EIF5A

eukaryotic translation initiation factor 5A

Basic information

Region (hg38): 17:7306999-7312463

Links

ENSG00000132507 ∙ NCBI:1984 ∙ OMIM:600187 ∙ HGNC:3300 ∙ Uniprot:P63241 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Faundes-Banka syndrome (Strong), mode of inheritance: AD
• Faundes-Banka syndrome (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Faundes-Banka syndrome	AD	Cardiovascular	Individuals may have congenital cardiovascular anomalies, and awareness may allow early identification and management	Cardiovascular; Craniofacial; Neurologic	33547280

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EIF5A gene.

• Faundes-Banka syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF5A 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		2	3	1		6
nonsense	1					1
start loss						0
frameshift		2	1			3
inframe indel						0
splice donor/acceptor (+/-2bp)		2	1			3
splice region				1		1
non coding					1	1
Total	1	6	5	2	1

Variants in EIF5A

This is a list of pathogenic ClinVar variants found in the EIF5A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7307083-C-A			Likely benign (Jun 01, 2023)
17-7307083-C-T		not specified	Uncertain significance (Oct 05, 2021)
17-7307116-G-A		EIF5A-related disorder • Faundes-Banka syndrome	Uncertain significance (Mar 26, 2024)
17-7309672-G-A		Faundes-Banka syndrome	Uncertain significance (Dec 06, 2023)
17-7309712-G-C		Neurodevelopmental disorder	Likely pathogenic (Dec 21, 2020)
17-7309759-G-A			Likely pathogenic (Sep 20, 2024)
17-7309778-C-A		Faundes-Banka syndrome	Pathogenic (Jun 09, 2021)
17-7309801-G-A		not specified	Likely pathogenic (Dec 18, 2023)
17-7311008-A-G			Benign (Mar 03, 2015)
17-7311041-CTT-C		Faundes-Banka syndrome	Likely pathogenic (Feb 03, 2023)
17-7311089-G-A			Uncertain significance (Dec 07, 2023)
17-7311123-G-A			Likely pathogenic (Mar 24, 2023)
17-7311367-T-TG		EIF5A-related disorder	Uncertain significance (Jun 22, 2023)
17-7311395-G-A			Pathogenic (Apr 24, 2024)
17-7311402-T-TA		Faundes-Banka syndrome	Pathogenic (Jan 18, 2024)
17-7311404-C-G		Faundes-Banka syndrome	Pathogenic (Jun 09, 2021)
17-7311404-C-T		Faundes-Banka syndrome	Pathogenic (Dec 28, 2023)
17-7311416-C-T			Uncertain significance (Oct 24, 2023)
17-7311422-C-T			Likely pathogenic (Apr 03, 2023)
17-7311422-CCT-C			Likely pathogenic (Apr 01, 2024)
17-7311574-C-T		not specified	Likely benign (Nov 01, 2017)
17-7311583-G-A			Likely benign (Oct 01, 2023)
17-7311587-C-A		not specified	Uncertain significance (Jun 16, 2024)
17-7311590-TC-AT		Faundes-Banka syndrome	Likely pathogenic (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF5A	protein_coding	protein_coding	ENST00000336452	5	5457

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.737	0.261	125746	0	2	125748	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.41	35	104	0.336	0.00000601	1199
Missense in Polyphen		0	20.38	0		266
Synonymous	-1.83	56	41.1	1.36	0.00000276	353
Loss of Function	2.43	1	8.74	0.114	4.70e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: mRNA-binding protein involved in translation elongation. Has an important function at the level of mRNA turnover, probably acting downstream of decapping. Involved in actin dynamics and cell cycle progression, mRNA decay and probably in a pathway involved in stress response and maintenance of cell wall integrity. With syntenin SDCBP, functions as a regulator of p53/TP53 and p53/TP53-dependent apoptosis. Regulates also TNF- alpha-mediated apoptosis. Mediates effects of polyamines on neuronal process extension and survival. May play an important role in brain development and function, and in skeletal muscle stem cell differentiation. Also described as a cellular cofactor of human T-cell leukemia virus type I (HTLV-1) Rex protein and of human immunodeficiency virus type 1 (HIV-1) Rev protein, essential for mRNA export of retroviral transcripts. {ECO:0000269|PubMed:15371445, ECO:0000269|PubMed:15452064, ECO:0000269|PubMed:16987817, ECO:0000269|PubMed:17187778, ECO:0000269|PubMed:17360499}.
• Pathway: Translation Factors;eIF5A regulation in response to inhibition of the nuclear export system;Post-translational protein modification;Metabolism of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation;Hypusine synthesis from eIF5A-lysine (Consensus)

Recessive Scores

• pRec: 0.298

Intolerance Scores

• loftool: 0.286
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.598
• ghis: 0.632

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eif5a

Gene ontology

• Biological process: mRNA export from nucleus;translational frameshifting;protein export from nucleus;nucleocytoplasmic transport;apoptotic process;positive regulation of cytosolic calcium ion concentration;aging;positive regulation of cell population proliferation;positive regulation of cardiac muscle cell apoptotic process;negative regulation of apoptotic process;positive regulation of translational elongation;positive regulation of translational termination;positive regulation of muscle cell differentiation;cellular response to thyroid hormone stimulus;positive regulation of reactive oxygen species metabolic process
• Cellular component: nucleus;annulate lamellae;nuclear pore;cytoplasm;endoplasmic reticulum membrane;cytosol;membrane;dendrite;neuronal cell body;synapse
• Molecular function: RNA binding;translation elongation factor activity;protein binding;U6 snRNA binding;ribosome binding;protein N-terminus binding