N6AMT1
GeneN-6 adenine-specific DNA methyltransferase 1, the group of 7BS protein methyltransferases
Gene summary
No gene description available in the current model. Review primary literature for detailed gene function and characteristics.
- C21orf127
- HEMK2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
GenCC 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 N6AMT1 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 28 | 2 | 30 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 28 | 2 | 0 | 30 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| No transcripts match your selected source or search query. | ||||
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Methylation
- Phase II - Conjugation of compounds
- Eukaryotic Translation Termination
- Translation
- Metabolism of proteins
Biological Process
- toxin metabolic process
- peptidyl-glutamine methylation
- arsonoacetate metabolic process
- positive regulation of cell growth
- methylation
Molecular Function
- nucleic acid binding
- protein binding
- protein methyltransferase activity
- S-adenosylmethionine-dependent methyltransferase activity
- site-specific DNA-methyltransferase (adenine-specific) activity
Cellular Component
- nucleus
- cytosol
- protein-containing complex
- eRF1 methyltransferase complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000303775
- Coding exons
- 6
- Length
- 13181
- Individuals with no LoFs
- 124720
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1007
- Defined
- 125727
- p
- 0.00401
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.230 | 123 | 116 | 1.06 | 0.00000549 | 1349 |
| Missense (PolyPhen) | 28 | 36.289 | 0.77158 | 422 | ||
| Synonymous | 0.0938 | 43 | 43.8 | 0.982 | 0.00000219 | 440 |
| Loss of Function | 0.0962 | 8 | 8.30 | 0.964 | 3.47e-7 | 112 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0033 | 0.0028 | notable |
| Latino/Admixed American | 0.0038 | 0.0034 | notable |
| Ashkenazi Jewish | 0.00093 | 0.00089 | rare |
| East Asian | 0.0045 | 0.0037 | notable |
| Finnish | 0.017 | 0.016 | notable |
| European (Non-Finnish) | 0.0037 | 0.0034 | notable |
| South Asian | 0.00044 | 0.00042 | rare |
| Other | 0.0029 | 0.0026 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Methyltransferase that can methylate both proteins and DNA, and to a lower extent, arsenic (PubMed:18539146, PubMed:21193388, PubMed:30017583). Catalytic subunit of a heterodimer with TRMT112, which catalyzes N5-methylation of Glu residue of proteins with a Gly-Gln-Xaa-Xaa-Xaa-Arg motif (PubMed:18539146) (By similarity). Methylates ETF1 on 'Gln-185'; ETF1 needs to be complexed to ERF3 in its GTP-bound form to be efficiently methylated (PubMed:18539146, PubMed:20606008). Also acts as a N(6)-adenine-specific DNA methyltransferase by mediating methylation of DNA on the 6th position of adenine (N(6)- methyladenosine) (PubMed:30017583). N(6)-methyladenosine (m6A) DNA is significantly enriched in exonic regions and is associated with gene transcriptional activation (PubMed:30017583). May also play a role in the modulation of arsenic-induced toxicity by mediating the conversion of monomethylarsonous acid (3+) into the less toxic dimethylarsonic acid (PubMed:21193388, PubMed:25997655). It however only plays a limited role in arsenic metabolism compared with AS3MT (PubMed:25997655). {ECO:0000250|UniProtKB:Q6SKR2, ECO:0000269|PubMed:18539146, ECO:0000269|PubMed:20606008, ECO:0000269|PubMed:21193388, ECO:0000269|PubMed:25997655, ECO:0000269|PubMed:30017583}.;
Recessive Scores
- pRec
- 0.0959
Intolerance Scores
- RVIS EVS
- 0.73
- RVIS percentile EVS
- 86.08
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.464
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |