PARS2 p.Arg103=
c.309A>G · VCV4822757
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -0.64 | GERP -3 |
| Overall | ||
| CADD | 5.922 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PARS2
- Protein
- p.Arg103=
- Coding
- c.309A>G
- MANE Select
- NM_152268
- Type
- single nucleotide variant
- Location
- chr1:54758853 (GRCh38)
- Gene constraint
- LOEUF 0.977 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30
- Residue 103
- a UniProt-annotated variant site (found in a patient with an aminoacyl-trna synthetase abnormality; uncertain significance)
Similar variants
- PARS2 p.Arg103Gln Uncertain significance ★★ ⚠ same residue
- PARS2 p.Gln296Ter Likely pathogenic ★★ same type
- PARS2 p.Ala372Thr Uncertain significance ★★ ⚠ same type
- PARS2 p.Arg186Gly Uncertain significance ★★ ⚠ same type
- PARS2 p.Arg186Lys Uncertain significance ★★ ⚠ same type
- PARS2 p.Arg189Gln Uncertain significance ★★ ⚠ same type
- PARS2 p.Arg195His Uncertain significance ★★ ⚠ same type
- PARS2 p.Arg200His 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/pars2-p-arg103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown