CMTR2
protein-codingcap methyltransferase 2, the group of 7BS 2'O-ribose DNA/RNA methyltransferases
Gene summary
Enables methyltransferase cap2 activity. Involved in 7-methylguanosine mRNA capping. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]
- FTSJD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0008903
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0005105
Submitter: Ambry Genetics
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CMTR2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018348.6. 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 | 95 | 7 | 102 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 95 | 7 | 0 | 102 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060818.4 | 1 | MANE Select | |
| Ensembl | ENSP00000411148.2 | 1 | MANE Select | |
| RefSeq | NP_001093112.1 | 1 | Standard | |
| RefSeq | NP_001311303.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pathways Affected in Adenoid Cystic Carcinoma
- mRNA capping
Biological Process
- 7-methylguanosine mRNA capping
- cap1 mRNA methylation
- cap2 mRNA methylation
Molecular Function
- mRNA (nucleoside-2'-O-)-methyltransferase activity
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000338099
- Coding exons
- 1
- Length
- 8327
- Individuals with no LoFs
- 125650
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 92
- Defined
- 125742
- p
- 0.000366
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.127 | 402 | 395 | 1.02 | 0.0000190 | 5148 |
| Missense (PolyPhen) | 96 | 116.4 | 0.82473 | 1600 | ||
| Synonymous | -0.488 | 153 | 146 | 1.05 | 0.00000726 | 1430 |
| Loss of Function | 0.983 | 17 | 22.0 | 0.774 | 0.00000108 | 300 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00023 | 0.00023 | rare |
| Ashkenazi Jewish | 0.00089 | 0.00089 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00048 | 0.00047 | rare |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that mediates mRNA cap2 2'-O-ribose methylation to the 5'-cap structure of mRNAs. Methylates the ribose of the second nucleotide of a m(7)GpppG-capped mRNA and small nuclear RNA (snRNA) (cap0) to produce m(7)GpppRmpNm (cap2). Recognizes a guanosine cap on RNA independently of its N(7) methylation status. Display cap2 methylation on both cap0 and cap1. Displays a preference for cap1 RNAs. {ECO:0000269|PubMed:21310715}.;
Intolerance Scores
- RVIS EVS
- 0.09
- RVIS percentile EVS
- 60.65
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- H
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |