NPM1 nucleophosmin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NPM1provided by HGNC
Official Full Name: nucleophosmin 1provided by HGNC
Primary source: HGNC:HGNC:7910
See related: Ensembl:ENSG00000181163 MIM:164040; AllianceGenome:HGNC:7910
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: B23; NPM
Summary: The protein encoded by this gene is involved in several cellular processes, including centrosome duplication, protein chaperoning, and cell proliferation. The encoded phosphoprotein shuttles between the nucleolus, nucleus, and cytoplasm, chaperoning ribosomal proteins and core histones from the nucleus to the cytoplasm. This protein is also known to sequester the tumor suppressor ARF in the nucleolus, protecting it from degradation until it is needed. Mutations in this gene are associated with acute myeloid leukemia. Dozens of pseudogenes of this gene have been identified. [provided by RefSeq, Aug 2017]
Expression: Ubiquitous expression in ovary (RPKM 256.2), lymph node (RPKM 146.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q35.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (171387116..171410900)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (171927442..171951228)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (170814120..170837904)

Chromosome 5 - NC_000005.10 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 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?

Molecular basis for RASSF10/NPM/RNF2 feedback cascade-mediated regulation of gastric cancer cell proliferation.
Title: Molecular basis for RASSF10/NPM/RNF2 feedback cascade-mediated regulation of gastric cancer cell proliferation.
Monocytic Differentiation of Human Acute Myeloid Leukemia Cells: A Proteomic and Phosphoproteomic Comparison of FAB-M4/M5 Patients with and without Nucleophosmin 1 Mutations.
Title: Monocytic Differentiation of Human Acute Myeloid Leukemia Cells: A Proteomic and Phosphoproteomic Comparison of FAB-M4/M5 Patients with and without Nucleophosmin 1 Mutations.
Targeting NPM1 Epigenetically Promotes Postinfarction Cardiac Repair by Reprogramming Reparative Macrophage Metabolism.
Title: Targeting NPM1 Epigenetically Promotes Postinfarction Cardiac Repair by Reprogramming Reparative Macrophage Metabolism.
MANF Promotes Unexplained Recurrent Miscarriages by Interacting with NPM1 and Downregulating Trophoblast Cell Migration and Invasion.
Title: MANF Promotes Unexplained Recurrent Miscarriages by Interacting with NPM1 and Downregulating Trophoblast Cell Migration and Invasion.
Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins.
Title: Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins.
Comprehensive Molecular Profiling of NPM1-Mutated Acute Myeloid Leukemia Using RNAseq Approach.
Title: Comprehensive Molecular Profiling of NPM1-Mutated Acute Myeloid Leukemia Using RNAseq Approach.
ZNF692 regulates nucleolar morphology by interacting with NPM1 and modifying its self-assembly properties.
Title: ZNF692 regulates nucleolar morphology by interacting with NPM1 and modifying its self-assembly properties.
Mutations highly specific for secondary AML are associated with poor outcomes in ELN favorable risk NPM1-mutated AML.
Title: Mutations highly specific for secondary AML are associated with poor outcomes in ELN favorable risk NPM1-mutated AML.
NPM1-Mutated Acute Myeloid Leukemia: Recent Developments and Open Questions.
Title: NPM1-Mutated Acute Myeloid Leukemia: Recent Developments and Open Questions.
AURKA inhibition induces Ewing's sarcoma apoptosis and ferroptosis through NPM1/YAP1 axis.
Title: AURKA inhibition induces Ewing's sarcoma apoptosis and ferroptosis through NPM1/YAP1 axis.

Submit: New GeneRIF Correction See all GeneRIFs (660)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Acute myeloid leukemia MedGen: C0023467 OMIM: 601626 GeneReviews: CEBPA-Associated Familial Acute Myeloid Leukemia (AML), ETV6 Thrombocytopenia and Predisposition to Leukemia, RUNX1 Familial Platelet Disorder with Associated Myeloid Malignancies, DDX41-Associated Familial Myelodysplastic Syndrome and Acute Myeloid Leukemia	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify nucleophosmin (NPM1; nucleolar phosphoprotein B23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify nucleophosmin (NPM1; nucleolar phosphoprotein B23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify nucleophosmin (NPM1; nucleolar phosphoprotein B23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify nucleophosmin (NPM1; nucleolar phosphoprotein B23), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Rev	rev	HIV-1 Rev interacting protein, nucleophosmin 1 (NPM1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with NPM1 is decreased by RRE	PubMed
	rev	HIV-1 Rev has a nucleolar distribution which is similar to B23.1, but with different trafficking rates	PubMed
	rev	interaction of B23 with Rev has been implicated in the cytotoxic activity of Rev	PubMed
	rev	amino acids 38-52 of Rev have been implicated in the association with B32	PubMed
	rev	B23 is associated with the nucleolar localization of Rev	PubMed
	rev	during nuclear import B23 forms a specific binding complex with Rev which is dissociated by RRE RNA and phosphorylation by casein kinase II (CK2)	PubMed
	rev	B23 stimulates the nuclear import of Rev, an effect that is increased when B23 is phosphorylated by casein kinase II (CK2)	PubMed
Tat	tat	Nucleophosmin (NPM1, nucleolar phosphoprotein B23, numatrin) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS	PubMed
	tat	HIV-1 Tat complexes with LARP7, MEPCE, SART3, NPM1, PPM1G, hnRNP-F, and 7SK RNA to form a Tat-7SK RNP complex to control HIV-1 transcription	PubMed
	tat	HIV-1 Tat upregulates the expression of nucleophosmin (NPM1, nucleolar phosphoprotein B23, numatrin) in Jurkat cells	PubMed
	tat	Acetylation of human histone chaperone NPK1 regulates nuclear localization of HIV-1 Tat and modulates Tat-mediated LTR-transactivation	PubMed
	tat	Overexpression of NPM1 enhances HIV-1 Tat-mediated transactivation by reducing the histone H1 occupancy on the chromatinized template of HIV-1 LTR	PubMed
	tat	The nucleolar shuttle protein B23 binds to HIV-1 Tat and data indicates B23 is necessary for the nucleolar localization of Tat	PubMed
Vpr	vpr	A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of nucleophosmin (NPM1, nucleolar phosphoprotein B23, numatrin) expression by HIV-1 Vpr in Vpr transduced macrophages	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80894 (e-PCR)
- UniSTS:92753

D16S2968 (e-PCR)
- UniSTS:3283

REN60444 (e-PCR)
- UniSTS:385244

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables NF-kappaB binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables Tat protein binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables rRNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribosomal large subunit binding	IDA Inferred from Direct Assay more info	PubMed
enables ribosomal small subunit binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables unfolded protein binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to UV	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular senescence	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in centrosome cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular protein transport	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of apoptotic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of apoptotic process	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of centrosome duplication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein kinase activity by regulation of protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleocytoplasmic transport	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleocytoplasmic transport	TAS Traceable Author Statement more info	PubMed
involved_in nucleosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell cycle G2/M phase transition	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of centriole replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of centrosome duplication	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of eIF2 alpha phosphorylation by dsRNA	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of endodeoxyribonuclease activity	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of endoribonuclease activity	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of mRNA stability involved in cellular response to UV	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribosomal large subunit biogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosomal large subunit export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosomal small subunit biogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosomal small subunit export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribosome assembly	TAS Traceable Author Statement more info	PubMed
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in focal adhesion	HDA more info	PubMed
located_in granular component	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	HDA more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-DNA complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
located_in spindle pole centrosome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nucleophosmin

Names: nucleolar protein NO38; nucleophosmin (nucleolar phosphoprotein B23, numatrin); nucleophosmin/nucleoplasmin family, member 1; testicular tissue protein Li 128

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.

Genomic

NG_016018.1 RefSeqGene

Range

5001..28181

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_458

mRNA and Protein(s)

NM_001037738.3 → NP_001032827.1 nucleophosmin isoform 3

See identical proteins and their annotated locations for NP_001032827.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) utilizes an alternate 3'-terminal exon, compared to variant 1, resulting in a shorter protein (isoform 3) with a distinct C-terminus.

Source sequence(s)

AC091980, AC093246, BC107754

Consensus CDS

CCDS43399.1

UniProtKB/TrEMBL

A0A140VJQ2, A4ZU86

Related

ENSP00000377408.2, ENST00000393820.2

Conserved Domains (1) summary

pfam03066
Location:18 → 117

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
NM_001355006.2 → NP_001341935.1 nucleophosmin isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1. Variants 1 and 7 both encode the same isoform (1).

Source sequence(s)

AC093246, AY347529

Consensus CDS

CCDS4376.1

UniProtKB/Swiss-Prot

A8K3N7, B5BU00, D3DQL6, P06748, P08693, Q12826, Q13440, Q13441, Q14115, Q5EU94, Q5EU95, Q5EU96, Q5EU97, Q5EU98, Q5EU99, Q6V962, Q8WTW5, Q96AT6, Q96DC4, Q96EA5, Q9BYG9, Q9UDJ7

UniProtKB/TrEMBL

A0A0S2Z491, A0A7I2V5S2

Related

ENSP00000428755.1, ENST00000517671.5

Conserved Domains (2) summary

pfam03066
Location:18 → 117

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain

pfam16276
Location:245 → 291

NPM1-C; Nucleophosmin C-terminal domain
NM_001355007.2 → NP_001341936.1 nucleophosmin isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AC091980, AC093246

Consensus CDS

CCDS93824.1

UniProtKB/TrEMBL

E5RI98, Q9BTI9

Related

ENSP00000429485.2, ENST00000521672.6

Conserved Domains (2) summary

pfam03066
Location:1 → 52

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain

pfam16276
Location:181 → 229

NPM1-C; Nucleophosmin C-terminal domain
NM_001355009.2 → NP_001341938.1 nucleophosmin isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) lacks an internal segment and has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AC091980, AC093246

UniProtKB/TrEMBL

A4ZU86

Related

ENSP00000503717.1, ENST00000679233.1

Conserved Domains (1) summary

pfam03066
Location:18 → 116

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain
NM_001355010.2 → NP_001341939.1 nucleophosmin isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (6) lacks several alternate internal exons compared to variant 1. The resulting isoform (6) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC091980, AC093246, BU661768

Conserved Domains (1) summary

pfam16276
Location:118 → 166

NPM1-C; Nucleophosmin C-terminal domain
NM_002520.7 → NP_002511.1 nucleophosmin isoform 1

See identical proteins and their annotated locations for NP_002511.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 and 7 both encode the same isoform (1).

Source sequence(s)

AC091980, AC093246

Consensus CDS

CCDS4376.1

UniProtKB/Swiss-Prot

A8K3N7, B5BU00, D3DQL6, P06748, P08693, Q12826, Q13440, Q13441, Q14115, Q5EU94, Q5EU95, Q5EU96, Q5EU97, Q5EU98, Q5EU99, Q6V962, Q8WTW5, Q96AT6, Q96DC4, Q96EA5, Q9BYG9, Q9UDJ7

UniProtKB/TrEMBL

A0A0S2Z491, A0A7I2V5S2

Related

ENSP00000296930.5, ENST00000296930.10

Conserved Domains (2) summary

pfam03066
Location:18 → 117

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain

pfam16276
Location:245 → 291

NPM1-C; Nucleophosmin C-terminal domain
NM_199185.4 → NP_954654.1 nucleophosmin isoform 2

See identical proteins and their annotated locations for NP_954654.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2) that lacks an internal segment, compared to isoform 1.

Source sequence(s)

AC093246, BC009623, BC021983, HM005441

Consensus CDS

CCDS4377.1

UniProtKB/TrEMBL

A0A0S2Z4G7, A0A7I2V5S2

Related

ENSP00000341168.6, ENST00000351986.10

Conserved Domains (2) summary

pfam03066
Location:18 → 116

Nucleoplasmin; Nucleoplasmin/nucleophosmin domain

pfam16276
Location:216 → 264

NPM1-C; Nucleophosmin C-terminal domain

RNA

NR_149149.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) uses an alternate splice junction and lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.

Source sequence(s)

AC091980, AC093246

Related

ENST00000678774.1