NPM3 Gene

Name	nucleophosmin/nucleoplasmin 3
Description	The protein encoded by this gene is related to the nuclear chaperone phosphoproteins, nucleoplasmin and nucleophosmin. This protein is strongly expressed in diverse cell types where it localizes primarily to the nucleus. Based on its similarity to nucleoplasmin and nucleophosmin, this protein likely functions as a molecular chaperone in the cell nucleus. [provided by RefSeq, Oct 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nNPM3 functions as a key modulator in chromatin remodeling during early embryogenesis. Although it lacks robust intrinsic nucleosome assembly activity on its own, NPM3 exerts its role by forming complexes with NPM1. This interaction facilitates sperm chromatin decondensation and nucleosome assembly after oocyte entry, while also modulating the RNA‐binding activity of NPM1 to aid its shuttling between the nucleoplasm and nucleolus. Moreover, as a member of the nucleophosmin/nucleoplasmin family, NPM3 is involved in the storage and organization of histones during the dramatic chromatin reorganization immediately following fertilization."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn the context of gametogenesis, particularly during spermiogenesis, NPM3 plays an important regulatory role through its interaction with transition protein 2 (TP2). TP2, which undergoes acetylation to modulate its chromatin-condensing properties, interacts with NPM3, suggesting that NPM3 contributes to the orchestration of the dynamic reorganization of chromatin as histones are replaced by more specific sperm nuclear proteins. In addition, although NPM3 itself does not display strong histone chaperone activity, it can negatively regulate the histone assembly function of NPM1 in vitro and yet markedly enhance transcriptional output in cellular systems."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nRecent evidence further implicates NPM3 in tumor biology, particularly in the modulation of the tumor microenvironment and immune evasion. In various cancers—including gastric, lung adenocarcinoma, and colorectal cancer—NPM3 expression is regulated post-transcriptionally by factors such as PUM1 and AGR2. These regulatory interactions promote NPM3 stabilization and its association with NPM1, thereby facilitating the nuclear translocation of NPM1 and upregulating the transcription of PD-L1, a key immune checkpoint protein. This AGR2–NPM3 and PUM1/NPM3/PD-L1 regulatory axis is emerging as a significant mechanism underlying immune escape and tumor progression."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "5", "end_ref": "7"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Mitsuru Okuwaki, Ayako Sumi, Miharu Hisaoka, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gks162"}], "href": "https://doi.org/10.1093/nar/gks162"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22362753"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22362753"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Ron M Finn, Katherine Ellard, José M Eirín-López, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Vertebrate nucleoplasmin and NASP: egg histone storage proteins with multiple chaperone activities."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "FASEB J (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1096/fj.12-216663"}], "href": "https://doi.org/10.1096/fj.12-216663"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22968912"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22968912"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Madapura M Pradeepa, Gupta Nikhil, Annavarapu Hari Kishore, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Acetylation of transition protein 2 (TP2) by KAT3B (p300) alters its DNA condensation property and interaction with putative histone chaperone NPM3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M109.052043"}], "href": "https://doi.org/10.1074/jbc.M109.052043"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19710011"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19710011"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Shrikanth S Gadad, Jayasha Shandilya, A Hari Kishore, et al. "}, {"type": "b", "children": [{"type": "t", "text": "NPM3, a member of the nucleophosmin/nucleoplasmin family, enhances activator-dependent transcription."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochemistry (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1021/bi9021632"}], "href": "https://doi.org/10.1021/bi9021632"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20073534"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20073534"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Han Wang, Zhijun Zhou, Junchang Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Pumilio1 regulates NPM3/NPM1 axis to promote PD-L1-mediated immune escape in gastric cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Lett (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.canlet.2023.216498"}], "href": "https://doi.org/10.1016/j.canlet.2023.216498"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38029539"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38029539"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Shan Wei, Jing Xing, Kaining Lu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "NPM3 as a novel oncogenic factor and poor prognostic marker contributes to cell proliferation and migration in lung adenocarcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hereditas (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s41065-023-00289-6"}], "href": "https://doi.org/10.1186/s41065-023-00289-6"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "37254219"}], "href": "https://pubmed.ncbi.nlm.nih.gov/37254219"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Andrea Martisova, Jakub Faktor, Tereza Sosolikova, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Characterization of the AGR2-NPM3 axis uncovers the AGR2 involvement in PD-L1 regulation in colorectal cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41598-024-72990-z"}], "href": "https://doi.org/10.1038/s41598-024-72990-z"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "39300184"}], "href": "https://pubmed.ncbi.nlm.nih.gov/39300184"}]}]}]}
Synonyms	PORMIN, TMEM123
Proteins	NPM3_HUMAN
NCBI Gene ID	10360
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

NPM3 has 7,324 functional associations with biological entities spanning 8 categories (molecular profile, organism, functional term, phrase or reference, chemical, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 112 datasets.

Click the + buttons to view associations for NPM3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

NPM3 Gene

Functional Associations

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

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of NPM3 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 NPM3 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 NPM3 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 NPM3 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 NPM3 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 NPM3 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 NPM3 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 NPM3 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 NPM3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of NPM3 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 NPM3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with NPM3 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with NPM3 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 NPM3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of NPM3 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 NPM3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing NPM3 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 NPM3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing NPM3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing NPM3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing NPM3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing NPM3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with NPM3 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 NPM3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing NPM3 protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with NPM3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with NPM3 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with NPM3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of NPM3 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by NPM3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with NPM3 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 NPM3 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 NPM3 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 NPM3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at NPM3 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 NPM3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of NPM3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing NPM3 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of NPM3 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with NPM3 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.