MRM2
protein-codingmitochondrial rRNA methyltransferase 2, the group of 7BS 2'O-ribose DNA/RNA methyltransferases
Gene summary
The protein encoded by this gene is a member of the S-adenosylmethionine-binding protein family. It is a nucleolar protein and it may be involved in the processing and modification of rRNA. This gene has been suggested to be involved in cell cycle control and DNA repair. [provided by RefSeq, Jul 2008]
- FTSJ2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032815
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0032815
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MRM2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013393.3. 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 | 8 | 1 | 9 | |||
| missense | 1 | 6 | 2 | 9 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 2 | 3 | |||
| Total | 2 | 0 | 9 | 8 | 3 | 22 |
Highest pathogenic variant AF is 0.000008351789
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037525.1 | 3 | MANE Select | |
| Ensembl | ENSP00000242257.8 | 3 | MANE Select | |
| Ensembl | ENSP00000392343.3 | 3 | Standard | |
| Ensembl | ENSP00000498090.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- rRNA processing
- rRNA modification in the mitochondrion
- Metabolism of RNA
- rRNA processing in the mitochondrion
Biological Process
- rRNA 2'-O-methylation
- rRNA processing
- cell population proliferation
- rRNA methylation
Molecular Function
- rRNA (uridine-2'-O-)-methyltransferase activity
Cellular Component
- nucleolus
- mitochondrion
- mitochondrial matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000242257
- Coding exons
- 3
- Length
- 7975
- Individuals with no LoFs
- 125705
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 41
- Defined
- 125746
- p
- 0.000163
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0869 | 150 | 153 | 0.980 | 0.00000954 | 1583 |
| Missense (PolyPhen) | 52 | 56.593 | 0.91884 | 608 | ||
| Synonymous | -0.375 | 67 | 63.2 | 1.06 | 0.00000410 | 523 |
| Loss of Function | 0.459 | 6 | 7.34 | 0.817 | 4.65e-7 | 70 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00071 | 0.00071 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00018 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: S-adenosyl-L-methionine-dependent 2'-O-ribose methyltransferase that catalyzes the formation of 2'-O- methyluridine at position 1369 (Um1369) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a universally conserved modification in the peptidyl transferase domain of the mtLSU rRNA. {ECO:0000269|PubMed:25009282, ECO:0000269|PubMed:25074936}.;
Recessive Scores
- pRec
- 0.143
Intolerance Scores
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 37.32
Essentials
- Essential (gene trap)
- K