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    VCPKMT valosin containing protein lysine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 79609, updated on 28-Oct-2024

    Summary

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    Official Symbol
    VCPKMTprovided by HGNC
    Official Full Name
    valosin containing protein lysine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:20352
    See related
    Ensembl:ENSG00000100483 MIM:615260; AllianceGenome:HGNC:20352
    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
    Also known as
    VCP-KMT; METTL21D; C14orf138
    Summary
    Enables ATPase binding activity and protein-lysine N-methyltransferase activity. Involved in negative regulation of ATP-dependent activity and peptidyl-lysine trimethylation. Located in cytosol. Part of protein-containing complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 3.1), testis (RPKM 3.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VCPKMT in Genome Data Viewer
    Location:
    14q21.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (50102716..50116572, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (44309674..44322811, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (50575355..50583290, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8345 Neighboring gene ribosomal protein S15a pseudogene 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:50541160-50541705 Neighboring gene RN7SK pseudogene 193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:50550650-50551156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8353 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:50605652-50606356 Neighboring gene SOS Ras/Rho guanine nucleotide exchange factor 2 Neighboring gene NANOG hESC enhancer GRCh37_chr14:50692526-50693052 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8354 Neighboring gene MPRA-validated peak2154 silencer Neighboring gene L-2-hydroxyglutarate dehydrogenase Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:50766206-50766899 Neighboring gene microRNA 4504

    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. Structural remodeling of AAA+ ATPase p97 by adaptor protein ASPL facilitates posttranslational methylation by METTL21D. Petrović S, et al. Proc Natl Acad Sci U S A, 2023 Jan 24. PMID 36656859, Free PMC Article
    2. Lysine methylation of VCP by a member of a novel human protein methyltransferase family. Kernstock S, et al. Nat Commun, 2012. PMID 22948820
    3. AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation. Hülsmann J, et al. Mol Cell Proteomics, 2018 Jul. PMID 29599191, Free PMC Article
    4. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. Cloutier P, et al. PLoS Genet, 2013. PMID 23349634, Free PMC Article
    5. Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family. Li X, et al. Mol Cell Proteomics, 2016 Sep. PMID 27432908, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural remodeling of AAA+ ATPase p97 by adaptor protein ASPL facilitates posttranslational methylation by METTL21D.
      Title: Structural remodeling of AAA+ ATPase p97 by adaptor protein ASPL facilitates posttranslational methylation by METTL21D.
    2. METTL21D is the methyltransferase responsible for lysine methylation of VCP.
      Title: Lysine methylation of VCP by a member of a novel human protein methyltransferase family.
    3. METTL21D trimethylates Lys-315 in VCP/p97 in a ASPCR1-dependent manner
      Title: A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity.
    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)

    Genotypes

    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

    Clone Names

    • FLJ13920

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables histone methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-lysine N-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein-lysine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein-lysine N-methyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of ATP-dependent activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in peptidyl-lysine methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in peptidyl-lysine trimethylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    part_of protein-containing complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein N-lysine methyltransferase METTL21D
    Names
    VCP lysine methyltransferase
    methyltransferase like 21D
    methyltransferase-like protein 21D
    protein-lysine methyltransferase METTL21D
    valosin containing protein lysine (K) methyltransferase

    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)

    1. NM_001040662.2 → NP_001035752.1  protein N-lysine methyltransferase METTL21D isoform b

      See identical proteins and their annotated locations for NP_001035752.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1, which results in a shorter protein (isoform B), compared to isoform A
      Source sequence(s)
      AK023982, AL109758, BI767189
      Consensus CDS
      CCDS41951.1
      UniProtKB/Swiss-Prot
      Q9H867
      Related
      ENSP00000379200.2, ENST00000395859.2
      Conserved Domains (1) summary
      pfam10294
      Location:22 → 191
      Methyltransf_16; Lysine methyltransferase

    2. NM_024558.3 → NP_078834.2  protein N-lysine methyltransferase METTL21D isoform a

      See identical proteins and their annotated locations for NP_078834.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (A).
      Source sequence(s)
      AK023982, AL109758, BI753530
      Consensus CDS
      CCDS9696.2
      UniProtKB/Swiss-Prot
      B7ZLA3, B7ZLA4, Q2M2X3, Q86T12, Q9H867
      Related
      ENSP00000379201.2, ENST00000395860.7
      Conserved Domains (1) summary
      pfam10294
      Location:22 → 195
      Methyltransf_16; Lysine methyltransferase

    RNA

    1. NR_049738.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region, compared to variant 1, which results in a frameshift and an early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record: however, the predicted protein is not represented because the product is significantly truncated and the transcript is a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC027585, BC105118, BX247997
      Related
      ENST00000491402.5

    2. NR_049739.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 5' coding region, compared to variant 1, which results in a frameshift and an early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record: however, the predicted protein is not represented because the product is significantly truncated and the transcript is a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC027585, BC105118, BX247997
      Related
      ENST00000484763.1

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      50102716..50116572 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017021640.3 → XP_016877129.1  protein N-lysine methyltransferase METTL21D isoform X2

    2. XM_005268060.5 → XP_005268117.1  protein N-lysine methyltransferase METTL21D isoform X1

      Conserved Domains (1) summary
      pfam10294
      Location:22 → 195
      Methyltransf_16; Lysine methyltransferase

    3. XM_047431773.1 → XP_047287729.1  protein N-lysine methyltransferase METTL21D isoform X3

    RNA

    1. XR_943532.2 RNA Sequence

    2. XR_007064045.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      44309674..44322811 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376713.1 → XP_054232688.1  protein N-lysine methyltransferase METTL21D isoform X2

    2. XM_054376712.1 → XP_054232687.1  protein N-lysine methyltransferase METTL21D isoform X1

    3. XM_054376714.1 → XP_054232689.1  protein N-lysine methyltransferase METTL21D isoform X3

    RNA

    1. XR_008488896.1 RNA Sequence

    2. XR_008488895.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H867.2 GenPept UniProtKB/Swiss-Prot:Q9H867

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