SERPING1 p.Gln474=
c.1422G>A · rs1450674538 · VCV1614452
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0493%, 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 0.52 | GERP -3.8, phastCons 0.99 |
| Overall | ||
| CADD | 5.484 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0493%
Middle Eastern · 3/6,082 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00716%
Overall
0.000744%
12/1,613,956 alleles · ultra-rare
exomes 8/1,461,774 · genomes 4/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0493% | 2,027 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| European (non-Finnish) | 0.000678% | 147,500 |
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.Gln474=
- Coding
- c.1422G>A
- MANE Select
- NM_000062
- dbSNP
- rs1450674538
- Type
- single nucleotide variant
- Location
- chr11:57614500 (GRCh38)
- Gene constraint
- LOEUF 0.278 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63 · 5 PDB
- Residue 474
- a UniProt-annotated variant site (in hae1)
Similar variants
- SERPING1 p.Gln474Ter Pathogenic ★★ same residue
- SERPING1 p.Gln474His 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
- SERPING1 p.Gln180His 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-gln474 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown