PARS2 p.Pro85=
c.255C>T · rs145866387 · VCV2071199
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0973%, afr)
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 -5.2 | GERP -3 |
| Overall | ||
| CADD | 4.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0973%
African / African-American · 73/75,054 alleles
Filtering AF
0.0793%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0727%
Overall
0.00768%
124/1,614,204 alleles · ultra-rare
exomes 81/1,461,878 · genomes 43/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0973% | 1,028 |
| Finnishnot grpmax-eligible | 0.025% | 4,002 |
| South Asian | 0.00769% | 13,012 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,252 |
| European (non-Finnish) | 0.0022% | 45,386 |
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.Pro85=
- Coding
- c.255C>T
- MANE Select
- NM_152268
- dbSNP
- rs145866387
- Type
- single nucleotide variant
- Location
- chr1:54758907 (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-pro85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown