AIMP2 p.Leu52=
c.156G>A · rs1290887880 · VCV2131572
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.30 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.071 | phastCons 0.91 |
| Overall | ||
| CADD | 7.292 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,179,992 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.00131%
2/152,194 alleles · very rare
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.Leu52=
- Coding
- c.156G>A
- MANE Select
- NM_006303
- dbSNP
- rs1290887880
- Type
- single nucleotide variant
- Location
- chr7:6015166 (GRCh38)
- Gene constraint
- LOEUF 1.107 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.65 · 13 PDB
- Residue 52
- an α-helix; a UniProt-annotated variant site (in hld17)
Similar variants
- AIMP2 p.Leu52Pro Uncertain significance ★★ ⚠ same residue
- AIMP2 p.Leu52Val Uncertain significance ★ ⚠ same residue
- 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
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-leu52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown