CPEB1
cytoplasmic polyadenylation element binding protein 1
Basic information
Region (hg38): 15:82543201-82648861
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (45 variants)
- not_provided (1 variants)
- Primary_amenorrhea (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPEB1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001365242.1. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 45 | 45 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 0 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CPEB1 | protein_coding | protein_coding | ENST00000568128 | 12 | 105662 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.00101 | 124449 | 0 | 5 | 124454 | 0.0000201 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.10 | 194 | 296 | 0.656 | 0.0000159 | 3655 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000132 | 0.000129 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000416 | 0.0000329 |
| Other | 0.000408 | 0.000331 |
dbNSFP
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}.;
- Pathway
- Oocyte meiosis - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Aurora A signaling
(Consensus)
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- loftool
- 0.0281
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.73
Haploinsufficiency Scores
- pHI
- 0.405
- hipred
- N
- hipred_score
- 0.492
- ghis
- 0.556
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.524
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cpeb1
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- mRNA processing;translation;cellular response to insulin stimulus;cellular response to amino acid stimulus;cellular response to hypoxia;positive regulation of mRNA polyadenylation;negative regulation of cytoplasmic translation
- Cellular component
- P-body;nucleus;nucleoplasm;cytoplasm;cytosol;postsynaptic density;cell junction;dendrite;neuron projection;synapse;postsynaptic membrane;messenger ribonucleoprotein complex
- 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;ribosome binding;metal ion binding