PRX p.Lys498=
c.1494A>G · rs879096800 · VCV1244085
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00828%, afr)
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 -0.74 | GERP -2, phastCons 0.044 |
| Overall | ||
| CADD | 0.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00828%
African / African-American · 6/72,484 alleles
Filtering AF
0.00357%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00245%
Overall
0.000998%
16/1,603,756 alleles · very rare
exomes 2/1,458,532 · genomes 14/145,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00828% | 12,081 |
| Admixed American | 0.00169% | 59,244 |
| Finnishnot grpmax-eligible | 0.00158% | 63,350 |
| European (non-Finnish) | 0.000681% | 146,914 |
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.Lys498=
- Coding
- c.1494A>G
- MANE Select
- NM_181882
- dbSNP
- rs879096800
- Type
- single nucleotide variant
- Location
- chr19:40396858 (GRCh38)
- Gene constraint
- LOEUF 1.321 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 35.74 · 1 PDB
- Residue 498
- the '55 x 5 aa approximate tandem repeats of [lvmag]-[psreqc]-[edkl]-[livmap]-[aqkhrpe]; that may have a tripeptide spacer of [lv]-p-[ker]' region
Similar variants
- 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
- PRX p.Arg897Ter 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-lys498 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown