Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.989%, afr)
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 -20 | GERP -2.9 |
| Overall | ||
| CADD | 0.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.989%
African / African-American · 742/75,022 alleles
Filtering AF
0.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.907%
Overall
0.0507%
819/1,614,008 alleles · rare
exomes 411/1,461,772 · genomes 408/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.989% | 101 |
| Admixed American | 0.0483% | 2,069 |
| Remaining individualsnot grpmax-eligible | 0.0336% | 2,976 |
| South Asian | 0.00439% | 22,767 |
| European (non-Finnish) | 0.00195% | 51,303 |
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
- PLAUR
- Protein
- p.Thr248=
- Coding
- c.744C>T
- MANE Select
- NM_002659
- dbSNP
- rs4251912
- Type
- single nucleotide variant
- Location
- chr19:43652235 (GRCh38)
- Gene constraint
- LOEUF 0.911 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.56 · 13 PDB
- Residue 248
- the upar/ly6 3 domain; a β-strand
Similar variants
- PLAUR p.His251= Likely benign ★★ same type
- PLAUR p.Met268Val Likely benign ★★ same type
- PLAUR p.Pro8= Benign/Likely benign ★★ same type
- PLAUR p.Ala106Asp Uncertain significance ★ ⚠ same type
- PLAUR p.Arg113Cys Uncertain significance ★ ⚠ same type
- PLAUR p.Arg113His Uncertain significance ★ ⚠ same type
- PLAUR p.Arg131Gly Uncertain significance ★ ⚠ same type
- PLAUR p.Arg164Cys 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/plaur-p-thr248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown