SERPING1 p.Ala440=
c.1320G>A · VCV4698862
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, 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 -2.6 | GERP -3.9 |
| Overall | ||
| CADD | 5.743 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,892 alleles
Filtering AF
0.00883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.00124%
20/1,613,932 alleles · ultra-rare
exomes 16/1,461,800 · genomes 4/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,612 |
| Admixed American | 0.00333% | 29,997 |
| African / African-American | 0.00267% | 37,455 |
| South Asian | 0.0022% | 45,543 |
| Finnishnot grpmax-eligible | 0.00156% | 63,944 |
| European (non-Finnish) | 0.000424% | 236,004 |
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.Ala440=
- Coding
- c.1320G>A
- MANE Select
- NM_000062
- Type
- single nucleotide variant
- Location
- chr11:57614398 (GRCh38)
- Gene constraint
- LOEUF 0.278 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63 · 5 PDB
- Residue 440
- a β-strand
Similar variants
- SERPING1 p.Ala440Val Likely benign ★ same residue
- SERPING1 c.1030-1G>T Pathogenic ★★ same type
- SERPING1 c.51+1G>T Pathogenic ★★ same type
- SERPING1 c.51+3A>C Pathogenic/Likely pathogenic ★★ same type
- SERPING1 c.51+3A>G Pathogenic ★★ same type
- SERPING1 c.52-1G>A Pathogenic ★★ same type
- SERPING1 c.550+1G>A Pathogenic ★★ same type
- SERPING1 c.551-1G>C Pathogenic/Likely pathogenic ★★ 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/serping1-p-ala440 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown