LRP2 p.Pro3886fs
c.11657_11663del · VCV4957581
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
LRP2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 62 of 79 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -1.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- LRP2
- Protein
- p.Pro3886fs
- Coding
- c.11657_11663del
- MANE Select
- NM_004525
- Type
- Deletion
- Location
- chr2:169166027 (GRCh38)
- Gene constraint
- LOEUF 0.352 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 3886
- the ldl-receptor class a 35 domain
Disease context
LRP2-related disorder
Similar variants
- LRP2 p.Pro4380fs Pathogenic/Likely pathogenic ★★ same condition
- LRP2 c.9998+1del Likely pathogenic ★ same condition
- LRP2 p.Val2460fs Likely pathogenic ★ same condition
- LRP2 p.Arg2095Ter Pathogenic/Likely pathogenic ★★ same condition
- LRP2 p.Arg233Ter Pathogenic ★★ same condition
- LRP2 p.Arg3554Ter Pathogenic/Likely pathogenic ★★ same condition
- LRP2 p.Cys4381fs Pathogenic/Likely pathogenic ★★ same condition
- LRP2 p.Arg2013His 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/lrp2-p-pro3886fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown