AARS2 p.Thr89=
c.267C>T · rs752629942 · VCV754432
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00695%, 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 Δ0.69 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -4.5 |
| Overall | ||
| CADD | 4.897 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00695%
European (non-Finnish) · 82/1,179,786 alleles
Filtering AF
0.00571%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00525%
Overall
0.00527%
85/1,613,806 alleles · very rare
exomes 83/1,461,590 · genomes 2/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00695% | 14,388 |
| Admixed American | 0.00333% | 30,000 |
| African / African-American | 0.00133% | 74,920 |
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
- AARS2
- Protein
- p.Thr89=
- Coding
- c.267C>T
- MANE Select
- NM_020745
- dbSNP
- rs752629942
- Type
- single nucleotide variant
- Location
- chr6:44312240 (GRCh38)
- Gene constraint
- LOEUF 0.752 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.05 · 3 PDB
Similar variants
- AARS2 c.2146-2A>G Pathogenic/Likely pathogenic ★★ same type
- AARS2 c.2255+1G>A Pathogenic ★★ same type
- AARS2 c.2598+1G>T Pathogenic/Likely pathogenic ★★ same type
- AARS2 p.Arg199Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- AARS2 p.Arg521Ter Pathogenic ★★ same type
- AARS2 p.Arg580Trp Likely pathogenic ★★ ⚠ same type
- AARS2 p.Arg592Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- AARS2 p.Arg958Ter Pathogenic/Likely pathogenic ★★ 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/aars2-p-thr89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown