rs3736228

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This is a protein-altering variant in the LRP5 gene.

Key Literature Trait Associations

Osteoporosis and Fracture Risk

rs3736228 causes a missense substitution p.Ala1330Val in LRP5, a co-receptor in the WNT/beta-catenin signalling pathway essential for osteoblast function. The Val allele disrupts a propeller domain contact required for efficient WNT ligand binding, reducing downstream beta-catenin signalling. Meta-analyses show that A/A homozygotes have significantly higher lumbar spine BMD than T-allele carriers. The T allele increases fracture/osteoporosis risk with OR 1.19 per allele, rising to OR 1.76 in homozygous T/T individuals.

Allele T
OR
β -0.080
p 2.0e-26
N 83,894
Meta-analysisLarge GWAS
European and East Asian
Allele T
OR 1.19
p 1.4e-2
Candidate gene study
Allele T
OR 1.06
p 1.0e-21
N 562,258
Large GWAS
European
Allele T
OR
p
N 16,705
Meta-analysis
multi-ancestry
Richards JB et al. Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study. Lancet (london, England) 371(9623):1505-12 (2008)
Allele T
OR 1.30
β -0.130
p 6.0e-12
N 8,557
Large GWAS
European

Appendicular lean mass

The rs3736228 T allele in LRP5 is associated with reduced appendicular lean mass (ALM), a measure of skeletal muscle mass in the limbs, in a large GWAS of 85,750 European adults (β=−0.084 units, p=1×10⁻⁹). This finding likely reflects pleiotropic effects of Wnt/LRP5 signaling on musculoskeletal tissue beyond bone, as the pathway plays roles in muscle development and maintenance. The clinical significance of this association is less established than the bone density signal, and the effect size is modest.

Hernandez Cordero AI et al. Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2. American Journal of Human Genetics 105(6):1222-1236 (2019)
Allele T
OR
β -0.084 ±0.013
p 1.0e-9
N 85,750
Large GWAS
European

GWAS Catalog Trait Associations (3)

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

ClinVar annotation

Benign★★★
12 submitters27 publications

not specified; not provided; Osteoporosis with pseudoglioma; Osteogenesis imperfecta; Uveal melanoma; Uterine carcinosarcoma; Adrenocortical carcinoma, hereditary; Colorectal cancer; Disorder of bone

View on ClinVar →

Research that mentions this SNP (9)

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
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
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
Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening
AssociationN=1,000Zhang YP et al.(2010)· Osteoporosis International

A replication study of 139 SNPs from three prior genome-wide association studies of bone mineral density in an independent sample of 1,000 unrelated US whites confirmed 38 SNPs (27% replication rate). Two SNPs achieved the most significant replication: rs3762397 in NR5A2 and rs3736228 in LRP5. Ten SNPs achieved combined p-values less than 3.6×10⁻⁴ across datasets, including rs3736228 (LRP5) with combined p=5.3×10⁻¹² for spinal BMD.

Traits studied:Bone mineral densityFemoral neck bone mineral density (FNBMD)Hip bone mineral density (HIPBMD)OsteoporosisSpinal bone mineral density (SPNBMD)
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
Complexity of the genotype-phenotype correlation in familial exudative vitreoretinopathy with mutations in theLRP5and/orFZD4genes
Case reportN=56Minghui Qin et al.(2005)· Human Mutation

Mutation screening of 56 unrelated FEVR patients identified 10 novel mutations in LRP5 and FZD4 genes (detection rate 25%, 14/56). Nine missense or frameshift mutations were found in LRP5 including c.1330C>T [p.R444C] and compound heterozygous mutations, while two mutations were found in FZD4. Notably, a synergistic effect was observed in a family carrying both c.1330C>T [p.R444C] in LRP5 and c.1250G>A [p.R417Q] in FZD4. Reduced bone density was identified as a feature specific to LRP5 mutations.

Traits studied:Bone mineral densityFamilial exudative vitreoretinopathy (FEVR)

Gene information from NCBI Gene. Variant classifications from ClinVar.

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