EIF4EBP2

eukaryotic translation initiation factor 4E binding protein 2

Basic information

Region (hg38): 10:70404145-70428618

Links

ENSG00000148730

∙ NCBI:1979 ∙ OMIM:602224 ∙ HGNC:3289 ∙ Uniprot:Q13542 ∙ 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 EIF4EBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF4EBP2 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 clinvar	1
missense			7 clinvar	1 clinvar		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	1

Variants in EIF4EBP2

This is a list of pathogenic ClinVar variants found in the EIF4EBP2 region.

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

Position	Phenotype	Significance	ClinVar
10-70404406-C-T	not specified	Uncertain significance (Aug 08, 2022)	2305609
10-70404418-G-A		Likely benign (Jun 09, 2018)	777852
10-70404422-C-T		Benign (Aug 09, 2018)	715427
10-70404468-G-A	not specified	Uncertain significance (Feb 17, 2024)	3088008
10-70404496-A-C	not specified	Uncertain significance (Mar 29, 2022)	2280719
10-70419929-A-T	not specified	Uncertain significance (Sep 20, 2023)	3088007
10-70419980-C-T	not specified	Uncertain significance (Dec 21, 2022)	2230513
10-70420052-T-G	not specified	Uncertain significance (May 08, 2023)	2523302
10-70420076-A-G	not specified	Uncertain significance (Aug 16, 2021)	2360398

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF4EBP2	protein_coding	protein_coding	ENST00000373218	3	24240

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.306	0.627	125595	0	1	125596	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0687	65	66.6	0.976	0.00000328	774
Missense in Polyphen		18	23.571	0.76364		255
Synonymous	0.104	24	24.7	0.973	0.00000124	225
Loss of Function	1.40	1	4.04	0.248	2.27e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Repressor of translation initiation involved in synaptic plasticity, learning and memory formation (By similarity). Regulates EIF4E activity by preventing its assembly into the eIF4F complex: hypophosphorylated form of EIF4EBP2 competes with EIF4G1/EIF4G3 and strongly binds to EIF4E, leading to repress translation. In contrast, hyperphosphorylated form dissociates from EIF4E, allowing interaction between EIF4G1/EIF4G3 and EIF4E, leading to initiation of translation (PubMed:25533957). EIF4EBP2 is enriched in brain and acts as a regulator of synapse activity and neuronal stem cell renewal via its ability to repress translation initiation (By similarity). Mediates the regulation of protein translation by hormones, growth factors and other stimuli that signal through the MAP kinase and mTORC1 pathways (By similarity). {ECO:0000250|UniProtKB:P70445, ECO:0000269|PubMed:25533957}.;
Pathway: Longevity regulating pathway - multiple species - Homo sapiens (human);RNA transport - Homo sapiens (human);Translation Factors (Consensus)

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.157
rvis_EVS: -0.16
rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

pHI: 0.299
hipred: Y
hipred_score: 0.669
ghis: 0.555

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.650

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Eif4ebp2
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);

Gene ontology

Biological process: translation;memory;insulin receptor signaling pathway;cAMP-mediated signaling;TOR signaling;social behavior;negative regulation of translational initiation;regulation of synaptic plasticity;modulation of chemical synaptic transmission
Cellular component: cytoplasm;postsynapse
Molecular function: protein binding;eukaryotic initiation factor 4E binding;translation repressor activity