EIF5B

eukaryotic translation initiation factor 5B

Basic information

Region (hg38): 2:99337389-99401326

Links

ENSG00000158417 ∙ NCBI:9669 ∙ OMIM:606086 ∙ HGNC:30793 ∙ Uniprot:O60841 ∙ 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 EIF5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF5B 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			40	2	1	43
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	41	2	3

Variants in EIF5B

This is a list of pathogenic ClinVar variants found in the EIF5B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-99337578-G-C		not specified	Uncertain significance (Nov 21, 2022)
2-99360261-G-A		not specified	Uncertain significance (Jul 19, 2022)
2-99360559-A-T			Benign (Sep 19, 2018)
2-99361230-A-G		not specified	Uncertain significance (Feb 10, 2022)
2-99361232-A-G		not specified	Uncertain significance (Aug 22, 2023)
2-99361277-A-G		not specified	Uncertain significance (Apr 08, 2022)
2-99361317-A-G		not specified	Uncertain significance (Mar 31, 2023)
2-99361344-A-T		not specified	Uncertain significance (Nov 30, 2021)
2-99361349-G-T		not specified	Uncertain significance (Dec 03, 2021)
2-99361373-A-G		not specified	Uncertain significance (Feb 09, 2022)
2-99361413-G-T		not specified	Uncertain significance (Dec 19, 2023)
2-99361565-T-G		not specified	Uncertain significance (Sep 14, 2023)
2-99361611-A-T			Benign/Likely benign (Jul 01, 2024)
2-99361631-G-C		not specified	Uncertain significance (Aug 01, 2022)
2-99361632-A-T		not specified	Uncertain significance (Aug 17, 2022)
2-99361659-T-C		not specified	Uncertain significance (Jan 19, 2022)
2-99361683-C-T		not specified	Uncertain significance (Sep 27, 2021)
2-99361754-G-A		not specified	Uncertain significance (May 07, 2024)
2-99361758-C-A		not specified	Uncertain significance (Dec 02, 2022)
2-99361767-C-G		not specified	Uncertain significance (Aug 16, 2021)
2-99361806-C-T		not specified	Uncertain significance (Jun 22, 2024)
2-99363663-A-G		not specified	Uncertain significance (Mar 18, 2024)
2-99363687-A-G		not specified	Uncertain significance (Mar 31, 2024)
2-99363860-G-A		not specified	Uncertain significance (Sep 22, 2022)
2-99364399-T-C			Benign (Sep 19, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF5B	protein_coding	protein_coding	ENST00000289371	24	63974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000190	124757	0	36	124793	0.000144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.62	424	606	0.700	0.0000301	8126
Missense in Polyphen		59	172.95	0.34114		2200
Synonymous	-0.259	203	198	1.02	0.00000949	2106
Loss of Function	6.38	9	64.2	0.140	0.00000349	872

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000495	0.000489
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000179	0.000167
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.000146	0.000115
Middle Eastern	0.000179	0.000167
South Asian	0.000330	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in translation initiation. Translational GTPase that catalyzes the joining of the 40S and 60S subunits to form the 80S initiation complex with the initiator methionine-tRNA in the P-site base paired to the start codon. GTP binding and hydrolysis induces conformational changes in the enzyme that renders it active for productive interactions with the ribosome. The release of the enzyme after formation of the initiation complex is a prerequisite to form elongation-competent ribosomes. {ECO:0000250|UniProtKB:P39730}.
• Pathway: RNA transport - Homo sapiens (human);Translation Factors;Eukaryotic Translation Initiation;Translation;Metabolism of proteins;eukaryotic protein translation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

• pRec: 0.211

Intolerance Scores

• loftool: 0.634
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.21

Haploinsufficiency Scores

• pHI: 0.972
• hipred: Y
• hipred_score: 0.672
• ghis: 0.558

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eif5b

Gene ontology

• Biological process: translational initiation;regulation of translational initiation
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: RNA binding;translation initiation factor activity;GTPase activity;protein binding;GTP binding;metal ion binding