PEX13

Chr 2AR

peroxisomal biogenesis factor 13

Also known as: NALD, PBD11A, PBD11B, ZWS

NCBI Gene: 5194ENSG00000162928UniProt: Q92968

This gene encodes a peroxisomal membrane protein that binds the type 1 peroxisomal targeting signal receptor via a SH3 domain located in the cytoplasm. Mutations and deficiencies in peroxisomal protein importing and peroxisome assembly lead to peroxisomal biogenesis disorders, an example of which is Zellweger syndrome. [provided by RefSeq, Oct 2008]

Primary Disease Associations & Inheritance

Peroxisome biogenesis disorder 11A (Zellweger)MIM #614883
AR
Peroxisome biogenesis disorder 11BMIM #614885
AR
488
ClinVar variants
50
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— PEX13
🧬
Gene-Disease Validity (ClinGen)
peroxisome biogenesis disorder · 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
50 Pathogenic / Likely Pathogenic· 241 VUS of 488 total submissions
Some data sources returned errors (1)

clinvar: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
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.
1.01LOEUF
pLI 0.000
Z-score 1.53
OE 0.58 (0.35–1.01)
Tolerant

Highly tolerant — LoF variants common in population

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.
-0.30Z-score
OE missense 1.06 (0.95–1.18)
230 obs / 217.7 exp
Tolerant

Tolerant to missense variation

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.0.58 (0.35–1.01)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.06 (0.95–1.18)
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.1.08
0≤1.21.6
LoF obs/exp: 9 / 15.5Missense obs/exp: 230 / 217.7Syn Z: -0.57

ClinVar Variant Classifications

488 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic37
Likely Pathogenic13
VUS241
Likely Benign177
Benign5
Conflicting15
37
Pathogenic
13
Likely Pathogenic
241
VUS
177
Likely Benign
5
Benign
15
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
18
1
18
0
37
Likely Pathogenic
3
0
10
0
13
VUS
1
195
44
1
241
Likely Benign
0
0
46
131
177
Benign
0
1
4
0
5
Conflicting
—15
Total22197122132488

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

View in ClinVar →

Protein Context — Lollipop Plot

PEX13 · protein map & ClinVar variants

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

Gene2Phenotype Curations

PEX13-related peroxisome biogenesis disorder 11B

definitive
ARLoss Of FunctionAbsent Gene Product
Eye
G2P ↗

PEX13-related peroxisome biogenesis disorder 11A (Zellweger)

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Peroxisome biogenesis disorder 11A (Zellweger)

MIM #614883

Molecular basis of disorder known

Autosomal recessive

Peroxisome biogenesis disorder 11B

MIM #614885

Molecular basis of disorder known

Autosomal recessive
📖
GeneReview available — PEX13
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response.
Zhang Z et al.·Genome Med
2022
Genotype-phenotype correlations and disease mechanisms in PEX13-related Zellweger spectrum disorders.
Borgia P et al.·Orphanet J Rare Dis
2022Functional
Severe Zellweger spectrum disorder due to a novel missense variant in the PEX13 gene: A case report and the literature review.
Su L et al.·Mol Genet Genomic Med
2024Case report
Functional analysis of PEX13 mutation in a Zellweger syndrome spectrum patient reveals novel homooligomerization of PEX13 and its role in human peroxisome biogenesis.
Krause C et al.·Hum Mol Genet
2013Functional
Isolation, characterization and mutation analysis of PEX13-defective Chinese hamster ovary cell mutants.
Toyama R et al.·Hum Mol Genet
1999
Clinical, biochemical and genetic aspects and neuronal migration in peroxisome biogenesis disorders.
Suzuki Y et al.·J Inherit Metab Dis
2001Review
It takes two peroxisome proliferator-activated receptors (PPAR-β/δ and PPAR-γ) to tango idiopathic pulmonary fibrosis.
Boateng E et al.·Respir Res
2024
PEX14 condensates recruit receptor and cargo pairs for peroxisomal protein import.
Wu J et al.·Nat Struct Mol Biol
2025
Hypomyelinating leukodystrophies in adults: Clinical and genetic features.
Di Bella D et al.·Eur J Neurol
2021
Zellweger syndrome caused by PEX13 deficiency: report of two novel mutations.
Al-Dirbashi OY et al.·Am J Med Genet A
2009
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