PLVAP p.Phe31=
c.93C>T · rs202209497 · VCV2896264
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0357%, eas)
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 -2.1 | GERP -3.2 |
| Overall | ||
| CADD | 8.492 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0357%
East Asian · 16/44,874 alleles
Filtering AF
0.0223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0182%
Overall
0.00248%
40/1,614,138 alleles · ultra-rare
exomes 34/1,461,890 · genomes 6/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0357% | 2,805 |
| Admixed American | 0.0217% | 4,617 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,254 |
| European (non-Finnish) | 0.000763% | 131,113 |
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
- PLVAP
- Protein
- p.Phe31=
- Coding
- c.93C>T
- MANE Select
- NM_031310
- dbSNP
- rs202209497
- Type
- single nucleotide variant
- Location
- chr19:17377196 (GRCh38)
- Gene constraint
- LOEUF 1.015 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.39
Similar variants
- PLVAP p.Arg358Ter Pathogenic ★★ same type
- PLVAP p.Ala292Val Uncertain significance ★★ ⚠ same type
- PLVAP p.Ala385Thr Uncertain significance ★★ ⚠ same type
- PLVAP p.Ala94Thr Uncertain significance ★★ ⚠ same type
- PLVAP p.Arg13Trp Uncertain significance ★★ ⚠ same type
- PLVAP p.Arg211Cys Uncertain significance ★★ ⚠ same type
- PLVAP p.Arg238His Uncertain significance ★★ ⚠ same type
- PLVAP p.Arg269Cys 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/plvap-p-phe31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown