LDLR p.Cys109Arg
c.324_325delinsTC · rs879254476 · VCV251154
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
3
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -4.8 |
| Regional constraint | o/e 1.00 | unconstrained · MANE · 42 kb · p 0.91 · regional, not allelic |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- LDLR
- Protein
- p.Cys109Arg
- Coding
- c.324_325delinsTC
- MANE Select
- NM_000527
- dbSNP
- rs879254476
- Type
- Indel
- Location
- chr19:11105230 (GRCh38)
- Gene constraint
- LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.81 · 36 PDB
- Residue 109
- an α-helix; a disulfide bond; the ldl-receptor class a 3 domain; a UniProt-annotated variant site (in fhcl1; uncertain significance; munster-1)
Similar variants
- LDLR p.Cys109Phe Pathogenic/Likely pathogenic ★★ same residue
- LDLR p.Cys109Ter Pathogenic ★★ same residue
- LDLR p.Cys109Tyr Pathogenic/Likely pathogenic ★★ same residue
- LDLR p.Cys109fs Pathogenic ★ same residue
- LDLR p.Cys109Gly Likely pathogenic ★ same residue
- LDLR p.Cys109Ser Likely pathogenic ★ same residue
- LDLR c.1359-31_1359-23delinsCGGCT Uncertain significance ★★★ same condition
- LDLR p.Arg257His 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/ldlr-p-cys109arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown