PLTP p.Ser66=
c.198T>A · VCV3713666
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0116%, 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 -7.6 | GERP -4.2 |
| Overall | ||
| CADD | 0.126 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0116%
European (non-Finnish) · 135/1,168,644 alleles
Filtering AF
0.00995%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00929%
Overall
0.00888%
142/1,599,676 alleles · ultra-rare
exomes 137/1,448,466 · genomes 5/151,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0116% | 8,657 |
| Remaining individualsnot grpmax-eligible | 0.00969% | 10,315 |
| African / African-American | 0.00135% | 74,292 |
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.Ser66=
- Coding
- c.198T>A
- MANE Select
- NM_006227
- Type
- single nucleotide variant
- Location
- chr20:45911154 (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-ser66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown