LDLR p.Cys82del
c.244_246del · rs1568591929 · VCV629952
Likely pathogenic
Multiple submitters
Classification
Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
2
familial hypercholesterolemia
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 5.8 | GERP 2.5, phastCons 1 |
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.Cys82del
- Coding
- c.244_246del
- MANE Select
- NM_000527
- dbSNP
- rs1568591929
- Type
- Deletion
- Location
- chr19:11102715 (GRCh38)
- Gene constraint
- LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.81 · 36 PDB
- Residue 82
- a disulfide bond; the ldl-receptor class a 2 domain
Similar variants
- LDLR p.Cys82Gly Pathogenic/Likely pathogenic ★★ same residue
- LDLR p.Cys82Phe Pathogenic/Likely pathogenic ★★ same residue
- LDLR p.Cys82Ser Likely pathogenic ★★ same residue
- LDLR p.Cys82Ter Pathogenic ★★ same residue
- LDLR p.Cys82Tyr Pathogenic/Likely pathogenic ★★ same residue
- LDLR p.Cys82fs Pathogenic ★ same residue
- LDLR p.Ala612fs Likely pathogenic ★★★ same condition
- LDLR p.Lys816fs Likely pathogenic ★★★ 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-cys82del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown