PEX2
protein-codingperoxisomal biogenesis factor 2, the group of Peroxins|Ring finger proteins
Gene summary
This gene encodes an integral peroxisomal membrane protein required for peroxisome biogenesis. The protein is thought to be involved in peroxisomal matrix protein import. Mutations in this gene result in one form of Zellweger syndrome and infantile Refsum disease. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]
- PXMP3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~20.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013932
Submitter: Myriad Women's Health
Inheritance Pattern: AR
Disease ID:MONDO:0100260
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0013933
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0013933
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0013933
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0019234
Submitter: ClinGen
PEX2 was first reported in relation to autosomal recessive peroxisomal biogenesis disorder in 1992 (Shimozawa et al., PMID: 1546315). Numerous variants have been reported in humans per ClinVar. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Summary of case-level and experimental data: 16.5 points. Variants (nonsense, missense, and frameshift) in this gene have been reported in at least 7 probands in 4 publications (PMIDS: 14630978, 21392394, 9452066, 1546315). The mechanism for disease is expected to be homozygoues loss of function. This gene-disease association is supported by expression studies, animal models, and in vitro functional assays. In summary, PEX2 is definitively associated with autosomal recessive peroxisomal biogenesis disorder. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time.
Inheritance Pattern: AR
Disease ID:MONDO:0019609
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0013932
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0019234
Submitter: PanelApp Australia
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 PEX2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000318.3. 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 | 4 | 141 | 1 | 146 | ||
| missense | 1 | 3 | 197 | 10 | 2 | 213 |
| nonsense | 12 | 15 | 1 | 28 | ||
| start loss | 0 | |||||
| frameshift | 16 | 48 | 1 | 65 | ||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 2 | |||
| Total | 29 | 67 | 204 | 151 | 3 | 454 |
Highest pathogenic variant AF is 0.00007434686
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000309.2 | 1 | MANE Select | |
| Ensembl | ENSP00000349543.4 | 1 | MANE Select | |
| RefSeq | NP_001073336.2 | 1 | Standard | |
| RefSeq | NP_001165557.2 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Peroxisome - Homo sapiens (human)
- Post-translational protein modification
- Metabolism of proteins
- Peroxisomal protein import
- Protein ubiquitination
Biological Process
- very long-chain fatty acid metabolic process
- negative regulation of transcription by RNA polymerase II
- protein targeting to peroxisome
- fatty acid beta-oxidation
- peroxisome organization
Molecular Function
- protein binding
- metal ion binding
Cellular Component
- peroxisomal membrane
- integral component of peroxisomal membrane
- membrane
- Cdc73/Paf1 complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000419564
- Coding exons
- 1
- Length
- 20787
- Individuals with no LoFs
- 125674
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 71
- Defined
- 125745
- p
- 0.000282
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0473 | 152 | 154 | 0.989 | 0.00000746 | 2000 |
| Missense (PolyPhen) | 46 | 46.31 | 0.99331 | 637 | ||
| Synonymous | 0.919 | 49 | 57.9 | 0.846 | 0.00000289 | 578 |
| Loss of Function | 1.11 | 7 | 11.0 | 0.638 | 6.33e-7 | 137 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.0024 | 0.0024 | notable |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00023 | 0.00023 | rare |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Somewhat implicated in the biogenesis of peroxisomes.;
- Disease
- DISEASE: Peroxisome biogenesis disorder complementation group 5 (PBD-CG5) [MIM:614866]: 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). Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 5A (PBD5A) [MIM:614866]: 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:1546315}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Peroxisome biogenesis disorder 5B (PBD5B) [MIM:614867]: 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:10528859}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.246
Intolerance Scores
- LoFtool
- 0.162
- RVIS EVS
- 0.4
- RVIS percentile EVS
- 76.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |