EEF1AKMT2
protein-codingEEF1A lysine methyltransferase 2, the group of 7BS protein lysine methyltransferases
Gene summary
Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine methylation. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
- C10orf138
- METTL10
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~43.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EEF1AKMT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_212554.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 32 | 5 | 37 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 32 | 6 | 0 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_997719.2 | 7 | MANE Select | |
| Ensembl | ENSP00000357829.2 | 7 | MANE Select | |
| RefSeq | NP_001291396.1 | 5 | Standard | |
| RefSeq | NP_001291397.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- Protein methylation
Biological Process
- protein methylation
- peptidyl-lysine methylation
Molecular Function
- methyltransferase activity
- protein-lysine N-methyltransferase activity
Cellular Component
- nucleus
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000368836
- Coding exons
- 6
- Length
- 43722
- Individuals with no LoFs
- 125712
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 125745
- p
- 0.000131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.253 | 128 | 136 | 0.939 | 0.00000622 | 1855 |
| Missense (PolyPhen) | 30 | 39.221 | 0.7649 | 528 | ||
| Synonymous | 0.333 | 50 | 53.1 | 0.942 | 0.00000254 | 578 |
| Loss of Function | 0.826 | 12 | 15.5 | 0.774 | 8.80e-7 | 183 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protein-lysine methyltransferase that selectively catalyzes the trimethylation of EEF1A at 'Lys-318'. {ECO:0000255|HAMAP-Rule:MF_03188, ECO:0000269|PubMed:25144183}.;
Recessive Scores
- pRec
- 0.0703
Intolerance Scores
- RVIS EVS
- 0.46
- RVIS percentile EVS
- 78.28
Essentials
- Essential (gene trap)
- N