AIMP2 p.Thr151=
c.453G>A · rs534008494 · VCV1368366
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, sas)
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 -12 | |
| Overall | ||
| CADD | 0.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
South Asian · 10/91,082 alleles
Filtering AF
0.00594%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00453%
Overall
0.00204%
33/1,613,996 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.011% | 9,108 |
| Admixed American | 0.00834% | 11,997 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,624 |
| Finnishnot grpmax-eligible | 0.00469% | 21,337 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| African / African-American | 0.00133% | 74,964 |
| European (non-Finnish) | 0.000763% | 131,112 |
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.Thr151=
- Coding
- c.453G>A
- MANE Select
- NM_006303
- dbSNP
- rs534008494
- Type
- single nucleotide variant
- Location
- chr7:6017924 (GRCh38)
- Gene constraint
- LOEUF 1.107 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.65 · 13 PDB
- Residue 151
- the 'interaction with prkn' region; a β-strand; a UniProt-annotated variant site (in hld17)
Similar variants
- AIMP2 p.Thr151Met 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
- AIMP2 p.Arg215His 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-thr151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown