Sugi Variant

Sugi Variant/LRP5

LRP5 — 2517 ClinVar variants

All ClinVar germline LRP5 variants across every classification, each assembled from ClinVar, gnomAD, AlphaMissense, conservation and more. 1164 flagged for review →

105 Pathogenic · 27 Pathogenic/Likely pathogenic · 82 Likely pathogenic · 154 Conflicting · 79 Benign · 56 Benign/Likely benign · 800 Likely benign · 1214 Uncertain significance

Full LRP5 gene report on Sugi Atlas → Gene function, pathways, protein structure, constraint & interactions

⚑ Evidence disagreements 1164

Variants where the independent computational evidence doesn't line up with the clinical picture — a QC signal for a second look, not a reclassification.

Predictors vs ClinVar 3

ClinVar calls these pathogenic, but the computational predictors lean tolerated — the highest-value review flag.

Predictors agree, ClinVar conflicts 62

ClinVar submitters conflict, but the independent predictors unanimously agree — a QC review flag, not a reclassification.

Predicted LoF vs a conflicting call 1

ClinVar submitters conflict, and it's a predicted loss-of-function change in a gene where LoF causes disease — flagged for review, not resolved (verify NMD-escape for C-terminal truncations). Non-missense.

Predictors lean, ClinVar uncertain 690

ClinVar classifies these uncertain (VUS), but the independent predictors unanimously lean one way — a triage signal for review, not a reclassification. · showing the 150 best-reviewed of 690

Predictors split 408

The independent predictors disagree with each other — read with care. · showing the 150 best-reviewed of 408

All LRP5 variants

Pathogenic 105

Pathogenic/Likely pathogenic 27

  • c.3236+2T>G Multiple submitters autosomal dominant osteopetrosis 1
  • c.4488+2_4488+17del Multiple submitters LRP5-related disorder
  • c.4488+2T>G Multiple submitters LRP5-related disorder
  • p.Ala242Thr Multiple submitters LRP5-related disorder
  • p.Arg353Gln Multiple submitters osteoporosis-pseudoglioma syndrome
  • p.Arg462Ter Multiple submitters osteoporosis
  • p.Arg494Gln Multiple submitters osteoporosis-pseudoglioma syndrome
  • p.Arg570Gln Multiple submitters Inborn genetic diseases ⚠
  • p.Asn198Ser Multiple submitters Bone mineral density quantitative trait locus 1
  • p.Asp424Asn Multiple submitters inherited retinal dystrophy
  • p.Asp69fs Multiple submitters LRP5-related disorder
  • p.Asp891fs Multiple submitters Autosomal recessive LRP5-related disorders
  • p.Cys1253Phe Multiple submitters LRP5-related disorder
  • p.Cys906fs Multiple submitters autosomal dominant osteopetrosis 1
  • p.Glu441Lys Multiple submitters LRP5-related disorder
  • p.Gly550Arg Multiple submitters LRP5-related disorder
  • p.Leu1397fs Multiple submitters LRP5-related disorder
  • p.Leu145fs Multiple submitters LRP5-related disorder
  • p.Leu458fs Multiple submitters exudative vitreoretinopathy 4
  • p.Met1369fs Multiple submitters autosomal dominant osteopetrosis 1
  • p.Met1Val Multiple submitters osteogenesis imperfecta
  • p.Phe1422fs Multiple submitters autosomal dominant osteopetrosis 1
  • p.Phe70Ter Multiple submitters LRP5-related disorder
  • p.Ser1484fs Multiple submitters LRP5-related disorder
  • p.Thr852Met Multiple submitters Bone mineral density quantitative trait locus 1
  • p.Trp1278Ter Multiple submitters osteogenesis imperfecta
  • p.Trp211Ter Multiple submitters LRP5-related disorder

Likely pathogenic 82

Conflicting classifications of pathogenicity 154

Benign 79

Benign/Likely benign 56

Likely benign 800

Showing the top 300 by review status; the full set is in the sitemap.

Uncertain significance 1214

Showing the top 300 by review status; the full set is in the sitemap.