AARS2 p.Lys107=
c.321A>G · rs769678972 · VCV3015343
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 -1.3 | GERP -4.1, phastCons 0.001 |
| Overall | ||
| CADD | 7.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,018 alleles
Filtering AF
0.000763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.00112%
18/1,614,126 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,009 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.00127% | 78,669 |
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.Lys107=
- Coding
- c.321A>G
- MANE Select
- NM_020745
- dbSNP
- rs769678972
- Type
- single nucleotide variant
- Location
- chr6:44312186 (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-lys107 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown