RNPEP
protein-codingarginyl aminopeptidase, the group of MicroRNA protein coding host genes|Aminopeptidases|M1 metallopeptidases
Gene summary
Predicted to enable metalloaminopeptidase activity. Predicted to be involved in proteolysis. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~23.8 kbGenCC 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 RNPEP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020216.4. 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 | 2 | 1 | 3 | |||
| missense | 97 | 2 | 1 | 100 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 100 | 2 | 2 | 104 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_064601.3 | 11 | MANE Select | |
| Ensembl | ENSP00000295640.4 | 11 | MANE Select | |
| RefSeq | NP_001306111.1 | 11 | Standard | |
| RefSeq | NP_001306112.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- proteolysis
- negative regulation of blood pressure
Molecular Function
- aminopeptidase activity
- epoxide hydrolase activity
- metalloexopeptidase activity
- zinc ion binding
Cellular Component
- extracellular region
- plasma membrane
- secretory granule
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000295640
- Coding exons
- 11
- Length
- 23776
- Individuals with no LoFs
- 125495
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 253
- Defined
- 125748
- p
- 0.00101
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.687 | 286 | 321 | 0.892 | 0.0000177 | 4192 |
| Missense (PolyPhen) | 107 | 131.31 | 0.81487 | 1636 | ||
| Synonymous | 1.02 | 118 | 133 | 0.888 | 0.00000806 | 1294 |
| Loss of Function | 0.432 | 27 | 29.5 | 0.914 | 0.00000149 | 344 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00031 | rare |
| Latino/Admixed American | 0.00043 | 0.00043 | rare |
| Ashkenazi Jewish | 0.0065 | 0.0065 | notable |
| East Asian | 0.00065 | 0.00065 | rare |
| Finnish | 0.0019 | 0.0019 | notable |
| European (Non-Finnish) | 0.00089 | 0.00089 | rare |
| South Asian | 0.00020 | 0.00016 | rare |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Exopeptidase which selectively removes arginine and/or lysine residues from the N-terminus of several peptide substrates including Arg(0)-Leu-enkephalin, Arg(0)-Met-enkephalin and Arg(- 1)-Lys(0)-somatostatin-14. Can hydrolyze leukotriene A4 (LTA-4) into leukotriene B4 (LTB-4) (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.226
Intolerance Scores
- RVIS EVS
- -0.6
- RVIS percentile EVS
- 18.14
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.356
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |