PEX11G
protein-codingperoxisomal biogenesis factor 11 gamma, the group of Peroxins
Gene summary
The protein encoded by this gene is a member of the PEX11 family. This family is reported to regulate the number and size of peroxisomes in evolutionarily distant organisms. The protein encoded by this gene may induce clustering of peroxisomes. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0019234
Submitter: ClinGen
The relationship between PEX11G and Peroxisome Biogenesis Disorder, an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of May, 2020. PEX11G is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. PEX11G has not been reported in relation to human disease, to the best of our knowledge. PMID: 26935981 reports that a homozygous PEX11G variant was identified by whole exome sequencing in a patient with mevalonate kinase deficiency. Two heterozygous variants in MVK as well as variants in other genes were detected in this patient. The authors suggest the PEX11G variant may be a modifier and implicated in the blurred vision phenotype in the patient. Of note, this variant is reported in gnomAD v2.1.1 at the highest MAF of 0.03814 in the non-Finnish European population with 62 homozygotes. Therefore, the PEX11G variant is not considered to be contributing towards any phenotype in the patient. In summary, no convincing evidence for a causal role for PEX11G in autosomal recessive peroxisome biogenesis disorder in humans has been reported (SOP Version 7).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PEX11G variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_080662.4. 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 | 63 | 1 | 64 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 67 | 2 | 1 | 70 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_542393.1 | 5 | MANE Select | |
| Ensembl | ENSP00000221480.1 | 5 | MANE Select | |
| RefSeq | NP_001257468.1 | 5 | Standard | |
| RefSeq | NP_001287810.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Peroxisome - Homo sapiens (human)
- Beta Oxidation of Very Long Chain Fatty Acids
- Adrenoleukodystrophy, X-linked
- Carnitine-acylcarnitine translocase deficiency
Biological Process
- peroxisome fission
- regulation of peroxisome size
Molecular Function
- protein binding
Cellular Component
- peroxisome
- integral component of peroxisomal membrane
- intrinsic component of peroxisomal membrane
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000221480
- Coding exons
- 5
- Length
- 20575
- Individuals with no LoFs
- 125659
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 81
- Defined
- 125740
- p
- 0.000322
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.349 | 140 | 129 | 1.09 | 0.00000822 | 1441 |
| Missense (PolyPhen) | 55 | 44.376 | 1.2394 | 549 | ||
| Synonymous | 0.907 | 49 | 57.8 | 0.848 | 0.00000349 | 525 |
| Loss of Function | -0.0765 | 11 | 10.7 | 1.03 | 6.23e-7 | 107 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.000060 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0015 | 0.0015 | notable |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.00023 | 0.00022 | rare |
| South Asian | 0.00073 | 0.00069 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Promotes membrane protrusion and elongation on the peroxisomal surface. {ECO:0000269|PubMed:20826455}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- LoFtool
- 0.836
- RVIS EVS
- 0.33
- RVIS percentile EVS
- 73.27
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.883
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |