RNMT
RNA guanine-7 methyltransferase, the group of 7BS DNA/RNA methyltransferases
Basic information
Region (hg38): 18:13726659-13764556
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (10 variants)
- not provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNMT gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 3 | |||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 2 |
Variants in RNMT
This is a list of pathogenic ClinVar variants found in the RNMT region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-13731521-G-A | Inborn genetic diseases | Uncertain significance (Nov 17, 2022) | ||
| 18-13731609-A-C | Inborn genetic diseases | Uncertain significance (Jan 26, 2022) | ||
| 18-13731662-G-A | Inborn genetic diseases | Uncertain significance (Sep 14, 2023) | ||
| 18-13731683-G-A | Inborn genetic diseases | Uncertain significance (Jul 20, 2022) | ||
| 18-13731702-T-G | Inborn genetic diseases | Uncertain significance (Sep 01, 2021) | ||
| 18-13731836-A-G | Inborn genetic diseases | Uncertain significance (Mar 25, 2022) | ||
| 18-13734511-A-G | Benign (Jul 18, 2018) | |||
| 18-13740200-A-C | Inborn genetic diseases | Uncertain significance (Jun 30, 2023) | ||
| 18-13740206-A-T | Inborn genetic diseases | Uncertain significance (Feb 08, 2023) | ||
| 18-13741577-G-A | Inborn genetic diseases | Uncertain significance (Sep 22, 2022) | ||
| 18-13741681-T-C | Inborn genetic diseases | Uncertain significance (Apr 22, 2022) | ||
| 18-13742558-G-C | Inborn genetic diseases | Uncertain significance (Aug 02, 2022) | ||
| 18-13742595-A-G | Inborn genetic diseases | Uncertain significance (Apr 20, 2023) | ||
| 18-13746263-T-C | Inborn genetic diseases | Uncertain significance (Jan 04, 2022) | ||
| 18-13746271-A-C | Inborn genetic diseases | Uncertain significance (Jan 10, 2022) | ||
| 18-13746277-C-T | Benign (Apr 07, 2018) | |||
| 18-13752326-C-T | Inborn genetic diseases | Uncertain significance (Feb 07, 2023) | ||
| 18-13754134-A-G | Likely benign (Jul 26, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RNMT | protein_coding | protein_coding | ENST00000383314 | 10 | 37899 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000566 | 0.994 | 125722 | 0 | 21 | 125743 | 0.0000835 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.630 | 215 | 243 | 0.886 | 0.0000121 | 3176 |
| Missense in Polyphen | 65 | 77.23 | 0.84165 | 1029 | ||
| Synonymous | -0.165 | 81 | 79.1 | 1.02 | 0.00000371 | 809 |
| Loss of Function | 2.45 | 11 | 23.9 | 0.460 | 0.00000120 | 340 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000679 | 0.0000679 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000179 | 0.000163 |
| Finnish | 0.0000467 | 0.0000462 |
| European (Non-Finnish) | 0.0000886 | 0.0000879 |
| Middle Eastern | 0.000179 | 0.000163 |
| South Asian | 0.000137 | 0.000131 |
| Other | 0.000191 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Catalytic subunit of the mRNA-capping methyltransferase RNMT:RAMAC complex that methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs (PubMed:9790902, PubMed:9705270, PubMed:10347220, PubMed:11114884, PubMed:22099306, PubMed:27422871). Binds RNA containing 5'-terminal GpppC (PubMed:11114884). {ECO:0000269|PubMed:10347220, ECO:0000269|PubMed:11114884, ECO:0000269|PubMed:22099306, ECO:0000269|PubMed:27422871, ECO:0000269|PubMed:9705270, ECO:0000269|PubMed:9790902}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);mRNA Processing;Disease;RNA Pol II CTD phosphorylation and interaction with CE during HIV infection;Gene expression (Transcription);Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Pol II CTD phosphorylation and interaction with CE;RNA Polymerase II Transcription;Metabolism of RNA;Infectious disease;mRNA capping;mRNA Capping
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.408
- hipred
- Y
- hipred_score
- 0.671
- ghis
- 0.555
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.740
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnmt
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- transcription by RNA polymerase II;7-methylguanosine mRNA capping;RNA 5'-cap (guanine-N7)-methylation;cellular response to leukemia inhibitory factor
- Cellular component
- fibrillar center;nucleus;nucleoplasm;mRNA cap binding complex;mRNA cap methyltransferase complex;receptor complex
- Molecular function
- RNA binding;mRNA (guanine-N7-)-methyltransferase activity;protein binding