RCE1
protein-codingRas converting CAAX endopeptidase 1
Gene summary
This gene encodes an integral membrane protein which is classified as a member of the metalloproteinase family. This enzyme is thought to function in the maintenance and processing of CAAX-type prenylated proteins. [provided by RefSeq, Jul 2008]
- RCE1A
- RCE1B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.7 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 RCE1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005133.3. 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 | 2 | 2 | ||||
| missense | 44 | 44 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 47 | 0 | 0 | 47 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005124.1 | 8 | MANE Select | |
| Ensembl | ENSP00000309163.3 | 8 | MANE Select | |
| RefSeq | NP_001027450.1 | 6 | Standard | |
| Ensembl | ENSP00000436600.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Terpenoid backbone biosynthesis - Homo sapiens (human)
- Post-translational protein modification
- Metabolism of proteins
- Ub-specific processing proteases
- Deubiquitination
Biological Process
- proteolysis
- protein deubiquitination
- CAAX-box protein processing
Molecular Function
- endopeptidase activity
- cysteine-type endopeptidase activity
- metalloendopeptidase activity
Cellular Component
- endoplasmic reticulum membrane
- cytosol
- integral component of plasma membrane
- membrane
- integral component of endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000309657
- Coding exons
- 8
- Length
- 3712
- Individuals with no LoFs
- 125736
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125747
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.782 | 158 | 188 | 0.840 | 0.0000104 | 2062 |
| Missense (PolyPhen) | 37 | 59.755 | 0.6192 | 624 | ||
| Synonymous | -2.43 | 110 | 82.0 | 1.34 | 0.00000439 | 731 |
| Loss of Function | 2.59 | 4 | 14.8 | 0.271 | 6.29e-7 | 160 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000035 | rare |
| South Asian | 0.000099 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Proteolytically removes the C-terminal three residues of farnesylated and geranylated proteins. Seems to be able to process K-Ras, N-Ras, H-Ras, RAP1B and G-gamma-1 (PubMed:10085068). {ECO:0000269|PubMed:10085068, ECO:0000269|PubMed:11038283, ECO:0000269|PubMed:19188362}.;
Recessive Scores
- pRec
- 0.140
Intolerance Scores
- LoFtool
- 0.205
- RVIS EVS
- -0.41
- RVIS percentile EVS
- 26.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.584
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |