PXDN

Chr 2AR

peroxidasin

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

NCBI Gene: 7837ENSG00000130508UniProt: Q92626

This gene encodes a heme-containing peroxidase that is secreted into the extracellular matrix. It is involved in extracellular matrix formation, and may function in the physiological and pathological fibrogenic response in fibrotic kidney. Mutations in this gene cause corneal opacification and other ocular anomalies, and also microphthalmia and anterior segment dysgenesis. [provided by RefSeq, Aug 2014]

Primary Disease Associations & Inheritance

Anterior segment dysgenesis 7, with sclerocorneaMIM #269400
AR
565
ClinVar variants
66
Pathogenic / LP
0.00
pLI score
0
Active trials
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
66 Pathogenic / Likely Pathogenic· 213 VUS of 565 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
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?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
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?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.37 (0.26–0.52)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.80 (0.75–0.85)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.10
0≤1.21.6
LoF obs/exp: 23 / 62.3Missense obs/exp: 752 / 942.8Syn Z: -1.69

ClinVar Variant Classifications

565 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic55
Likely Pathogenic11
VUS213
Likely Benign189
Benign91
Conflicting6
55
Pathogenic
11
Likely Pathogenic
213
VUS
189
Likely Benign
91
Benign
6
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
8
3
44
0
55
Likely Pathogenic
2
1
8
0
11
VUS
0
186
27
0
213
Likely Benign
0
10
86
93
189
Benign
0
5
62
24
91
Conflicting
—6
Total10205227117565

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.

Gene2Phenotype Curations

PXDN-related anterior segment dysgenesis with sclerocornea

strong
ARLoss Of FunctionAbsent Gene Product
Dev. DisordersEye
G2P ↗
frameshift variantstop gainedmissense variant

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
PEROXIDASIN; PXDN
MIM #605158 · *

Anterior segment dysgenesis 7, with sclerocornea

MIM #269400

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Baicalin affects the progression of diabetic retinopathy through the RAGE/PXDN/PI3K/AKT pathway.
Gao Y et al.·J Transl Med
2025
Proteomic Profiling of Advanced Melanoma Patients to Predict Therapeutic Response to Anti-PD-1 Therapy.
Zila N et al.·Clin Cancer Res
2024Cohort
The oncogenic role and prognostic value of PXDN in human stomach adenocarcinoma.
Tian Y et al.·BMC Cancer
2024
Proteomic networks and related genetic variants associated with smoking and chronic obstructive pulmonary disease.
Konigsberg IR et al.·BMC Genomics
2024
Novel mutations in PXDN cause microphthalmia and anterior segment dysgenesis.
Choi A et al.·Eur J Hum Genet
2015
Novel heterozygous variants in PXDN cause different anterior segment dysgenesis phenotypes in monozygotic twins.
Zhu AY et al.·Ophthalmic Genet
2021Case report
Differential DNA methylation analysis of SUMF2, ADAMTS5, and PXDN provides novel insights into colorectal cancer prognosis prediction in Taiwan.
Su JQ et al.·World J Gastroenterol
2022
Whole-genome sequencing analysis of clozapine-induced myocarditis.
Narang A et al.·Pharmacogenomics J
2022
Identification of Novel Variants in LTBP2 and PXDN Using Whole-Exome Sequencing in Developmental and Congenital Glaucoma.
Micheal S et al.·PLoS One
2016
Germline mosaic transmission of a novel duplication of PXDN and MYT1L to two male half-siblings with autism.
Meyer KJ et al.·Psychiatr Genet
2012
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools