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GeneBe

RNMT

RNA guanine-7 methyltransferase, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 18:13726659-13764556

Links

ENSG00000101654NCBI:8731OMIM:603514HGNC:10075Uniprot:O43148AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNMT gene.

  • Inborn genetic diseases (15 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.

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
1
clinvar
2
clinvar
3
missense
15
clinvar
15
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 15 1 2

Variants in RNMT

This is a list of pathogenic ClinVar variants found in the RNMT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
18-13731521-G-A Inborn genetic diseases Uncertain significance (Nov 17, 2022)2329698
18-13731609-A-C Inborn genetic diseases Uncertain significance (Jan 26, 2022)2273009
18-13731662-G-A Inborn genetic diseases Uncertain significance (Sep 14, 2023)2623997
18-13731683-G-A Inborn genetic diseases Uncertain significance (Jul 20, 2022)2302502
18-13731702-T-G Inborn genetic diseases Uncertain significance (Sep 01, 2021)2248544
18-13731836-A-G Inborn genetic diseases Uncertain significance (Mar 25, 2022)2226297
18-13734511-A-G Benign (Jul 18, 2018)758114
18-13740200-A-C Inborn genetic diseases Uncertain significance (Jun 30, 2023)2608968
18-13740206-A-T Inborn genetic diseases Uncertain significance (Feb 08, 2023)2458522
18-13741577-G-A Inborn genetic diseases Uncertain significance (Sep 22, 2022)2216882
18-13741681-T-C Inborn genetic diseases Uncertain significance (Apr 22, 2022)2284885
18-13742558-G-C Inborn genetic diseases Uncertain significance (Aug 02, 2022)2360510
18-13742595-A-G Inborn genetic diseases Uncertain significance (Apr 20, 2023)2539437
18-13746263-T-C Inborn genetic diseases Uncertain significance (Jan 04, 2022)2207629
18-13746271-A-C Inborn genetic diseases Uncertain significance (Jan 10, 2022)2356978
18-13746277-C-T Benign (Apr 07, 2018)773596
18-13752326-C-T Inborn genetic diseases Uncertain significance (Feb 07, 2023)2481611
18-13754134-A-G Likely benign (Jul 26, 2018)757966

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNMTprotein_codingprotein_codingENST00000383314 1037899
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00005660.9941257220211257430.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6302152430.8860.00001213176
Missense in Polyphen6577.230.841651029
Synonymous-0.1658179.11.020.00000371809
Loss of Function2.451123.90.4600.00000120340

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006790.0000679
Ashkenazi Jewish0.000.00
East Asian0.0001790.000163
Finnish0.00004670.0000462
European (Non-Finnish)0.00008860.0000879
Middle Eastern0.0001790.000163
South Asian0.0001370.000131
Other0.0001910.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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