PRDX1 p.Pro99=
c.297C>T · rs752317535 · VCV2078536
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0717%, amr)
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 0.56 | GERP -2.6, phastCons 0.99 |
| Overall | ||
| CADD | 9.132 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0717%
Admixed American · 43/60,000 alleles
Filtering AF
0.0546%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0486%
Overall
0.00304%
49/1,614,130 alleles · ultra-rare
exomes 42/1,461,878 · genomes 7/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0717% | 1,395 |
| African / African-American | 0.00667% | 14,989 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
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
- PRDX1
- Protein
- p.Pro99=
- Coding
- c.297C>T
- MANE Select
- NM_181697
- dbSNP
- rs752317535
- Type
- single nucleotide variant
- Location
- chr1:45514959 (GRCh38)
- Gene constraint
- LOEUF 1.322 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.29 · 20 PDB
- Residue 99
- the thioredoxin domain
Similar variants
- PRDX1 p.Pro99Ser Uncertain significance ★ ⚠ same residue
- PRDX1 c.515-1G>T Pathogenic ★★ same type
- PRDX1 p.Asn101Ser Uncertain significance ★★ ⚠ same type
- PRDX1 p.Ile57Thr Uncertain significance ★★ ⚠ same type
- PRDX1 p.Val153Leu Uncertain significance ★★ ⚠ same type
- PRDX1 c.107-15C>T Benign/Likely benign ★★ same type
- PRDX1 c.107-33A>G Benign ★★ same type
- PRDX1 c.260+68T>C Benign ★★ 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/prdx1-p-pro99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown