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PEX2 peroxisomal biogenesis factor 2 [ Homo sapiens (human) ]

Gene ID: 5828, updated on 2-Nov-2024

Summary

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Official Symbol
PEX2provided by HGNC
Official Full Name
peroxisomal biogenesis factor 2provided by HGNC
Primary source
HGNC:HGNC:9717
See related
Ensembl:ENSG00000164751 MIM:170993; AllianceGenome:HGNC:9717
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PAF1; PMP3; ZWS3; PBD5A; PBD5B; PMP35; PXMP3; RNF72
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]
Expression
Ubiquitous expression in thyroid (RPKM 10.2), urinary bladder (RPKM 7.9) and 25 other tissues See more
Orthologs
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Genomic context

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See PEX2 in Genome Data Viewer
Location:
8q21.13
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (76980258..77001044, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (77409691..77430483, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (77892494..77913280, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ZFHX4 antisense RNA 1 Neighboring gene VISTA enhancer hs1318 Neighboring gene zinc finger homeobox 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:77676670-77677613 Neighboring gene VISTA enhancer hs774 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19305 Neighboring gene VISTA enhancer hs1681 Neighboring gene Sharpr-MPRA regulatory region 11833 Neighboring gene microRNA 3149 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 18 Neighboring gene MPRA-validated peak7079 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:78000945-78001521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19306 Neighboring gene VISTA enhancer hs742 Neighboring gene uncharacterized LOC105375909

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Ring finger in the peroxisome assembly factor-1. Patarca R, et al. FEBS Lett, 1992 Nov 2. PMID 1426230
  2. Genomic organization and characterization of human PEX2 encoding a 35-kDa peroxisomal membrane protein. Biermanns M, et al. Biochem Biophys Res Commun, 2000 Jul 14. PMID 10891359
  3. A deleterious mutation in the PEX2 gene causes Zellweger syndrome in individuals of Ashkenazi Jewish descent. Fedick A, et al. Clin Genet, 2014 Apr. PMID 23590336
  4. Autosomal recessive cerebellar ataxia caused by mutations in the PEX2 gene. Sevin C, et al. Orphanet J Rare Dis, 2011 Mar 10. PMID 21392394, Free PMC Article
  5. A novel mutation, R125X in peroxisome assembly factor-1 responsible for Zellweger syndrome. Shimozawa N, et al. Hum Mutat, 1998. PMID 9452066

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. we report here that PEX2 and other peroxins are essential for the viability of liver cancer cells
    Title: Disruption of peroxisome function leads to metabolic stress, mTOR inhibition, and lethality in liver cancer cells.
  2. PEX2 is required for peroxisome autophagy during starvation.
    Title: PEX2 is the E3 ubiquitin ligase required for pexophagy during starvation.
  3. the carrier frequencies for two PEX2 mutations causative of the severe Zellweger syndrome spectrum phenotype in Ashkenazi Jews
    Title: A deleterious mutation in the PEX2 gene causes Zellweger syndrome in individuals of Ashkenazi Jewish descent.
  4. Ischemic wound healing is retarded in mice subjected to recombinant PEX2 injections or viral transduction with PEX2-lentivurus.
    Title: Elevation of hemopexin-like fragment of matrix metalloproteinase-2 tissue levels inhibits ischemic wound healing and angiogenesis.
  5. Genetic screening of PEX2 and other PEX genes involved in peroxisomal biogenesis is warranted in children and adults with ARCA
    Title: Autosomal recessive cerebellar ataxia caused by mutations in the PEX2 gene.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature.
  7. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  8. The cause of the syndrome in this patient was a point mutation that resulted in the premature termination of peroxisome assembly factor-1.
    Title: A human gene responsible for Zellweger syndrome that affects peroxisome assembly.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Peroxisome biogenesis disorder 5A (Zellweger)
MedGen: C3553940 OMIM: 614866 GeneReviews: Not available
not available
Peroxisome biogenesis disorder 5B
MedGen: C3542026 OMIM: 614867 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
A novel common variant in DCST2 is associated with length in early life and height in adulthood.
EBI GWAS Catalog
GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog
Many sequence variants affecting diversity of adult human height.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin protein ligase activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cellular response to reactive oxygen species IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in fatty acid beta-oxidation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in fatty acid beta-oxidation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of epithelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of fibroblast proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in peroxisome organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peroxisome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in pexophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein destabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein import into peroxisome matrix IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein import into peroxisome matrix, receptor recycling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein import into peroxisome matrix, substrate release ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in protein monoubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein monoubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in response to amino acid starvation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in very long-chain fatty acid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in very long-chain fatty acid metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Cdc73/Paf1 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Cdc73/Paf1 complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 
located_in peroxisomal membrane HDA PubMed 
is_active_in peroxisomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in peroxisomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in peroxisomal membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in peroxisomal membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
peroxisome biogenesis factor 2
Names
35 kDa peroxisomal membrane protein
RING finger protein 72
peroxisomal membrane protein 3, 35kDa
peroxisome assembly factor 1
NP_000309.2
NP_001073336.2
NP_001165557.2
NP_001165558.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008371.2 RefSeqGene

    Range
    5966..25786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000318.3 → NP_000309.2  peroxisome biogenesis factor 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) and variants 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC090810
    Consensus CDS
    CCDS6221.1
    UniProtKB/Swiss-Prot
    P28328, Q567S6, Q9BW41
    UniProtKB/TrEMBL
    B2R7I6
    Related
    ENSP00000349543.4, ENST00000357039.9
    Conserved Domains (2) summary
    cd16526
    Location:243 → 284
    RING-HC_PEX2; RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins
    pfam04757
    Location:27 → 224
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

  2. NM_001079867.2 → NP_001073336.2  peroxisome biogenesis factor 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC090810
    Consensus CDS
    CCDS6221.1
    UniProtKB/Swiss-Prot
    P28328, Q567S6, Q9BW41
    UniProtKB/TrEMBL
    B2R7I6
    Related
    ENSP00000428638.1, ENST00000522527.5
    Conserved Domains (2) summary
    cd16526
    Location:243 → 284
    RING-HC_PEX2; RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins
    pfam04757
    Location:27 → 224
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

  3. NM_001172086.2 → NP_001165557.2  peroxisome biogenesis factor 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC090810
    Consensus CDS
    CCDS6221.1
    UniProtKB/Swiss-Prot
    P28328, Q567S6, Q9BW41
    UniProtKB/TrEMBL
    B2R7I6
    Conserved Domains (2) summary
    cd16526
    Location:243 → 284
    RING-HC_PEX2; RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins
    pfam04757
    Location:27 → 224
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

  4. NM_001172087.2 → NP_001165558.2  peroxisome biogenesis factor 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC090810
    Consensus CDS
    CCDS6221.1
    UniProtKB/Swiss-Prot
    P28328, Q567S6, Q9BW41
    UniProtKB/TrEMBL
    B2R7I6
    Related
    ENSP00000428590.1, ENST00000520103.5
    Conserved Domains (2) summary
    cd16526
    Location:243 → 284
    RING-HC_PEX2; RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins
    pfam04757
    Location:27 → 224
    Pex2_Pex12; Pex2 / Pex12 amino terminal region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    76980258..77001044 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    77409691..77430483 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P28328.2 GenPept UniProtKB/Swiss-Prot:P28328

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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