TRMT61A
Basic information
Region (hg38): 14:103529195-103537073
Previous symbols: [ "C14orf172" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRMT61A gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in TRMT61A
This is a list of pathogenic ClinVar variants found in the TRMT61A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-103530034-C-T | not specified | Uncertain significance (May 18, 2023) | ||
| 14-103530283-G-A | not specified | Uncertain significance (May 15, 2024) | ||
| 14-103532684-G-A | not specified | Uncertain significance (Nov 16, 2021) | ||
| 14-103532704-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
| 14-103532705-G-A | not specified | Uncertain significance (Jun 28, 2022) | ||
| 14-103532758-G-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 14-103532786-T-G | not specified | Uncertain significance (May 12, 2024) | ||
| 14-103532837-T-C | not specified | Uncertain significance (Jun 17, 2024) | ||
| 14-103534618-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| 14-103534627-T-C | not specified | Uncertain significance (Jun 05, 2023) | ||
| 14-103534747-C-T | not specified | Uncertain significance (Jan 23, 2023) | ||
| 14-103534748-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 14-103534753-G-A | not specified | Uncertain significance (Jan 04, 2024) | ||
| 14-103534757-C-T | not specified | Uncertain significance (Oct 14, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRMT61A | protein_coding | protein_coding | ENST00000389749 | 3 | 7890 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0244 | 0.921 | 124960 | 0 | 22 | 124982 | 0.0000880 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.28 | 160 | 212 | 0.753 | 0.0000155 | 1818 |
| Missense in Polyphen | 36 | 71.476 | 0.50366 | 624 | ||
| Synonymous | 0.253 | 92 | 95.1 | 0.967 | 0.00000730 | 641 |
| Loss of Function | 1.65 | 4 | 9.48 | 0.422 | 4.91e-7 | 91 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000111 | 0.000111 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000112 | 0.000106 |
| Middle Eastern | 0.000111 | 0.000111 |
| South Asian | 0.000133 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalytic subunit of tRNA (adenine-N(1)-)- methyltransferase, which catalyzes the formation of N(1)- methyladenine at position 58 (m1A58) in initiator methionyl-tRNA (PubMed:16043508). Catalytic subunit of mRNA N(1)- methyltransferase complex, which mediates methylation of adenosine residues at the N(1) position of a small subset of mRNAs: N(1) methylation takes place in tRNA T-loop-like structures of mRNAs and is only present at low stoichiometries (PubMed:29107537, PubMed:29072297). {ECO:0000269|PubMed:16043508, ECO:0000269|PubMed:29072297, ECO:0000269|PubMed:29107537}.;
- Pathway
- tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA
(Consensus)
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- loftool
- 0.487
- rvis_EVS
- -0.67
- rvis_percentile_EVS
- 15.62
Haploinsufficiency Scores
- pHI
- 0.158
- hipred
- N
- hipred_score
- 0.422
- ghis
- 0.668
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.689
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trmt61a
- Phenotype
Gene ontology
- Biological process
- tRNA methylation;mRNA methylation
- Cellular component
- nucleus;nucleoplasm;tRNA (m1A) methyltransferase complex
- Molecular function
- tRNA (adenine-N1-)-methyltransferase activity;mRNA (adenine-N1-)-methyltransferase activity