PLVAP p.Pro410=
c.1230C>G · rs373942287 · VCV2890881
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.19%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.9 | GERP -2.2 |
| Overall | ||
| CADD | 0.159 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.19%
South Asian · 173/91,078 alleles
Filtering AF
0.167%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.158%
Overall
0.0119%
192/1,613,874 alleles · rare
exomes 183/1,461,538 · genomes 9/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.19% | 526 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| East Asian | 0.00223% | 44,886 |
| African / African-American | 0.00133% | 75,054 |
| European (non-Finnish) | 0.000593% | 168,531 |
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.Pro410=
- Coding
- c.1230C>G
- MANE Select
- NM_031310
- dbSNP
- rs373942287
- Type
- single nucleotide variant
- Location
- chr19:17360782 (GRCh38)
- Gene constraint
- LOEUF 1.015 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.39
- Residue 410
- a UniProt-annotated variant site (in diar10); a UniProt-annotated variant site (in diar10; the protein is not expressed in the patient biopsy tissues); the 'disordered' region
Similar variants
- PLVAP p.Pro410Thr Uncertain significance ★ ⚠ same residue
- 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
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-pro410 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown