LRP1 p.Ser438=
c.1314T>C · VCV4917300
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000763%, nfe)
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 -13 | GERP -4.5 |
| Overall | ||
| CADD | 1.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000763%
European (non-Finnish) · 9/1,179,962 alleles
Filtering AF
0.000359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00026%
Overall
0.000558%
9/1,613,632 alleles · very rare
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
- LRP1
- Protein
- p.Ser438=
- Coding
- c.1314T>C
- MANE Select
- NM_173177 · reported on NM_002332
- Type
- single nucleotide variant
- Location
- chr12:57156180 (GRCh38)
- Structure
- AlphaFold pLDDT 88.37
Similar variants
- LRP1 p.Ala1564Thr Uncertain significance ★★ same type
- LRP1 p.Arg228Gln Uncertain significance ★★ same type
- LRP1 p.Arg2440Trp Uncertain significance ★★ ⚠ same type
- LRP1 p.Arg539Gln Uncertain significance ★★ same type
- LRP1 p.Asp4483Tyr Uncertain significance ★★ same type
- LRP1 p.Ser2907Pro Uncertain significance ★★ same type
- LRP1 p.Val3296Ile Uncertain significance ★★ ⚠ same type
- C1D p.Glu4= Benign ★★ same type
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/lrp1-p-ser438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown