PLTP p.Leu179=
c.537C>T · rs138461220 · VCV1461717
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0878%, 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 0.49 | GERP -3.1, phastCons 0.99 |
| Overall | ||
| CADD | 7.114 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0878%
European (non-Finnish) · 1,031/1,173,790 alleles
Filtering AF
0.0834%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0816%
Overall
0.0695%
1,112/1,599,792 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0878% | 1,138 |
| Remaining individualsnot grpmax-eligible | 0.0853% | 1,172 |
| African / African-American | 0.0187% | 5,355 |
| Admixed American | 0.0176% | 5,687 |
| Finnishnot grpmax-eligible | 0.00317% | 31,566 |
| South Asian | 0.00226% | 44,166 |
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.Leu179=
- Coding
- c.537C>T
- MANE Select
- NM_006227
- dbSNP
- rs138461220
- Type
- single nucleotide variant
- Location
- chr20:45907853 (GRCh38)
- Gene constraint
- LOEUF 1.002 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.36
- Residue 179
- a disulfide bond
Similar variants
- PLTP p.Leu179Phe Uncertain significance ★★ ⚠ same residue
- 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
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-leu179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown