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NHP2 NHP2 ribonucleoprotein [ Homo sapiens (human) ]

Gene ID: 55651, updated on 27-Nov-2024

Summary

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Official Symbol
NHP2provided by HGNC
Official Full Name
NHP2 ribonucleoproteinprovided by HGNC
Primary source
HGNC:HGNC:14377
See related
Ensembl:ENSG00000145912 MIM:606470; AllianceGenome:HGNC:14377
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
DKCB2; NHP2P; NOLA2
Summary
This gene is a member of the H/ACA snoRNPs (small nucleolar ribonucleoproteins) gene family. snoRNPs are involved in various aspects of rRNA processing and modification and have been classified into two families: C/D and H/ACA. The H/ACA snoRNPs also include the DKC1, NOLA1 and NOLA3 proteins. These four H/ACA snoRNP proteins localize to the dense fibrillar components of nucleoli and to coiled (Cajal) bodies in the nucleus. Both 18S rRNA production and rRNA pseudouridylation are impaired if any one of the four proteins is depleted. The four H/ACA snoRNP proteins are also components of the telomerase complex. This gene encodes a protein related to Saccharomyces cerevisiae Nhp2p. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in esophagus (RPKM 36.2), brain (RPKM 32.1) and 25 other tissues See more
Orthologs
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Genomic context

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See NHP2 in Genome Data Viewer
Location:
5q35.3
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (178149463..178153885, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (178699722..178704144, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (177576464..177580886, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16711 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:177541661-177542174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16712 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177547789-177548591 Neighboring gene NEDD4 binding protein 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177550999-177551800 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177553540-177554200 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177554863-177555523 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177556537-177557188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177557189-177557840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177559119-177559648 Neighboring gene required for meiotic nuclear division 5 homolog B Neighboring gene Sharpr-MPRA regulatory region 11782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177577953-177578454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177590971-177591472 Neighboring gene NAD(P)HX epimerase pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:177607056-177607598 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177607599-177608139 Neighboring gene germ cell-less 2, spermatogenesis associated

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Control of box C/D snoRNP assembly by N(6)-methylation of adenine. Huang L, et al. EMBO Rep, 2017 Sep. PMID 28623187, Free PMC Article
  2. NHP2 downregulation counteracts hTR-mediated activation of the DNA damage response at ALT telomeres. Raghunandan M, et al. EMBO J, 2021 Mar 15. PMID 33595114, Free PMC Article
  3. Mutations in the telomerase component NHP2 cause the premature ageing syndrome dyskeratosis congenita. Vulliamy T, et al. Proc Natl Acad Sci U S A, 2008 Jun 10. PMID 18523010, Free PMC Article
  4. Expression of the human homologue of the small nucleolar RNA-binding protein NHP2 gene during monocytic differentiation of U937 cells. Kang HS, et al. Biochim Biophys Acta, 2002 May 3. PMID 12020816
  5. A novel mutation (p.Y24N) in NHP2 leads to idiopathic pulmonary fibrosis and lung carcinoma chronic obstructive lung disease by disrupting the expression and nucleocytoplasmic localization of NHP2. Liu L, et al. Biochim Biophys Acta Mol Basis Dis, 2023 Jun. PMID 36933847

