EIF2S2

eukaryotic translation initiation factor 2 subunit beta, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 20:34088308-34112243

Previous symbols: [ "EIF2" ]

Links

ENSG00000125977 ∙ NCBI:8894 ∙ OMIM:603908 ∙ HGNC:3266 ∙ Uniprot:P20042 ∙ 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 EIF2S2 gene.

• not provided (3 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF2S2 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	1	3
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	2	1

Variants in EIF2S2

This is a list of pathogenic ClinVar variants found in the EIF2S2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-34089745-A-G			Likely benign (Jul 20, 2018)
20-34089747-G-A		not specified	Uncertain significance (Apr 07, 2022)
20-34096758-C-G		not specified	Uncertain significance (Aug 02, 2021)
20-34097422-G-A			Benign (Mar 29, 2018)
20-34105429-C-G			Likely benign (Aug 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF2S2	protein_coding	protein_coding	ENST00000374980	9	24035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.953	0.0467	125737	0	4	125741	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.90	61	166	0.368	0.00000819	2234
Missense in Polyphen		8	47.762	0.1675		733
Synonymous	0.225	55	57.2	0.962	0.00000298	562
Loss of Function	3.55	2	18.4	0.108	0.00000111	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000269	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.
• Pathway: RNA transport - Homo sapiens (human);Translation Factors;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;double stranded rna induced gene expression;skeletal muscle hypertrophy is regulated via akt-mtor pathway;Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;Recycling of eIF2:GDP;Eukaryotic Translation Initiation;Translation;Metabolism of proteins;Transport of small molecules;regulation of eif2;ABC-family proteins mediated transport;eukaryotic protein translation;Ribosomal scanning and start codon recognition;L13a-mediated translational silencing of Ceruloplasmin expression;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

• pRec: 0.190

Intolerance Scores

• loftool: 0.428
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.917
• hipred: Y
• hipred_score: 0.802
• ghis: 0.580

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eif2s2
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: in utero embryonic development;male germ cell proliferation;translational initiation;male gonad development;transmembrane transport
• Cellular component: nucleus;cytoplasm;cytosol;eukaryotic translation initiation factor 2 complex
• Molecular function: RNA binding;translation initiation factor activity;protein binding;translation factor activity, RNA binding;metal ion binding