PEX2

protein-coding

peroxisomal 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]

Previous symbols:
  • PXMP3

MANE transcript

NM_000318.3

Inheritance

AR

ClinVar variants

P:96U:204B:154

Top phenotype

Peroxisome biogenesis disorder 5A; Peroxisome biogenesis disorder 5B

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr8:76,980,258-77,001,044

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~20.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

peroxisome biogenesis disorder 5A (Zellweger)DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013932

Submitter: Myriad Women's Health

peroxisome biogenesis disorder due to PEX2 defectDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100260

Submitter: Natera

peroxisome biogenesis disorder 5BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013933

Submitter: G2P

peroxisome biogenesis disorder 5BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013933

Submitter: Ambry Genetics

peroxisome biogenesis disorder 5BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013933

Submitter: Labcorp Genetics (formerly Invitae)

peroxisome biogenesis disorderDEFINITIVE

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.

Zellweger spectrum disordersSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019609

Submitter: Orphanet

peroxisome biogenesis disorder 5A (Zellweger)DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013932

Submitter: G2P

peroxisome biogenesis disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019234

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Peroxisome biogenesis disorder 5A; Peroxisome biogenesis disorder 5BAR

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

Refs: 1546315; 7541833; 10528859; 14630978; 17041890; 21392394Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PEX2 variants in ClinVar

10 Conditions Cataloged
Peroxisome biogenesis disorder 5A (Zellweger)Total: 378
Zellweger spectrum disordersTotal: 84
not providedTotal: 62
Inborn genetic diseasesTotal: 56
PEX2-related disorderTotal: 44
Peroxisome biogenesis disorder 5BTotal: 42
not specifiedTotal: 23
Peroxisome biogenesis disorderTotal: 13

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
141
clinvar
1
clinvar
146
missense
1
clinvar
3
clinvar
197
clinvar
10
clinvar
2
clinvar
213
nonsense
12
clinvar
15
clinvar
1
clinvar
28
start loss
0
frameshift
16
clinvar
48
clinvar
1
clinvar
65
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
Total29672041513454

Highest pathogenic variant AF is 0.00007434686

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000318.3RefSeqNP_000309.21MANE Select
ENST00000357039.9EnsemblENSP00000349543.41MANE Select
NM_001079867.2RefSeqNP_001073336.21Standard
NM_001172086.2RefSeqNP_001165557.21Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.04731521540.9890.000007462000
Missense (PolyPhen)4646.310.99331637
Synonymous0.9194957.90.8460.00000289578
Loss of Function1.11711.00.6386.33e-7137

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000190.00018rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish0.00240.0024notable
East Asian0.000220.00022rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000230.00023rare
South Asian0.000260.00026rare
Other0.000490.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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