AMBP p.Pro25=
c.75G>A · VCV4090493
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.245%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.8 | GERP -3.1 |
| Overall | ||
| CADD | 0.834 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.245%
South Asian · 223/91,082 alleles
Filtering AF
0.218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.208%
Overall
0.0221%
356/1,613,844 alleles · rare
exomes 326/1,461,508 · genomes 30/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.245% | 408 |
| East Asian | 0.241% | 415 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,167 |
| Admixed American | 0.00666% | 15,008 |
| 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
- AMBP
- Protein
- p.Pro25=
- Coding
- c.75G>A
- MANE Select
- NM_001633
- Type
- single nucleotide variant
- Location
- chr9:114078135 (GRCh38)
- Gene constraint
- LOEUF 1.017 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.03 · 11 PDB
Similar variants
- AMBP p.Pro25Arg Uncertain significance ★ ⚠ same residue
- AMBP p.Ala13Thr Uncertain significance ★ ⚠ same type
- AMBP p.Ala19Val Uncertain significance ★ ⚠ same type
- AMBP p.Ala255Thr Uncertain significance ★ ⚠ same type
- AMBP p.Ala285Val Uncertain significance ★ ⚠ same type
- AMBP p.Ala304Thr Uncertain significance ★ ⚠ same type
- AMBP p.Ala48Thr Uncertain significance ★ ⚠ same type
- AMBP p.Ala74Thr Uncertain significance ★ ⚠ 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/ambp-p-pro25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown