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LRP5 low density lipoprotein receptor-related protein 5 [ Homo sapiens (human) ]

Gene ID: 4041, updated on 30-Jun-2015
Official Symbol
LRP5provided by HGNC
Official Full Name
low density lipoprotein receptor-related protein 5provided by HGNC
Primary source
HGNC:HGNC:6697
See related
Ensembl:ENSG00000162337; HPRD:04616; MIM:603506; Vega:OTTHUMG00000167570
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; OPTA1; 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]
Orthologs
See LRP5 in Epigenomics, MapViewer
Location:
11q13.4
Exon count:
27
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 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 uncharacterized LOC102724209 Neighboring gene chromosome 11 open reading frame 24 Neighboring gene uncharacterized LOC101928175 Neighboring gene protein phosphatase 6, regulatory subunit 3 Neighboring gene galanin/GMAP prepropeptide

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Bone mineral density quantitative trait locus 1
MedGen: C1866079 OMIM: 601884 GeneReviews: Not available
Compare labs
Exudative vitreoretinopathy 4 Compare labs
Familial exudative vitreoretinopathy Compare labs
Osteopetrosis autosomal dominant type 1
MedGen: C1843330 OMIM: 607634 GeneReviews: Not available
Compare labs
Osteoporosis
MedGen: C0029458 OMIM: 166710 GeneReviews: Not available
Compare labs
Osteoporosis with pseudoglioma
MedGen: C0432252 OMIM: 259770 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
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Wnt-activated receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
 
Wnt-protein binding IBA
Inferred from Biological aspect of Ancestor
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NOT toxin transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
Wnt signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
Wnt signaling pathway involved in dorsal/ventral axis specification IDA
Inferred from Direct Assay
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 IEA
Inferred from Electronic Annotation
more info
 
apoptotic process involved in patterning of blood vessels IEA
Inferred from Electronic Annotation
more info
 
bone marrow development IMP
Inferred from Mutant Phenotype
more info
PubMed 
bone morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
bone remodeling IEA
Inferred from Electronic Annotation
more info
 
branching involved in mammary gland duct morphogenesis IEA
Inferred from Electronic Annotation
more info
 
canonical Wnt signaling pathway IDA
Inferred from Direct Assay
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 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 IEA
Inferred from Electronic Annotation
more info
 
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
 
positive regulation of canonical Wnt signaling pathway TAS
Traceable Author Statement
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 proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of sequence-specific DNA binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription from RNA polymerase II promoter 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 bone remodeling IEA
Inferred from Electronic Annotation
more info
 
regulation of canonical Wnt signaling pathway 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
 
retina morphogenesis in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
retinal blood vessel morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
somatic stem cell maintenance IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
mitochondrion 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 
Preferred Names
low-density lipoprotein receptor-related protein 5
Names
low density lipoprotein receptor-related protein 7

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_015835.1 RefSeqGene

    Range
    4970..141636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001291902.1NP_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, BC098397, BC150595, DN999254
    UniProtKB/Swiss-Prot
    O75197
    Conserved Domains (3) 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 ...
    pfam14670
    Location:325360
    FXa_inhibition; Coagulation Factor Xa inhibitory site
  2. NM_002335.3NP_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, BC150595, DN999254
    Consensus CDS
    CCDS8181.1
    UniProtKB/Swiss-Prot
    O75197
    Related
    ENSP00000294304, OTTHUMP00000236183, ENST00000294304, OTTHUMT00000395088
    Conserved Domains (6) 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 ...
    pfam00058
    Location:163203
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:299336
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cd05819
    Location:686712
    NHL; NHL repeat [structural motif]
    cl18310
    Location:685878
    NHL; NHL repeat unit of beta-propeller proteins

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p2 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011545029.1XP_011543331.1  

    Conserved Domains (6) 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 ...
    pfam00058
    Location:172212
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:308345
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cd05819
    Location:695721
    NHL; NHL repeat [structural motif]
    cl18310
    Location:694887
    NHL; NHL repeat unit of beta-propeller proteins
  2. XM_011545030.1XP_011543332.1  

    Conserved Domains (6) 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 ...
    pfam00058
    Location:172212
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:308345
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cd05819
    Location:695721
    NHL; NHL repeat [structural motif]
    cl18310
    Location:694887
    NHL; NHL repeat unit of beta-propeller proteins
  3. XM_011545031.1XP_011543333.1  

    Conserved Domains (6) 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 ...
    pfam00058
    Location:172212
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:308345
    FXa_inhibition; Coagulation Factor Xa inhibitory site
    cd05819
    Location:695721
    NHL; NHL repeat [structural motif]
    cl18310
    Location:694887
    NHL; NHL repeat unit of beta-propeller proteins
  4. XM_005273994.2XP_005274051.1  

    Conserved Domains (4) 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 ...
    pfam00058
    Location:163203
    Ldl_recept_b; Low-density lipoprotein receptor repeat class B
    pfam14670
    Location:299336
    FXa_inhibition; Coagulation Factor Xa inhibitory site

RNA

  1. XR_949926.1 RNA Sequence

  2. XR_949925.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018922.2 Alternate CHM1_1.1

    Range
    67964539..68100925
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)