CPEB1
protein-codingcytoplasmic polyadenylation element binding protein 1
Gene summary
This gene encodes a member of the cytoplasmic polyadenylation element binding protein family. This highly conserved protein binds to a specific RNA sequence, called the cytoplasmic polyadenylation element, found in the 3' untranslated region of some mRNAs. The encoded protein functions in both the cytoplasm and the nucleus. It is involved in the regulation of mRNA translation, as well as processing of the 3' untranslated region, and may play a role in cell proliferation and tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~105.7 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 CPEB1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001365242.1. 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 | 2 | |||
| missense | 60 | 60 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 60 | 1 | 1 | 62 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001352171.1 | 12 | MANE Select | |
| Ensembl | ENSP00000507835.1 | 12 | MANE Select | |
| RefSeq | NP_001073001.1 | 10 | Standard | |
| RefSeq | NP_001073002.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Oocyte meiosis - Homo sapiens (human)
- Progesterone-mediated oocyte maturation - Homo sapiens (human)
- Aurora A signaling
Biological Process
- mRNA processing
- translation
- cellular response to insulin stimulus
- cellular response to amino acid stimulus
- cellular response to hypoxia
Molecular Function
- translation repressor activity, mRNA regulatory element binding
- mRNA 3'-UTR binding
- protein binding
- translation factor activity, RNA binding
- mRNA 3'-UTR AU-rich region binding
Cellular Component
- P-body
- nucleus
- nucleoplasm
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000568128
- Coding exons
- 12
- Length
- 105662
- Individuals with no LoFs
- 124449
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 124454
- p
- 0.0000201
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.10 | 194 | 296 | 0.656 | 0.0000159 | 3655 |
| Missense (PolyPhen) | 45 | 114.48 | 0.39307 | 1442 | ||
| Synonymous | -0.325 | 114 | 110 | 1.04 | 0.00000564 | 1129 |
| Loss of Function | 4.63 | 2 | 28.8 | 0.0694 | 0.00000181 | 309 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000042 | 0.000033 | rare |
| Other | 0.00041 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sequence-specific RNA-binding protein that regulates mRNA cytoplasmic polyadenylation and translation initiation during oocyte maturation, early development and at postsynapse sites of neurons. Binds to the cytoplasmic polyadenylation element (CPE), an uridine-rich sequence element (consensus sequence 5'-UUUUUAU- 3') within the mRNA 3'-UTR. RNA binding results in a clear conformational change analogous to the Venus fly trap mechanism (PubMed:24990967). In absence of phosphorylation and in association with TACC3 is also involved as a repressor of translation of CPE-containing mRNA; a repression that is relieved by phosphorylation or degradation (By similarity). Involved in the transport of CPE-containing mRNA to dendrites; those mRNAs may be transported to dendrites in a translationally dormant form and translationally activated at synapses (By similarity). Its interaction with APLP1 promotes local CPE-containing mRNA polyadenylation and translation activation (By similarity). Induces the assembly of stress granules in the absence of stress. Required for cell cycle progression, specifically for prophase entry (PubMed:26398195). {ECO:0000250|UniProtKB:P70166, ECO:0000269|PubMed:15731006, ECO:0000269|PubMed:15966895, ECO:0000269|PubMed:24990967, ECO:0000269|PubMed:26398195}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.0281
- RVIS EVS
- -0.56
- RVIS percentile EVS
- 19.73
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.524
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |