LDLR p.Cys160Phe
c.479_480delinsTT · rs1135402767 · VCV431510
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
hypercholesterolemia, familial, 1
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 12 | GERP 2.5, phastCons 1 |
| 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.Cys160Phe
- Coding
- c.479_480delinsTT
- MANE Select
- NM_000527
- dbSNP
- rs1135402767
- Type
- Indel
- Location
- chr19:11105385 (GRCh38)
- Gene constraint
- LOEUF 1.091 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.81 · 36 PDB
- Residue 160
- the 'binding to getah virus e1-e2 spike glycoproteins' region; a β-strand; a disulfide bond; the ldl-receptor class a 4 domain; a UniProt-annotated variant site (in fhcl1; uncertain significance)
Similar variants
- LDLR p.Cys160Tyr Uncertain significance ★★★ ⚠ same residue
- LDLR p.Cys160Arg Pathogenic/Likely pathogenic ★★ same residue
- LDLR p.Cys160Gly Pathogenic/Likely pathogenic ★★ same residue
- LDLR c.1359-31_1359-23delinsCGGCT Uncertain significance ★★★ same condition
- LDLR p.Arg257His Uncertain significance ★★★ same condition
- LDLR p.Arg744Gln Uncertain significance ★★★ same condition
- LDLR p.Asp224_Lys225delinsPhe Uncertain significance ★★★ same condition
- LDLR p.Val653Ala 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-cys160phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown