SERPINE1 p.Phe38=
c.114C>T · rs780207027 · VCV3046476
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, amr)
Conditions
1
SERPINE1-related disorder
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 -9.1 | GERP -3.1 |
| Overall | ||
| CADD | 8.642 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
Admixed American · 8/59,988 alleles
Filtering AF
0.00662%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00483%
Overall
0.00366%
59/1,614,028 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0133% | 7,499 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| European (non-Finnish) | 0.0039% | 25,653 |
| African / African-American | 0.00133% | 74,916 |
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.Phe38=
- Coding
- c.114C>T
- MANE Select
- NM_000602
- dbSNP
- rs780207027
- Type
- single nucleotide variant
- Location
- chr7:101128507 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI 0.03 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.68 · 29 PDB
- Residue 38
- an α-helix
Disease context
SERPINE1-related disorder
Similar variants
- SERPINE1 p.Asn232Ser Likely benign same condition
- 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
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-phe38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown