PLAT p.Ser513=
c.1539G>A · rs13306824 · VCV708039
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.38%, 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 -9.9 | GERP -3.8 |
| Overall | ||
| CADD | 0.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.38%
East Asian · 1,517/44,822 alleles
Filtering AF
3.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.19%
Overall
0.121%
1,950/1,612,996 alleles · low-frequency
exomes 1,738/1,460,768 · genomes 212/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.38% | 30 |
| Remaining individualsnot grpmax-eligible | 0.387% | 258 |
| South Asian | 0.129% | 777 |
| Admixed American | 0.0485% | 2,063 |
| African / African-American | 0.0293% | 3,409 |
| Middle Eastern | 0.0165% | 6,058 |
| European (non-Finnish) | 0.00187% | 53,611 |
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.Ser513=
- Coding
- c.1539G>A
- MANE Select
- NM_000930
- dbSNP
- rs13306824
- Type
- single nucleotide variant
- Location
- chr8:42176143 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.28 · 11 PDB
- Residue 513
- the peptidase s1 domain; an active site
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.Thr205Asn Likely 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-ser513 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown