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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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VCPKMT
valosin containing protein lysine methyltransferase
Chromosome 14 · 14q21.3
NCBI Gene: 79609Ensembl: ENSG00000100483.15HGNC: HGNC:20352UniProt: Q9H867
16PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingpeptidyl-lysine trimethylationcytosolcytoplasmcolorectal carcinomaDNA methylationosteoarthritis, kneeosteoarthritis, hip
✦AI Summary

VCPKMT (METTL21D) is a highly specific protein lysine methyltransferase that catalyzes the trimethylation of lysine 315 (Lys315) in valosin-containing protein (VCP/p97), a crucial AAA+ ATPase 12. The enzyme functions by first disassembling p97 hexamers into monomeric units, making the buried Lys315 residue accessible for methylation 2. This process is facilitated by the adaptor protein ASPL, which structurally remodels p97 to expose the target lysine residue 3. Structural studies reveal that VCPKMT recognizes monomeric p97 through specific molecular interactions involving the N/D1 domains 2. While trimethylation of Lys315 may decrease VCP ATPase activity, knockout studies in mice demonstrate that VCPKMT is dispensable for normal development and survival under unstressed conditions 1. Notably, VCPKMT expression has been associated with cancer progression, as it was identified as part of a three-gene signature predictive of positive surgical margins in tongue squamous cell carcinomas 4. The enzyme appears to be highly substrate-specific, with VCP being its primary target 1.

Sources cited
1
VCPKMT specifically trimethylates VCP at Lys315 and is dispensable for mouse development
PMID: 26544960
2
VCPKMT disassembles p97 hexamers and methylates Lys315, with structural details of recognition
PMID: 37456834
3
ASPL facilitates VCPKMT-mediated methylation by remodeling p97 structure
PMID: 36656859
4
VCPKMT expression associated with positive surgical margins in tongue cancer
PMID: 31178206
⚠Limited data available — This gene has 4 indexed publications. Summary and analysis may be incomplete.
Disease Associationsⓘ20
colorectal carcinomaOpen Targets
0.07Suggestive
DNA methylationOpen Targets
0.07Suggestive
osteoarthritis, hipOpen Targets
0.06Suggestive
osteoarthritis, kneeOpen Targets
0.06Suggestive
knee fractureOpen Targets
0.05Suggestive
chronic laryngitisOpen Targets
0.05Suggestive
type 2 diabetes mellitusOpen Targets
0.05Suggestive
paralytic strabismusOpen Targets
0.05Suggestive
duodenal ulcerOpen Targets
0.04Suggestive
diabetes mellitusOpen Targets
0.04Suggestive
hyperinsulinism due to INSR deficiencyOpen Targets
0.03Suggestive
hyperinsulinemic hypoglycemia, familial, 8Open Targets
0.03Suggestive
neoplasmOpen Targets
0.03Suggestive
chronic kidney diseaseOpen Targets
0.01Suggestive
colorectal cancerOpen Targets
0.01Suggestive
Pick diseaseOpen Targets
0.00Suggestive
cancerOpen Targets
0.00Suggestive
type 1 diabetes mellitusOpen Targets
0.00Suggestive
soft tissue sarcomaOpen Targets
0.00Suggestive
tongue neoplasmOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
VCPProtein interaction85%UBXN6Protein interaction85%EEF2KMTProtein interaction75%METTL18Protein interaction73%EEF1AKMT2Protein interaction59%METTL22Protein interaction58%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
28%
Lung
27%
Liver
27%
Ovary
25%
Heart
14%
Gene Interaction Network
Click a node to explore
VCPKMTVCPUBXN6EEF2KMTMETTL18EEF1AKMT2METTL22
PROTEIN STRUCTURE
Preparing viewer…
PDB4LG1 · 1.80 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.67LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF1.18 [0.85–1.67]
RankingsWhere VCPKMT stands among ~20K protein-coding genes
  • #15,436of 20,598
    Most Researched16
  • #15,964of 17,882
    Most Constrained (LOEUF)1.67
Genes detectedVCPKMT
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase.
PMID: 37456834
iScience · 2023
1.00
2
Recessive marfanoid syndrome with herniation associated with a homozygous mutation in Fibulin-3.
PMID: 32006683
Eur J Med Genet · 2020
0.90
3
A three-gene expression signature associated with positive surgical margins in tongue squamous cell carcinomas: Predicting surgical resectability from tumour biology?
PMID: 31178206
Oral Oncol · 2019
0.80
4
Lysine Methylation of the Valosin-Containing Protein (VCP) Is Dispensable for Development and Survival of Mice.
PMID: 26544960
PLoS One · 2015
0.70
5
Structural remodeling of AAA+ ATPase p97 by adaptor protein ASPL facilitates posttranslational methylation by METTL21D.
PMID: 36656859
Proc Natl Acad Sci U S A · 2023
0.60