TYW3
Basic information
Region (hg38): 1:74733152-74766678
Previous symbols: [ "C1orf171" ]
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 TYW3 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in TYW3
This is a list of pathogenic ClinVar variants found in the TYW3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-74733293-A-C | not specified | Uncertain significance (Jul 19, 2023) | ||
| 1-74736560-G-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 1-74738690-A-G | not specified | Uncertain significance (Dec 02, 2021) | ||
| 1-74738719-T-A | not specified | Uncertain significance (Apr 11, 2023) | ||
| 1-74738724-C-G | not specified | Uncertain significance (Dec 31, 2023) | ||
| 1-74738738-C-T | not specified | Uncertain significance (Apr 09, 2024) | ||
| 1-74752328-A-G | not specified | Uncertain significance (Jan 03, 2022) | ||
| 1-74752349-G-A | not specified | Uncertain significance (Dec 16, 2023) | ||
| 1-74752364-A-G | not specified | Uncertain significance (Apr 26, 2023) | ||
| 1-74763925-A-G | not specified | Uncertain significance (Feb 10, 2022) | ||
| 1-74763932-C-T | not specified | Uncertain significance (May 31, 2024) | ||
| 1-74763937-A-T | not specified | Uncertain significance (May 18, 2023) | ||
| 1-74763940-A-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 1-74764007-A-G | not specified | Uncertain significance (Mar 28, 2023) | ||
| 1-74764015-C-T | not specified | Uncertain significance (Sep 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TYW3 | protein_coding | protein_coding | ENST00000370867 | 6 | 33527 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00169 | 0.901 | 125730 | 0 | 18 | 125748 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.357 | 149 | 137 | 1.09 | 0.00000646 | 1733 |
| Missense in Polyphen | 40 | 42.237 | 0.94704 | 526 | ||
| Synonymous | -0.397 | 51 | 47.5 | 1.07 | 0.00000214 | 448 |
| Loss of Function | 1.44 | 6 | 11.2 | 0.535 | 5.38e-7 | 130 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000126 | 0.000125 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000721 | 0.0000703 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000144 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA (By similarity). {ECO:0000250}.;
- Pathway
- Synthesis of wybutosine at G37 of tRNA(Phe);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA;wybutosine biosynthesis;7-(3-amino-3-carboxypropyl)-wyosine biosynthesis
(Consensus)
Recessive Scores
- pRec
- 0.0776
Intolerance Scores
- loftool
- 0.790
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.23
Haploinsufficiency Scores
- pHI
- 0.0435
- hipred
- N
- hipred_score
- 0.355
- ghis
- 0.548
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.551
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tyw3
- Phenotype
Gene ontology
- Biological process
- tRNA methylation;wybutosine biosynthetic process
- Cellular component
- cytoplasm
- Molecular function
- tRNA methyltransferase activity