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Aliases for VLDLR Gene

Aliases for VLDLR Gene

  • Very Low Density Lipoprotein Receptor 2 3
  • VLDL Receptor 3 4
  • CARMQ1 3 6
  • VLDL-R 3 4
  • Very Low-Density Lipoprotein Receptor 3
  • VLDLRCH 3
  • CAMRQ1 3
  • CHRMQ1 3

External Ids for VLDLR Gene

Summaries for VLDLR Gene

Entrez Gene Summary for VLDLR Gene

  • 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]

GeneCards Summary for VLDLR Gene

VLDLR (Very Low Density Lipoprotein Receptor) is a Protein Coding gene. Diseases associated with VLDLR include cerebellar hypoplasia and mental retardation with or without quadrupedal locomotion 1 and cerebellar hypoplasia. Among its related pathways are Guidance Cues and Growth Cone Motility and Reelin signaling pathway. GO annotations related to this gene include calcium ion binding and glycoprotein binding. An important paralog of this gene is LRP1B.

UniProtKB/Swiss-Prot for VLDLR Gene

  • Binds VLDL and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. Binding to Reelin induces tyrosine phosphorylation of Dab1 and modulation of Tau phosphorylation (By similarity).

Gene Wiki entry for VLDLR Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VLDLR Gene

Genomics for VLDLR Gene

Genomic Location for VLDLR Gene

Start:
2,621,774 bp from pter
End:
2,660,053 bp from pter
Size:
38,280 bases
Orientation:
Plus strand

Genomic View for VLDLR Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VLDLR Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VLDLR Gene

Regulatory Elements for VLDLR Gene

Proteins for VLDLR Gene

  • Protein details for VLDLR Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P98155-VLDLR_HUMAN
    Recommended name:
    Very low-density lipoprotein receptor
    Protein Accession:
    P98155
    Secondary Accessions:
    • B2RMZ7
    • D3DRH6
    • Q5VVF6

    Protein attributes for VLDLR Gene

    Size:
    873 amino acids
    Molecular mass:
    96098 Da
    Quaternary structure:
    • Binds to the extracellular matrix protein Reelin. Interacts with VLDLR. Interacts with SNX17 (By similarity). Interacts with DAB1. Receptor for the minor-group human rhinoviruses (HRVs); binds protein VP1 through the second and third LDL-receptor class A domains. Interacts with PCSK9.

    Three dimensional structures from OCA and Proteopedia for VLDLR Gene

    Alternative splice isoforms for VLDLR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VLDLR Gene

Proteomics data for VLDLR Gene at MOPED

Post-translational modifications for VLDLR Gene

  • Ubiquitinated at Lys-839 by MYLIP leading to degradation.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys828 and Lys839
  • Glycosylation at Thr71, Asn151, Thr277, Asn765, and Asn781

Other Protein References for VLDLR Gene

No data available for DME Specific Peptides for VLDLR Gene

Domains for VLDLR Gene

Gene Families for VLDLR Gene

HGNC:
  • LDLR :Low density lipoprotein receptors

UniProtKB/Swiss-Prot:

VLDLR_HUMAN
Domain:
  • Contains 3 EGF-like domains.:
    • P98155
  • Contains 8 LDL-receptor class A domains.:
    • P98155
Similarity:
  • Contains 6 LDL-receptor class B repeats.:
    • P98155
genes like me logo Genes that share domains with VLDLR: view

Function for VLDLR Gene

Molecular function for VLDLR Gene

GENATLAS Biochemistry: very low density lipoprotein/ApoE receptor,containing a CGG repeat in 5utr,(may be a susceptibility gene for late onset senile Alzheimer disease)
UniProtKB/Swiss-Prot Function: Binds VLDL and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. Binding to Reelin induces tyrosine phosphorylation of Dab1 and modulation of Tau phosphorylation (By similarity).

Gene Ontology (GO) - Molecular Function for VLDLR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001948 glycoprotein binding IPI 10571240
GO:0005041 low-density lipoprotein receptor activity TAS 10380922
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 10571241
GO:0030229 very-low-density lipoprotein particle receptor activity IDA 8083232
genes like me logo Genes that share ontologies with VLDLR: view
genes like me logo Genes that share phenotypes with VLDLR: view

Animal Models for VLDLR Gene

MGI Knock Outs for VLDLR:

miRNA for VLDLR Gene

miRTarBase miRNAs that target VLDLR

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for VLDLR Gene

Localization for VLDLR Gene

Subcellular locations from UniProtKB/Swiss-Prot for VLDLR Gene

Membrane; Single-pass type I membrane protein. Membrane, clathrin-coated pit; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VLDLR Gene COMPARTMENTS Subcellular localization image for VLDLR gene
Compartment Confidence
plasma membrane 4
extracellular 3
peroxisome 2
cytoskeleton 1
endoplasmic reticulum 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for VLDLR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space --
GO:0005886 plasma membrane TAS 10380922
GO:0005905 coated pit IEA --
GO:0016020 membrane IDA 15082773
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with VLDLR: view

Pathways for VLDLR Gene

genes like me logo Genes that share pathways with VLDLR: view

Pathways by source for VLDLR Gene

Gene Ontology (GO) - Biological Process for VLDLR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0006869 lipid transport IEA --
GO:0006898 receptor-mediated endocytosis IDA 10571240
GO:0007165 signal transduction TAS 10380922
GO:0007399 nervous system development TAS 10380922
genes like me logo Genes that share ontologies with VLDLR: view

Compounds for VLDLR Gene

(11) Novoseek inferred chemical compound relationships for VLDLR Gene

Compound -log(P) Hits PubMed IDs
lipid 39.3 12
cholesterol 38.7 14
fatty acid 20 3
sterol 15.8 2
triacylglycerol 6.01 2
genes like me logo Genes that share compounds with VLDLR: view

Transcripts for VLDLR Gene

Unigene Clusters for VLDLR Gene

Very low density lipoprotein receptor:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for VLDLR Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b ^ 16a · 16b ·
SP1: - - -
SP2: -
SP3:
SP4: -
SP5: -
SP6: -
SP7:
SP8:
SP9:

ExUns: 16c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for VLDLR Gene

GeneLoc Exon Structure for
VLDLR
ECgene alternative splicing isoforms for
VLDLR

Expression for VLDLR Gene

mRNA expression in normal human tissues for VLDLR Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for VLDLR Gene

This gene is overexpressed in Ovary (5.6) and Heart - Left Ventricle (5.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for VLDLR Gene

SOURCE GeneReport for Unigene cluster for VLDLR Gene Hs.370422

mRNA Expression by UniProt/SwissProt for VLDLR Gene

P98155-VLDLR_HUMAN
Tissue specificity: Abundant in heart and skeletal muscle; also ovary and kidney; not in liver
genes like me logo Genes that share expressions with VLDLR: view

Orthologs for VLDLR Gene

This gene was present in the common ancestor of animals.

Orthologs for VLDLR Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VLDLR 36
  • 99.62 (n)
  • 99.54 (a)
VLDLR 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VLDLR 36
  • 91.16 (n)
  • 95.15 (a)
VLDLR 37
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VLDLR 36
  • 91.56 (n)
  • 95.88 (a)
VLDLR 37
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vldlr 36
  • 90.95 (n)
  • 95.99 (a)
Vldlr 16
Vldlr 37
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VLDLR 37
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VLDLR 37
  • 71 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vldlr 36
  • 91.07 (n)
  • 95.99 (a)
chicken
(Gallus gallus)
Aves VLDL 37
  • 80 (a)
OneToOne
VLDLR 36
  • 79.1 (n)
  • 84.29 (a)
lizard
(Anolis carolinensis)
Reptilia VLDLR 37
  • 71 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.998 36
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.8622 36
vldlr 36
  • 72.39 (n)
  • 76.28 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.11520 36
zebrafish
(Danio rerio)
Actinopterygii vldlr 36
  • 68.57 (n)
  • 71.58 (a)
vldlr 37
  • 70 (a)
OneToOne
zgc55792 36
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002186 36
  • 50.34 (n)
  • 43.13 (a)
fruit fly
(Drosophila melanogaster)
Insecta LpR1 36
  • 51.1 (n)
  • 44.85 (a)
LpR1 37
  • 33 (a)
ManyToMany
LpR2 37
  • 33 (a)
ManyToMany
CG4861 38
  • 40 (a)
worm
(Caenorhabditis elegans)
Secernentea T13C2.6 36
  • 50.53 (n)
  • 40.26 (a)
T13C2.6 37
  • 33 (a)
OneToMany
B0244.8 38
  • 37 (a)
R01H2.3 38
  • 38 (a)
Species with no ortholog for VLDLR:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VLDLR Gene

ENSEMBL:
Gene Tree for VLDLR (if available)
TreeFam:
Gene Tree for VLDLR (if available)

Paralogs for VLDLR Gene

Paralogs for VLDLR Gene

Selected SIMAP similar genes for VLDLR Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for VLDLR Gene

genes like me logo Genes that share paralogs with VLDLR: view

Variants for VLDLR Gene

Sequence variations from dbSNP and Humsavar for VLDLR Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type MAF
rs3421 -- 2,654,048(+) TTCTT(A/G)TCCAC utr-variant-3-prime
rs6143 Likely benign 2,645,719(+) TGGGC(C/T)GATCT reference, synonymous-codon
rs6144 -- 2,645,557(+) AACCC(A/T)GACTT intron-variant, splice-acceptor-variant
rs6145 Likely benign 2,651,962(+) AAGTA(G/T)ATTTC intron-variant
rs6146 - 2,644,802(+) GCTAC(A/G)AGTGT missense, reference

Structural Variations from Database of Genomic Variants (DGV) for VLDLR Gene

Variant ID Type Subtype PubMed ID
nsv892069 CNV Gain 21882294
nsv892070 CNV Gain 21882294
nsv892071 CNV Loss 21882294
nsv892072 CNV Loss 21882294
nsv824819 CNV Gain 20364138
nsv892073 CNV Gain 21882294
nsv527298 CNV Loss 19592680
nsv892074 CNV Loss 21882294
nsv892075 CNV Loss 21882294
nsv892076 CNV Gain 21882294

Relevant External Links for VLDLR Gene

HapMap Linkage Disequilibrium report
VLDLR
Human Gene Mutation Database (HGMD)
VLDLR

Disorders for VLDLR Gene

(1) OMIM Diseases for VLDLR Gene (192977)

UniProtKB/Swiss-Prot

VLDLR_HUMAN
  • Cerebellar ataxia, mental retardation, and dysequilibrium syndrome 1 (CAMRQ1) [MIM:224050]: A congenital, non-progressive cerebellar ataxia associated with disturbed equilibrium, delayed ambulation, mental retardation, cerebellar hypoplasia and mild cerebral gyral simplification. Additional features include short stature, strabismus, pes planus and, rarely, seizures. {ECO:0000269 PubMed:16080122}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for VLDLR Gene

(15) Novoseek inferred disease relationships for VLDLR Gene

Disease -log(P) Hits PubMed IDs
cerebellar hypoplasia 70.3 2
alzheimers disease 47.6 12
hypertriglyceridemia 38.3 2
senile plaques 33.3 3
atherosclerosis 28.8 3

Relevant External Links for VLDLR

GeneTests
VLDLR
GeneReviews
VLDLR
Genetic Association Database (GAD)
VLDLR
Human Genome Epidemiology (HuGE) Navigator
VLDLR
genes like me logo Genes that share disorders with VLDLR: view

Publications for VLDLR Gene

  1. Genetic association of the very low density lipoprotein (VLDL) receptor gene with sporadic Alzheimer's disease. (PMID: 7550352) Okuizumi K. … Tsuji S. (Nat. Genet. 1995) 3 23 49
  2. Human very-low-density lipoprotein receptor complementary DNA and deduced amino acid sequence and localization of its gene (VLDLR) to chromosome band 9p24 by fluorescence in situ hybridization. (PMID: 8020981) Oka K. … Chan L. (Genomics 1994) 3 4 23
  3. VLDL receptor polymorphism, cognitive impairment, and dementia. (PMID: 11342683) Helbecque N. … Amouyel P. (Neurology 2001) 3 23 49
  4. Association analysis of polymorphic CGG repeat in 5' UTR of the reelin and VLDLR genes with schizophrenia. (PMID: 12363388) Akahane A. … Nanko S. (Schizophr. Res. 2002) 3 23 49
  5. A cellular receptor of human rhinovirus type 2, the very-low-density lipoprotein receptor, binds to two neighboring proteins of the viral capsid. (PMID: 12857919) Neumann E. … Hewat E.A. (J. Virol. 2003) 3 4 23

Products for VLDLR Gene

Sources for VLDLR Gene

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