PRDX1

Chr 1AR

peroxiredoxin 1

Also known as: MSP23, NKEF-A, NKEFA, PAG, PAGA, PAGB, PRX1, PRXI

NCBI Gene: 5052ENSG00000117450UniProt: Q06830OMIM: 176763

This gene encodes a thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, protecting cells against oxidative stress. Mutations cause methylmalonic aciduria and homocystinuria, cblC type, through digenic inheritance, which involves defects in vitamin B12 metabolism. The gene shows very low constraint against loss-of-function variants (pLI near zero) and follows autosomal recessive inheritance.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
DNmechanismARLOEUF 1.911 OMIM phenotype
Clinical Summary— PRDX1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
10 unique Pathogenic / Likely Pathogenic· 51 VUS of 109 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — PRDX1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.91LOEUF
pLI 0.000
Z-score -1.08
OE 1.40 (0.88–1.91)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.20Z-score
OE missense 0.95 (0.81–1.11)
103 obs / 108.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE1.40 (0.88–1.91)
0≤0.351.4
Missense OE0.95 (0.81–1.11)
0≤0.61.4
Synonymous OE1.03
0≤1.21.6
LoF obs/exp: 12 / 8.6Missense obs/exp: 103 / 108.9Syn Z: -0.13
DN
0.6259th %ile
GOF
0.5955th %ile
LOF
0.3842th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

109 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic7
Likely Pathogenic3
VUS51
Likely Benign24
Benign12
7
Pathogenic
3
Likely Pathogenic
51
VUS
24
Likely Benign
12
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
0
6
0
7
Likely Pathogenic
1
0
2
0
3
VUS
4
28
18
1
51
Likely Benign
0
0
10
14
24
Benign
0
0
11
1
12
Total628471697

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PRDX1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients