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

    Gene ID: 5828, updated on 11-Apr-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
    mouse all
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    Genomic context

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    Location:
    8q21.13
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (76980258..77001044, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (77409691..77430483, complement)
    105.20220307 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
    • 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. Disruption of peroxisome function leads to metabolic stress, mTOR inhibition, and lethality in liver cancer cells. Cai M, et al. Cancer Lett, 2018 May 1. PMID 29458144
    2. 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
    3. 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
    4. 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
    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 (56) 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
    		Compare labs
    Peroxisome biogenesis disorder 5B
    MedGen: C3542026 OMIM: 614867 GeneReviews: Not available
    		Compare labs

    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)

    Genotypes

    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_2023_10

    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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