PEX10

Chr 1AR

peroxisomal biogenesis factor 10

Also known as: NALD, PBD6A, PBD6B, RNF69

NCBI Gene: 5192ENSG00000157911UniProt: O60683OMIM: 602859

The protein imports peroxisomal matrix proteins and localizes to the peroxisomal membrane. Mutations cause peroxisome biogenesis disorders within the Zellweger spectrum, ranging from neonatal adrenoleukodystrophy to Zellweger syndrome, inherited in an autosomal recessive pattern. The pathogenic mechanism involves dominant-negative effects.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismARLOEUF 0.862 OMIM phenotypes
Clinical Summary— PEX10
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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
136 unique Pathogenic / Likely Pathogenic· 192 VUS of 617 total submissions
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
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GeneReview available — PEX10
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
0.86LOEUF
pLI 0.001
Z-score 1.99
OE 0.48 (0.28–0.86)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.29Z-score
OE missense 1.06 (0.95–1.18)
229 obs / 216.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.48 (0.28–0.86)
0≤0.351.4
Missense OE1.06 (0.95–1.18)
0≤0.61.4
Synonymous OE1.00
0≤1.21.6
LoF obs/exp: 8 / 16.8Missense obs/exp: 229 / 216.8Syn Z: 0.01
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitivePEX10-related peroxisome biogenesis disorder 6BLOFAR
definitivePEX10-related peroxisome biogenesis disorder 6A (Zellweger)LOFAR

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

DN
0.6840th %ile
GOF
0.5759th %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

617 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic86
Likely Pathogenic50
VUS192
Likely Benign252
Benign15
Conflicting17
86
Pathogenic
50
Likely Pathogenic
192
VUS
252
Likely Benign
15
Benign
17
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
35
4
47
0
86
Likely Pathogenic
45
4
1
0
50
VUS
2
161
25
4
192
Likely Benign
2
4
94
152
252
Benign
0
2
13
0
15
Conflicting
—17
Total84175180156612

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

View in ClinVar →

Protein Context — Lollipop Plot

PEX10 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
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
Ataxia with novel compound heterozygous PEX10 mutations and a literature review of PEX10-related peroxisome biogenesis disorders.
Zhang C et al.·Clin Neurol Neurosurg
2019Review
High rate of hypomorphic variants as the cause of inherited ataxia and related diseases: study of a cohort of 366 families.
Benkirane M et al.·Genet Med
2021Cohort
Expanding the spectrum of PEX10-related peroxisomal biogenesis disorders: slowly progressive recessive ataxia.
Renaud M et al.·J Neurol
2016
[Abnormal expression of PEX10 gene may be related to epilepsy associated with 1p36 copy number variations].
Zhang Y et al.·Zhonghua Yi Xue Yi Chuan Xue Za Zhi
2015
Identification of novel compound heterozygous variants in the PEX10 gene in a Han-Chinese family with PEX10-related peroxisome biogenesis disorders.
Huang X et al.·PLoS One
2025
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