EEF1A1

eukaryotic translation elongation factor 1 alpha 1

Basic information

Region (hg38): 6:73489307-73525587

Previous symbols: [ "EF1A", "EEF1A", "LENG7" ]

Links

ENSG00000156508 ∙ NCBI:1915 ∙ OMIM:130590 ∙ HGNC:3189 ∙ Uniprot:P68104 ∙ 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 EEF1A1 gene.

• Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency (120 variants)
• not provided (29 variants)
• not specified (7 variants)
• Inborn genetic diseases (7 variants)
• Abnormal brain morphology (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF1A1 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	2
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	6	2	69	46	13	136
Total	6	2	70	46	15

Highest pathogenic variant AF is 0.00000658

Variants in EEF1A1

This is a list of pathogenic ClinVar variants found in the EEF1A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-73491915-G-A			Benign (Jun 25, 2018)
6-73491953-A-T			Benign (Jun 14, 2018)
6-73492090-C-T			Benign (Jun 23, 2018)
6-73492103-CA-C			Benign (Jan 06, 2020)
6-73492103-CAA-C			Benign (Aug 10, 2019)
6-73492214-A-C		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (Apr 29, 2022)
6-73492217-CTT-C		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (Sep 27, 2023)
6-73492218-T-G		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (Aug 19, 2022)
6-73492220-T-C		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (May 05, 2022)
6-73492222-A-G		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (Jan 26, 2022)
6-73492224-A-G		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (Oct 03, 2022)
6-73492235-G-A		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency • Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
6-73492236-C-T		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Uncertain significance (Sep 14, 2021)
6-73492238-C-G		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Uncertain significance (Oct 28, 2023)
6-73492238-C-T		Inborn genetic diseases	Uncertain significance (Nov 13, 2023)
6-73492238-C-CT		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Pathogenic (Jul 27, 2023)
6-73492240-C-G		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (Aug 28, 2023)
6-73492240-C-T		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (Aug 16, 2023)
6-73492241-G-A		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Uncertain significance (Aug 30, 2023)
6-73492242-A-ATGT		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Uncertain significance (Aug 28, 2023)
6-73492246-T-C		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Likely benign (Dec 22, 2023)
6-73492254-A-G		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Uncertain significance (Oct 22, 2022)
6-73492263-T-C		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency • MTO1-related disorder	Likely benign (Jan 19, 2024)
6-73492268-A-G		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Uncertain significance (May 04, 2022)
6-73492272-A-G		Mitochondrial hypertrophic cardiomyopathy with lactic acidosis due to MTO1 deficiency	Uncertain significance (Dec 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF1A1	protein_coding	protein_coding	ENST00000316292	7	8048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0214	125719	0	9	125728	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.72	90	258	0.348	0.0000127	3012
Missense in Polyphen		16	67.64	0.23655		940
Synonymous	-5.29	156	91.6	1.70	0.00000456	921
Loss of Function	3.50	1	16.2	0.0618	7.45e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000975	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000615
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. With PARP1 and TXK, forms a complex that acts as a T helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production. {ECO:0000269|PubMed:17177976}.
• Pathway: Legionellosis - Homo sapiens (human);RNA transport - Homo sapiens (human);Translation Factors;Neutrophil degranulation;HSF1 activation;west nile virus;Translation;Cellular responses to stress;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Cellular responses to external stimuli;EGFR1;Cellular response to heat stress;Protein methylation;Peptide chain elongation;Eukaryotic Translation Elongation (Consensus)

Recessive Scores

• pRec: 0.696

Intolerance Scores

• loftool: 0.0919
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.988
• hipred: Y
• hipred_score: 0.783
• ghis: 0.644

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eef1a1
• Phenotype: immune system phenotype; hematopoietic 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

Gene ontology

• Biological process: translation;translational elongation;neutrophil degranulation;cellular response to epidermal growth factor stimulus;regulation of chaperone-mediated autophagy
• Cellular component: extracellular region;extracellular space;nucleus;nucleolus;cytoplasm;cytosol;eukaryotic translation elongation factor 1 complex;plasma membrane;membrane;cortical actin cytoskeleton;ruffle membrane;secretory granule lumen;extracellular exosome;cytoplasmic side of lysosomal membrane;ficolin-1-rich granule lumen
• Molecular function: tRNA binding;RNA binding;translation elongation factor activity;GTPase activity;protein binding;GTP binding;protein kinase binding