rs4988321

This is a variant in the LRP5 gene that changes a valine to an methionine.

GWAS Catalog Trait Associations (9)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

heel bone mineral density

Morris JA et al. An atlas of genetic influences on osteoporosis in humans and mice. Nature Genetics 51(2):258-266 (2019)
Allele G
OR 0.06
p 2.0e-35
N 426,824
Large GWAS
European
Allele G
OR 0.07
p 3.0e-23
N 142,487
Large GWAS
European

pelvis bone mineral density

Allele A
OR 0.17
p 1.0e-20
N 31,873
Large GWAS
European

bone tissue density

Allele A
OR 0.17
p 3.0e-20
N 31,986
Large GWAS
European

trunk bone mineral density

Allele A
OR 0.17
p 2.0e-19
N 31,986
Large GWAS
European

spine bone mineral density

Allele A
OR 0.17
p 1.0e-18
N 31,986
Large GWAS
European

bone fracture

Nethander M et al. An atlas of genetic determinants of forearm fracture. Nature Genetics 55(11):1820-1830 (2023)
Allele A
OR 1.12
p 3.0e-17
N 1,020,094
Large GWAS
European

forced expiratory volume

Allele G
OR 0.03
p 8.0e-15
N 373,397
Large GWAS
European

BMI-adjusted hip circumference

Allele A
OR 0.04
p 2.0e-10
N 219,872
Major Consortium StudyLarge GWAS
European

osteoporosis

Verma A et al. Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele G
OR 0.16
p 9.0e-15
N 442,537
Major Consortium StudyLarge GWAS
European

ClinVar annotation

Uncertain Significance★★★
18 submitters34 publications

Autosomal dominant osteopetrosis 1 (OPTA1); Bone mineral density quantitative trait locus 1 (BMND1); Exudative vitreoretinopathy 1 (EVR1); Exudative vitreoretinopathy 4 (EVR4); Increased bone mineral density; Osteogenesis imperfecta (OI); Osteoporosis; Osteoporosis with pseudoglioma (OPPG); Polycystic liver disease 4 with or without kidney cysts; Retinal dystrophy; Worth disease; not specified

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Research that mentions this SNP (7)

Polymorphism of LRP5, but not of TNFRSF11B, is associated with a decrease in bone mineral density in postmenopausal maya‐mestizo women
AssociationN=483Thelma Canto‐Cetina et al.(2013)· American Journal of Human Biology

A case-control study of 483 postmenopausal women examined associations between three SNPs (rs3736228 and rs4988321 in LRP5, rs1800795 in IL-6) and osteoporosis/osteopenia at multiple skeletal sites using dual-energy X-ray absorptiometry and real-time PCR genotyping. LRP5 polymorphisms were significantly associated with osteoporosis at the lumbar spine (rs3736228 p=0.018, rs4988321 p=0.032) and proximal femur (rs3736228 p=0.008, rs4988321 p=0.003), while IL-6 rs1800795 GG genotype was a risk factor for hip osteoporosis (p=0.045 for genotypes). The findings support LRP5 and IL-6 polymorphisms as contributing to postmenopausal osteoporosis development.

Traits studied:Bone mineral densityOsteopeniaOsteoporosis
Genetic variation in the SMAD3 gene is associated with hip and knee osteoarthritis
AssociationN=206Ana M. Valdes et al.(2010)· Arthritis &amp; Rheumatism

This Japanese cohort study of 206 elderly women (mean age 69.7 years) from the Obuse registry investigated associations between genetic variants and osteoarthritis (OA) prevalence. LRP5 rs3736228 showed significant associations with knee/hip OA (OR 7.28, 95% CI 2.22-28.08) and osteoporosis (OR 5.24, 95% CI 0.95-26.98). MTHFR rs1801133 showed a protective association with knee OA prevalence (OR 0.58, 95% CI 0.35-0.97). Other variants (LRP5 rs312009, GDF5 rs143383, SMAD3 rs12901499) showed no significant associations.

Traits studied:Hip osteoarthritisKnee osteoarthritisOsteoarthritisOsteoporosis
The role of cigarette smoking and statins in the development of postmenopausal osteoporosis: a pilot study utilizing the Marshfield Clinic Personalized Medicine Cohort
AssociationN=602Giampietro PF et al.(2010)· Osteoporosis International

A nested case-control study of 309 postmenopausal osteoporotic women and 293 controls found that the IL6 -634G>C SNP (rs1800796) was associated with osteoporosis (OR 2.51, p=0.0047), independent of smoking or statin use. Additionally, the LRP5 C135242T SNP (rs545382) showed association with osteoporosis specifically in cigarette smokers (OR 2.8, p=0.03), suggesting a gene-environment interaction.

Traits studied:Bone mineral densityOsteoporosis
Common Genetic Variation in the DKK1 Gene is Associated with Hip Axis Length but not with Bone Mineral Density and Bone Turnover Markers in Young Adult Men: Results from the Odense Androgen Study
AssociationN=783Elke Piters et al.(2010)· Calcified Tissue International

A population-based candidate gene study of 783 young Danish men examining associations between DKK1 polymorphisms and bone phenotypes. The study found no association between DKK1 variants and bone mineral density (BMD) or bone turnover markers, but identified a significant association between rs1569198 and hip axis length (HAL, P=0.012; P=0.004 in nonsedentary men), with each minor allele increasing HAL by 0.74-0.96 mm. The association with HAL was independent of BMD and height, suggesting a potential effect on hip fracture risk.

Traits studied:Bone mineral density (BMD)Bone turnover markersHip axis length (HAL)Hip fracture riskHip geometryOsteoporosis
LRP5 Polymorphisms and Response to Risedronate Treatment in Osteoporotic Men
AssociationN=249Marcin Kruk et al.(2009)· Calcified Tissue International

This study examined LRP5 polymorphisms in relation to bone mineral density (BMD) and response to risedronate treatment in 249 osteoporotic or osteopenic men over 24 months. The A1330V polymorphism was significantly associated with hip BMD at baseline, with Val/Val homozygotes having 8.4% higher total-hip BMD (P=0.009), 7.5% higher femoral neck BMD (P=0.015), and 11.7% higher trochanter BMD (P=0.002) compared to other genotype groups. However, no association was found between either LRP5 polymorphism (A1330V or V667M) and response to bisphosphonate treatment.

Traits studied:Bone mineral densityOsteoporosisResponse to risedronate treatment
Large-Scale Analysis of Association Between &lt;emph type="ital"&gt;LRP5&lt;/emph&gt; and &lt;emph type="ital"&gt;LRP6&lt;/emph&gt; Variants and Osteoporosis
AssociationN=37,534van Meurs JB et al.(2008)· JAMA

Large-scale GENOMOS consortium analysis of 37,534 individuals found that two common LRP5 variants (Val667Met: rs4988321 and Ala1330Val: rs3736228) are significantly associated with reduced bone mineral density and increased fracture risk. The Met667 allele was associated with 20 mg/cm² lower lumbar spine BMD (P=3.3×10⁻⁸) and OR 1.26 for vertebral fractures; Val1330 showed 14 mg/cm² lower lumbar spine BMD (P=2.6×10⁻⁹) and OR 1.12 for vertebral fractures. The LRP6 variant (Ile1062Val: rs2302685) was not associated with osteoporosis phenotypes.

Traits studied:Bone mineral densityFracture riskOsteoporosisVertebral fractures
Polymorphisms in the Low-Density Lipoprotein Receptor-Related Protein 5 (LRP5) Gene Are Associated with Peak Bone Mass in Non-sedentary Men: Results from the Odense Androgen Study
AssociationN=783Brixen K. et al.(2007)· Calcified Tissue International

This study investigated two polymorphisms in the LRP5 gene (Ala1330Val rs3736228 and Val667Met rs4988321) and their association with peak bone mass in 783 young Danish men. In non-sedentary (physically active) subjects, each copy of the T-allele at Ala1330Val was associated with a -0.21 Z-score change in lumbar spine BMD (p=0.02), and each A-allele at Val667Met showed a -0.26 Z-score change (p=0.04). The findings suggest a gene-environment interaction between LRP5 polymorphisms and physical activity in determining peak bone mass.

Traits studied:Bone mineral densityOsteoporosisPeak bone mass

About LRP5

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]

View all LRP5 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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