CMTR1
protein-codingcap methyltransferase 1, the group of G-patch domain containing|7BS 2'O-ribose DNA/RNA methyltransferases
Gene summary
Enables methyltransferase cap1 activity. Involved in 7-methylguanosine mRNA capping. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- KIAA0082
- FTSJD2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.6 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 CMTR1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015050.3. 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 | 72 | 2 | 74 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 72 | 2 | 0 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055865.1 | 23 | MANE Select | |
| Ensembl | ENSP00000362550.4 | 23 | MANE Select | |
| Ensembl | ENSP00000414233.1 | 9 | Standard | |
| Ensembl | ENSP00000393893.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- mRNA capping
Biological Process
- 7-methylguanosine mRNA capping
- mRNA methylation
- cap1 mRNA methylation
Molecular Function
- nucleic acid binding
- mRNA (nucleoside-2'-O-)-methyltransferase activity
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373451
- Coding exons
- 23
- Length
- 49609
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125748
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.32 | 287 | 495 | 0.580 | 0.0000294 | 5554 |
| Missense (PolyPhen) | 49 | 131.28 | 0.37326 | 1611 | ||
| Synonymous | -0.0389 | 180 | 179 | 1.00 | 0.0000102 | 1556 |
| Loss of Function | 5.50 | 8 | 49.9 | 0.160 | 0.00000287 | 539 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000060 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that mediates mRNA cap1 2'-O-ribose methylation to the 5'-cap structure of mRNAs. Methylates the ribose of the first nucleotide of a m(7)GpppG-capped mRNA and small nuclear RNA (snRNA) to produce m(7)GpppRm (cap1). Displays a preference for cap0 transcripts. Cap1 modification is linked to higher levels of translation. May be involved in the interferon response pathway. {ECO:0000269|PubMed:18533109, ECO:0000269|PubMed:20713356, ECO:0000269|PubMed:21310715}.;
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- RVIS EVS
- -1.09
- RVIS percentile EVS
- 7.11
Essentials
- Essential (CRISPR)
- E
- Essential (gene trap)
- K
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |