METTL24
protein-codingmethyltransferase like 24
Gene summary
Predicted to enable methyltransferase activity. Predicted to be involved in methylation. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]
- C6orf186
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~114.4 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 METTL24 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001123364.3. 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 | 1 | 1 | ||||
| missense | 69 | 1 | 70 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 71 | 1 | 0 | 72 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001116836.1 | 5 | MANE Select | |
| Ensembl | ENSP00000344071.4 | 5 | MANE Select | |
| RefSeq | NP_001341523.1 | 2 | Standard | |
| RefSeq | NP_001341524.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- methylation
Molecular Function
- methyltransferase activity
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000338882
- Coding exons
- 5
- Length
- 112345
- Individuals with no LoFs
- 124390
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 201
- Defined
- 124592
- p
- 0.000811
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.491 | 137 | 154 | 0.889 | 0.00000798 | 2351 |
| Missense (PolyPhen) | 65 | 75.561 | 0.86023 | 1063 | ||
| Synonymous | 0.983 | 45 | 54.2 | 0.830 | 0.00000264 | 714 |
| Loss of Function | 0.820 | 9 | 12.1 | 0.745 | 5.13e-7 | 159 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0.00041 | 0.00041 | rare |
| Ashkenazi Jewish | 0.00010 | 0.00010 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00083 | 0.00084 | rare |
| European (Non-Finnish) | 0.0011 | 0.0011 | notable |
| South Asian | 0.0014 | 0.0013 | notable |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 1.26
- RVIS percentile EVS
- 93.53
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |