EEF1B2

eukaryotic translation elongation factor 1 beta 2, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 2:206159585-206162928

Links

ENSG00000114942 ∙ NCBI:1933 ∙ OMIM:600655 ∙ HGNC:3208 ∙ Uniprot:P24534 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive non-syndromic intellectual disability (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EEF1B2 gene.

• Global developmental delay (2 variants)
• Moderate global developmental delay;Intellectual disability;Seizure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF1B2 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				2		2
missense			14			14
nonsense	2					2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region					1	1
non coding						0
Total	3	0	14	2	0

Variants in EEF1B2

This is a list of pathogenic ClinVar variants found in the EEF1B2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-206160044-A-G			Uncertain significance (Sep 01, 2022)
2-206160060-G-C		Global developmental delay	Pathogenic (-)
2-206160597-A-G			Likely benign (Aug 01, 2022)
2-206160691-T-TA		Global developmental delay	Pathogenic (-)
2-206160709-A-G		Inborn genetic diseases	Uncertain significance (Dec 28, 2023)
2-206161383-C-T		Inborn genetic diseases	Uncertain significance (Dec 28, 2023)
2-206161385-T-G			Likely benign (Apr 01, 2023)
2-206161438-A-G		Inborn genetic diseases	Uncertain significance (Mar 07, 2023)
2-206161446-G-A			Uncertain significance (Dec 01, 2022)
2-206161466-T-G		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
2-206161480-G-A			Benign (Mar 29, 2018)
2-206162042-G-A		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
2-206162044-G-A		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
2-206162090-C-A		Moderate global developmental delay;Seizure;Intellectual disability	Pathogenic (Aug 05, 2019)
2-206162545-G-A		Inborn genetic diseases	Uncertain significance (Jan 26, 2022)
2-206162555-T-G		EEF1B2-related condition	Uncertain significance (Jul 03, 2024)
2-206162590-G-A		Inborn genetic diseases	Uncertain significance (Oct 08, 2024)
2-206162602-G-C		Inborn genetic diseases	Uncertain significance (May 24, 2023)
2-206162737-G-A		Inborn genetic diseases	Uncertain significance (Jul 31, 2024)
2-206162737-G-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
2-206162774-A-G		Inborn genetic diseases	Uncertain significance (Mar 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF1B2	protein_coding	protein_coding	ENST00000392222	6	3344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0663	0.921	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.327	114	124	0.917	0.00000606	1474
Missense in Polyphen		14	20.186	0.69354		278
Synonymous	-0.347	51	47.9	1.06	0.00000266	414
Loss of Function	2.17	4	12.2	0.329	5.12e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000110	0.000109
South Asian	0.0000332	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: EF-1-beta and EF-1-delta stimulate the exchange of GDP bound to EF-1-alpha to GTP.
• Pathway: Translation Factors;Translation;Metabolism of proteins;Eukaryotic Translation Elongation (Consensus)

Recessive Scores

• pRec: 0.277

Intolerance Scores

• loftool: 0.367
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.279
• hipred: Y
• hipred_score: 0.731
• ghis: 0.607

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eef1b2

Gene ontology

• Biological process: translational elongation;response to ethanol
• Cellular component: nucleus;cytoplasm;endoplasmic reticulum;cytosol;eukaryotic translation elongation factor 1 complex
• Molecular function: translation elongation factor activity;protein binding