PEX13
protein-codingperoxisomal biogenesis factor 13, the group of Peroxins
Gene summary
This gene encodes a peroxisomal membrane protein that binds the type 1 peroxisomal targeting signal receptor via a SH3 domain located in the cytoplasm. Mutations and deficiencies in peroxisomal protein importing and peroxisome assembly lead to peroxisomal biogenesis disorders, an example of which is Zellweger syndrome. [provided by RefSeq, Oct 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~34.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0019234
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0013949
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0019234
Submitter: ClinGen
The relationship between PEX13 and peroxisome biogenesis disorder (types 11A and 11B included), an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of August, 2019. PEX13 encodes a peroxisome membrane protein involved in PTS1 and PTS2 import. Peroxisomal biogenesis disorders are caused by defects in various stages of peroxisomal protein import and/or peroxisome biogenesis, involving at least 14 PEX genes. PEX13 belongs to complementation group H or group 13, and mutations in the gene result in cells devoid of peroxisomes (Waterham and Ebberink 2012, PMID 22871920). PEX13 was first reported in relation to autosomal recessive Peroxisome biogenesis disorder in 1999. (Shimozawa et al, 1999; PMID: 10332040, Liu et al, 1999; PMID: 10441568). At least 9 nonsense, splice site, frameshift, deletion/duplication and missense variants have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Summary of Case Level Data (11 points): Variants in this gene have been reported in at least 9 probands in 5 publications (PMIDs: 10332040, 21031596, 17041890, 10441568, 19449432). The mechanism for disease is expected to be homozygous loss of function. Summary of experimental data (5 points): This gene-disease association is supported by in vitro functional assays and animal models. PEX13 interacts with PEX19 and PEX14 (PMID: 12096124, 15798189). Mouse models of PEX13 recapitulate the human disease (PMIDs: 12897163, 29187321) and functional experiments show impaired PTS1 and PTS2 import in PEX13-deficient cells (PMIDs: 21669930, 8858165). In summary, PEX13 is definitively associated with autosomal recessive peroxisome biogenesis disorder. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the Peroxisomal Disorders GCEP on October 4, 2019.
Inheritance Pattern: AR
Disease ID:MONDO:0019609
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0013950
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0013949
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Renal
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PEX13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002618.4. 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 | 3 | 159 | 162 | |||
| missense | 1 | 3 | 267 | 13 | 1 | 285 |
| nonsense | 12 | 6 | 2 | 20 | ||
| start loss | 1 | 1 | ||||
| frameshift | 17 | 4 | 21 | |||
| splice donor/acceptor (+/-2bp) | 4 | 1 | 5 | |||
| Total | 30 | 17 | 274 | 172 | 1 | 494 |
Highest pathogenic variant AF is 0.00008432519
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002609.1 | 4 | MANE Select | |
| Ensembl | ENSP00000295030.4 | 4 | MANE Select | |
| Ensembl | ENSP00000384738.1 | 2 | Standard | |
| Ensembl | ENSP00000384738.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| pex13 | Danio rerio | Structure: hepatocyte Quality: decreased amount abnormal |
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
- Oxidation of Branched Chain Fatty Acids
- Adrenoleukodystrophy, X-linked
- Carnitine-acylcarnitine translocase deficiency
Biological Process
- fatty acid alpha-oxidation
- neuron migration
- suckling behavior
- protein targeting to peroxisome
- locomotory behavior
Molecular Function
- protein binding
Cellular Component
- peroxisome
- peroxisomal membrane
- integral component of peroxisomal membrane
- membrane
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000295030
- Coding exons
- 4
- Length
- 34766
- Individuals with no LoFs
- 125728
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125746
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.297 | 230 | 218 | 1.06 | 0.0000113 | 2606 |
| Missense (PolyPhen) | 62 | 67.083 | 0.92422 | 867 | ||
| Synonymous | -0.574 | 83 | 76.6 | 1.08 | 0.00000362 | 840 |
| Loss of Function | 1.53 | 9 | 15.5 | 0.582 | 8.38e-7 | 184 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the peroxisomal translocation machinery with PEX14 and PEX17. Functions as a docking factor for the predominantly cytoplasmic PTS1 receptor (PAS10/PEX5). Involved in the import of PTS1 and PTS2 proteins.;
- Disease
- DISEASE: Peroxisome biogenesis disorder complementation group 13 (PBD-CG13) [MIM:614883]: A peroxisomal disorder arising from a failure of protein import into the peroxisomal membrane or matrix. The peroxisome biogenesis disorders (PBD group) are genetically heterogeneous with at least 14 distinct genetic groups as concluded from complementation studies. Include disorders are: Zellweger syndrome (ZWS), neonatal adrenoleukodystrophy (NALD), infantile Refsum disease (IRD), and classical rhizomelic chondrodysplasia punctata (RCDP). ZWS, NALD and IRD are distinct from RCDP and constitute a clinical continuum of overlapping phenotypes known as the Zellweger spectrum (PBD-ZSS). {ECO:0000269|PubMed:10332040, ECO:0000269|PubMed:19449432}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 11A (PBD11A) [MIM:614883]: A fatal peroxisome biogenesis disorder belonging to the Zellweger disease spectrum and clinically characterized by severe neurologic dysfunction with profound psychomotor retardation, severe hypotonia and neonatal seizures, craniofacial abnormalities, liver dysfunction, and biochemically by the absence of peroxisomes. Additional features include cardiovascular and skeletal defects, renal cysts, ocular abnormalities, and hearing impairment. Most severely affected individuals with the classic form of the disease (classic Zellweger syndrome) die within the first year of life. {ECO:0000269|PubMed:10332040, ECO:0000269|PubMed:19449432}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 11B (PBD11B) [MIM:614885]: A peroxisome biogenesis disorder that includes neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease (IRD), two milder manifestations of the Zellweger disease spectrum. The clinical course of patients with the NALD and IRD presentation is variable and may include developmental delay, hypotonia, liver dysfunction, sensorineural hearing loss, retinal dystrophy and vision impairment. Children with the NALD presentation may reach their teens, while patients with the IRD presentation may reach adulthood. The clinical conditions are often slowly progressive in particular with respect to loss of hearing and vision. The biochemical abnormalities include accumulation of phytanic acid, very long chain fatty acids (VLCFA), di- and trihydroxycholestanoic acid and pipecolic acid. {ECO:0000269|PubMed:10332040, ECO:0000269|PubMed:10441568}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.216
Intolerance Scores
- LoFtool
- 0.511
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 75.29
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.955
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |