PEX11A
protein-codingperoxisomal 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
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
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
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 3 | |||
| missense | 46 | 3 | 49 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 48 | 4 | 0 | 52 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003838.1 | 3 | MANE Select | |
| Ensembl | ENSP00000300056.3 | 3 | MANE Select | |
| RefSeq | NP_001258501.1 | 3 | Standard | |
| RefSeq | NP_001258502.1 | 1 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.100 | 132 | 135 | 0.976 | 0.00000691 | 1593 |
| Missense (PolyPhen) | 32 | 42.349 | 0.75563 | 573 | ||
| Synonymous | 0.0749 | 50 | 50.7 | 0.987 | 0.00000236 | 510 |
| Loss of Function | 0.372 | 10 | 11.4 | 0.881 | 7.56e-7 | 115 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00027 | 0.00026 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |