CPEB3

cytoplasmic polyadenylation element binding protein 3, the group of RNA binding motif containing

Basic information

Region (hg38): 10:92046692-92291078

Links

ENSG00000107864 ∙ NCBI:22849 ∙ OMIM:610606 ∙ HGNC:21746 ∙ Uniprot:Q8NE35 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CPEB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CPEB3 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					1	1
missense			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	1

Variants in CPEB3

This is a list of pathogenic ClinVar variants found in the CPEB3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-92052234-T-G		not specified	Uncertain significance (Jun 27, 2023)
10-92052267-G-A		not specified	Uncertain significance (May 04, 2022)
10-92052307-C-A		not specified	Uncertain significance (Dec 09, 2023)
10-92111170-T-C		not specified	Uncertain significance (May 13, 2024)
10-92143080-C-T		not specified	Uncertain significance (Feb 06, 2023)
10-92143109-G-A		not specified	Uncertain significance (Sep 20, 2023)
10-92145058-T-C		not specified	Uncertain significance (Jul 05, 2023)
10-92192480-C-T		not specified	Uncertain significance (Dec 16, 2023)
10-92192537-A-G		not specified	Uncertain significance (Dec 19, 2022)
10-92192636-C-T		not specified	Uncertain significance (Jul 08, 2021)
10-92239507-C-A		not specified	Uncertain significance (Jan 26, 2023)
10-92239511-G-A			Benign (May 24, 2018)
10-92239525-C-T		not specified	Uncertain significance (Mar 28, 2022)
10-92239558-C-T		not specified	Uncertain significance (Aug 13, 2021)
10-92239579-G-T		not specified	Uncertain significance (Dec 27, 2023)
10-92239591-C-G		not specified	Uncertain significance (Mar 06, 2023)
10-92239592-G-T		not specified	Uncertain significance (Jul 27, 2021)
10-92239674-A-G		not specified	Likely benign (Nov 12, 2021)
10-92239705-T-C		not specified	Uncertain significance (Aug 17, 2022)
10-92239736-G-C		not specified	Uncertain significance (Dec 14, 2022)
10-92239758-T-C		not specified	Uncertain significance (Sep 28, 2022)
10-92239804-G-C		not specified	Uncertain significance (Nov 29, 2023)
10-92239810-G-T		not specified	Uncertain significance (Oct 29, 2021)
10-92239898-G-C		not specified	Uncertain significance (Feb 14, 2023)
10-92239939-T-C		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CPEB3	protein_coding	protein_coding	ENST00000265997	9	244396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00154	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	252	395	0.638	0.0000213	4518
Missense in Polyphen		48	117.02	0.41018		1238
Synonymous	-0.446	165	158	1.05	0.00000882	1382
Loss of Function	4.52	2	27.7	0.0722	0.00000148	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000320	0.0000320
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sequence-specific RNA-binding protein which acts as a translational repressor in the basal unstimulated state but, following neuronal stimulation, acts as a translational activator (By similarity). In contrast to CPEB1, does not bind to the cytoplasmic polyadenylation element (CPE), a uridine-rich sequence element within the mRNA 3'-UTR, but binds to a U-rich loop within a stem-loop structure (By similarity). Required for the consolidation and maintenance of hippocampal-based long term memory (By similarity). In the basal state, binds to the mRNA 3'- UTR of the glutamate receptors GRIA2/GLUR2 mRNA and negatively regulates their translation (By similarity). Also represses the translation of DLG4, GRIN1, GRIN2A and GRIN2B (By similarity). When activated, acts as a translational activator of GRIA1 and GRIA2 (By similarity). In the basal state, suppresses SUMO2 translation but activates it following neuronal stimulation (By similarity). Binds to the 3'-UTR of TRPV1 mRNA and represses TRPV1 translation which is required to maintain normal thermoception (By similarity). Binds actin mRNA, leading to actin translational repression in the basal state and to translational activation following neuronal stimulation (By similarity). Negatively regulates target mRNA levels by binding to TOB1 which recruits CNOT7/CAF1 to a ternary complex and this leads to target mRNA deadenylation and decay (PubMed:21336257). In addition to its role in translation, binds to and inhibits the transcriptional activation activity of STAT5B without affecting its dimerization or DNA-binding activity. This, in turn, represses transcription of the STAT5B target gene EGFR which has been shown to play a role in enhancing learning and memory performance (PubMed:20639532). In contrast to CPEB1, CPEB2 and CPEB4, not required for cell cycle progression (PubMed:26398195). {ECO:0000250|UniProtKB:Q7TN99, ECO:0000269|PubMed:20639532, ECO:0000269|PubMed:21336257, ECO:0000269|PubMed:26398195}.
• Pathway: Oocyte meiosis - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0637
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.783
• hipred: Y
• hipred_score: 0.728
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.297

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cpeb3
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;translation;long-term memory;negative regulation of translation;positive regulation of translation;regulation of synaptic plasticity;positive regulation of nuclear-transcribed mRNA poly(A) tail shortening;regulation of dendritic spine development;positive regulation of dendritic spine development;3'-UTR-mediated mRNA destabilization;cellular response to amino acid stimulus;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;negative regulation of cytoplasmic translational elongation;positive regulation of mRNA polyadenylation;negative regulation of cytoplasmic translation
• Cellular component: nucleus;cytoplasm;postsynaptic density;CCR4-NOT complex;cell junction;dendrite;neuron projection;synapse;postsynaptic membrane;apical dendrite;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;RNA stem-loop binding;mRNA 3'-UTR AU-rich region binding;ribosome binding