PEX11B

Chr 1AR

peroxisomal biogenesis factor 11 beta

Also known as: PEX11-BETA, PEX11beta, PEX14B

NCBI Gene: 8799 ENSG00000131779 UniProt: O96011 OMIM: 603867

The protein facilitates peroxisomal proliferation by promoting membrane protrusion and elongation on the peroxisomal surface and recruiting dynamin-related GTPase to regulate peroxisome division. Mutations cause peroxisome biogenesis disorder 14B, inherited in an autosomal recessive pattern. The gene shows relatively low constraint to loss-of-function variants (pLI 0.0001, LOEUF 1.08), suggesting the disorder requires biallelic loss of function.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene facilitates peroxisomal proliferation and interacts with PEX19. The encoded protein is found in the peroxisomal membrane. Several transcript variants, some protein-coding and some not protein-coding, have been found for this gene. [provided by RefSeq, Dec 2012]

GeneReviews OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 1.081 OMIM phenotype

Clinical Summary— PEX11B

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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

17 unique Pathogenic / Likely Pathogenic· 136 VUS of 267 total submissions

Explore recent and relevant literature in Research Assistant →

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GeneReview available — PEX11B

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?

1.08LOEUF

pLI 0.000

Z-score 1.36

OE 0.60 (0.35–1.08)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.31Z-score

OE missense 1.07 (0.94–1.22)

156 obs / 145.6 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.60 (0.35–1.08)

0≤0.351.4

Missense OE?1.07 (0.94–1.22)

0≤0.61.4

Synonymous OE?0.85

0≤1.21.6

LoF obs/exp: 8 / 13.4Missense obs/exp: 156 / 145.6Syn Z: 0.90

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

definitivePEX11B-related peroxisome biogenesis disorder 14BLOFAR

This gene — mechanism propensity

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

0.80top 25%

GOF

0.6736th %ile

LOF

0.2679th %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

267 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5

Likely Pathogenic12

VUS136

Likely Benign99

Benign5

Conflicting10

Pathogenic

Likely Pathogenic

136

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	3	0	2	0	5
Likely Pathogenic	10	1	1	0	12
VUS	1	125	6	4	136
Likely Benign	0	1	37	61	99
Benign	0	0	4	1	5
Conflicting	—				10
Total	14	127	50	66	267

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

View in ClinVar →

134 pathogenic / likely-pathogenic (of 214) ClinVar copy-number / structural variants overlap PEX11B — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →