AIMP2 p.Cys23=
c.69C>T · rs201425558 · VCV1571764
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0483%, nfe)
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 5.9 | phastCons 1 |
| Overall | ||
| CADD | 16.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0483%
European (non-Finnish) · 570/1,179,900 alleles
Filtering AF
0.045%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0437%
Overall
0.04%
645/1,611,244 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0483% | 2,070 |
| South Asian | 0.0396% | 2,527 |
| Remaining individualsnot grpmax-eligible | 0.0385% | 2,596 |
| African / African-American | 0.008% | 12,497 |
| Finnishnot grpmax-eligible | 0.0079% | 12,665 |
| Admixed American | 0.00667% | 14,991 |
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
- AIMP2
- Protein
- p.Cys23=
- Coding
- c.69C>T
- MANE Select
- NM_006303
- dbSNP
- rs201425558
- Type
- single nucleotide variant
- Location
- chr7:6009432 (GRCh38)
- Gene constraint
- LOEUF 1.107 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.65 · 13 PDB
Similar variants
- PMS2 c.-2146C>A Benign ★★★ same type
- PMS2 c.-2559T>A Benign ★★★ same type
- PMS2 c.-323G>T Benign ★★★ same type
- AIMP2 p.Tyr35Ter Likely pathogenic ★★ same type
- AIMP2 p.Ala240Val Uncertain significance ★★ ⚠ same type
- AIMP2 p.Arg215Cys Uncertain significance ★★ ⚠ same type
- AIMP2 p.Arg215His Uncertain significance ★★ ⚠ same type
- AIMP2 p.Arg33Lys 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/aimp2-p-cys23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown