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    NHP2 NHP2 ribonucleoprotein [ Homo sapiens (human) ]

    Gene ID: 55651, updated on 10-Dec-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
    mouse all
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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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. 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
    2. 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
    3. NHP2 deficiency impairs rRNA biogenesis and causes pulmonary fibrosis and Høyeraal-Hreidarsson syndrome. Benyelles M, et al. Hum Mol Genet, 2020 Apr 15. PMID 31985013
    4. 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
    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 (125) 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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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