PEX3 Gene

Name	peroxisomal biogenesis factor 3
Description	The product of this gene is involved in peroxisome biosynthesis and integrity. It assembles membrane vesicles before the matrix proteins are translocated. Peroxins (PEXs) are proteins that are essential for the assembly of functional peroxisomes. The peroxisome biogenesis disorders (PBDs) are a group of genetically heterogeneous autosomal recessive, lethal diseases characterized by multiple defects in peroxisome function. The peroxisomal biogenesis disorders are a heterogeneous group with at least 14 complementation groups and with more than 1 phenotype being observed in cases falling into particular complementation groups. Although the clinical features of PBD patients vary, cells from all PBD patients exhibit a defect in the import of one or more classes of peroxisomal matrix proteins into the organelle. Defects in this gene are a cause Zellweger syndrome (ZWS). [provided by RefSeq, Oct 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nPEX3 is a key membrane‐anchored peroxin that functions as an essential docking receptor for the cytosolic chaperone PEX19 during peroxisomal membrane protein (PMP) import. Structural and biochemical studies have revealed that PEX3 contains a conserved hydrophobic groove that specifically interacts with an α‐helical motif in PEX19. This interaction is critical for recruiting newly synthesized class I PMPs to peroxisomes, thereby ensuring efficient peroxisome biogenesis. Such docking events have been mapped down to key residues—such as Trp‐104—in PEX3 that form direct contacts with PEX19 and are indispensable for its function."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "6"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its canonical role at the peroxisomal membrane, PEX3 also participates in an endoplasmic reticulum (ER)‐dependent pathway for peroxisome formation. Newly synthesized PEX3 is inserted co‐translationally into the ER via the Sec61 translocon and then trafficked to pre‐existing or nascent peroxisomes via vesicular carriers. Moreover, the PEX19/PEX3 system has been implicated in the posttranslational insertion of monotopic hairpin proteins into the ER, thereby coordinating the biogenesis of lipid droplets and peroxisomes. Biophysical analyses further reveal that PEX3 can interact with amphipathic lipids, hinting at additional roles in membrane remodeling and protein sorting to other organelles."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "7", "end_ref": "14"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nDeficiencies or mutations in PEX3 have profound clinical consequences, as illustrated by its link to Zellweger spectrum disorders where aberrant peroxisome biogenesis leads to “mosaic” peroxisome distribution and metabolic dysfunction. In addition, altered PEX3 expression patterns have emerged in proteomic screens as potential biomarkers in melanoma and lung cancer, suggesting that its function may extend to modulating secretory pathway components such as collagen-related proteins. Together, these observations underscore the pivotal role of PEX3 not only in peroxisome formation but also in diverse cellular processes, with implications for understanding and treating human disease."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "15", "end_ref": "18"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Yi Fang, James C Morrell, Jacob M Jones, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PEX3 functions as a PEX19 docking factor in the import of class I peroxisomal membrane proteins."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biol (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1083/jcb.200311131"}], "href": "https://doi.org/10.1083/jcb.200311131"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15007061"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15007061"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Yuji Matsuzono, Takashi Matsuzaki, Yukio Fujiki "}, {"type": "b", "children": [{"type": "t", "text": "Functional domain mapping of peroxin Pex19p: interaction with Pex3p is essential for function and translocation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.03100"}], "href": "https://doi.org/10.1242/jcs.03100"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16895967"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16895967"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Yasuhiko Sato, Hiroyuki Shibata, Hiroaki Nakano, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Characterization of the interaction between recombinant human peroxin Pex3p and Pex19p: identification of TRP-104 IN Pex3p as a critical residue for the interaction."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M706139200"}], "href": "https://doi.org/10.1074/jbc.M706139200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18174172"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18174172"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Friederike Schmidt, Nora Treiber, Georg Zocher, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Insights into peroxisome function from the structure of PEX3 in complex with a soluble fragment of PEX19."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M110.138503"}], "href": "https://doi.org/10.1074/jbc.M110.138503"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20554521"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20554521"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Yasuhiko Sato, Hiroyuki Shibata, Toru Nakatsu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO J (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/emboj.2010.293"}], "href": "https://doi.org/10.1038/emboj.2010.293"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21102411"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21102411"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Friederike Schmidt, Denise Dietrich, Roy Eylenstein, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Pex3p-dependent peroxisomal biogenesis initiates in the endoplasmic reticulum of human fibroblasts."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biochem (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcb.22210"}], "href": "https://doi.org/10.1002/jcb.22210"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19479899"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19479899"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Manuel P Pinto, Cláudia P Grou, Marc Fransen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The cytosolic domain of PEX3, a protein involved in the biogenesis of peroxisomes, binds membrane lipids."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochim Biophys Acta (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbamcr.2009.08.007"}], "href": "https://doi.org/10.1016/j.bbamcr.2009.08.007"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19715730"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19715730"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Alexander Aranovich, Rong Hua, Andrew D Rutenberg, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PEX16 contributes to peroxisome maintenance by constantly trafficking PEX3 via the ER."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.146282"}], "href": "https://doi.org/10.1242/jcs.146282"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25002403"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25002403"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Katarina Hattula, Daniel Hirschberg, Nisse Kalkkinen, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Human Peroxin PEX3 Is Co-translationally Integrated into the ER and Exits the ER in Budding Vesicles."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Traffic (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/tra.12350"}], "href": "https://doi.org/10.1111/tra.12350"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26572236"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26572236"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Bianca Schrul, Ron R Kopito "}, {"type": "b", "children": [{"type": "t", "text": "Peroxin-dependent targeting of a lipid-droplet-destined membrane protein to ER subdomains."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Cell Biol (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ncb3373"}], "href": "https://doi.org/10.1038/ncb3373"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27295553"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27295553"}]}, {"type": "r", "ref": 13, "children": [{"type": "t", "text": "Yasunori Yamamoto, Toshiaki Sakisaka "}, {"type": "b", "children": [{"type": "t", "text": "The peroxisome biogenesis factors posttranslationally target reticulon homology domain-containing proteins to the endoplasmic reticulum membrane."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41598-018-20797-0"}], "href": "https://doi.org/10.1038/s41598-018-20797-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29396426"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29396426"}]}, {"type": "r", "ref": 14, "children": [{"type": "t", "text": "Renate L M Jansen, Ida J van der Klei "}, {"type": "b", "children": [{"type": "t", "text": "The peroxisome biogenesis factors Pex3 and Pex19: multitasking proteins with disputed functions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "FEBS Lett (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/1873-3468.13340"}], "href": "https://doi.org/10.1002/1873-3468.13340"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30776093"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30776093"}]}, {"type": "r", "ref": 15, "children": [{"type": "t", "text": "Daniela D'Arcangelo, Claudia Giampietri, Mario Muscio, et al. 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Synonyms	PBD10B, TRG18, PBD10A
Proteins	PEX3_HUMAN
NCBI Gene ID	8504
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

PEX3 has 6,917 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 119 datasets.

Click the + buttons to view associations for PEX3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

PEX3 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by PEX3 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PEX3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of PEX3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of PEX3 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of PEX3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of PEX3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PEX3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of PEX3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PEX3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PEX3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of PEX3 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of PEX3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of PEX3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with PEX3 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with PEX3 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PEX3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of PEX3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of PEX3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with PEX3 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of PEX3 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing PEX3 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of PEX3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing PEX3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing PEX3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing PEX3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with PEX3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with PEX3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of PEX3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with PEX3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with PEX3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by PEX3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving PEX3 gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving PEX3 gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with PEX3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with PEX3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with PEX3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with PEX3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with PEX3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at PEX3 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PEX3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.