See all (123) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A novel mutation (p.Y24N) in NHP2 leads to idiopathic pulmonary fibrosis and lung carcinoma chronic obstructive lung disease by disrupting the expression and nucleocytoplasmic localization of NHP2.
    Title: A novel mutation (p.Y24N) in NHP2 leads to idiopathic pulmonary fibrosis and lung carcinoma chronic obstructive lung disease by disrupting the expression and nucleocytoplasmic localization of NHP2.
  2. NHP2 downregulation counteracts hTR-mediated activation of the DNA damage response at ALT telomeres.
    Title: NHP2 downregulation counteracts hTR-mediated activation of the DNA damage response at ALT telomeres.
  3. NHP2 deficiency impairs rRNA biogenesis and causes pulmonary fibrosis and Hoyeraal-Hreidarsson syndrome.
    Title: NHP2 deficiency impairs rRNA biogenesis and causes pulmonary fibrosis and Høyeraal-Hreidarsson syndrome.
  4. In this work, we have uncovered a putative role of epigenetic regulation in a subset of human snoRNP complexes that are involved in the site-specific modification of RNA. We find that a subset of box C/D snoRNAs are methylated at the 1n position and that this blocks both 15.5k binding and the formation of the kinked conformation in vivo.
    Title: Control of box C/D snoRNP assembly by N(6)-methylation of adenine.
  5. Indian aplastic anemia patients did not have NHP2 mutations.
    Title: Detection of mutations in TERT, the genes for telomerase reverse transcriptase, in Indian patients of aplastic anaemia: a pilot study.
  6. Effects of dyskeratosis congenita mutations in NHP2 on assembly of H/ACA pre-RNPs
    Title: Effects of dyskeratosis congenita mutations in dyskerin, NHP2 and NOP10 on assembly of H/ACA pre-RNPs.
  7. The analysis of two other proteins, NHP2 and GAR1, that together with dyskerin and NOP10 are key components of telomerase and small nucleolar ribonucleoprotein (snoRNP) complexes, is described.
    Title: Mutations in the telomerase component NHP2 cause the premature ageing syndrome dyskeratosis congenita.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Mutations in TERT, the gene for telomerase reverse transcriptase, in aplastic anemia.
  9. NOLA2 expression in patients with squamous cell lung cancer increased by 70% which makes it a highly informative marker of squamous cell lung cancer
    Title: [The NOLA2 and RPS3A genes as highly informative markers for human squamous cell lung cancer].
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human NHP2 ribonucleoprotein homolog (yeast) (NHP2) at amino acid residues 27-28 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables U3 snoRNA binding IEA
Inferred from Electronic Annotation
more info
  
enables box H/ACA snoRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables box H/ACA snoRNA binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables mRNA 3'-UTR binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables telomerase RNA binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in rRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in rRNA pseudouridine synthesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in snRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in snoRNA guided rRNA pseudouridine synthesis IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within telomerase RNA localization to Cajal body HMP PubMed 
involved_in telomere maintenance via telomerase IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in telomere maintenance via telomerase NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in telomere maintenance via telomerase TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of box H/ACA scaRNP complex TAS
Traceable Author Statement
more info
 PubMed 
part_of box H/ACA snoRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of box H/ACA snoRNP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of box H/ACA snoRNP complex TAS
Traceable Author Statement
more info
 PubMed 
part_of box H/ACA telomerase RNP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of box H/ACA telomerase RNP complex TAS
Traceable Author Statement
more info
 PubMed 
located_in chromosome, telomeric region HDA PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of sno(s)RNA-containing ribonucleoprotein complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of telomerase holoenzyme complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of telomerase holoenzyme complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of telomerase holoenzyme complex TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
H/ACA ribonucleoprotein complex subunit 2
Names
NHP2 ribonucleoprotein homolog
NHP2-like protein
nucleolar protein family A, member 2 (H/ACA small nucleolar RNPs)
snoRNP protein NHP2

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

  1. NG_011765.1 RefSeqGene

    Range
    5001..9498
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_346

mRNA and Protein(s)

  1. NM_001034833.2 → NP_001030005.1  H/ACA ribonucleoprotein complex subunit 2 isoform b

    See identical proteins and their annotated locations for NP_001030005.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon compared to variant 1, that causes a frameshift. The resulting protein (isoform b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AJ293309, BG827491, BM913344
    Consensus CDS
    CCDS34308.1
    UniProtKB/TrEMBL
    J3QSY4
    Related
    ENSP00000366276.2, ENST00000314397.9
    Conserved Domains (1) summary
    cd21104
    Location:32 → 74
    SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13

  2. NM_001396110.1 → NP_001383039.1  H/ACA ribonucleoprotein complex subunit 2 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC136632
    UniProtKB/TrEMBL
    D6RCB9
    Related
    ENSP00000423803.1, ENST00000514354.5
    Conserved Domains (1) summary
    COG1358
    Location:34 → 111
    Rpl7Ae; Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure and biogenesis]

  3. NM_017838.4 → NP_060308.1  H/ACA ribonucleoprotein complex subunit 2 isoform a

    See identical proteins and their annotated locations for NP_060308.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform a).
    Source sequence(s)
    AJ293309, BC000009, BE797477
    Consensus CDS
    CCDS4432.1
    UniProtKB/Swiss-Prot
    A6NKY8, Q9NX24, Q9P095
    Related
    ENSP00000274606.4, ENST00000274606.8
    Conserved Domains (1) summary
    cd21104
    Location:32 → 130
    SNU13; U4/U6.U5 small nuclear ribonucleoprotein SNU13

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    178149463..178153885 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    178699722..178704144 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NX24.1 GenPept UniProtKB/Swiss-Prot:Q9NX24

Gene LinkOut

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