CPEB3

protein-coding

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

Gene summary

Enables mRNA 3'-UTR binding activity and translation factor activity, RNA binding. Involved in cellular response to amino acid stimulus and regulation of gene expression. Located in cytoplasm; neuron projection; and nucleus. Part of CCR4-NOT complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_014912.5

Inheritance

—

ClinVar variants

U:97B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr10:92,046,692-92,291,078

External References & Databases

Ensembl (ENSG00000107864)

Transcript & Mutation Effects

hg38 • Region Span ~244.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CPEB3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014912.5. 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 clinvar	1
missense			95 clinvar	1 clinvar		96
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	97	1	1	99

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 93 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014912.5	RefSeq	NP_055727.3	9	MANE Select
ENST00000265997.5	Ensembl	ENSP00000265997.4	9	MANE Select
NM_001178137.2	RefSeq	NP_001171608.1	9	Standard
ENST00000412050.8	Ensembl	ENSP00000398310.2	9	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)

Biological Process

negative regulation of transcription by RNA polymerase II
translation
long-term memory
negative regulation of translation
positive regulation of translation

Molecular Function

translation repressor activity, mRNA regulatory element binding
RNA binding
mRNA 3'-UTR binding
protein binding
translation factor activity, RNA binding

Cellular Component

nucleus
cytoplasm
postsynaptic density
CCR4-NOT complex
cell junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265997
Coding exons: 9
Length: 244396
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.56	252	395	0.638	0.0000213	4518
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000032	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.0637
RVIS EVS: -0.43
RVIS percentile EVS: 25.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.297

Gene Damage Prediction

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