CPEB1

cytoplasmic polyadenylation element binding protein 1

Basic information

Region (hg38): 15:82543201-82648861

Links

ENSG00000214575 ∙ NCBI:64506 ∙ OMIM:607342 ∙ HGNC:21744 ∙ Uniprot:Q9BZB8 ∙ 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 CPEB1 gene.

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.

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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	28	0	1

Variants in CPEB1

This is a list of pathogenic ClinVar variants found in the CPEB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-82546483-A-C		not specified	Uncertain significance (Sep 16, 2021)
15-82547216-T-C		not specified	Uncertain significance (Feb 27, 2024)
15-82549585-C-T		not specified	Uncertain significance (Jan 04, 2024)
15-82549604-G-C		not specified	Uncertain significance (Feb 15, 2023)
15-82552547-G-A		not specified	Uncertain significance (Jul 25, 2023)
15-82552566-G-C		not specified	Uncertain significance (Apr 17, 2023)
15-82553517-C-T		not specified	Uncertain significance (Sep 06, 2022)
15-82553542-T-C		not specified	Uncertain significance (Jul 19, 2022)
15-82553887-T-C		not specified	Uncertain significance (Jun 10, 2024)
15-82553914-C-T		not specified	Uncertain significance (Oct 05, 2022)
15-82553963-A-C		not specified	Uncertain significance (Jun 22, 2023)
15-82555946-T-C			Benign (Dec 31, 2019)
15-82556029-C-T		not specified	Uncertain significance (Sep 21, 2021)
15-82556112-C-T		not specified	Uncertain significance (Feb 23, 2023)
15-82557840-G-C		not specified	Uncertain significance (Dec 07, 2021)
15-82557848-C-T		not specified	Uncertain significance (Jan 26, 2022)
15-82557849-G-A		not specified	Uncertain significance (Feb 23, 2023)
15-82557861-G-A		not specified	Uncertain significance (Nov 22, 2023)
15-82557960-C-T		not specified	Uncertain significance (Sep 22, 2022)
15-82557975-G-A		not specified	Uncertain significance (Aug 08, 2023)
15-82571346-G-A		not specified	Uncertain significance (Jun 22, 2023)
15-82571385-G-A		not specified	Uncertain significance (Jan 06, 2023)
15-82571398-G-C		not specified	Uncertain significance (Jun 17, 2024)
15-82571478-G-A		not specified	Uncertain significance (Mar 07, 2024)
15-82571484-G-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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