VCPKMT

valosin containing protein lysine methyltransferase, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 14:50108632-50116600

Previous symbols: [ "C14orf138", "METTL21D" ]

Links

ENSG00000100483 ∙ NCBI:79609 ∙ OMIM:615260 ∙ HGNC:20352 ∙ Uniprot:Q9H867 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VCPKMT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VCPKMT gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17			17
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in VCPKMT

This is a list of pathogenic ClinVar variants found in the VCPKMT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-50109709-A-G		not specified	Uncertain significance (Mar 29, 2024)
14-50112616-G-A		not specified	Uncertain significance (Apr 04, 2024)
14-50112618-T-G		not specified	Uncertain significance (Apr 23, 2024)
14-50112624-C-G		not specified	Uncertain significance (Oct 12, 2021)
14-50112655-C-T		not specified	Uncertain significance (May 29, 2024)
14-50112685-G-T		not specified	Uncertain significance (Feb 03, 2022)
14-50112686-G-A		not specified	Uncertain significance (Sep 20, 2023)
14-50112716-G-A		not specified	Uncertain significance (Aug 14, 2023)
14-50114347-T-C		not specified	Uncertain significance (Apr 12, 2023)
14-50114365-C-T		not specified	Uncertain significance (Dec 08, 2023)
14-50114373-T-C		not specified	Uncertain significance (Mar 19, 2024)
14-50115846-T-C		not specified	Uncertain significance (Oct 06, 2022)
14-50115856-A-T		not specified	Uncertain significance (Feb 13, 2024)
14-50115895-C-T		not specified	Uncertain significance (Jun 05, 2023)
14-50115903-T-C		not specified	Uncertain significance (Nov 29, 2023)
14-50116163-T-G		not specified	Uncertain significance (Jan 11, 2023)
14-50116344-G-A		not specified	Uncertain significance (Jun 10, 2024)
14-50116413-A-G		not specified	Uncertain significance (Oct 25, 2022)
14-50116454-A-C		not specified	Uncertain significance (Nov 15, 2018)
14-50116501-G-C		not specified	Uncertain significance (Jan 24, 2023)
14-50116518-G-A		not specified	Uncertain significance (Dec 17, 2023)
14-50116518-G-T		not specified	Uncertain significance (Jun 02, 2024)
14-50116524-T-G		not specified	Uncertain significance (May 29, 2024)
14-50116527-A-G		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VCPKMT	protein_coding	protein_coding	ENST00000395860	6	7969

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.55e-11	0.0172	125649	1	98	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.61	169	119	1.42	0.00000551	1474
Missense in Polyphen		36	39.137	0.91986		444
Synonymous	-2.18	69	49.5	1.39	0.00000245	442
Loss of Function	-0.836	14	11.0	1.27	5.30e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000191	0.000183
Ashkenazi Jewish	0.00	0.00
East Asian	0.00196	0.00196
Finnish	0.00	0.00
European (Non-Finnish)	0.0000845	0.0000791
Middle Eastern	0.00196	0.00196
South Asian	0.00162	0.00154
Other	0.000518	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-lysine N-methyltransferase that specifically trimethylates 'Lys-315' of VCP/p97; this modification may decrease VCP ATPase activity. {ECO:0000269|PubMed:22948820, ECO:0000269|PubMed:23349634}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein methylation (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.174
• ghis: 0.470

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vcpkmt
• Phenotype: homeostasis/metabolism phenotype; normal phenotype

Gene ontology

• Biological process: protein methylation;peptidyl-lysine methylation;peptidyl-lysine trimethylation;negative regulation of ATPase activity
• Cellular component: cytoplasm;cytosol;protein-containing complex
• Molecular function: protein binding;protein-lysine N-methyltransferase activity;ATPase binding