EEF1D

eukaryotic translation elongation factor 1 delta

Basic information

Region (hg38): 8:143579697-143599541

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.

not_specified (120 variants)
not_provided (23 variants)
EEF1D-related_disorder (13 variants)
Neurodevelopmental_disorder_with_thin_corpus_callosum,_hypotonia,_and_absent_language (5 variants)
Neurodevelopmental_disorder (2 variants)
Inborn_genetic_diseases (2 variants)
EEF1D-related_intellectual_disabilities (2 variants)
Myelodysplastic_syndrome_associated_with_isolated_del(5q) (1 variants)
EEF1D-associated_Neurodevelopmental_Syndrome (1 variants)
Autosomal_recessive_non-syndromic_intellectual_disability (1 variants)
Moyamoya_angiopathy (1 variants)

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. These statistics are base on transcript: NM_001130053.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	4 clinvar	9
missense	1 clinvar	1 clinvar	114 clinvar	12 clinvar	4 clinvar	132
nonsense	1 clinvar	2 clinvar	1 clinvar			4
start loss						0
frameshift	1 clinvar	1 clinvar	1 clinvar			3
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar			2
Total	3	5	117	17	8

Highest pathogenic variant AF is 0.00000378082

Loading clinvar variants...

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
Phenotype

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