TRMT112
Basic information
Region (hg38): 11:64316460-64318074
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (13 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT112 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016404.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRMT112 | protein_coding | protein_coding | ENST00000544844 | 4 | 1625 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.139 | 0.787 | 125731 | 0 | 17 | 125748 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.928 | 96 | 73.6 | 1.30 | 0.00000324 | 806 |
| Missense in Polyphen | 24 | 15.418 | 1.5566 | 196 | ||
| Synonymous | -1.18 | 39 | 30.7 | 1.27 | 0.00000136 | 256 |
| Loss of Function | 1.45 | 2 | 5.74 | 0.349 | 2.53e-7 | 60 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000114 | 0.000114 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000659 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as an activator of both rRNA/tRNA and protein methyltransferases (PubMed:25851604). Together with methyltransferase BUD23, methylates the N(7) position of a guanine in 18S rRNA (PubMed:25851604). The heterodimer with HEMK2/N6AMT1 catalyzes N5-methylation of ETF1 on 'Gln-185', using S-adenosyl L- methionine as methyl donor (PubMed:18539146). The heterodimer with ALKBH8 catalyzes the methylation of 5-carboxymethyl uridine to 5- methylcarboxymethyl uridine at the wobble position of the anticodon loop in target tRNA species (PubMed:20308323). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production (PubMed:25851604). {ECO:0000269|PubMed:18539146, ECO:0000269|PubMed:20308323, ECO:0000269|PubMed:25851604}.;
- Pathway
- tRNA modification in the nucleus and cytosol;tRNA processing;rRNA processing;Methylation;Phase II - Conjugation of compounds;Eukaryotic Translation Termination;Translation;Metabolism of proteins;Metabolism of RNA;Biological oxidations;Metabolism;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol
(Consensus)
Intolerance Scores
- loftool
- 0.509
- rvis_EVS
- -0.08
- rvis_percentile_EVS
- 47.79
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.183
- ghis
- 0.657
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.925
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trmt112
- Phenotype
Gene ontology
- Biological process
- peptidyl-glutamine methylation;tRNA methylation;rRNA (guanine-N7)-methylation;positive regulation of rRNA processing
- Cellular component
- nucleoplasm;cytosol;protein-containing complex;perinuclear region of cytoplasm
- Molecular function
- protein binding;protein methyltransferase activity;rRNA (guanine) methyltransferase activity;protein heterodimerization activity