Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.4%, afr)
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 -8.2 | GERP -3.2 |
| Overall | ||
| CADD | 0.059 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.4%
African / African-American · 1,047/75,038 alleles
Filtering AF
1.33%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.3%
Overall
0.0729%
1,177/1,614,140 alleles · low-frequency
exomes 606/1,461,832 · genomes 571/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.4% | 72 |
| Remaining individualsnot grpmax-eligible | 0.11% | 906 |
| Admixed American | 0.075% | 1,334 |
| Middle Eastern | 0.0495% | 2,020 |
| South Asian | 0.00878% | 11,385 |
| European (non-Finnish) | 0.000424% | 235,997 |
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
- PLAT
- Protein
- p.Val389=
- Coding
- c.1167C>G
- MANE Select
- NM_000930
- dbSNP
- rs8178781
- Type
- single nucleotide variant
- Location
- chr8:42180297 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.28 · 11 PDB
- Residue 389
- the peptidase s1 domain; a β-strand
Similar variants
- PLAT p.Arg184Gly Uncertain significance ★★ ⚠ same type
- PLAT p.Val280Met Uncertain significance ★★ ⚠ same type
- PLAT p.Ala34Asp Likely benign ★★ same type
- PLAT p.Ala493= Benign/Likely benign ★★ same type
- PLAT p.Arg561Ter Benign ★★ same type
- PLAT p.Pro543= Likely benign ★★ same type
- PLAT p.Ser154= Likely benign ★★ same type
- PLAT p.Ser513= Benign ★★ 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/plat-p-val389 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown