CPEB4

cytoplasmic polyadenylation element binding protein 4, the group of RNA binding motif containing

Basic information

Region (hg38): 5:173888348-173961980

Links

ENSG00000113742 ∙ NCBI:80315 ∙ OMIM:610607 ∙ HGNC:21747 ∙ Uniprot:Q17RY0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPEB4 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	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 (Dec 20, 2021)
5-173890203-C-A		not specified	Uncertain significance (Apr 27, 2022)
5-173890317-T-C		not specified	Uncertain significance (Oct 17, 2023)
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: gnomAD

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: dbNSFP

• 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