PEX3

Chr 6AR

peroxisomal biogenesis factor 3

Also known as: PBD10A, PBD10B, TRG18

The protein assembles membrane vesicles during peroxisome biogenesis before matrix protein translocation occurs. Mutations cause peroxisome biogenesis disorders including Zellweger syndrome, inherited in an autosomal recessive pattern. The pathogenic mechanism involves dominant-negative effects where mutant proteins disrupt normal peroxisome assembly and function.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismARLOEUF 0.562 OMIM phenotypes
Clinical SummaryPEX3
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Gene-Disease Validity (ClinGen)
peroxisome biogenesis disorder · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.31) despite low pLI — interpret in context.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.56LOEUF
pLI 0.016
Z-score 3.26
OE 0.31 (0.180.56)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.19Z-score
OE missense 0.76 (0.660.87)
145 obs / 191.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.31 (0.180.56)
00.351.4
Missense OE0.76 (0.660.87)
00.61.4
Synonymous OE0.89
01.21.6
LoF obs/exp: 8 / 25.9Missense obs/exp: 145 / 191.1Syn Z: 0.70
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongPEX3-related peroxisome biogenesis disorder 10BOTHERAR
definitivePEX3-related peroxisome biogenesis disorderLOFAR

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

DN
0.6939th %ile
GOF
0.6053th %ile
LOF
0.3066th %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

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

PEX3 · 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

No active trials found for this gene.

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Clinical Literature
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