EEF1A2

eukaryotic translation elongation factor 1 alpha 2

Basic information

Region (hg38): 20:63488012-63499239

Previous symbols: [ "STNL", "STN" ]

Links

ENSG00000101210 ∙ NCBI:1917 ∙ OMIM:602959 ∙ HGNC:3192 ∙ Uniprot:Q05639 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy, 33 (Moderate), mode of inheritance: AD
• autosomal dominant non-syndromic intellectual disability (Supportive), mode of inheritance: AD
• undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
• developmental and epileptic encephalopathy, 33 (Strong), mode of inheritance: AD
• complex neurodevelopmental disorder (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 33; Intellectual developmental disorder, autosomal dominant 38	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	23033978; 23647072; 24697219

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EEF1A2 gene.

• Developmental and epileptic encephalopathy, 33 (351 variants)
• not provided (182 variants)
• Inborn genetic diseases (64 variants)
• not specified (49 variants)
• Intellectual disability, autosomal dominant 38 (14 variants)
• Intellectual disability, autosomal dominant 38;Developmental and epileptic encephalopathy, 33 (10 variants)
• EEF1A2-related developmental and degenerative epileptic-dyskinetic encephalopathy (9 variants)
• Intellectual disability (4 variants)
• EEF1A2-related disorders (2 variants)
• Developmental and epileptic encephalopathy, 33;Intellectual disability, autosomal dominant 38 (2 variants)
• EEF1A2-related condition (1 variants)
• Developmental disorder (1 variants)
• Neurodevelopmental disorder (1 variants)
• See cases (1 variants)
• Autosomal dominant epilepsy (1 variants)
• Hereditary spastic paraplegia 46 (1 variants)
• Seizure;Autism;Global developmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF1A2 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	160	11	173
missense	7	22	110	10	1	150
nonsense			3			3
start loss						0
frameshift		1	1			2
inframe indel			3			3
splice donor/acceptor (+/-2bp)			3			3
splice region			11	31	3	45
non coding				64	36	100
Total	7	23	122	234	48

Variants in EEF1A2

This is a list of pathogenic ClinVar variants found in the EEF1A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63488052-G-A			Likely benign (Jan 01, 2024)
20-63488301-C-T			Likely benign (Sep 23, 2020)
20-63488306-CCGCCTTCTG-C		not specified • Developmental and epileptic encephalopathy, 33	Conflicting classifications of pathogenicity (Dec 27, 2023)
20-63488307-C-T		Developmental and epileptic encephalopathy, 33 • Inborn genetic diseases	Likely benign (Oct 25, 2022)
20-63488308-G-A		Developmental and epileptic encephalopathy, 33	Uncertain significance (Jan 19, 2024)
20-63488310-C-T		Developmental and epileptic encephalopathy, 33	Likely benign (May 08, 2023)
20-63488311-T-C		Intellectual disability, autosomal dominant 38	Uncertain significance (Nov 11, 2021)
20-63488316-C-T		Developmental and epileptic encephalopathy, 33	Likely benign (Sep 15, 2020)
20-63488321-T-C		Developmental and epileptic encephalopathy, 33	Uncertain significance (Apr 25, 2022)
20-63488325-C-T		Developmental and epileptic encephalopathy, 33	Likely benign (Jan 15, 2024)
20-63488334-G-C		Developmental and epileptic encephalopathy, 33	Likely benign (Nov 05, 2022)
20-63488334-G-T		Developmental and epileptic encephalopathy, 33	Likely benign (Apr 26, 2022)
20-63488339-C-T		Developmental and epileptic encephalopathy, 33	Uncertain significance (May 17, 2022)
20-63488345-C-T		Developmental and epileptic encephalopathy, 33 • Intellectual disability, autosomal dominant 38;Developmental and epileptic encephalopathy, 33	Uncertain significance (May 26, 2022)
20-63488346-G-A		Developmental and epileptic encephalopathy, 33	Likely benign (Sep 29, 2022)
20-63488346-G-C		Developmental and epileptic encephalopathy, 33	Likely benign (Sep 19, 2023)
20-63488349-G-A			Likely benign (Apr 20, 2018)
20-63488351-C-T		Developmental and epileptic encephalopathy, 33	Benign (Jun 04, 2023)
20-63488352-G-A		Developmental and epileptic encephalopathy, 33	Likely benign (Dec 23, 2021)
20-63488355-G-A		not specified • Developmental and epileptic encephalopathy, 33 • Inborn genetic diseases • EEF1A2-related disorder	Benign (Jan 30, 2024)
20-63488355-G-T		Developmental and epileptic encephalopathy, 33 • Inborn genetic diseases	Uncertain significance (Jun 25, 2022)
20-63488356-CTCT-C			Uncertain significance (Sep 17, 2021)
20-63488358-C-T		Developmental and epileptic encephalopathy, 33	Likely benign (Dec 12, 2022)
20-63488362-T-C		Developmental and epileptic encephalopathy, 33	Uncertain significance (Mar 26, 2023)
20-63488364-C-T		not specified • Developmental and epileptic encephalopathy, 33 • Inborn genetic diseases	Benign (Feb 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF1A2	protein_coding	protein_coding	ENST00000217182	7	11140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00442	124323	0	1	124324	0.00000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.82	69	306	0.225	0.0000212	3026
Missense in Polyphen		18	163.77	0.10991		1594
Synonymous	0.831	128	141	0.911	0.0000116	933
Loss of Function	3.71	0	16.0	0.00	7.83e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000897	0.00000897
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.
• Disease: DISEASE: Epileptic encephalopathy, early infantile, 33 (EIEE33) [MIM:616409]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. {ECO:0000269|PubMed:23033978, ECO:0000269|PubMed:23647072}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Mental retardation, autosomal dominant 38 (MRD38) [MIM:616393]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD38 common features are severe intellectual disability, autistic behavior, absent speech, neonatal hypotonia, epilepsy and progressive microcephaly. {ECO:0000269|PubMed:24697219}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Legionellosis - Homo sapiens (human);RNA transport - Homo sapiens (human);Translation Factors;Translation;Metabolism of proteins;Purine metabolism;EGFR1;Eukaryotic Translation Elongation (Consensus)

Recessive Scores

• pRec: 0.476

Intolerance Scores

• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.502
• hipred: Y
• hipred_score: 0.851
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eef1a2
• Phenotype: immune system 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); 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); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; muscle phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: eef1a2
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: translation;translational elongation;response to inorganic substance;positive regulation of apoptotic process;response to electrical stimulus;positive regulation of lipid kinase activity;regulation of chaperone-mediated autophagy
• Cellular component: nucleus;cytoplasm;eukaryotic translation elongation factor 1 complex;neuronal cell body;myelin sheath;synapse;cytoplasmic side of lysosomal membrane
• Molecular function: translation elongation factor activity;GTPase activity;protein binding;GTP binding;translation factor activity, RNA binding;protein kinase binding