NPM2 nucleophosmin/nucleoplasmin 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NPM2provided by HGNC
Official Full Name: nucleophosmin/nucleoplasmin 2provided by HGNC
Primary source: HGNC:HGNC:7930
See related: Ensembl:ENSG00000158806 MIM:608073; AllianceGenome:HGNC:7930
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Predicted to enable RNA binding activity; chromatin binding activity; and histone binding activity. Involved in several processes, including blastocyst development; oocyte differentiation; and regulation of cell cycle process. Located in chromatin and nucleus. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in thyroid (RPKM 3.7), brain (RPKM 3.7) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8p21.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (22024134..22036897)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (22298091..22310854)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (21881645..21894408)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hexavalent chromium causes centrosome amplification by inhibiting the binding between TMOD2 and NPM2.
Title: Hexavalent chromium causes centrosome amplification by inhibiting the binding between TMOD2 and NPM2.
Loss of NPM2 expression is a potential immunohistochemical marker for malignant peritoneal mesothelioma: a single-center study of 92 cases.
Title: Loss of NPM2 expression is a potential immunohistochemical marker for malignant peritoneal mesothelioma: a single-center study of 92 cases.
Studies indicate that histone chalerones nucleoplasmin (NPM2/NPM3) preferentially associated with histones H2A-H2B in the egg and the nuclear autoantigenic sperm protein (NASP) families.
Title: Vertebrate nucleoplasmin and NASP: egg histone storage proteins with multiple chaperone activities.
Characterization of the sperm chromatin decondensation and nucleosome assembly activities of homo- and hetero-oligomers of NPM1,NPM2 and NPM3.
Title: Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling.
The crystal structure of a truncated Npm2-core shows that the N-terminal domains of Npm2 and Np form similar pentamers, providing insights into the mechanism of histone binding by nucleoplasmins.
Title: Crystal structure and function of human nucleoplasmin (npm2): a histone chaperone in oocytes and embryos.
Observational study of gene-disease association. (HuGE Navigator)
Title: Centrosome-related genes, genetic variation, and risk of breast cancer.
Promoter methylation and differential gene expression of five markers: COL1A2, NPM2, HSPB6, DDIT4L and MT1G were validated by sequencing of bisulfite-modified DNA and real-time reverse transcriptase PCR, respectively.
Title: Genome-wide screen of promoter methylation identifies novel markers in melanoma.
Expression of NPM2 in HeLa cells
Title: Increased expression of a COOH-truncated nucleophosmin resulting from alternative splicing is associated with cellular resistance to ionizing radiation in HeLa cells.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables enzyme binding	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	TAS Traceable Author Statement more info	PubMed
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in blastocyst development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in oocyte differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of DNA replication	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of meiotic nuclear division	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of exit from mitosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in single fertilization	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nucleoplasmin-2

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.

mRNA and Protein(s)

NM_001286680.2 → NP_001273609.1 nucleoplasmin-2 isoform 1

See identical proteins and their annotated locations for NP_001273609.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).

Source sequence(s)

AY262113, DB262972

Consensus CDS

CCDS6018.1

UniProtKB/Swiss-Prot

B3KSU0, D3DSQ8, Q6NVH6, Q86SE8

Related

ENSP00000427741.1, ENST00000518119.6

Conserved Domains (1) summary

pfam03066
Location:18 → 119

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
NM_001286681.2 → NP_001273610.1 nucleoplasmin-2 isoform 2

See identical proteins and their annotated locations for NP_001273610.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an exon in the 3' coding region which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC091171

Consensus CDS

CCDS75703.1

UniProtKB/TrEMBL

E5RFQ8

Related

ENSP00000370941.5, ENST00000381530.9

Conserved Domains (1) summary

pfam03066
Location:18 → 119

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
NM_001413113.1 → NP_001400042.1 nucleoplasmin-2 isoform 1

Status: VALIDATED

Source sequence(s)

AC091171

UniProtKB/Swiss-Prot

B3KSU0, D3DSQ8, Q6NVH6, Q86SE8
NM_001413114.1 → NP_001400043.1 nucleoplasmin-2 isoform 3

Status: VALIDATED

Source sequence(s)

AC091171
NM_001413115.1 → NP_001400044.1 nucleoplasmin-2 isoform 4

Status: VALIDATED

Source sequence(s)

AC091171
NM_001413116.1 → NP_001400045.1 nucleoplasmin-2 isoform 1

Status: VALIDATED

Source sequence(s)

AC091171

UniProtKB/Swiss-Prot

B3KSU0, D3DSQ8, Q6NVH6, Q86SE8

Related

ENSP00000381032.1, ENST00000397940.5
NM_001413117.1 → NP_001400046.1 nucleoplasmin-2 isoform 5

Status: VALIDATED

Source sequence(s)

AC091171
NM_001413118.1 → NP_001400047.1 nucleoplasmin-2 isoform 5

Status: VALIDATED

Source sequence(s)

AC091171
NM_001413119.1 → NP_001400048.1 nucleoplasmin-2 isoform 5

Status: VALIDATED

Source sequence(s)

AC091171
NM_001413120.1 → NP_001400049.1 nucleoplasmin-2 isoform 4

Status: VALIDATED

Source sequence(s)

AC091171
NM_001413121.1 → NP_001400050.1 nucleoplasmin-2 isoform 2

Status: VALIDATED

Source sequence(s)

AC091171

UniProtKB/TrEMBL

E5RFQ8

Related

ENSP00000481018.1, ENST00000615914.1
NM_182795.2 → NP_877724.1 nucleoplasmin-2 isoform 1

See identical proteins and their annotated locations for NP_877724.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform (1).

Source sequence(s)

AC091171

Consensus CDS

CCDS6018.1

UniProtKB/Swiss-Prot

B3KSU0, D3DSQ8, Q6NVH6, Q86SE8

Conserved Domains (1) summary

pfam03066
Location:18 → 119

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain