EEF1AKMT3
protein-codingEEF1A lysine methyltransferase 3, the group of 7BS protein lysine methyltransferases
Gene summary
Enables heat shock protein binding activity and protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine methylation. Located in centrosome and cytoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jun 2026]
- FAM119B
- METTL21B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.0 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 EEF1AKMT3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015433.3. 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 | 0 | |||||
| missense | 38 | 1 | 39 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 40 | 1 | 0 | 41 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056248.2 | 3 | MANE Select | |
| Ensembl | ENSP00000300209.8 | 3 | MANE Select | |
| RefSeq | NP_996797.1 | 4 | Standard | |
| Ensembl | ENSP00000327425.5 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- peptidyl-lysine methylation
Molecular Function
- protein binding
- methyltransferase activity
- protein-lysine N-methyltransferase activity
- heat shock protein binding
Cellular Component
- cytoplasm
- centrosome
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000300209
- Coding exons
- 3
- Length
- 11050
- Individuals with no LoFs
- 125686
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 62
- Defined
- 125748
- p
- 0.000247
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.831 | 103 | 130 | 0.795 | 0.00000606 | 1463 |
| Missense (PolyPhen) | 49 | 54.481 | 0.8994 | 609 | ||
| Synonymous | 1.50 | 45 | 59.7 | 0.753 | 0.00000281 | 480 |
| Loss of Function | 0.596 | 6 | 7.79 | 0.770 | 3.37e-7 | 81 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00087 | 0.00086 | rare |
| Latino/Admixed American | 0.00035 | 0.00035 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00022 | 0.00022 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00082 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protein-lysine methyltransferase that selectively methylates EEF1A1 and EEF1A2 at 'Lys-165' in an aminoacyl-tRNA and GTP-dependent manner. EEF1A1 methylation by EEF1AKMT3 is dynamic as well as inducible by stress conditions, such as ER-stress, and plays a regulatory role on mRNA translation. {ECO:0000269|PubMed:28108655}.;
Intolerance Scores
- RVIS EVS
- 0.46
- RVIS percentile EVS
- 78.46
Essentials
- Essential (gene trap)
- N