MEPCE
protein-codingmethylphosphate capping enzyme, the group of 7BS DNA/RNA methyltransferases|7SK snRNP complex
Gene summary
Enables 7SK snRNA binding activity and RNA 5'-gamma-phosphate methyltransferase activity. Involved in RNA modification; positive regulation of protein localization to Cajal body; and positive regulation of snRNA transcription by RNA polymerase II. Located in nucleus. Part of 7SK snRNP. [provided by Alliance of Genome Resources, Jul 2025]
- BCDIN3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MEPCE variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_019606.6. 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 | 1 | ||||
| missense | 112 | 4 | 116 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 118 | 4 | 0 | 122 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_062552.2 | 4 | MANE Select | |
| Ensembl | ENSP00000308546.2 | 4 | MANE Select | |
| RefSeq | NP_001181919.1 | 4 | Standard | |
| RefSeq | NP_001181920.1 | 4 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| mepce | Danio rerio | Structure: brain Quality: degenerate abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of transcription by RNA polymerase II
- RNA methylation
- snRNA metabolic process
- negative regulation of chromatin binding
- snRNA modification
Molecular Function
- RNA binding
- O-methyltransferase activity
- RNA methyltransferase activity
- S-adenosylmethionine-dependent methyltransferase activity
- snRNA binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000310512
- Coding exons
- 4
- Length
- 5329
- Individuals with no LoFs
- 125615
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125618
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.99 | 259 | 366 | 0.707 | 0.0000226 | 4353 |
| Missense (PolyPhen) | 61 | 140.01 | 0.43568 | 1565 | ||
| Synonymous | -2.66 | 196 | 154 | 1.27 | 0.00000869 | 1544 |
| Loss of Function | 4.21 | 1 | 22.6 | 0.0442 | 0.00000147 | 239 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.0000090 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that adds a methylphosphate cap at the 5'-end of 7SK snRNA, leading to stabilize it. {ECO:0000269|PubMed:17643375}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- RVIS EVS
- -0.89
- RVIS percentile EVS
- 10.3
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.916
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |