LRP5 p.Ala97=
c.291C>T · rs146667935 · VCV745716
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.7 | GERP -4.2 |
| Overall | ||
| CADD | 1.922 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Amishnot grpmax-eligible | 1.64% | 61 |
| European (non-Finnish)grpmax | 0.0885% | 1,130 |
| Remaining individualsnot grpmax-eligible | 0.0784% | 1,276 |
| Admixed American | 0.02% | 5,003 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.00666% | 15,008 |
| Finnishnot grpmax-eligible | 0.00625% | 15,991 |
| South Asian | 0.00439% | 22,770 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| East Asian | 0.00223% | 44,878 |
Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- LRP5
- Protein
- p.Ala97=
- Coding
- c.291C>T
- MANE Select
- NM_002335
- dbSNP
- rs146667935
- Type
- single nucleotide variant
- Location
- chr11:68348046 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.94 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.65
- Residue 97
- the 'beta-propeller 1' region; a UniProt-annotated variant site (in)
Disease context
osteogenesis imperfecta — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Osteogenesis imperfecta (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, X-linked recessive
- Onset
- All ages
- Prevalence
- 1-5 / 10 000 (Worldwide)
Similar variants
- LRP5 p.Ala97Val Likely benign ★★ same residue
- LRP5 p.Ala97Ser Uncertain significance ★ ⚠ same residue
- LRP5 c.884-2A>G Likely pathogenic ★★ same condition
- LRP5 p.Met1Val Pathogenic/Likely pathogenic ★★ same condition
- LRP5 p.Trp1278Ter Pathogenic/Likely pathogenic ★★ same condition
- LRP5 p.Ala1265Pro Uncertain significance ★★ ⚠ same condition
- LRP5 p.Ala465Thr Uncertain significance ★★ ⚠ same condition
- LRP5 p.Arg178Leu Uncertain significance ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/lrp5-p-ala97 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown