METTL1
Basic information
Region (hg38): 12:57768471-57772119
Previous symbols: [ "C12orf1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
- Abnormality_of_neuronal_migration (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005371.6. 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 | 8 | |||||
| missense | 45 | 45 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 8 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| METTL1 | protein_coding | protein_coding | ENST00000324871 | 6 | 4323 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00196 | 0.916 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.239 | 157 | 166 | 0.948 | 0.00000960 | 1782 |
| Missense in Polyphen | 50 | 57.192 | 0.87424 | 585 | ||
| Synonymous | -0.207 | 67 | 64.9 | 1.03 | 0.00000374 | 559 |
| Loss of Function | 1.52 | 6 | 11.6 | 0.518 | 4.90e-7 | 146 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000362 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. {ECO:0000255|HAMAP-Rule:MF_03055, ECO:0000269|PubMed:12403464}.;
- Pathway
- tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA
(Consensus)
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- loftool
- 0.409
- rvis_EVS
- -0.63
- rvis_percentile_EVS
- 17.03
Haploinsufficiency Scores
- pHI
- 0.204
- hipred
- Y
- hipred_score
- 0.617
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.810
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mettl1
- Phenotype
Gene ontology
- Biological process
- tRNA modification;tRNA methylation;RNA (guanine-N7)-methylation;tRNA (guanine-N7)-methylation
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytosol
- Molecular function
- tRNA binding;protein binding;tRNA (guanine-N7-)-methyltransferase activity