SERPING1 p.Ser460=
c.1380C>T · rs772014083 · VCV1771279
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
Conditions
1
Inborn genetic diseases
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 -3.9 |
| Overall | ||
| CADD | 0.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,084 alleles
Filtering AF
0.0058%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0026%
Overall
0.00366%
59/1,613,988 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,042 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,621 |
| African / African-American | 0.004% | 24,972 |
| European (non-Finnish) | 0.00381% | 26,223 |
| Admixed American | 0.00333% | 30,003 |
| South Asian | 0.00329% | 30,361 |
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
- SERPING1
- Protein
- p.Ser460=
- Coding
- c.1380C>T
- MANE Select
- NM_000062
- dbSNP
- rs772014083
- Type
- single nucleotide variant
- Location
- chr11:57614458 (GRCh38)
- Gene constraint
- LOEUF 0.278 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63 · 5 PDB
Similar variants
- SERPING1 p.Ser460Pro Likely pathogenic ★ same residue
- SERPING1 p.Ser460Tyr Likely pathogenic ★ same residue
- SERPING1 p.Ser460Cys Likely pathogenic same residue
- SERPING1 c.51+3A>G Pathogenic ★★ same condition
- SERPING1 p.Asp408Gly Pathogenic/Likely pathogenic ★★ ⚠ same condition
- SERPING1 p.Pro498Leu Likely pathogenic ★★ ⚠ same condition
- SERPING1 p.Asp144Gly Uncertain significance ★★ ⚠ same condition
- SERPING1 p.Asp424Glu Uncertain significance ★★ ⚠ same condition
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/serping1-p-ser460 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown