PRX p.Arg953=
c.2859A>G · rs369688519 · VCV2649878
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
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 -0.61 | GERP -4.3, phastCons 0.079 |
| Overall | ||
| CADD | 3.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,179,952 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,634 alleles · very rare
exomes 1/1,461,894 · genomes 1/151,740 · 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
- PRX
- Protein
- p.Arg953=
- Coding
- c.2859A>G
- MANE Select
- NM_181882
- dbSNP
- rs369688519
- Type
- single nucleotide variant
- Location
- chr19:40395493 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 35.74 · 1 PDB
Similar variants
- PRX p.Arg953Ter Pathogenic ★★ same residue
- PRX c.184+2T>C Likely pathogenic ★★ same type
- PRX p.Arg1070Ter Pathogenic/Likely pathogenic ★★ same type
- PRX p.Arg196Ter Pathogenic/Likely pathogenic ★★ same type
- PRX p.Arg364Ter Pathogenic ★★ same type
- PRX p.Arg368Ter Pathogenic/Likely pathogenic ★★ same type
- PRX p.Arg392Ter Pathogenic/Likely pathogenic ★★ same type
- PRX p.Arg464Ter 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/prx-p-arg953 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown