PEX11A

protein-coding

peroxisomal biogenesis factor 11 alpha, the group of Peroxins

Gene summary

This gene is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. This gene product interacts with peroxisomal membrane protein 19 and may respond to outside stimuli to increase peroxisome abundance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]

MANE transcript

NM_003847.3

Inheritance

AR

ClinVar variants

U:48B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr15:89,677,764-89,690,783

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~13.0 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

peroxisome biogenesis disorderNO_KNOWN

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: ClinGen

The relationship between PEX11A and Peroxisome Biogenesis Disorder, an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of May, 2020. PEX11A is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. PEX11A has not been reported in relation to human disease, to the best of our knowledge. Minimal evidence supporting the role of this gene in disease is available from experimental data. Summary of experimental data (1 point): Since PEX11A has not been implicated in human disease, no mouse models that recapitulate a phenotype are reported. At least three Pex11a knock-out mouse models are reported, one of which is noted to show no external phenotypes or peroxisome defects (PMID: 12417726). Two other models by Weng et al (PMID: 23169785, PMID: 25113963) show the Pex11a deficiency may lead to alterations in peroxisome abundance, function and variability in expression of genes involved in fatty acid oxidation. The authors suggest that these are models for steatosis and hypertension/albuminuria. In summary, no convincing evidence for a causal role for PEX11A in autosomal recessive peroxisome biogenesis disorder has been reported. Although there is minimal evidence from animal models to support the role of PEX11A in disease, no reports have directly implicated the gene in humans. (SOP Version 7).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEX11A variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 49
not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003847.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
3
missense
46
clinvar
3
clinvar
49
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00484052
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003847.3RefSeqNP_003838.13MANE Select
ENST00000300056.8EnsemblENSP00000300056.33MANE Select
NM_001271572.2RefSeqNP_001258501.13Standard
NM_001271573.2RefSeqNP_001258502.11Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Peroxisome - Homo sapiens (human)
  • Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)

Biological Process

  • peroxisome organization
  • signal transduction
  • peroxisome membrane biogenesis
  • peroxisome fission
  • regulation of lipid metabolic process

Molecular Function

  • protein binding
  • protein homodimerization activity

Cellular Component

  • peroxisome
  • peroxisomal membrane
  • integral component of peroxisomal membrane
  • protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000300056
Coding exons
3
Length
13020
Individuals with no LoFs
125697
Homozygous LoFs
0
Heterozygous LoFs
49
Defined
125746
p
0.000195
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.1001321350.9760.000006911593
Missense (PolyPhen)3242.3490.75563573
Synonymous0.07495050.70.9870.00000236510
Loss of Function0.3721011.40.8817.56e-7115

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000370.00037rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian0.000380.00038rare
Finnish00.0absent
European (Non-Finnish)0.000270.00026rare
South Asian0.0000980.000098rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: May be involved in peroxisomal proliferation and may regulate peroxisomes division (PubMed:9792670). May mediate binding of coatomer proteins to the peroxisomal membrane (By similarity). Promotes membrane protrusion and elongation on the peroxisomal surface (PubMed:20826455). {ECO:0000250|UniProtKB:O70597, ECO:0000269|PubMed:20826455, ECO:0000269|PubMed:9792670}.;

Recessive Scores

pRec
0.130

Intolerance Scores

LoFtool
0.738
RVIS EVS
-0.45
RVIS percentile EVS
24

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.939

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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