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Aliases for VCPKMT Gene

Aliases for VCPKMT Gene

  • Valosin Containing Protein Lysine Methyltransferase 2 3 5
  • Valosin Containing Protein Lysine (K) Methyltransferase 2 3
  • Methyltransferase-Like Protein 21D 3 4
  • VCP Lysine Methyltransferase 3 4
  • Methyltransferase Like 21D 2 3
  • C14orf138 3 4
  • METTL21D 3 4
  • VCP-KMT 3 4
  • Valosin-Containing Protein Lysine Methyltransferase 4
  • Protein-Lysine Methyltransferase METTL21D 3
  • Chromosome 14 Open Reading Frame 138 2
  • EC 2.1.1.- 4

External Ids for VCPKMT Gene

Previous HGNC Symbols for VCPKMT Gene

  • C14orf138
  • METTL21D

Previous GeneCards Identifiers for VCPKMT Gene

  • GC14M050577

Summaries for VCPKMT Gene

GeneCards Summary for VCPKMT Gene

VCPKMT (Valosin Containing Protein Lysine Methyltransferase) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and Protein methylation. Gene Ontology (GO) annotations related to this gene include protein-lysine N-methyltransferase activity. An important paralog of this gene is METTL21A.

UniProtKB/Swiss-Prot for VCPKMT Gene

  • Protein-lysine N-methyltransferase that specifically trimethylates Lys-315 of VCP/p97; this modification may decrease VCP ATPase activity.

Additional gene information for VCPKMT Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VCPKMT Gene

Genomics for VCPKMT Gene

GeneHancer (GH) Regulatory Elements for VCPKMT Gene

Promoters and enhancers for VCPKMT Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14I050115 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 584.3 +0.0 40 2.3 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B ZNF207 VCPKMT RHOQP1 LRR1 ENSG00000270062 ATP5S LINC01588 LINC01599 SOS2
GH14I050114 Enhancer 0.4 ENCODE dbSUPER 550.8 +1.8 1782 0.2 VCPKMT ATP5S LINC01588 LINC01599
GH14I050080 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 40.3 +31.5 31472 8.9 HDGF PKNOX1 SMAD1 BMI1 BATF KLF5 IRF4 TCF12 SCRT2 ZNF207 ENSG00000251792 GC14P050088 VCPKMT RNU6-189P DNAAF2 ATP5S LINC01588 ARF6 KLHDC2 NEMF
GH14I050229 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 24.3 -115.0 -114953 4.2 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 SOS2 VCPKMT ATP5S LOC105370486
GH14I049891 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 19.6 +220.8 220840 8.9 HDGF PKNOX1 CLOCK SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ARF6 LRR1 VCPKMT RHOQP1 POLE2 ENSG00000270062 RPL36AL ENSG00000282885 RNU6-189P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VCPKMT on UCSC Golden Path with GeneCards custom track

Genomic Locations for VCPKMT Gene

Genomic Locations for VCPKMT Gene
7,969 bases
Minus strand

Genomic View for VCPKMT Gene

Genes around VCPKMT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VCPKMT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VCPKMT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VCPKMT Gene

Proteins for VCPKMT Gene

  • Protein details for VCPKMT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein-lysine methyltransferase METTL21D
    Protein Accession:
    Secondary Accessions:
    • B7ZLA3
    • B7ZLA4
    • Q2M2X3
    • Q86T12

    Protein attributes for VCPKMT Gene

    229 amino acids
    Molecular mass:
    25807 Da
    Quaternary structure:
    • Interacts with ALKBH6. Interacts with ASPSCR1 and UBXN6; interaction with ASPSCR1, but not with UBXN6, enhances VCP methylation.
    • Sequence=CAD62329.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for VCPKMT Gene

    Alternative splice isoforms for VCPKMT Gene


neXtProt entry for VCPKMT Gene

Post-translational modifications for VCPKMT Gene

  • Ubiquitination at isoforms=122
  • Modification sites at PhosphoSitePlus

Other Protein References for VCPKMT Gene

No data available for DME Specific Peptides for VCPKMT Gene

Domains & Families for VCPKMT Gene

Gene Families for VCPKMT Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VCPKMT Gene

Suggested Antigen Peptide Sequences for VCPKMT Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the methyltransferase superfamily. METTL21 family.
  • Belongs to the methyltransferase superfamily. METTL21 family.
genes like me logo Genes that share domains with VCPKMT: view

Function for VCPKMT Gene

Molecular function for VCPKMT Gene

UniProtKB/Swiss-Prot Function:
Protein-lysine N-methyltransferase that specifically trimethylates Lys-315 of VCP/p97; this modification may decrease VCP ATPase activity.

Enzyme Numbers (IUBMB) for VCPKMT Gene

Phenotypes From GWAS Catalog for VCPKMT Gene

Gene Ontology (GO) - Molecular Function for VCPKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22948820
GO:0008168 methyltransferase activity IEA --
GO:0016279 protein-lysine N-methyltransferase activity TAS --
GO:0016740 transferase activity IEA --
GO:0051117 ATPase binding IPI 23349634
genes like me logo Genes that share ontologies with VCPKMT: view
genes like me logo Genes that share phenotypes with VCPKMT: view

Animal Models for VCPKMT Gene

MGI Knock Outs for VCPKMT:

Animal Model Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VCPKMT Gene

Localization for VCPKMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for VCPKMT Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VCPKMT gene
Compartment Confidence
cytosol 5
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VCPKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 23349634
GO:0005829 cytosol TAS --
GO:0043234 protein complex IDA 23349634
genes like me logo Genes that share ontologies with VCPKMT: view

Pathways & Interactions for VCPKMT Gene

genes like me logo Genes that share pathways with VCPKMT: view

Pathways by source for VCPKMT Gene

SIGNOR curated interactions for VCPKMT Gene

Is activated by:

Gene Ontology (GO) - Biological Process for VCPKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006479 protein methylation TAS --
GO:0018022 peptidyl-lysine methylation IMP 23349634
GO:0018023 peptidyl-lysine trimethylation IDA 22948820
GO:0032259 methylation IEA --
GO:0032780 negative regulation of ATPase activity IMP 23349634
genes like me logo Genes that share ontologies with VCPKMT: view

Drugs & Compounds for VCPKMT Gene

No Compound Related Data Available

Transcripts for VCPKMT Gene

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for VCPKMT Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c · 9d
SP1: - - - - - -
SP2: - - - - -
SP3: - - - - -
SP4: - - - - - -
SP5: - - - -
SP6: - -
SP7: -

Relevant External Links for VCPKMT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for VCPKMT Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VCPKMT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VCPKMT Gene

This gene is overexpressed in Oral epithelium (44.3), Lymph node (15.3), and Fetal ovary (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VCPKMT Gene

NURSA nuclear receptor signaling pathways regulating expression of VCPKMT Gene:


Evidence on tissue expression from TISSUES for VCPKMT Gene

  • Nervous system(4.3)
  • Blood(4.2)
genes like me logo Genes that share expression patterns with VCPKMT: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VCPKMT Gene

Orthologs for VCPKMT Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VCPKMT Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia METTL21D 33
  • 100 (n)
  • 100 (a)
(Canis familiaris)
Mammalia VCPKMT 34
  • 95 (a)
  • 91.85 (n)
(Bos Taurus)
Mammalia VCPKMT 34
  • 94 (a)
  • 91.8 (n)
(Mus musculus)
Mammalia Mettl21d 34
  • 90 (a)
Vcpkmt 33 16
  • 87.43 (n)
(Rattus norvegicus)
Mammalia LOC102548559 33
  • 86.55 (n)
(Ornithorhynchus anatinus)
Mammalia VCPKMT 34
  • 78 (a)
(Monodelphis domestica)
Mammalia VCPKMT 34
  • 65 (a)
(Gallus gallus)
Aves METTL21D 33
  • 66.67 (n)
  • 64 (a)
(Anolis carolinensis)
Reptilia VCPKMT 34
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia vcpkmt 33
  • 66.98 (n)
Str.15857 33
(Danio rerio)
Actinopterygii vcpkmt 33 34
  • 61.05 (n)
(Caenorhabditis elegans)
Secernentea C42C1.13 33 34
  • 47.37 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 34
  • 28 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G73320 33
  • 48.82 (n)
(Oryza sativa)
Liliopsida Os06g0101100 33
  • 47.62 (n)
Species where no ortholog for VCPKMT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VCPKMT Gene

Gene Tree for VCPKMT (if available)
Gene Tree for VCPKMT (if available)

Paralogs for VCPKMT Gene

Paralogs for VCPKMT Gene

(1) SIMAP similar genes for VCPKMT Gene using alignment to 1 proteins: Pseudogenes for VCPKMT Gene

genes like me logo Genes that share paralogs with VCPKMT: view

Variants for VCPKMT Gene

Sequence variations from dbSNP and Humsavar for VCPKMT Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs10658395 benign, Noonan syndrome 9 50,118,857(-) AAAAAAAAAA/AAAAAAAAA/AAAAAAAAAAA/AAAAAAAAAAAA/AAAAAAAAAAAAA upstream_transcript_variant
rs138133010 likely-benign, Noonan syndrome 9 50,118,599(-) C/A/T upstream_transcript_variant
rs140995728 likely-benign, Noonan syndrome 9 50,118,391(-) G/A/C upstream_transcript_variant
rs143166880 uncertain-significance, Noonan syndrome 9 50,118,840(-) G/T upstream_transcript_variant
rs146802994 likely-benign, Noonan syndrome 9 50,118,513(-) A/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for VCPKMT Gene

Variant ID Type Subtype PubMed ID
esv28926 CNV gain+loss 19812545
nsv564835 CNV gain 21841781

Variation tolerance for VCPKMT Gene

Residual Variation Intolerance Score: 55% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.13; 84.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VCPKMT Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VCPKMT Gene

Disorders for VCPKMT Gene

Additional Disease Information for VCPKMT

No disorders were found for VCPKMT Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VCPKMT Gene

Publications for VCPKMT Gene

  1. Lysine methylation of VCP by a member of a novel human protein methyltransferase family. (PMID: 22948820) Kernstock S … Falnes PØ (Nature communications 2012) 2 3 4 58
  2. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. (PMID: 23349634) Cloutier P … Coulombe B (PLoS genetics 2013) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for VCPKMT Gene

Sources for VCPKMT Gene

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