ETFBKMT
protein-codingelectron transfer flavoprotein subunit beta lysine methyltransferase, the group of 7BS protein lysine methyltransferases
Gene summary
Enables heat shock protein binding activity and protein-lysine N-methyltransferase activity. Involved in negative regulation of fatty acid beta-oxidation using acyl-CoA dehydrogenase. Located in mitochondrial matrix. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]
- C12orf72
- METTL20
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.0 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 ETFBKMT variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001135863.2. 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 | 4 | 4 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 2 | |||
| Total | 0 | 0 | 5 | 2 | 0 | 7 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001129335.1 | 3 | MANE Select | |
| Ensembl | ENSP00000350353.3 | 3 | MANE Select | |
| RefSeq | NP_001129336.1 | 3 | Standard | |
| RefSeq | NP_776163.1 | 3 | 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
- peptidyl-lysine trimethylation
- negative regulation of electron transfer activity
- negative regulation of fatty acid beta-oxidation using acyl-CoA dehydrogenase
Molecular Function
- protein-lysine N-methyltransferase activity
- heat shock protein binding
Cellular Component
- cytoplasm
- mitochondrial matrix
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000357721
- Coding exons
- 3
- Length
- 25955
- Individuals with no LoFs
- 124625
- Homozygous LoFs
- 11
- Heterozygous LoFs
- 1111
- Defined
- 125747
- p
- 0.00447
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.257 | 127 | 135 | 0.938 | 0.00000634 | 1720 |
| Missense (PolyPhen) | 49 | 47.017 | 1.0422 | 543 | ||
| Synonymous | 0.951 | 40 | 48.4 | 0.826 | 0.00000219 | 505 |
| Loss of Function | -0.423 | 12 | 10.5 | 1.14 | 6.00e-7 | 113 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0011 | 0.0011 | notable |
| Latino/Admixed American | 0.0050 | 0.0050 | notable |
| Ashkenazi Jewish | 0.0011 | 0.0011 | notable |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.011 | 0.010 | notable |
| European (Non-Finnish) | 0.0047 | 0.0047 | notable |
| South Asian | 0.0044 | 0.0044 | notable |
| Other | 0.0052 | 0.0051 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protein-lysine methyltransferase that selectively trimethylates the flavoprotein ETFB in mitochondria (PubMed:25023281, PubMed:25416781). Thereby, may negatively regulate the function of ETFB in electron transfer from Acyl-CoA dehydrogenases to the main respiratory chain (PubMed:25416781). {ECO:0000269|PubMed:25023281, ECO:0000269|PubMed:25416781}.;
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- RVIS EVS
- 0.75
- RVIS percentile EVS
- 86.57
Essentials
- Essential (gene trap)
- N