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    PEX16 peroxisomal biogenesis factor 16 [ Homo sapiens (human) ]

    Gene ID: 9409, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PEX16provided by HGNC
    Official Full Name
    peroxisomal biogenesis factor 16provided by HGNC
    Primary source
    HGNC:HGNC:8857
    See related
    Ensembl:ENSG00000121680 MIM:603360; AllianceGenome:HGNC:8857
    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
    PBD8A; PBD8B
    Summary
    The protein encoded by this gene is an integral peroxisomal membrane protein. An inactivating nonsense mutation localized to this gene was observed in a patient with Zellweger syndrome of the complementation group CGD/CG9. Expression of this gene product morphologically and biochemically restores the formation of new peroxisomes, suggesting a role in peroxisome organization and biogenesis. Alternative splicing has been observed for this gene and two variants have been described. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 7.9), spleen (RPKM 6.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PEX16 in Genome Data Viewer
    Location:
    11p11.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (45909663..45918822, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (46065593..46074744, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (45931214..45939428, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902668 Neighboring gene Sharpr-MPRA regulatory region 31 Neighboring gene mitogen-activated protein kinase 8 interacting protein 1 Neighboring gene Sharpr-MPRA regulatory region 10000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45927125-45927626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45927627-45928126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45929145-45930090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:45938484-45939236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4673 Neighboring gene Frey regulator of sperm-oocyte fusion 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:45956286-45957284 Neighboring gene LARGE xylosyl- and glucuronyltransferase 2 Neighboring gene PHD finger protein 21A Neighboring gene ReSE screen-validated silencer GRCh37_chr11:45975728-45975893 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:45986871-45987068 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:46003193-46004090 Neighboring gene Sharpr-MPRA regulatory region 8215 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:46015337-46015518 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:46015959-46016504 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:46022272-46022894 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:46033641-46034224 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:46141064-46141221 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3293 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3294

    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. Identification of an unusual variant peroxisome biogenesis disorder caused by mutations in the PEX16 gene. Ebberink MS, et al. J Med Genet, 2010 Sep. PMID 20647552
    2. Knockdown of PEX16 Induces Autophagic Degradation of Peroxisomes. Wei X, et al. Int J Mol Sci, 2021 Jul 26. PMID 34360754, Free PMC Article
    3. A novel aberrant splicing mutation of the PEX16 gene in two patients with Zellweger syndrome. Shimozawa N, et al. Biochem Biophys Res Commun, 2002 Mar 22. PMID 11890679
    4. Mutation in PEX16 is causal in the peroxisome-deficient Zellweger syndrome of complementation group D. Honsho M, et al. Am J Hum Genet, 1998 Dec. PMID 9837814, Free PMC Article
    5. The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER. Kim PK, et al. J Cell Biol, 2006 May 22. PMID 16717127, Free PMC Article

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Knockdown of PEX16 Induces Autophagic Degradation of Peroxisomes.
      Title: Knockdown of PEX16 Induces Autophagic Degradation of Peroxisomes.
    2. PEX16 mediates the peroxisomal trafficking of two distinct peroxisomal membrane proteins, PEX3 and PMP34, via the endoplasmic reticulum
      Title: PEX16 contributes to peroxisome maintenance by constantly trafficking PEX3 via the ER.
    3. Data show that knockdown of Sec16B but not Sec16A by RNAi affected the morphology of peroxisomes, inhibited the transport of Pex16 from the ER to peroxisomes, and suppressed expression of Pex3.
      Title: Sec16B is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (Pex16) in mammalian cells.
    4. An unusual variant peroxisome biogenesis disorder caused by mutations in the PEX16 gene, with a relatively mild clinical phenotype and an unexpected phenotype in fibroblasts, was identified.
      Title: Identification of an unusual variant peroxisome biogenesis disorder caused by mutations in the PEX16 gene.
    5. aberrant splicing mutation of the PEX16 gene in patients with Zellweger syndrome
      Title: A novel aberrant splicing mutation of the PEX16 gene in two patients with Zellweger syndrome.
    6. PEX16 regulates peroxisome assembly by being cotranslationally inserted into the ER and serving to recruit other peroxisomal membrane proteins to membranes.
      Title: The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER.
    7. Pex16p functions in peroxisome membrane assembly, more likely upstream of Pex3p
      Title: The membrane biogenesis peroxin Pex16p. Topogenesis and functional roles in peroxisomal membrane assembly.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Peroxisome biogenesis disorder
    MedGen: C1832200 GeneReviews: Zellweger Spectrum Disorder
    		not available
    Peroxisome biogenesis disorder 8A (Zellweger)
    MedGen: C3553959 OMIM: 614876 GeneReviews: Not available
    		not available
    Peroxisome biogenesis disorder 8B
    MedGen: C3553960 OMIM: 614877 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    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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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ER-dependent peroxisome localization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ER-dependent peroxisome organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in peroxisome membrane biogenesis 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 
    acts_upstream_of_or_within protein import into peroxisome matrix IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein import into peroxisome membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein targeting to peroxisome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein to membrane docking IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    located_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
    		  
    located_in peroxisome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    peroxisomal biogenesis factor 16
    Names
    peroxin 16
    peroxisomal membrane protein PEX16
    peroxisome biogenesis factor 16

    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_008460.2 RefSeqGene

      Range
      5945..14159
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004813.4 → NP_004804.2  peroxisomal biogenesis factor 16 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate terminal exon. The encoded isoform (1) is shorter than isoform 2 and has a unique C-terminus.
      Source sequence(s)
      AB016531, AC068385, AF118240, BC000467, BM746616
      Consensus CDS
      CCDS31472.1
      UniProtKB/Swiss-Prot
      Q9BWB9, Q9Y5Y5
      Related
      ENSP00000368024.5, ENST00000378750.10
      Conserved Domains (1) summary
      pfam08610
      Location:10 → 329
      Pex16; Peroxisomal membrane protein (Pex16)

    2. NM_057174.3 → NP_476515.2  peroxisomal biogenesis factor 16 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate terminal exon. The resulting protein (isoform 2) is longer and has a unique C-terminus compared to isoform 1.
      Source sequence(s)
      AC068385
      Consensus CDS
      CCDS7917.1
      Related
      ENSP00000241041.3, ENST00000241041.7
      Conserved Domains (1) summary
      pfam08610
      Location:10 → 317
      Pex16; Peroxisomal membrane protein (Pex16)

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      45909663..45918822 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427888.1 → XP_047283844.1  peroxisomal biogenesis factor 16 isoform X2

      UniProtKB/TrEMBL
      E9PP98
      Related
      ENSP00000434654.1, ENST00000532681.5

    2. XM_047427886.1 → XP_047283842.1  peroxisomal biogenesis factor 16 isoform X1

    3. XM_047427887.1 → XP_047283843.1  peroxisomal biogenesis factor 16 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      46065593..46074744 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370542.1 → XP_054226517.1  peroxisomal biogenesis factor 16 isoform X2

    2. XM_054370541.1 → XP_054226516.1  peroxisomal biogenesis factor 16 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5Y5.2 GenPept UniProtKB/Swiss-Prot:Q9Y5Y5

    Gene LinkOut

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

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