AIMP2 p.Pro39=
c.117G>C · rs566052179 · VCV2657294
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00227%, 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 -1.2 | |
| Overall | ||
| CADD | 2.774 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00227%
South Asian · 2/88,134 alleles
Filtering AF
0.000377%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000141%
Overall
0.00014%
2/1,426,446 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.Pro39=
- Coding
- c.117G>C
- MANE Select
- NM_006303
- dbSNP
- rs566052179
- Type
- single nucleotide variant
- Location
- chr7:6009480 (GRCh38)
- Gene constraint
- LOEUF 1.107 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.65 · 13 PDB
- Residue 39
- a UniProt-annotated variant site (in hld17)
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-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown