EIF2B4

eukaryotic translation initiation factor 2B subunit delta

Basic information

Region (hg38): 2:27364351-27370338

Links

ENSG00000115211 ∙ ∙ OMIM:606687 ∙ HGNC:3260 ∙ Uniprot:Q9UI10 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• leukoencephalopathy with vanishing white matter 1 (Definitive), mode of inheritance: AR
• leukoencephalopathy with vanishing white matter (Strong), mode of inheritance: AR
• ovarioleukodystrophy (Supportive), mode of inheritance: AR
• leukoencephalopathy with vanishing white matter 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukoencephalopathy with vanishing white matter 4	AR	Obstetric	Individuals with Ovarioleukodystrophy may suffer from premature ovarian failure, and measures to allow reproduction (eg,through egg preservation) may be desired	Endocrine; Neurologic; Obstetric	11704758; 11835386; 14566705; 15054402; 15776425; 18263758; 20301435
The evidence is unclear, but it is possible that certain circumstances may aggravate the condition and accelerate neurological decline, including head trauma (children may benefit from wearing helmets), contact sports, and stressful situations (including high body temperature, and prophylactic measures and rapid treatment related to infections may be beneficial)

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EIF2B4 gene.

• not provided (192 variants)
• Vanishing white matter disease (58 variants)
• Inborn genetic diseases (22 variants)
• not specified (14 variants)
• Leukoencephalopathy with vanishing white matter 4 (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF2B4 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			4	50	3	57
missense		4	86	5	1	96
nonsense	1		1			2
start loss						0
frameshift	5	1	1			7
inframe indel			3			3
splice donor/acceptor (+/-2bp)		3				3
splice region	1		4	5	3	13
non coding			5	33	11	49
Total	6	8	100	88	15

Highest pathogenic variant AF is 0.0000132

Variants in EIF2B4

This is a list of pathogenic ClinVar variants found in the EIF2B4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27364361-G-A		Vanishing white matter disease	Uncertain significance (Jan 13, 2018)
2-27364399-G-A		Vanishing white matter disease • EIF2B4-related disorder	Benign (Sep 13, 2023)
2-27364403-C-T			Likely benign (Jan 18, 2023)
2-27364405-G-A		not specified	Uncertain significance (Nov 19, 2023)
2-27364406-G-A			Likely benign (Aug 06, 2023)
2-27364408-C-T		Inborn genetic diseases	Uncertain significance (Feb 23, 2023)
2-27364411-T-GA			Uncertain significance (Dec 07, 2021)
2-27364421-T-G			Likely benign (Dec 01, 2023)
2-27364436-T-C			Likely benign (Apr 08, 2023)
2-27364439-A-G			Likely benign (Jun 03, 2023)
2-27364462-G-A			Likely benign (Jul 18, 2023)
2-27364466-C-T			Likely benign (Jan 29, 2024)
2-27364467-G-A		Vanishing white matter disease	Uncertain significance (Oct 25, 2018)
2-27364481-C-T			Likely benign (Jul 25, 2023)
2-27364484-A-G		Vanishing white matter disease	Uncertain significance (Jan 12, 2018)
2-27364492-G-A			Uncertain significance (Aug 07, 2022)
2-27364496-A-C			Likely benign (Jul 29, 2023)
2-27364502-A-G			Likely benign (Jan 08, 2024)
2-27364507-A-G		Leukoencephalopathy with vanishing white matter 4	Pathogenic (Jun 01, 2003)
2-27364510-C-T		Inborn genetic diseases	Uncertain significance (Nov 01, 2022)
2-27364513-G-A			Likely benign (Sep 30, 2023)
2-27364515-T-C			Uncertain significance (Dec 21, 2022)
2-27364524-C-T			Uncertain significance (Dec 26, 2023)
2-27364525-G-A		Leukoencephalopathy with vanishing white matter 4	Pathogenic (Nov 01, 2003)
2-27364532-T-C			Likely benign (Jul 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF2B4	protein_coding	protein_coding	ENST00000451130	12	6135

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.961	0.0388	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.798	257	296	0.869	0.0000188	3428
Missense in Polyphen		75	109.24	0.68658		1333
Synonymous	-1.35	133	115	1.16	0.00000596	1173
Loss of Function	4.18	4	27.8	0.144	0.00000165	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000439	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the exchange of eukaryotic initiation factor 2-bound GDP for GTP.
• Disease: DISEASE: Leukodystrophy with vanishing white matter (VWM) [MIM:603896]: A leukodystrophy that occurs mainly in children. Neurological signs include progressive cerebellar ataxia, spasticity, inconstant optic atrophy and relatively preserved mental abilities. The disease is chronic-progressive with, in most individuals, additional episodes of rapid deterioration following febrile infections or minor head trauma. While childhood onset is the most common form of the disorder, some severe forms are apparent at birth. A severe, early-onset form seen among the Cree and Chippewayan populations of Quebec and Manitoba is called Cree leukoencephalopathy. Milder forms may not become evident until adolescence or adulthood. Some females with milder forms of the disease who survive to adolescence exhibit ovarian dysfunction. This variant of the disorder is called ovarioleukodystrophy. {ECO:0000269|PubMed:11835386, ECO:0000269|PubMed:12707859, ECO:0000269|PubMed:15776425}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: RNA transport - Homo sapiens (human);Translation Factors;Recycling of eIF2:GDP;Eukaryotic Translation Initiation;Translation;Metabolism of proteins;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.0313
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.715
• hipred: Y
• hipred_score: 0.706
• ghis: 0.570

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.902

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eif2b4
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: ovarian follicle development;translational initiation;regulation of translation;response to heat;response to glucose;oligodendrocyte development;myelination;response to peptide hormone;T cell receptor signaling pathway
• Cellular component: cytoplasm;cytosol;eukaryotic translation initiation factor 2B complex
• Molecular function: translation initiation factor activity;guanyl-nucleotide exchange factor activity;protein binding;translation initiation factor binding