Aliases for NPM2 Gene

Aliases for NPM2 Gene

  • Nucleophosmin/Nucleoplasmin 2 2 3 5
  • Nucleoplasmin-2 3 4
  • NPM2 5

External Ids for NPM2 Gene

Previous GeneCards Identifiers for NPM2 Gene

  • GC00U990477
  • GC08U900224
  • GC08P021903
  • GC08P021904
  • GC08P021939
  • GC08P021881
  • GC08P020424

Summaries for NPM2 Gene

GeneCards Summary for NPM2 Gene

NPM2 (Nucleophosmin/Nucleoplasmin 2) is a Protein Coding gene. Diseases associated with NPM2 include Ceroid Lipofuscinosis, Neuronal, 8, Northern Epilepsy Variant. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and enzyme binding. An important paralog of this gene is NPM1.

UniProtKB/Swiss-Prot Summary for NPM2 Gene

  • Core histones chaperone involved in chromatin reprogramming, specially during fertilization and early embryonic development. Probably involved in sperm DNA decondensation during fertilization.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NPM2 Gene

Genomics for NPM2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NPM2 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
GH08J022023 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 605.7 +1.1 1093 0.8 GATAD2A TFE3 ZIC2 RBFOX2 EZH2 POLR2A ZNF341 KMT2B SOX13 MGA NPM2 NONHSAG049702.2 SNODB541 FGF17
GH08J022026 Promoter/Enhancer 1 Ensembl ENCODE 605.7 +1.7 1738 0.3 GATAD2A RBFOX2 EZH2 KMT2B TAF1 REST ZBTB26 TGIF2 CTCF TEAD1 NPM2 NONHSAG049702.2 SNODB541 FGF17
GH08J022024 Promoter 0.7 Ensembl 600.7 +0.4 393 0.2 POLR2A DPF2 MAZ ZNF3 GLIS1 ZBTB33 L3MBTL2 EZH2 NONHSAG049702.2 NPM2 FGF17
GH08J022021 Enhancer 0.3 Ensembl 600.7 -1.2 -1207 0.2 SCRT2 ZNF384 NPM2 piR-36416 XPO7
GH08J022022 Enhancer 0.3 Ensembl 600.7 -0.6 -607 0.2 SCRT2 NONHSAG049702.2 NPM2 piR-36416 XPO7
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NPM2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NPM2

Top Transcription factor binding sites by QIAGEN in the NPM2 gene promoter:
  • ATF6
  • Evi-1
  • FOXD3
  • FOXI1
  • FOXJ2
  • FOXJ2 (long isoform)
  • FOXL1
  • GATA-1
  • HFH-1
  • HFH-3

Genomic Locations for NPM2 Gene

Genomic Locations for NPM2 Gene
chr8:22,023,308-22,036,908
(GRCh38/hg38)
Size:
13,601 bases
Orientation:
Plus strand
chr8:21,881,636-21,894,408
(GRCh37/hg19)
Size:
12,773 bases
Orientation:
Plus strand

Genomic View for NPM2 Gene

Genes around NPM2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPM2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPM2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPM2 Gene

Proteins for NPM2 Gene

  • Protein details for NPM2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86SE8-NPM2_HUMAN
    Recommended name:
    Nucleoplasmin-2
    Protein Accession:
    Q86SE8
    Secondary Accessions:
    • B3KSU0
    • D3DSQ8
    • Q6NVH6

    Protein attributes for NPM2 Gene

    Size:
    214 amino acids
    Molecular mass:
    24152 Da
    Quaternary structure:
    • Homopentamer, when bound to H2A-H2B dimers only. Homodecamer of two stacked pentamers, when bound to H2A-H2B dimers and H3-H4 tetramers simultaneously.

    Three dimensional structures from OCA and Proteopedia for NPM2 Gene

    Alternative splice isoforms for NPM2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NPM2 Gene

Post-translational modifications for NPM2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NPM2 Gene

Domains & Families for NPM2 Gene

Gene Families for NPM2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NPM2 Gene

InterPro:
Blocks:
  • Nucleoplasmin
ProtoNet:

Suggested Antigen Peptide Sequences for NPM2 Gene

GenScript: Design optimal peptide antigens:
  • Nucleoplasmin-2 (NPM2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q86SE8

UniProtKB/Swiss-Prot:

NPM2_HUMAN :
  • The acidic tract A2 mediates histone binding.
  • Belongs to the nucleoplasmin family.
Domain:
  • The acidic tract A2 mediates histone binding.
Family:
  • Belongs to the nucleoplasmin family.
genes like me logo Genes that share domains with NPM2: view

Function for NPM2 Gene

Molecular function for NPM2 Gene

UniProtKB/Swiss-Prot Function:
Core histones chaperone involved in chromatin reprogramming, specially during fertilization and early embryonic development. Probably involved in sperm DNA decondensation during fertilization.

Phenotypes From GWAS Catalog for NPM2 Gene

Gene Ontology (GO) - Molecular Function for NPM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IBA 21873635
GO:0003723 RNA binding IBA 21873635
GO:0005515 protein binding IPI 25416956
GO:0019899 enzyme binding IEA --
GO:0042393 histone binding TAS 12581654
genes like me logo Genes that share ontologies with NPM2: view
genes like me logo Genes that share phenotypes with NPM2: view

Animal Models for NPM2 Gene

MGI Knock Outs for NPM2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NPM2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for NPM2 Gene

Localization for NPM2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NPM2 Gene

Nucleus. Note=Found in the oocyte nucleus before nuclear membrane breakdown, after which it is redistributed to the cytoplasm. {ECO:0000250}.

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 NPM2 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NPM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000789 cytoplasmic chromatin IDA 12714744
GO:0000790 nuclear chromatin IDA 12714744
GO:0005634 nucleus IEA,IDA 12714744
GO:0005654 nucleoplasm IBA 21873635
GO:0005730 nucleolus IBA 21873635
genes like me logo Genes that share ontologies with NPM2: view

Pathways & Interactions for NPM2 Gene

PathCards logo

SuperPathways for NPM2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for NPM2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001824 blastocyst development IMP 12714744
GO:0006325 chromatin organization IEA --
GO:0006338 chromatin remodeling IDA 12714744
GO:0007096 regulation of exit from mitosis IMP 12714744
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with NPM2: view

No data available for Pathways by source and SIGNOR curated interactions for NPM2 Gene

Drugs & Compounds for NPM2 Gene

No Compound Related Data Available

Transcripts for NPM2 Gene

mRNA/cDNA for NPM2 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NPM2

Alternative Splicing Database (ASD) splice patterns (SP) for NPM2 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10
SP1: - -
SP2:
SP3:
SP4: - -
SP5: - - -
SP6: - - -
SP7: -

Relevant External Links for NPM2 Gene

GeneLoc Exon Structure for
NPM2

Expression for NPM2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NPM2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NPM2 Gene

This gene is overexpressed in Brain - Cortex (x6.5), Brain - Frontal Cortex (BA9) (x5.6), and Brain - Anterior cingulate cortex (BA24) (x5.2).

Protein differential expression in normal tissues from HIPED for NPM2 Gene

This gene is overexpressed in Spinal cord (37.6), Frontal cortex (15.3), and Retina (14.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NPM2 Gene



Protein tissue co-expression partners for NPM2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NPM2

SOURCE GeneReport for Unigene cluster for NPM2 Gene:

Hs.131055

Evidence on tissue expression from TISSUES for NPM2 Gene

  • Nervous system(4.6)
  • Skin(4.3)
genes like me logo Genes that share expression patterns with NPM2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NPM2 Gene

Orthologs for NPM2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NPM2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NPM2 30 31
  • 99.37 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia NPM2 30 31
  • 77.93 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Npm2 30
  • 75.49 (n)
Cow
(Bos Taurus)
Mammalia NPM2 30 31
  • 74.83 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Npm2 30 17 31
  • 74.82 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 51 (a)
OneToMany
-- 31
  • 34 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia NPM2 31
  • 48 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia NPM2 31
  • 39 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia npm2 30
  • 56.2 (n)
African clawed frog
(Xenopus laevis)
Amphibia npm-A 30
Zebrafish
(Danio rerio)
Actinopterygii npm2b 31
  • 36 (a)
OneToOne
Species where no ortholog for NPM2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Chicken (Gallus gallus)
  • 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 Vase (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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for NPM2 Gene

ENSEMBL:
Gene Tree for NPM2 (if available)
TreeFam:
Gene Tree for NPM2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NPM2: view image

Paralogs for NPM2 Gene

Paralogs for NPM2 Gene

(2) SIMAP similar genes for NPM2 Gene using alignment to 4 proteins:

  • NPM2_HUMAN
  • E5RFQ8_HUMAN
  • E5RGN1_HUMAN
  • Q6NVH6_HUMAN
genes like me logo Genes that share paralogs with NPM2: view

Variants for NPM2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NPM2 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
788549 Benign: not provided 22,034,113(+) A/C SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for NPM2 Gene

Structural Variations from Database of Genomic Variants (DGV) for NPM2 Gene

Variant ID Type Subtype PubMed ID
dgv7132n100 CNV gain 25217958
esv2759604 CNV loss 17122850
nsv528590 CNV loss 19592680
nsv610764 CNV loss 21841781
nsv831263 CNV loss 17160897
nsv951112 CNV deletion 24416366

Variation tolerance for NPM2 Gene

Residual Variation Intolerance Score: 75.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.56; 44.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NPM2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPM2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPM2 Gene

Disorders for NPM2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for NPM2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
ceroid lipofuscinosis, neuronal, 8, northern epilepsy variant
  • ceroid lipofuscinosis, neuronal, 8
- elite association - COSMIC cancer census association via MalaCards
Search NPM2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NPM2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with NPM2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NPM2 Gene

Publications for NPM2 Gene

  1. Roles of NPM2 in chromatin and nucleolar organization in oocytes and embryos. (PMID: 12714744) Burns KH … Matzuk MM (Science (New York, N.Y.) 2003) 2 3 4
  2. Crystal structure and function of human nucleoplasmin (npm2): a histone chaperone in oocytes and embryos. (PMID: 21863821) Platonova O … Akey CW (Biochemistry 2011) 3 4
  3. Centrosome-related genes, genetic variation, and risk of breast cancer. (PMID: 20508983) Olson JE … Couch FJ (Breast cancer research and treatment 2011) 3 41
  4. New insights into the nucleophosmin/nucleoplasmin family of nuclear chaperones. (PMID: 17187372) Frehlick LJ … Ausió J (BioEssays : news and reviews in molecular, cellular and developmental biology 2007) 4 23
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for NPM2 Gene

Sources for NPM2 Gene