PXDN

Chr 2AR

peroxidasin

Also known as: ASGD7, COPOA, D2S448, D2S448E, MG50, PRG2, PXN, VPO

NCBI Gene: 7837ENSG00000130508UniProt: Q92626OMIM: 605158

This gene encodes a heme-containing peroxidase that catalyzes the formation of sulfilimine cross-links in collagen IV, which is essential for basement membrane integrity and extracellular matrix assembly. Mutations cause anterior segment dysgenesis with sclerocornea, microphthalmia, and other ocular anomalies affecting eye development. The condition follows autosomal recessive inheritance.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.521 OMIM phenotype
Clinical Summary— PXDN
🧬
Gene-Disease Validity (ClinGen)
anterior segment dysgenesis 7 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
26 unique Pathogenic / Likely Pathogenic· 243 VUS of 397 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.52LOEUF
pLI 0.000
Z-score 4.62
OE 0.37 (0.26–0.52)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
2.21Z-score
OE missense 0.80 (0.75–0.85)
752 obs / 942.8 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.37 (0.26–0.52)
0≤0.351.4
Missense OE0.80 (0.75–0.85)
0≤0.61.4
Synonymous OE1.10
0≤1.21.6
LoF obs/exp: 23 / 62.3Missense obs/exp: 752 / 942.8Syn Z: -1.69
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongPXDN-related anterior segment dysgenesis with sclerocorneaLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6937th %ile
GOF
0.6053th %ile
LOF
0.3164th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

ClinVar Variant Classifications

397 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic19
Likely Pathogenic7
VUS243
Likely Benign93
Benign12
Conflicting1
19
Pathogenic
7
Likely Pathogenic
243
VUS
93
Likely Benign
12
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
7
0
12
0
19
Likely Pathogenic
7
0
0
0
7
VUS
0
226
17
0
243
Likely Benign
0
10
30
53
93
Benign
0
0
9
3
12
Conflicting
—1
Total142366856375

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

View in ClinVar →

Protein Context — Lollipop Plot

PXDN · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
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