RNMT

protein-coding

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

Gene summary

Enables RNA binding activity and mRNA 5'-cap (guanine-N7-)-methyltransferase activity. Involved in 7-methylguanosine mRNA capping. Located in fibrillar center and nucleoplasm. Part of mRNA cap methyltransferase RNMT:RAMAC complex; mRNA capping enzyme complex; and signaling receptor complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_003799.3

Inheritance

—

ClinVar variants

U:62B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr18:13,726,660-13,764,556

External References & Databases

Ensembl (ENSG00000101654)

Transcript & Mutation Effects

hg38 • Region Span ~37.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RNMT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 56

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003799.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	2 clinvar	4
missense			58 clinvar	1 clinvar		59
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	62	2	2	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003799.3	RefSeq	NP_003790.1	10	MANE Select
ENST00000383314.7	Ensembl	ENSP00000372804.2	10	MANE Select
NM_001308263.2	RefSeq	NP_001295192.1	10	Standard
NM_001378132.1	RefSeq	NP_001365061.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mRNA surveillance pathway - Homo sapiens (human)
mRNA Processing
Disease
RNA Pol II CTD phosphorylation and interaction with CE during HIV infection
Gene expression (Transcription)

Biological Process

transcription by RNA polymerase II
7-methylguanosine mRNA capping
RNA 5'-cap (guanine-N7)-methylation
cellular response to leukemia inhibitory factor

Molecular Function

RNA binding
mRNA (guanine-N7-)-methyltransferase activity
protein binding

Cellular Component

fibrillar center
nucleus
nucleoplasm
mRNA cap binding complex
mRNA cap methyltransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000383314
Coding exons: 10
Length: 37899
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125743
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.630	215	243	0.886	0.0000121	3176
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000068	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00018	0.00016	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.00014	0.00013	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

RVIS EVS: 0.08
RVIS percentile EVS: 60.09

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.740

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium