LRP1 p.Ser508=
c.1524C>T · rs144836356 · VCV3051825
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0418%, 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 -20 | GERP -5 |
| Overall | ||
| CADD | 4.216 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0418%
European (non-Finnish) · 489/1,170,492 alleles
Filtering AF
0.0387%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0374%
Overall
0.0329%
524/1,593,826 alleles · ultra-rare
exomes 497/1,441,480 · genomes 27/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0418% | 2,394 |
| Finnishnot grpmax-eligible | 0.0263% | 3,809 |
| Remaining individualsnot grpmax-eligible | 0.0162% | 6,163 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0102% | 9,836 |
| African / African-American | 0.00534% | 18,713 |
| Admixed American | 0.00502% | 19,929 |
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.Ser508=
- Coding
- c.1524C>T
- MANE Select
- NM_002332
- dbSNP
- rs144836356
- Type
- single nucleotide variant
- Location
- chr12:57156883 (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-ser508 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown