Human Gene LRP5 (ENST00000294304.12_4) from GENCODE V47lift37
  Description: LDL receptor related protein 5, transcript variant 1 (from RefSeq NM_002335.4)
Gencode Transcript: ENST00000294304.12_4
Gencode Gene: ENSG00000162337.12_8
Transcript (Including UTRs)
   Position: hg19 chr11:68,080,059-68,216,743 Size: 136,685 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr11:68,080,183-68,216,538 Size: 136,356 Coding Exon Count: 23 

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Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:68,080,059-68,216,743)mRNA (may differ from genome)Protein (1615 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LRP5_HUMAN
DESCRIPTION: RecName: Full=Low-density lipoprotein receptor-related protein 5; Short=LRP-5; Flags: Precursor;
FUNCTION: Component of the Wnt-Fzd-LRP5-LRP6 complex that triggers beta-catenin signaling through inducing aggregation of receptor- ligand complexes into ribosome-sized signalsomes. Cell-surface coreceptor of Wnt/beta-catenin signaling, which plays a pivotal role in bone formation. The Wnt-induced Fzd/LRP6 coreceptor complex recruits DVL1 polymers to the plasma membrane which, in turn, recruits the AXIN1/GSK3B-complex to the cell surface promoting the formation of signalsomes and inhibiting AXIN1/GSK3- mediated phosphorylation and destruction of beta-catenin. Appears be required for postnatal control of vascular regression in the eye. Required for posterior patterning of the epiblast during gastrulation.
SUBUNIT: Homodimer; disulfide-linked. Forms phosphorylated oligomer aggregates on Wnt-signaling (By similarity). Component of a Wnt-signaling complex that contains a WNT protein, a FZD protein and LRP5 or LRP6. Interacts with FZD8; the interaction is formed on WNT-binding and signaling. Interacts (via the phosphorylated PPPSP motif domains) with AXIN1; the interaction prevents inhibition of beta-catenin phosphorylation and signaling and is enhanced in the presence of GSK3B and WNT1 or WNT3A. Interacts (via beta-propeller regions 3 and 4) with DKK1; the interaction, enhanced by MESD and/or KREMEN, inhibits beta-catenin signaling by preventing GSK3-mediated phosphorylation of the PPPSP motifs and subsequent, AXIN1 binding. Interacts with MESD; the interaction prevents the formation of LRP5 aggregates, targets LRP5 to the plasma membrane and, when complexed with KREMEN2, increases DKK1 binding. Interacts with CSNK1E. Interacts with SOST; the interaction antagonizes canonical Wnt signaling. Interacts with APCDD1.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein. Endoplasmic reticulum (By similarity). Note=Chaperoned to the plasma membrane by MESD (By similarity).
TISSUE SPECIFICITY: Widely expressed, with the highest level of expression in the liver and in aorta.
PTM: Phosphorylation of cytoplasmic PPPSP motifs regulates the signal transduction of the Wnt signaling pathway through acting as a docking site for AXIN1 (By similarity).
POLYMORPHISM: Genetic variations in LRP5 define the bone mineral density quantitative trait locus 1 (BMND1) [MIM:601884]. Variance in bone mineral density influences bone mass and contributes to size determination in the general population.
DISEASE: Defects in LRP5 are the cause of vitreoretinopathy exudative type 4 (EVR4) [MIM:601813]. EVR4 is a disorder of the retinal vasculature characterized by an abrupt cessation of growth of peripheral capillaries, leading to an avascular peripheral retina. This may lead to compensatory retinal neovascularization, which is thought to be induced by hypoxia from the initial avascular insult. New vessels are prone to leakage and rupture causing exudates and bleeding, followed by scarring, retinal detachment and blindness. Clinical features can be highly variable, even within the same family. Patients with mild forms of the disease are asymptomatic, and their only disease related abnormality is an arc of avascular retina in the extreme temporal periphery. EVR4 inheritance can be autosomal dominant or recessive.
DISEASE: Genetic variations in LRP5 are a cause of susceptibility to osteoporosis (OSTEOP) [MIM:166710]; also known as senile osteoporosis or postmenopausal osteoporosis. Osteoporosis is characterized by reduced bone mass, disruption of bone microarchitecture without alteration in the composition of bone. Osteoporotic bones are more at risk of fracture.
DISEASE: Defects in LRP5 are the cause of osteoporosis- pseudoglioma syndrome (OPPG) [MIM:259770]; also known as osteogenesis imperfecta ocular form. OPPG is a recessive disorder characterized by very low bone mass and blindness. Individualy with OPPG are prone to develop bone fractures and deformations and have various eye abnormalities, including phthisis bulbi, retinal detachments, falciform folds or persistent vitreal vasculature.
DISEASE: Defects in LRP5 are a cause of high bone mass trait (HBM) [MIM:601884]. HBM is a rare phenotype characterized by exceptionally dense bones. HBM individuals show otherwise a completely normal skeletal structure and no other unusual clinical findings.
DISEASE: Defects in LRP5 are a cause of endosteal hyperostosis Worth type (WENHY) [MIM:144750]; also known as autosomal dominant osteosclerosis. WENHY is an autosomal dominant sclerosing bone dysplasia clinically characterized by elongation of the mandible, increased gonial angle, flattened forehead, and the presence of a slowly enlarging osseous prominence of the hard palate (torus palatinus). Serum calcium, phosphorus and alkaline phosphatase levels are normal. Radiologically, it is characterized by early thickening of the endosteum of long bones, the skull and of the mandible. With advancing age, the trabeculae of the metaphysis become thickened. WENHY becomes clinically and radiologically evident by adolescence, does not cause deformity except in the skull and mandible, and is not associated with bone pain or fracture. Affected patients have normal height, proportion, intelligence and longevity.
DISEASE: Defects in LRP5 are the cause of osteopetrosis autosomal dominant type 1 (OPTA1) [MIM:607634]. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. OPTA1 is characterized by generalized osteosclerosis most pronounced in the cranial vault. Patients are often asymptomatic, but some suffer from pain and hearing loss. It appears to be the only type of osteopetrosis not associated with an increased fracture rate.
DISEASE: Defects in LRP5 are the cause of van Buchem disease type 2 (VBCH2)[MIM:607636]. VBCH2 is an autosomal dominant sclerosing bone dysplasia characterized by cranial osteosclerosis, thickened calvaria and cortices of long bones, enlarged mandible and normal serum alkaline phosphatase levels.
SIMILARITY: Belongs to the LDLR family.
SIMILARITY: Contains 4 EGF-like domains.
SIMILARITY: Contains 3 LDL-receptor class A domains.
SIMILARITY: Contains 20 LDL-receptor class B repeats.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/LRP5";

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: LRP5
Diseases sorted by gene-association score: osteoporosis-pseudoglioma syndrome* (1724), hyperostosis, endosteal* (1677), osteopetrosis, autosomal dominant 1* (1580), van buchem disease, type 2* (1300), exudative vitreoretinopathy* (899), exudative vitreoretinopathy 4* (800), osteoporosis* (441), worth's syndrome* (417), osteosclerosis-developmental delay-craniosynostosis syndrome* (350), high bone mass trait* (341), exudative vitreoretinopathy 1* (316), van buchem disease* (281), polycystic liver disease* (263), lrp5-related autosomal dominant osteopetrosis* (100), lrp5-related familial exudative vitreoretinopathy, autosomal recessive* (100), lrp5-related familial exudative vitreoretinopathy, autosomal dominant* (100), idiopathic juvenile osteoporosis* (68), hyperostosis (25), osteopetrosis (19), norrie disease (19), craniodiaphyseal dysplasia (17), sclerosteosis (16), mass syndrome (15), retinal detachment (15), camurati-engelmann disease (12), glanders (9), osteopathia striata with cranial sclerosis (8), leukocoria (8), sialolithiasis (6), diabetes mellitus, insulin-dependent, 4 (6), hypotrichosis simplex (6), premenstrual tension (6), isolated microphthalmia (6), peroneal nerve paralysis (5), facial nerve disease (5), facial paralysis (5), bone fracture (5), vertebrobasilar insufficiency (5), bone remodeling disease (4), bone resorption disease (4), retinal vascular disease (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.64 RPKM in Minor Salivary Gland
Total median expression: 604.09 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -65.90124-0.531 Picture PostScript Text
3' UTR -42.60205-0.208 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011042 - 6-blade_b-propeller_TolB-like
IPR000742 - EG-like_dom
IPR023415 - LDLR_class-A_CS
IPR000033 - LDLR_classB_rpt
IPR002172 - LDrepeatLR_classA_rpt
IPR017049 - Low_density_Lipo_rcpt-rel_p5/6

Pfam Domains:
PF00057 - Low-density lipoprotein receptor domain class A
PF00058 - Low-density lipoprotein receptor repeat class B
PF14670 - Coagulation Factor Xa inhibitory site

SCOP Domains:
50729 - PH domain-like
50952 - Soluble quinoprotein glucose dehydrogenase
50956 - Thermostable phytase (3-phytase)
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like
57424 - LDL receptor-like module
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on O75197
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017147 Wnt-protein binding
GO:0042813 Wnt-activated receptor activity
GO:0071936 coreceptor activity involved in Wnt signaling pathway
GO:1904928 coreceptor activity involved in canonical Wnt signaling pathway
GO:0019534 toxin transporter activity

Biological Process:
GO:0001702 gastrulation with mouth forming second
GO:0001944 vasculature development
GO:0002053 positive regulation of mesenchymal cell proliferation
GO:0002076 osteoblast development
GO:0006007 glucose catabolic process
GO:0006897 endocytosis
GO:0007275 multicellular organism development
GO:0008203 cholesterol metabolic process
GO:0008217 regulation of blood pressure
GO:0008284 positive regulation of cell proliferation
GO:0009314 response to radiation
GO:0009952 anterior/posterior pattern specification
GO:0016055 Wnt signaling pathway
GO:0033690 positive regulation of osteoblast proliferation
GO:0035019 somatic stem cell population maintenance
GO:0035108 limb morphogenesis
GO:0035426 extracellular matrix-cell signaling
GO:0042074 cell migration involved in gastrulation
GO:0042632 cholesterol homeostasis
GO:0042733 embryonic digit morphogenesis
GO:0042981 regulation of apoptotic process
GO:0043434 response to peptide hormone
GO:0044332 Wnt signaling pathway involved in dorsal/ventral axis specification
GO:0045600 positive regulation of fat cell differentiation
GO:0045668 negative regulation of osteoblast differentiation
GO:0045840 positive regulation of mitotic nuclear division
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046849 bone remodeling
GO:0046850 regulation of bone remodeling
GO:0048539 bone marrow development
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0060033 anatomical structure regression
GO:0060042 retina morphogenesis in camera-type eye
GO:0060070 canonical Wnt signaling pathway
GO:0060348 bone development
GO:0060349 bone morphogenesis
GO:0060444 branching involved in mammary gland duct morphogenesis
GO:0060603 mammary gland duct morphogenesis
GO:0060612 adipose tissue development
GO:0060764 cell-cell signaling involved in mammary gland development
GO:0060828 regulation of canonical Wnt signaling pathway
GO:0061178 regulation of insulin secretion involved in cellular response to glucose stimulus
GO:0061299 retina vasculature morphogenesis in camera-type eye
GO:0061304 retinal blood vessel morphogenesis
GO:0071901 negative regulation of protein serine/threonine kinase activity
GO:1902262 apoptotic process involved in blood vessel morphogenesis

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0043235 receptor complex
GO:1990851 Wnt-Frizzled-LRP5/6 complex
GO:1990909 Wnt signalosome


-  Descriptions from all associated GenBank mRNAs
  AB017498 - Homo sapiens LRP5 mRNA for Lipoprotein Receptor Related Protein 5, complete cds.
LF385266 - JP 2014500723-A/192769: Polycomb-Associated Non-Coding RNAs.
AF077820 - Homo sapiens LDL receptor member LR3 mRNA, complete cds.
BC150595 - Homo sapiens low density lipoprotein receptor-related protein 5, mRNA (cDNA clone MGC:183505 IMAGE:9056965), complete cds.
AF064548 - Homo sapiens low-density lipoprotein receptor-related protein 5 (LRP5) mRNA, complete cds.
BC098397 - Homo sapiens low density lipoprotein receptor-related protein 5, mRNA (cDNA clone IMAGE:30527697).
MA620843 - JP 2018138019-A/192769: Polycomb-Associated Non-Coding RNAs.
AF088027 - Homo sapiens full length insert cDNA clone ZC19E01.
LF344187 - JP 2014500723-A/151690: Polycomb-Associated Non-Coding RNAs.
LF344186 - JP 2014500723-A/151689: Polycomb-Associated Non-Coding RNAs.
LF344183 - JP 2014500723-A/151686: Polycomb-Associated Non-Coding RNAs.
LF344180 - JP 2014500723-A/151683: Polycomb-Associated Non-Coding RNAs.
LF344179 - JP 2014500723-A/151682: Polycomb-Associated Non-Coding RNAs.
LF344178 - JP 2014500723-A/151681: Polycomb-Associated Non-Coding RNAs.
LF344175 - JP 2014500723-A/151678: Polycomb-Associated Non-Coding RNAs.
MA579764 - JP 2018138019-A/151690: Polycomb-Associated Non-Coding RNAs.
MA579763 - JP 2018138019-A/151689: Polycomb-Associated Non-Coding RNAs.
MA579760 - JP 2018138019-A/151686: Polycomb-Associated Non-Coding RNAs.
MA579757 - JP 2018138019-A/151683: Polycomb-Associated Non-Coding RNAs.
MA579756 - JP 2018138019-A/151682: Polycomb-Associated Non-Coding RNAs.
MA579755 - JP 2018138019-A/151681: Polycomb-Associated Non-Coding RNAs.
MA579752 - JP 2018138019-A/151678: Polycomb-Associated Non-Coding RNAs.
LF344173 - JP 2014500723-A/151676: Polycomb-Associated Non-Coding RNAs.
DQ570511 - Homo sapiens piRNA piR-30623, complete sequence.
LF344172 - JP 2014500723-A/151675: Polycomb-Associated Non-Coding RNAs.
JD065066 - Sequence 46090 from Patent EP1572962.
LF344170 - JP 2014500723-A/151673: Polycomb-Associated Non-Coding RNAs.
LF344169 - JP 2014500723-A/151672: Polycomb-Associated Non-Coding RNAs.
LF344168 - JP 2014500723-A/151671: Polycomb-Associated Non-Coding RNAs.
LF344167 - JP 2014500723-A/151670: Polycomb-Associated Non-Coding RNAs.
LF344166 - JP 2014500723-A/151669: Polycomb-Associated Non-Coding RNAs.
LF344164 - JP 2014500723-A/151667: Polycomb-Associated Non-Coding RNAs.
LF344161 - JP 2014500723-A/151664: Polycomb-Associated Non-Coding RNAs.
LF344160 - JP 2014500723-A/151663: Polycomb-Associated Non-Coding RNAs.
MF459052 - Homo sapiens LRP5, partial sequence.
LF344158 - JP 2014500723-A/151661: Polycomb-Associated Non-Coding RNAs.
JD325795 - Sequence 306819 from Patent EP1572962.
LF344157 - JP 2014500723-A/151660: Polycomb-Associated Non-Coding RNAs.
JD544613 - Sequence 525637 from Patent EP1572962.
JD220564 - Sequence 201588 from Patent EP1572962.
MA579750 - JP 2018138019-A/151676: Polycomb-Associated Non-Coding RNAs.
MA579749 - JP 2018138019-A/151675: Polycomb-Associated Non-Coding RNAs.
MA579747 - JP 2018138019-A/151673: Polycomb-Associated Non-Coding RNAs.
MA579746 - JP 2018138019-A/151672: Polycomb-Associated Non-Coding RNAs.
MA579745 - JP 2018138019-A/151671: Polycomb-Associated Non-Coding RNAs.
MA579744 - JP 2018138019-A/151670: Polycomb-Associated Non-Coding RNAs.
MA579743 - JP 2018138019-A/151669: Polycomb-Associated Non-Coding RNAs.
MA579741 - JP 2018138019-A/151667: Polycomb-Associated Non-Coding RNAs.
MA579738 - JP 2018138019-A/151664: Polycomb-Associated Non-Coding RNAs.
MA579737 - JP 2018138019-A/151663: Polycomb-Associated Non-Coding RNAs.
MA579735 - JP 2018138019-A/151661: Polycomb-Associated Non-Coding RNAs.
MA579734 - JP 2018138019-A/151660: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O75197 (Reactome details) participates in the following event(s):

R-HSA-1458875 WNT binds to FZD and LRP5/6
R-HSA-3769397 SOST binds LRP5/6
R-HSA-3769401 DKK and KRM bind LRP5/6
R-HSA-1504188 FZD recruits DVL to the receptor complex
R-HSA-4641249 ZNRF3,RNF43 binds the FZD:LRP5/6 receptor complex
R-HSA-4641236 USP8 deubiquitinates FZD to potentiate WNT signaling
R-HSA-4641253 ZNRF3 ubiquitinates FZD to promote its downregulation
R-HSA-201691 Phosphorylation of LRP5/6 cytoplasmic domain by CSNKI
R-NUL-1458902 frog CK1gamma phosphorylates LRP5/6
R-HSA-201677 Phosphorylation of LRP5/6 cytoplasmic domain by membrane-associated GSK3beta
R-HSA-1504186 DVL recruits GSK3beta:AXIN1 to the receptor complex
R-HSA-5339717 Misspliced LRP5 mutants have enhanced beta-catenin-dependent signaling
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-3772470 Negative regulation of TCF-dependent signaling by WNT ligand antagonists
R-HSA-4791275 Signaling by WNT in cancer
R-HSA-4641263 Regulation of FZD by ubiquitination
R-HSA-5340588 RNF mutants show enhanced WNT signaling and proliferation
R-HSA-195721 Signaling by WNT
R-HSA-4641262 Disassembly of the destruction complex and recruitment of AXIN to the membrane
R-HSA-5663202 Diseases of signal transduction
R-HSA-162582 Signal Transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000294304.1, ENST00000294304.10, ENST00000294304.11, ENST00000294304.2, ENST00000294304.3, ENST00000294304.4, ENST00000294304.5, ENST00000294304.6, ENST00000294304.7, ENST00000294304.8, ENST00000294304.9, LR3 , LRP5 , LRP5_HUMAN, LRP7 , NM_002335, O75197, Q96TD6, Q9UES7, Q9UP66, uc317lgm.1, uc317lgm.2
UCSC ID: ENST00000294304.12_4
RefSeq Accession: NM_002335.4
Protein: O75197 (aka LRP5_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.