PLAT p.Ser154=
c.462C>T · rs561637468 · VCV745888
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0498%, mid)
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 -4.9 | GERP -3.5 |
| Overall | ||
| CADD | 0.638 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0498%
Middle Eastern · 3/6,026 alleles
Filtering AF
0.0135%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.00466%
75/1,609,342 alleles · ultra-rare
exomes 71/1,456,962 · genomes 4/152,380 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0498% | 2,009 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,806 |
| African / African-American | 0.00932% | 10,724 |
| South Asian | 0.00659% | 15,177 |
| European (non-Finnish) | 0.00407% | 24,579 |
| Finnishnot grpmax-eligible | 0.00336% | 29,764 |
| Admixed American | 0.00167% | 60,014 |
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.Ser154=
- Coding
- c.462C>T
- MANE Select
- NM_000930
- dbSNP
- rs561637468
- Type
- single nucleotide variant
- Location
- chr8:42187475 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.28 · 11 PDB
- Residue 154
- the kringle 1 domain
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.Ser513= 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-ser154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown