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

Gene ID: 79609, updated on 5-Mar-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 ATPase activity and peptidyl-lysine trimethylation. Located in cytosol. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 3.1), testis (RPKM 3.0) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (50102716..50116572, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (44309674..44322811, complement)
105.20220307 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
  • 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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_2023_10

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

Gene LinkOut

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