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    NVL nuclear VCP like [ Homo sapiens (human) ]

    Gene ID: 4931, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NVLprovided by HGNC
    Official Full Name
    nuclear VCP likeprovided by HGNC
    Primary source
    HGNC:HGNC:8070
    See related
    Ensembl:ENSG00000143748 MIM:602426; AllianceGenome:HGNC:8070
    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
    NVL2
    Summary
    This gene encodes a member of the AAA (ATPases associated with diverse cellular activities) superfamily. Multiple transcript variants encoding different isoforms have been found for this gene. Two encoded proteins, described as major and minor isoforms, have been localized to distinct regions of the nucleus. The largest encoded protein (major isoform) has been localized to the nucleolus and shown to participate in ribosome biosynthesis (PMID: 15469983, 16782053), while the minor isoform has been localized to the nucleoplasmin. [provided by RefSeq, Aug 2011]
    Expression
    Ubiquitous expression in skin (RPKM 7.5), lymph node (RPKM 5.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NVL in Genome Data Viewer
    Location:
    1q42.11
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (224227345..224330172, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (223416266..223519053, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (224415047..224517874, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224370121-224370951 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224370952-224371781 Neighboring gene Sharpr-MPRA regulatory region 9300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2603 Neighboring gene delta 4-desaturase, sphingolipid 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1851 Neighboring gene uncharacterized LOC101927143 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_5412 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224402200-224402893 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:224405308-224405505 Neighboring gene uncharacterized LOC101927164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224442412-224443337 Neighboring gene Sharpr-MPRA regulatory region 1236 Neighboring gene microRNA 320b-2 Neighboring gene MPRA-validated peak721 silencer Neighboring gene RNA, U6 small nuclear 1008, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2608 Neighboring gene Sharpr-MPRA regulatory region 12366 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:224523487-224523975 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:224527150-224527870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:224528593-224529312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2609 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:224544931-224545431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2611 Neighboring gene cornichon family member 4

    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 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. The NVL gene confers risk for both major depressive disorder and schizophrenia in the Han Chinese population. Wang M, et al. Prog Neuropsychopharmacol Biol Psychiatry, 2015 Oct 1. PMID 25891250
    2. Structure and function of the N-terminal nucleolin binding domain of nuclear valosin-containing protein-like 2 (NVL2) harboring a nucleolar localization signal. Fujiwara Y, et al. J Biol Chem, 2011 Jun 17. PMID 21474449, Free PMC Article
    3. NVL: a new member of the AAA family of ATPases localized to the nucleus. Germain-Lee EL, et al. Genomics, 1997 Aug 15. PMID 9286697
    4. Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2. Ishida YI, et al. Int J Biochem Cell Biol, 2021 Mar. PMID 33422691
    5. The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs. Lingaraju M, et al. Nat Commun, 2019 Jul 29. PMID 31358741, Free PMC Article

    See all (87) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.
      Title: Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2.
    2. Data show that the nuclear exosome adaptors nuclear valosin-containing protein-like (NVL) and zinc finger, CCHC domain containing 8 protein (ZCCHC8) bind the Mtr4 exosome RNA helicase (MTR4) KOW domain on a surface.
      Title: The MTR4 helicase recruits nuclear adaptors of the human RNA exosome using distinct arch-interacting motifs.
    3. knockdown of WDR74 leads to significant defects in the pre-rRNA cleavage within the internal transcribed spacer 1, occurring in an early stage of the processing pathway. When the dissociation of WDR74 from the MTR4-containing exonuclease complex was impaired upon expression of mutant NVL2, the same processing defect, with partial migration of WDR74 from the nucleolus towards the nucleoplasm, was observed.
      Title: WDR74 participates in an early cleavage of the pre-rRNA processing pathway in cooperation with the nucleolar AAA-ATPase NVL2.
    4. Results indicated that the NVL gene may contain overlapping common genetic risk factors for major depressive disorder and schizophrenia in the Han Chinese population
      Title: The NVL gene confers risk for both major depressive disorder and schizophrenia in the Han Chinese population.
    5. results suggest that WDR74 is a novel regulatory protein of the MTR4-exsosome complex whose interaction is regulated by NVL2 and is involved in ribosome biogenesis
      Title: AAA-ATPase NVL2 acts on MTR4-exosome complex to dissociate the nucleolar protein WDR74.
    6. suggest that NVL2 is involved in pre-rRNA processing by associating with the nuclear exosome complex and that MPP6 is required for maintaining the integrity of this rRNA processing complex
      Title: NVL2, a nucleolar AAA-ATPase, is associated with the nuclear exosome and is involved in pre-rRNA processing.
    7. these findings suggest that NVL2 is essential for telomerase biogenesis and provides an alternative approach for inhibiting telomerase activity in cancer.
      Title: The AAA-ATPase NVL2 is a telomerase component essential for holoenzyme assembly.
    8. NVL2 might facilitate the dissociation and recycling of nucleolin, thereby promoting efficient ribosome biogenesis
      Title: Structure and function of the N-terminal nucleolin binding domain of nuclear valosin-containing protein-like 2 (NVL2) harboring a nucleolar localization signal.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    10. interaction of NVL2 with ribosomal protein L5 is ATP-dependent and likely contributes to the nucleolar translocation of NVL2
      Title: NVL2 is a nucleolar AAA-ATPase that interacts with ribosomal protein L5 through its nucleolar localization sequence.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 ATP binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables ATP hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding HDA PubMed 
    enables preribosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables preribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of protein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of positive regulation of telomere maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in rRNA processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of protein localization to nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ribosomal large subunit biogenesis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ribosomal large subunit biogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in ribosome biogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ribosome biogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in telomerase holoenzyme complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in membrane HDA PubMed 
    part_of nuclear exosome (RNase complex) IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of telomerase holoenzyme complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    nuclear valosin-containing protein-like
    Names
    NVLp

    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_029641.1 RefSeqGene

      Range
      5018..107845
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243146.2 → NP_001230075.1  nuclear valosin-containing protein-like isoform 3

      See identical proteins and their annotated locations for NP_001230075.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks three alternate coding exons in the 5' coding region, uses a downstream initiation codon, and contains an alternate in-frame exon, compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC092809, AK297396, BP284587, BU683548
      Consensus CDS
      CCDS58062.1
      UniProtKB/Swiss-Prot
      O15381
      Related
      ENSP00000341362.4, ENST00000340871.8
      Conserved Domains (3) summary
      COG0464
      Location:68 → 663
      SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
      pfam00004
      Location:429 → 559
      AAA; ATPase family associated with various cellular activities (AAA)
      cl21455
      Location:409 → 445
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. NM_001243147.2 → NP_001230076.1  nuclear valosin-containing protein-like isoform 4

      See identical proteins and their annotated locations for NP_001230076.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC092809, AK298244, BP284587, BU683548
      Consensus CDS
      CCDS58063.1
      UniProtKB/TrEMBL
      B4DLM8
      Related
      ENSP00000417826.1, ENST00000469075.5
      Conserved Domains (5) summary
      COG0464
      Location:193 → 761
      SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
      pfam00004
      Location:527 → 657
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam16725
      Location:2 → 72
      Nucleolin_bd; Nucleolin binding domain
      cl11522
      Location:75 → 125
      Tom22; Mitochondrial import receptor subunit Tom22
      cl21455
      Location:507 → 543
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    3. NM_002533.4 → NP_002524.2  nuclear valosin-containing protein-like isoform 1

      See identical proteins and their annotated locations for NP_002524.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1, also known as NVL.2 or the major isoform).
      Source sequence(s)
      AC092809, AK293923, BP284587, BU683548, U68140
      Consensus CDS
      CCDS1541.1
      UniProtKB/Swiss-Prot
      B4DMC4, B4DP98, O15381, Q96EM7
      UniProtKB/TrEMBL
      B4DLM8
      Related
      ENSP00000281701.6, ENST00000281701.11
      Conserved Domains (4) summary
      COG0464
      Location:284 → 852
      SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
      pfam00004
      Location:618 → 748
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam16725
      Location:2 → 72
      Nucleolin_bd; Nucleolin binding domain
      cl21455
      Location:598 → 634
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    4. NM_206840.3 → NP_996671.1  nuclear valosin-containing protein-like isoform 2

      See identical proteins and their annotated locations for NP_996671.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon and uses a downstream start codon compared to variant 1. The resulting protein (isoform 2, also known as NVL.1 or the minor isoform) is shorter and has a distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC092809, AK293923, BP284587, BU683548, U78772
      Consensus CDS
      CCDS1542.1
      UniProtKB/TrEMBL
      B4DLM8
      Related
      ENSP00000375747.2, ENST00000391875.6
      Conserved Domains (1) summary
      cl27568
      Location:137 → 750
      TIP49; TIP49 C-terminus

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      224227345..224330172 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001383.2 → XP_016856872.1  nuclear valosin-containing protein-like isoform X5

      UniProtKB/TrEMBL
      B4DLM8

    2. XM_011544196.1 → XP_011542498.1  nuclear valosin-containing protein-like isoform X4

      UniProtKB/TrEMBL
      B4DLM8
      Conserved Domains (4) summary
      COG0464
      Location:284 → 879
      SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
      pfam00004
      Location:645 → 775
      AAA; ATPase family associated with various cellular activities (AAA)
      pfam16725
      Location:2 → 72
      Nucleolin_bd; Nucleolin binding domain
      cl21455
      Location:625 → 661
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    3. XM_017001379.2 → XP_016856868.1  nuclear valosin-containing protein-like isoform X2

      UniProtKB/TrEMBL
      B4DLM8

    4. XM_017001378.2 → XP_016856867.1  nuclear valosin-containing protein-like isoform X1

      UniProtKB/TrEMBL
      B4DLM8

    5. XM_047421613.1 → XP_047277569.1  nuclear valosin-containing protein-like isoform X7

    6. XM_017001380.3 → XP_016856869.1  nuclear valosin-containing protein-like isoform X3

      UniProtKB/TrEMBL
      B4DLM8

    7. XM_047421631.1 → XP_047277587.1  nuclear valosin-containing protein-like isoform X12

    8. XM_047421621.1 → XP_047277577.1  nuclear valosin-containing protein-like isoform X10

    9. XM_047421618.1 → XP_047277574.1  nuclear valosin-containing protein-like isoform X8

    10. XM_017001384.2 → XP_016856873.1  nuclear valosin-containing protein-like isoform X6

      UniProtKB/TrEMBL
      B4DLM8

    11. XM_047421637.1 → XP_047277593.1  nuclear valosin-containing protein-like isoform X14

    12. XM_047421635.1 → XP_047277591.1  nuclear valosin-containing protein-like isoform X13

    13. XM_047421626.1 → XP_047277582.1  nuclear valosin-containing protein-like isoform X11

    14. XM_017001385.3 → XP_016856874.1  nuclear valosin-containing protein-like isoform X9

      UniProtKB/TrEMBL
      B4DLM8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      223416266..223519053 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336810.1 → XP_054192785.1  nuclear valosin-containing protein-like isoform X5

    2. XM_054336809.1 → XP_054192784.1  nuclear valosin-containing protein-like isoform X4

    3. XM_054336807.1 → XP_054192782.1  nuclear valosin-containing protein-like isoform X2

    4. XM_054336806.1 → XP_054192781.1  nuclear valosin-containing protein-like isoform X1

    5. XM_054336812.1 → XP_054192787.1  nuclear valosin-containing protein-like isoform X7

    6. XM_054336808.1 → XP_054192783.1  nuclear valosin-containing protein-like isoform X3

    7. XM_054336817.1 → XP_054192792.1  nuclear valosin-containing protein-like isoform X12

    8. XM_054336815.1 → XP_054192790.1  nuclear valosin-containing protein-like isoform X10

    9. XM_054336813.1 → XP_054192788.1  nuclear valosin-containing protein-like isoform X8

    10. XM_054336811.1 → XP_054192786.1  nuclear valosin-containing protein-like isoform X6

    11. XM_054336819.1 → XP_054192794.1  nuclear valosin-containing protein-like isoform X14

    12. XM_054336818.1 → XP_054192793.1  nuclear valosin-containing protein-like isoform X13

    13. XM_054336816.1 → XP_054192791.1  nuclear valosin-containing protein-like isoform X11

    14. XM_054336814.1 → XP_054192789.1  nuclear valosin-containing protein-like isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15381.1 GenPept UniProtKB/Swiss-Prot:O15381

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