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, Oc... See more...

Aliases for NPM3 Gene

Aliases for NPM3 Gene

  • Nucleophosmin/Nucleoplasmin 3 2 3 5
  • Nucleoplasmin-3 3 4
  • Nucleophosmin/Nucleoplasmin Family, Member 3 3
  • TMEM123 3
  • PORMIN 3

External Ids for NPM3 Gene

Previous GeneCards Identifiers for NPM3 Gene

  • GC10M102434
  • GC10M102774
  • GC10M103672
  • GC10M103205
  • GC10M103532
  • GC10M097171

Summaries for NPM3 Gene

Entrez Gene Summary for NPM3 Gene

  • 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]

GeneCards Summary for NPM3 Gene

NPM3 (Nucleophosmin/Nucleoplasmin 3) is a Protein Coding gene. Diseases associated with NPM3 include Lung Papillary Adenocarcinoma. An important paralog of this gene is NPM1.

UniProtKB/Swiss-Prot Summary for NPM3 Gene

  • Plays a role in the regulation of diverse cellular processes such as ribosome biogenesis, chromatin remodeling or protein chaperoning (PubMed:22362753, PubMed:20073534). Modulates the histone chaperone function and the RNA-binding activity of nucleolar phosphoprotein B23/NPM (PubMed:22362753). Efficiently mediates chromatin remodeling when included in a pentamer containing NPM3 and NPM (PubMed:15596447).

Gene Wiki entry for NPM3 Gene

Additional gene information for NPM3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NPM3 Gene

Genomics for NPM3 Gene

GeneHancer (GH) Regulatory Elements for NPM3 Gene

Promoters and enhancers for NPM3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J101781 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 507.4 -0.2 -162 3.3 ZBTB40 ZNF217 TCF12 POLR2G USF1 SP1 PHF8 ZBTB10 POLR2A ZNF623 NPM3 NFKB2 WBP1L lnc-NPM3-1 OGA
GH10J101814 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 6.7 -33.7 -33696 5.9 RXRA FOXK2 ZBTB40 ZNF217 EP300 ZSCAN5C SIN3A MYC NRF1 POLR2G KCNIP2-AS1 OGA HPS6 PPRC1 MRPL43 GBF1 LDB1 TWNK SUFU NPM3
GH10J101828 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 6.4 -47.6 -47568 4.4 ZBTB40 ZNF217 EP300 ZSCAN5C TCF12 SIN3A NRF1 SP1 ZFX ZNF639 PPRC1 LDB1 LZTS2 GBF1 MRPL43 HPS6 ENSG00000272572 NOLC1 KCNIP2-AS1 SUFU
GH10J101778 Promoter/Enhancer 2 VISTA FANTOM5 Ensembl ENCODE CraniofacialAtlas 6.6 +3.2 3219 3.2 RXRA CTCF ZIC2 ZBTB10 TCF7 ZNF423 ZBTB26 SAP30 REST KLF7 FGF8 HPS6 NPM3 LOC105378457
GH10J101835 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 6.4 -56.7 -56719 8.5 CTCF SIN3A NRF1 TEAD4 ZNF639 ZNF10 ZIC2 REST GABPA ZBTB26 LOC101927445 KCNIP2 HPS6 KCNIP2-AS1 NPM3 SUFU MRPL43 lnc-HPS6-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPM3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NPM3

Top Transcription factor binding sites by QIAGEN in the NPM3 gene promoter:
  • MyoD

Genomic Locations for NPM3 Gene

Genomic Locations for NPM3 Gene
chr10:101,781,325-101,783,413
(GRCh38/hg38)
Size:
2,089 bases
Orientation:
Minus strand
chr10:103,541,082-103,543,170
(GRCh37/hg19)
Size:
2,089 bases
Orientation:
Minus strand

Genomic View for NPM3 Gene

Genes around NPM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPM3 Gene

Proteins for NPM3 Gene

  • Protein details for NPM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75607-NPM3_HUMAN
    Recommended name:
    Nucleoplasmin-3
    Protein Accession:
    O75607
    Secondary Accessions:
    • Q9UNY6

    Protein attributes for NPM3 Gene

    Size:
    178 amino acids
    Molecular mass:
    19344 Da
    Quaternary structure:
    • Interacts with NPM (via N-terminus) (PubMed:15596447). Forms a pentamer with NPM at a ratio 4:1 (NPM3/NPM). Two pentamers form a decamer (PubMed:22362753).

neXtProt entry for NPM3 Gene

Post-translational modifications for NPM3 Gene

Other Protein References for NPM3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NPM3 Gene

Domains & Families for NPM3 Gene

Gene Families for NPM3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NPM3 Gene

Blocks:
  • Nucleoplasmin
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NPM3 Gene

GenScript: Design optimal peptide antigens:
  • Nucleoplasmin-3 (NPM3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75607

UniProtKB/Swiss-Prot:

NPM3_HUMAN :
  • Belongs to the nucleoplasmin family.
Family:
  • Belongs to the nucleoplasmin family.
genes like me logo Genes that share domains with NPM3: view

Function for NPM3 Gene

Molecular function for NPM3 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the regulation of diverse cellular processes such as ribosome biogenesis, chromatin remodeling or protein chaperoning (PubMed:22362753, PubMed:20073534). Modulates the histone chaperone function and the RNA-binding activity of nucleolar phosphoprotein B23/NPM (PubMed:22362753). Efficiently mediates chromatin remodeling when included in a pentamer containing NPM3 and NPM (PubMed:15596447).

Phenotypes From GWAS Catalog for NPM3 Gene

Gene Ontology (GO) - Molecular Function for NPM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IBA 21873635
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 22190034
GO:0042393 histone binding IBA 21873635
genes like me logo Genes that share ontologies with NPM3: view
genes like me logo Genes that share phenotypes with NPM3: view

Animal Models for NPM3 Gene

MGI Knock Outs for NPM3:
  • Npm3 Npm3<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

miRNA for NPM3 Gene

miRTarBase miRNAs that target NPM3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NPM3 Gene

Localization for NPM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPM3 Gene

Nucleus. Nucleus, nucleolus. Note=Mainly found in the granular component of the nucleolus. {ECO:0000269 PubMed:22362753}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NPM3 gene
Compartment Confidence
nucleus 5
cytoskeleton 4
cytosol 4
extracellular 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Cytosol (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NPM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IBA 21873635
GO:0005730 nucleolus IDA,IBA --
GO:0005737 cytoplasm IBA 21873635
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with NPM3: view

Pathways & Interactions for NPM3 Gene

PathCards logo

SuperPathways for NPM3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NPM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006338 chromatin remodeling IBA 21873635
GO:0006364 rRNA processing IEA --
GO:0009303 rRNA transcription IEA --
genes like me logo Genes that share ontologies with NPM3: view

No data available for Pathways by source and SIGNOR curated interactions for NPM3 Gene

Drugs & Compounds for NPM3 Gene

No Compound Related Data Available

Transcripts for NPM3 Gene

mRNA/cDNA for NPM3 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NPM3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b
SP1: -
SP2: - -
SP3: - -
SP4:

Relevant External Links for NPM3 Gene

GeneLoc Exon Structure for
NPM3

Expression for NPM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NPM3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NPM3 Gene

This gene is overexpressed in Pancreas (20.0), Bone marrow stromal cell (8.7), and Ovary (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NPM3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NPM3

SOURCE GeneReport for Unigene cluster for NPM3 Gene:

Hs.90691

mRNA Expression by UniProt/SwissProt for NPM3 Gene:

O75607-NPM3_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for NPM3 Gene

  • Skin(4.3)
genes like me logo Genes that share expression patterns with NPM3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NPM3 Gene

Orthologs for NPM3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NPM3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NPM3 31 30
  • 100 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NPM3 31
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia NPM3 31 30
  • 88.69 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NPM3 31 30
  • 87.43 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Npm3 17 31 30
  • 82.29 (n)
rat
(Rattus norvegicus)
Mammalia Npm3 30
  • 80.98 (n)
oppossum
(Monodelphis domestica)
Mammalia NPM3 31
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves NPM3 31 30
  • 67.88 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NPM3 31
  • 56 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii npm1b 31
  • 17 (a)
ManyToMany
Species where no ortholog for NPM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for NPM3 Gene

ENSEMBL:
Gene Tree for NPM3 (if available)
TreeFam:
Gene Tree for NPM3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NPM3: view image

Paralogs for NPM3 Gene

Paralogs for NPM3 Gene

(2) SIMAP similar genes for NPM3 Gene using alignment to 1 proteins:

  • NPM3_HUMAN

Pseudogenes.org Pseudogenes for NPM3 Gene

genes like me logo Genes that share paralogs with NPM3: view

Variants for NPM3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NPM3 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs2735420 - p.Asn80Ile
rs34376117 - p.Ser16Asn

Additional dbSNP identifiers (rs#s) for NPM3 Gene

Structural Variations from Database of Genomic Variants (DGV) for NPM3 Gene

Variant ID Type Subtype PubMed ID
dgv171n67 CNV gain 20364138
nsv951003 CNV deletion 24416366

Variation tolerance for NPM3 Gene

Residual Variation Intolerance Score: 64.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.19; 4.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPM3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPM3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPM3 Gene

Disorders for NPM3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NPM3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
lung papillary adenocarcinoma
  • papillary adenocarcinoma of the lung
- elite association - COSMIC cancer census association via MalaCards
Search NPM3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NPM3

genes like me logo Genes that share disorders with NPM3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NPM3 Gene

Publications for NPM3 Gene

  1. Cloning, expression and nuclear localization of human NPM3, a member of the nucleophosmin/nucleoplasmin family of nuclear chaperones. (PMID: 11722795) Shackleford GM … MacArthur CA (BMC genomics 2001) 2 3 4 23 54
  2. Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling. (PMID: 22362753) Okuwaki M … Nagata K (Nucleic acids research 2012) 3 4 54
  3. NPM3, a member of the nucleophosmin/nucleoplasmin family, enhances activator-dependent transcription. (PMID: 20073534) Gadad SS … Kundu TK (Biochemistry 2010) 3 4 54
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  5. BioID Performed on Golgi Enriched Fractions Identify C10orf76 as a GBF1 Binding Protein Essential for Golgi Maintenance and Secretion. (PMID: 31519766) Chan CJ … Melançon P (Molecular & cellular proteomics : MCP 2019) 3 54

Products for NPM3 Gene

Sources for NPM3 Gene