PLTP p.Val187=
c.561C>T · rs2229452 · VCV1600405
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.55%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.30 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.26 | gain · loss 0.12 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -3.3, phastCons 0.96 |
| Overall | ||
| CADD | 13.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.55%
African / African-American · 1,165/75,018 alleles
Filtering AF
1.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.45%
Overall
0.0801%
1,292/1,613,762 alleles · low-frequency
exomes 652/1,461,474 · genomes 640/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.55% | 64 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,136 |
| Admixed American | 0.0817% | 1,224 |
| South Asian | 0.0022% | 45,435 |
| European (non-Finnish) | 0.00178% | 56,188 |
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
- PLTP
- Protein
- p.Val187=
- Coding
- c.561C>T
- MANE Select
- NM_006227
- dbSNP
- rs2229452
- Type
- single nucleotide variant
- Location
- chr20:45907744 (GRCh38)
- Gene constraint
- LOEUF 1.002 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.36
Similar variants
- PLTP p.Ala155Thr Uncertain significance ★★ ⚠ same type
- PLTP p.Ala155Val Uncertain significance ★★ ⚠ same type
- PLTP p.Arg177Cys Uncertain significance ★★ ⚠ same type
- PLTP p.Arg251Gln Uncertain significance ★★ ⚠ same type
- PLTP p.Arg372His Uncertain significance ★★ ⚠ same type
- PLTP p.Arg380Gln Uncertain significance ★★ ⚠ same type
- PLTP p.Arg391Cys Uncertain significance ★★ ⚠ same type
- PLTP p.Arg394Pro Uncertain significance ★★ ⚠ 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/pltp-p-val187 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown