EIF5A2

eukaryotic translation initiation factor 5A2

Basic information

Region (hg38): 3:170888418-170908644

Links

ENSG00000163577

∙ NCBI:56648 ∙ OMIM:605782 ∙ HGNC:3301 ∙ Uniprot:Q9GZV4 ∙ 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 EIF5A2 gene.

not_specified (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF5A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020390.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			10 clinvar			10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF5A2	protein_coding	protein_coding	ENST00000295822	4	20279

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000211	0.513	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	53	85.1	0.623	0.00000419	1000
Missense in Polyphen		9	17.365	0.51827		234
Synonymous	0.299	27	29.1	0.929	0.00000156	285
Loss of Function	0.404	6	7.17	0.837	3.73e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000706	0.0000703
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000332	0.0000327
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. Functions as a regulator of 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 (By similarity). {ECO:0000250, ECO:0000269|PubMed:14622290}.;
Pathway: EMT transition in Colorectal Cancer;Post-translational protein modification;Metabolism of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation;Hypusine synthesis from eIF5A-lysine (Consensus)

Recessive Scores

pRec: 0.136

Intolerance Scores

loftool: 0.540
rvis_EVS: 0.08
rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

pHI: 0.492
hipred: N
hipred_score: 0.459
ghis: 0.601

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Eif5a2
Phenotype: normal phenotype;

Gene ontology

Biological process: translational frameshifting;spermatogenesis;positive regulation of cell population proliferation;polyamine homeostasis;protein transport;positive regulation of translational elongation;positive regulation of translational termination;mRNA transport
Cellular component: nuclear pore;endoplasmic reticulum membrane;cytosol;intracellular membrane-bounded organelle
Molecular function: translation elongation factor activity;protein binding;ribosome binding