PARS2 p.Pro92=
c.276A>G · rs758254364 · VCV2418554
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -3 |
| Overall | ||
| CADD | 0.703 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,002 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000372%
6/1,614,060 alleles · very rare
exomes 5/1,461,880 · genomes 1/152,180 · joint denominator
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
- PARS2
- Protein
- p.Pro92=
- Coding
- c.276A>G
- MANE Select
- NM_152268
- dbSNP
- rs758254364
- Type
- single nucleotide variant
- Location
- chr1:54758886 (GRCh38)
- Gene constraint
- LOEUF 0.977 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30
Similar variants
- PARS2 p.Gln296Ter Likely pathogenic ★★ same type
- PARS2 p.Ala372Thr Uncertain significance ★★ ⚠ same type
- PARS2 p.Arg103Gln 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-pro92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown