CPEB4
cytoplasmic polyadenylation element binding protein 4, the group of RNA binding motif containing
Basic information
Region (hg38): 5:173888349-173961980
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPEB4 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 0 | 0 |
Variants in CPEB4
This is a list of pathogenic ClinVar variants found in the CPEB4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-173889746-G-A | not specified | Uncertain significance (Jun 05, 2023) | ||
| 5-173889849-C-A | not specified | Uncertain significance (Jul 17, 2023) | ||
| 5-173890106-G-C | not specified | Uncertain significance (Feb 16, 2023) | ||
| 5-173890134-G-A | not specified | Uncertain significance (Apr 23, 2024) | ||
| 5-173890201-A-T | not specified | Uncertain significance (Jun 13, 2024) | ||
| 5-173890203-C-A | not specified | Uncertain significance (Apr 27, 2022) | ||
| 5-173890288-A-T | not specified | Uncertain significance (Mar 29, 2024) | ||
| 5-173890317-T-C | not specified | Uncertain significance (Oct 17, 2023) | ||
| 5-173890322-G-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 5-173890377-G-A | not specified | Uncertain significance (Dec 01, 2023) | ||
| 5-173890554-T-G | not specified | Uncertain significance (Jul 13, 2022) | ||
| 5-173890650-A-G | not specified | Uncertain significance (Jan 22, 2024) | ||
| 5-173890755-A-G | not specified | Uncertain significance (Dec 09, 2023) | ||
| 5-173890778-G-T | not specified | Uncertain significance (Oct 26, 2021) | ||
| 5-173890857-C-T | not specified | Uncertain significance (Aug 19, 2023) | ||
| 5-173944971-G-T | not specified | Uncertain significance (Jan 26, 2023) | ||
| 5-173945014-C-T | not specified | Uncertain significance (Dec 16, 2022) | ||
| 5-173945059-T-G | not specified | Uncertain significance (Mar 17, 2023) | ||
| 5-173949529-G-A | not specified | Uncertain significance (Sep 22, 2022) | ||
| 5-173955968-G-A | Uncertain significance (Aug 20, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CPEB4 | protein_coding | protein_coding | ENST00000265085 | 10 | 73697 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.986 | 0.0145 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.31 | 228 | 418 | 0.545 | 0.0000225 | 4808 |
| Missense in Polyphen | 47 | 127.54 | 0.36851 | 1390 | ||
| Synonymous | 0.686 | 145 | 156 | 0.930 | 0.00000850 | 1432 |
| Loss of Function | 4.69 | 5 | 34.9 | 0.143 | 0.00000205 | 357 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000314 | 0.0000314 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Sequence-specific RNA-binding protein that binds to the cytoplasmic polyadenylation element (CPE), an uridine-rich sequence element (consensus sequence 5'-UUUUUAU-3') within the mRNA 3'-UTR (PubMed:24990967). RNA binding results in a clear conformational change analogous to the Venus fly trap mechanism (PubMed:24990967). Regulates activation of unfolded protein response (UPR) in the process of adaptation to ER stress in liver, by maintaining translation of CPE-regulated mRNAs in conditions in which global protein synthesis is inhibited (By similarity). Required for cell cycle progression, specifically for cytokinesis and chromosomal segregation (PubMed:26398195). Plays a role as an oncogene promoting tumor growth and progression by positively regulating translation of t-plasminogen activator/PLAT (PubMed:22138752). Stimulates proliferation of melanocytes (PubMed:27857118). In contrast to CPEB1 and CPEB3, does not play role in synaptic plasticity, learning and memory (By similarity). {ECO:0000250|UniProtKB:Q7TN98, ECO:0000269|PubMed:22138752, ECO:0000269|PubMed:24990967, ECO:0000269|PubMed:26398195, ECO:0000269|PubMed:27857118}.;
- Pathway
- Oocyte meiosis - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- 0.225
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 37.32
Haploinsufficiency Scores
- pHI
- 0.678
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.547
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.964
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cpeb4
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system 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); skeleton phenotype; cellular phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- response to ischemia;translation;ionotropic glutamate receptor signaling pathway;cellular response to decreased oxygen levels;cellular response to glucose starvation;negative regulation of neuron apoptotic process;cellular response to amino acid stimulus;negative regulation of cytoplasmic translation
- Cellular component
- nucleus;cytoplasm;endoplasmic reticulum;postsynaptic density;cell junction;dendrite;growth cone;neuron projection;dendritic spine;synapse;postsynaptic membrane;perinuclear region of cytoplasm;messenger ribonucleoprotein complex
- Molecular function
- translation repressor activity, mRNA regulatory element binding;RNA binding;mRNA 3'-UTR binding;protein binding;translation factor activity, RNA binding;ribosome binding;metal ion binding