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LRP5 LDL receptor related protein 5 [ Homo sapiens (human) ]

Gene ID: 4041, updated on 1-Aug-2020

Summary

Official Symbol
LRP5provided by HGNC
Official Full Name
LDL receptor related protein 5provided by HGNC
Primary source
HGNC:HGNC:6697
See related
Ensembl:ENSG00000162337 MIM:603506
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
HBM; LR3; OPS; EVR1; EVR4; LRP7; OPPG; BMND1; LRP-5; LRP-7; OPTA1; PCLD4; VBCH2
Summary
This gene encodes a transmembrane low-density lipoprotein receptor that binds and internalizes ligands in the process of receptor-mediated endocytosis. This protein also acts as a co-receptor with Frizzled protein family members for transducing signals by Wnt proteins and was originally cloned on the basis of its association with type 1 diabetes mellitus in humans. This protein plays a key role in skeletal homeostasis and many bone density related diseases are caused by mutations in this gene. Mutations in this gene also cause familial exudative vitreoretinopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
Expression
Ubiquitous expression in fat (RPKM 20.9), small intestine (RPKM 15.5) and 24 other tissues See more
Orthologs

Genomic context

See LRP5 in Genome Data Viewer
Location:
11q13.2
Exon count:
28
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (68298866..68449275)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (68080077..68216743)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369363 Neighboring gene chromosome 11 open reading frame 24 Neighboring gene protein phosphatase 6 regulatory subunit 3 Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 pseudogene 2 Neighboring gene uncharacterized LOC107984343 Neighboring gene galanin and GMAP prepropeptide

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

Associated conditions

Description Tests
Autosomal dominant osteopetrosis 1
MedGen: C1843330 OMIM: 607634 GeneReviews: Not available
Compare labs
Bone mineral density quantitative trait locus 1
MedGen: C1866079 OMIM: 601884 GeneReviews: Not available
Compare labs
Exudative vitreoretinopathy 1 Compare labs
Exudative vitreoretinopathy 4 Compare labs
Osteoporosis with pseudoglioma
MedGen: C0432252 OMIM: 259770 GeneReviews: Not available
Compare labs
POLYCYSTIC LIVER DISEASE 4 WITH OR WITHOUT KIDNEY CYSTS
MedGen: C4693479 OMIM: 617875 GeneReviews: Not available
Compare labs
Postmenopausal osteoporosis
MedGen: C0029458 OMIM: 166710 GeneReviews: Not available
Compare labs
Van Buchem disease type 2
MedGen: C1843323 OMIM: 607636 GeneReviews: Not available
Compare labs
Worth disease
MedGen: C0432273 OMIM: 144750 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2015-04-02)

ClinGen Genome Curation Page
Haploinsufficency

Some evidence for dosage pathogenicity (Last evaluated (2015-04-02)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
NHGRI GWA Catalog
Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
NHGRI GWA Catalog
Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
NHGRI GWA Catalog
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Wnt-activated receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
Wnt-activated receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Wnt-protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Wnt-protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Wnt-protein binding TAS
Traceable Author Statement
more info
PubMed 
coreceptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
coreceptor activity involved in Wnt signaling pathway IPI
Inferred from Physical Interaction
more info
PubMed 
coreceptor activity involved in canonical Wnt signaling pathway NAS
Non-traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NOT toxin transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
adipose tissue development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
adipose tissue development IMP
Inferred from Mutant Phenotype
more info
PubMed 
anatomical structure regression IEA
Inferred from Electronic Annotation
more info
 
anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apoptotic process involved in blood vessel morphogenesis IEA
Inferred from Electronic Annotation
more info
 
bone marrow development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bone marrow development IMP
Inferred from Mutant Phenotype
more info
PubMed 
bone morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
bone morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
bone remodeling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
branching involved in mammary gland duct morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
canonical Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
canonical Wnt signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
canonical Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell migration involved in gastrulation IEA
Inferred from Electronic Annotation
more info
 
cell-cell signaling involved in mammary gland development IEA
Inferred from Electronic Annotation
more info
 
cholesterol homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cholesterol homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
cholesterol metabolic process IEA
Inferred from Electronic Annotation
more info
 
embryonic digit morphogenesis IEA
Inferred from Electronic Annotation
more info
 
endocytosis IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix-cell signaling IEA
Inferred from Electronic Annotation
more info
 
gastrulation with mouth forming second IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glucose catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein serine/threonine kinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
osteoblast development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of fat cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of mesenchymal cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of mitotic nuclear division IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of osteoblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of osteoblast proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
regulation of blood pressure IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of insulin secretion involved in cellular response to glucose stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to peptide hormone IEA
Inferred from Electronic Annotation
more info
 
response to radiation IEA
Inferred from Electronic Annotation
more info
 
retina morphogenesis in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
retinal blood vessel morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retinal blood vessel morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
somatic stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
toxin transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Wnt signalosome NAS
Non-traceable Author Statement
more info
PubMed 
Wnt-Frizzled-LRP5/6 complex TAS
Traceable Author Statement
more info
PubMed 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma 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 

General protein information

Preferred Names
low-density lipoprotein receptor-related protein 5
Names
low density lipoprotein receptor-related protein 5
low density lipoprotein receptor-related protein 7

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_015835.2 RefSeqGene

    Range
    4952..141636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001291902.2NP_001278831.1  low-density lipoprotein receptor-related protein 5 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in its 5' UTR and uses and alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AB017498, AI583742, AP000807, AP002813, BC098397, BC150595, DN999254
    UniProtKB/Swiss-Prot
    O75197
    Conserved Domains (6) summary
    smart00135
    Location:129171
    LY; Low-density lipoprotein-receptor YWTD domain
    cd00112
    Location:755789
    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 ...
    cd05819
    Location:139175
    NHL; NHL repeat [structural motif]
    pfam00057
    Location:677714
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam14670
    Location:2459
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl18310
    Location:104297
    NHL; NHL repeat unit of beta-propeller proteins
  2. NM_002335.4NP_002326.2  low-density lipoprotein receptor-related protein 5 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002326.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AB017498, AI583742, AP000807, AP002813, BC150595, DN999254
    Consensus CDS
    CCDS8181.1
    UniProtKB/Swiss-Prot
    O75197
    Related
    ENSP00000294304.6, ENST00000294304.12
    Conserved Domains (7) summary
    smart00135
    Location:408450
    LY; Low-density lipoprotein-receptor YWTD domain
    cd00112
    Location:13361370
    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 ...
    cd05819
    Location:720756
    NHL; NHL repeat [structural motif]
    pfam00057
    Location:12581295
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:163203
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:299336
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl18310
    Location:685878
    NHL; NHL repeat unit of beta-propeller proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    68298866..68449275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545029.1XP_011543331.1  low-density lipoprotein receptor-related protein 5 isoform X1

    Conserved Domains (7) summary
    smart00135
    Location:417459
    LY; Low-density lipoprotein-receptor YWTD domain
    cd00112
    Location:13451379
    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 ...
    cd05819
    Location:729765
    NHL; NHL repeat [structural motif]
    pfam00057
    Location:12671304
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:172212
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:308345
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl18310
    Location:694887
    NHL; NHL repeat unit of beta-propeller proteins
  2. XM_011545030.1XP_011543332.1  low-density lipoprotein receptor-related protein 5 isoform X3

    Conserved Domains (7) summary
    smart00135
    Location:417459
    LY; Low-density lipoprotein-receptor YWTD domain
    cd00112
    Location:13451379
    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 ...
    cd05819
    Location:729765
    NHL; NHL repeat [structural motif]
    pfam00057
    Location:12671304
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:172212
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:308345
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl18310
    Location:694887
    NHL; NHL repeat unit of beta-propeller proteins
  3. XM_011545031.1XP_011543333.1  low-density lipoprotein receptor-related protein 5 isoform X4

    Conserved Domains (7) summary
    smart00135
    Location:417459
    LY; Low-density lipoprotein-receptor YWTD domain
    cd00112
    Location:13451379
    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 ...
    cd05819
    Location:729765
    NHL; NHL repeat [structural motif]
    pfam00057
    Location:12671304
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:172212
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:308345
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl18310
    Location:694887
    NHL; NHL repeat unit of beta-propeller proteins
  4. XM_005273994.2XP_005274051.1  low-density lipoprotein receptor-related protein 5 isoform X2

    Conserved Domains (7) summary
    smart00135
    Location:408450
    LY; Low-density lipoprotein-receptor YWTD domain
    cd00112
    Location:13361370
    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 ...
    cd05819
    Location:720756
    NHL; NHL repeat [structural motif]
    pfam00057
    Location:12581295
    Ldl_recept_a; Low-density lipoprotein receptor domain class A
    pfam00058
    Location:163203
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:299336
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cl18310
    Location:685878
    NHL; NHL repeat unit of beta-propeller proteins
  5. XM_017017735.1XP_016873224.1  low-density lipoprotein receptor-related protein 5 isoform X5

  6. XM_017017736.1XP_016873225.1  low-density lipoprotein receptor-related protein 5 isoform X6

RNA

  1. XR_949926.2 RNA Sequence

  2. XR_949925.2 RNA Sequence

    Related
    ENST00000529993.5
  3. XR_001747874.1 RNA Sequence

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