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

Gene ID: 9409, updated on 2-Nov-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
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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 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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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
MedGen: C1832200 GeneReviews: Zellweger Spectrum Disorder
Compare labs
Peroxisome biogenesis disorder 8A (Zellweger)
MedGen: C3553959 OMIM: 614876 GeneReviews: Not available
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Peroxisome biogenesis disorder 8B
MedGen: C3553960 OMIM: 614877 GeneReviews: Not available
Compare labs

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

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