RNMT

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

Basic information

Region (hg38): 18:13726660-13764556

Links

ENSG00000101654 ∙ NCBI:8731 ∙ OMIM:603514 ∙ HGNC:10075 ∙ Uniprot:O43148 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	2	3
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	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		not specified	Uncertain significance (Nov 17, 2022)
18-13731552-A-G		not specified	Uncertain significance (Jan 23, 2024)
18-13731579-C-T		not specified	Uncertain significance (Nov 20, 2023)
18-13731609-A-C		not specified	Uncertain significance (Jan 26, 2022)
18-13731662-G-A		not specified	Uncertain significance (Sep 14, 2023)
18-13731683-G-A		not specified	Uncertain significance (Jul 20, 2022)
18-13731702-T-G		not specified	Uncertain significance (Sep 01, 2021)
18-13731836-A-G		not specified	Uncertain significance (Mar 25, 2022)
18-13734511-A-G			Benign (Jul 18, 2018)
18-13740200-A-C		not specified	Uncertain significance (Jun 30, 2023)
18-13740206-A-T		not specified	Uncertain significance (Feb 08, 2023)
18-13741577-G-A		not specified	Uncertain significance (Sep 22, 2022)
18-13741681-T-C		not specified	Uncertain significance (Apr 22, 2022)
18-13742558-G-C		not specified	Uncertain significance (Aug 02, 2022)
18-13742595-A-G		not specified	Uncertain significance (Apr 20, 2023)
18-13746263-T-C		not specified	Uncertain significance (Jan 04, 2022)
18-13746271-A-C		not specified	Uncertain significance (Apr 15, 2024)
18-13746277-C-T			Benign (Apr 07, 2018)
18-13746289-T-G		not specified	Uncertain significance (Mar 25, 2024)
18-13752326-C-T		not specified	Uncertain significance (Feb 07, 2023)
18-13754134-A-G			Likely benign (Jul 26, 2018)

GnomAD

Source: gnomAD

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: 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

• 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