PEX13

Chr 2AR

peroxisomal biogenesis factor 13

Also known as: NALD, PBD11A, PBD11B, ZWS

NCBI Gene: 5194 ENSG00000162928 UniProt: Q92968 OMIM: 601789

This gene encodes a peroxisomal membrane protein that binds the type 1 peroxisomal targeting signal receptor via a cytoplasmic SH3 domain, facilitating protein import into peroxisomes. Mutations cause autosomal recessive peroxisome biogenesis disorders including Zellweger syndrome (PBD11A) and the milder PBD11B phenotype. Loss-of-function mutations disrupt peroxisomal protein import and peroxisome assembly, leading to the characteristic metabolic and developmental abnormalities seen in these disorders.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt, Mechanism

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]

GeneReviews OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 1.012 OMIM phenotypes

Clinical Summary— PEX13

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Gene-Disease Validity (ClinGen)

peroxisome biogenesis disorder · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

46 unique Pathogenic / Likely Pathogenic· 331 VUS of 624 total submissions

Explore recent and relevant literature in Research Assistant →

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GeneReview available — PEX13

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?

1.01LOEUF

pLI 0.000

Z-score 1.53

OE 0.58 (0.35–1.01)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.30Z-score

OE missense 1.06 (0.95–1.18)

230 obs / 217.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.58 (0.35–1.01)

0≤0.351.4

Missense OE?1.06 (0.95–1.18)

0≤0.61.4

Synonymous OE?1.08

0≤1.21.6

LoF obs/exp: 9 / 15.5Missense obs/exp: 230 / 217.7Syn Z: -0.57

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

definitivePEX13-related peroxisome biogenesis disorder 11BLOFAR

definitivePEX13-related peroxisome biogenesis disorder 11A (Zellweger)LOFAR

This gene — mechanism propensity

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

0.6937th %ile

GOF

0.6247th %ile

LOF

0.3355th %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

624 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic35

Likely Pathogenic11

VUS331

Likely Benign197

Benign13

Conflicting25

Pathogenic

Likely Pathogenic

331

VUS

197

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	32	1	2	0	35
Likely Pathogenic	9	1	1	0	11
VUS	2	262	65	2	331
Likely Benign	0	2	53	142	197
Benign	0	1	12	0	13
Conflicting	—				25
Total	43	267	133	144	612

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

View in ClinVar →

21 pathogenic / likely-pathogenic (of 32) ClinVar copy-number / structural variants overlap PEX13 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →