679..2654485)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101930053 Neighboring gene uncharacterized LOC105375956 Neighboring gene uncharacterized LOC101930048 Neighboring gene VLDLR antisense RNA 1 Neighboring gene uncharacterized LOC105375957 Neighboring gene potassium voltage-gated channel modifier subfamily V member 2 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

NHGRI GWAS Catalog

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

Homology

Clone Names

  • FLJ35024

Gene Ontology Provided by GOA

Function Evidence Code Pubs
apolipoprotein binding IDA
Inferred from Direct Assay
more info
PubMed 
apolipoprotein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
calcium-dependent protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
cargo receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
low-density lipoprotein particle receptor activity TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
reelin receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
very-low-density lipoprotein particle binding IDA
Inferred from Direct Assay
more info
PubMed 
very-low-density lipoprotein particle receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
very-low-density lipoprotein particle receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
axon guidance TAS
Traceable Author Statement
more info
 
cholesterol metabolic process IEA
Inferred from Electronic Annotation
more info
 
dendrite morphogenesis IEA
Inferred from Electronic Annotation
more info
 
glycoprotein transport IDA
Inferred from Direct Assay
more info
PubMed 
lipid transport IEA
Inferred from Electronic Annotation
more info
 
low-density lipoprotein particle receptor catabolic process TAS
Traceable Author Statement
more info
 
memory TAS
Traceable Author Statement
more info
PubMed 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
positive regulation of dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein kinase activity IEA
Inferred from Electronic Annotation
more info
 
receptor-mediated endocytosis IDA
Inferred from Direct Assay
more info
PubMed 
reelin-mediated signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
signal transduction TAS
Traceable Author Statement
more info
PubMed 
ventral spinal cord development IEA
Inferred from Electronic Annotation
more info
 
very-low-density lipoprotein particle clearance IDA
Inferred from Direct Assay
more info
PubMed 
very-low-density lipoprotein particle clearance TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
clathrin-coated pit IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
lysosomal membrane TAS
Traceable Author Statement
more info
 
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 
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)

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_012741.1 RefSeqGene

    Range
    4982..39311
    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/Swiss-Prot
    P98155
    UniProtKB/TrEMBL
    Q5VVF5
    Related
    ENSP00000371531.2, ENST00000382099.2
    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
    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
    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
    P98155
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    2621786..2660056
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_002956805.1 RNA Sequence

  2. XR_001746373.2 RNA Sequence

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