EEF1D

eukaryotic translation elongation factor 1 delta

Basic information

Region (hg38): 8:143579696-143599541

Links

ENSG00000104529 ∙ NCBI:1936 ∙ OMIM:130592 ∙ HGNC:3211 ∙ Uniprot:P29692 ∙ 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 EEF1D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF1D 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				5	8	13
missense			52	8	4	64
nonsense			1			1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)		1	1			2
splice region				1		1
non coding				1	1	2
Total	0	2	54	14	13

Variants in EEF1D

This is a list of pathogenic ClinVar variants found in the EEF1D region.

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

Position	Type	Phenotype	Significance	ClinVar
8-143579812-C-T		not specified	Uncertain significance (Feb 06, 2023)
8-143580011-C-T		Inborn genetic diseases	Uncertain significance (Nov 08, 2017)
8-143580028-G-C		not specified	Uncertain significance (Jun 11, 2021)
8-143580060-C-T		EEF1D-related disorder	Benign (Feb 19, 2019)
8-143580113-C-T		not specified	Uncertain significance (Jan 17, 2023)
8-143580163-C-T		not specified	Uncertain significance (Oct 22, 2021)
8-143580164-G-A		Neurodevelopmental disorder • not specified	Uncertain significance (Mar 31, 2023)
8-143580165-C-G		EEF1D-related disorder	Benign (Apr 03, 2019)
8-143580183-G-A		EEF1D-related disorder	Benign (Oct 17, 2019)
8-143580192-C-T		EEF1D-related disorder	Likely benign (Oct 28, 2019)
8-143580199-T-C		not specified	Uncertain significance (Dec 03, 2021)
8-143580511-T-C		not specified	Uncertain significance (Mar 07, 2023)
8-143580550-G-C		not specified	Uncertain significance (May 15, 2024)
8-143580571-C-A		EEF1D-related disorder	Likely benign (Nov 21, 2022)
8-143580594-C-T		not specified	Uncertain significance (Jul 13, 2021)
8-143580606-G-A		not specified	Uncertain significance (May 15, 2024)
8-143580617-C-G		not specified	Uncertain significance (Feb 12, 2024)
8-143580662-G-A			Likely benign (Sep 01, 2022)
8-143580670-C-G		not specified	Uncertain significance (Oct 05, 2023)
8-143580675-G-A		not specified	Uncertain significance (Jan 22, 2024)
8-143580711-C-T		not specified	Uncertain significance (Jul 06, 2022)
8-143580724-C-T		not specified	Uncertain significance (Nov 01, 2022)
8-143581053-C-T		Myelodysplastic syndrome associated with isolated del(5q)	Likely pathogenic (Mar 25, 2024)
8-143581077-G-A		not specified	Uncertain significance (Jul 12, 2022)
8-143581088-G-A		not specified	Uncertain significance (Jun 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF1D	protein_coding	protein_coding	ENST00000423316	8	19845

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.99e-7	0.983	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0820	409	404	1.01	0.0000280	4113
Missense in Polyphen		97	108.05	0.89777		1232
Synonymous	-1.12	200	181	1.11	0.0000134	1318
Loss of Function	2.20	14	26.1	0.536	0.00000138	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000893	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: EF-1-beta and EF-1-delta stimulate the exchange of GDP bound to EF-1-alpha to GTP, regenerating EF-1- alpha for another round of transfer of aminoacyl-tRNAs to the ribosome.
• Pathway: Herpes simplex infection - Homo sapiens (human);Translation Factors;Translation;Metabolism of proteins;Eukaryotic Translation Elongation (Consensus)

Intolerance Scores

• loftool: 0.00868
• rvis_EVS: 0.34
• rvis_percentile_EVS: 73.73

Haploinsufficiency Scores

• pHI: 0.601
• hipred: Y
• hipred_score: 0.655
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eef1d

Gene ontology

• Biological process: translational elongation;positive regulation of I-kappaB kinase/NF-kappaB signaling;cellular response to ionizing radiation
• Cellular component: fibrillar center;nucleus;cytoplasm;endoplasmic reticulum;cytosol;eukaryotic translation elongation factor 1 complex
• Molecular function: DNA binding;translation elongation factor activity;protein binding;translation factor activity, RNA binding;cadherin binding