AIMP2 p.Thr90=
c.270C>T · rs61751884 · VCV711474
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.79%, afr)
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 -1 | phastCons 0.001 |
| Overall | ||
| CADD | 8.537 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.79%
African / African-American · 2,097/75,030 alleles
Filtering AF
2.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.65%
Overall
0.143%
2,314/1,614,158 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.79% | 36 |
| Admixed American | 0.163% | 612 |
| Remaining individualsnot grpmax-eligible | 0.144% | 695 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.00439% | 22,771 |
| European (non-Finnish) | 0.00195% | 51,305 |
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.Thr90=
- Coding
- c.270C>T
- MANE Select
- NM_006303
- dbSNP
- rs61751884
- Type
- single nucleotide variant
- Location
- chr7:6015280 (GRCh38)
- Gene constraint
- LOEUF 1.107 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.65 · 13 PDB
- Residue 90
- the 'interaction with prkn' region; a UniProt-annotated variant site (in hld17)
Similar variants
- AIMP2 p.Thr90Ala 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-thr90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown