SERPINE1 p.Thr319=
c.957C>T · rs762047141 · VCV3027120
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
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 -20 | GERP -3.5 |
| Overall | ||
| CADD | 0.079 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,078 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000682%
11/1,614,036 alleles · very rare
exomes 9/1,461,888 · genomes 2/152,148 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,359 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| African / African-American | 0.00133% | 74,930 |
| European (non-Finnish) | 0.000508% | 196,673 |
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
- SERPINE1
- Protein
- p.Thr319=
- Coding
- c.957C>T
- MANE Select
- NM_000602
- dbSNP
- rs762047141
- Type
- single nucleotide variant
- Location
- chr7:101135551 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.03 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.68 · 29 PDB
Similar variants
- SERPINE1 c.*617T>A Uncertain significance ★★ same type
- SERPINE1 p.Asp240Gly Uncertain significance ★★ ⚠ same type
- SERPINE1 p.Gly196Ser Uncertain significance ★★ ⚠ same type
- SERPINE1 p.Leu175Pro Uncertain significance ★★ ⚠ same type
- SERPINE1 p.Phe157Leu Uncertain significance ★★ ⚠ same type
- SERPINE1 p.Pro372Ala Uncertain significance ★★ ⚠ same type
- SERPINE1 c.1088-106A>G Benign ★★ same type
- SERPINE1 c.1088-9C>T Benign/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/serpine1-p-thr319 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown