EEF1D

protein-coding

eukaryotic translation elongation factor 1 delta

Gene summary

This gene encodes a subunit of the elongation factor-1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome. This subunit, delta, functions as guanine nucleotide exchange factor. It is reported that following HIV-1 infection, this subunit interacts with HIV-1 Tat. This interaction results in repression of translation of host cell proteins and enhanced translation of viral proteins. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. Related pseudogenes have been defined on chromosomes 1, 6, 7, 9, 11, 13, 17, 19.[provided by RefSeq, Aug 2010]

MANE transcript

NM_001130053.5

Inheritance

ClinVar variants

P:12U:148B:26

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr8:143,579,697-143,599,541

External References & Databases

Ensembl (ENSG00000104529)

Transcript & Mutation Effects

hg38 • Region Span ~19.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EEF1D variants in ClinVar

11 Conditions Cataloged

not specifiedTotal: 135

not providedTotal: 29

EEF1D-related disorderTotal: 13

Neurodevelopmental disorder with thin corpus callosum, hypotonia, and absent languageTotal: 10

Neurodevelopmental disorderTotal: 2

Inborn genetic diseasesTotal: 2

EEF1D-related intellectual disabilitiesTotal: 2

Myelodysplastic syndrome associated with isolated del(5q)Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001130053.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	5 clinvar	4 clinvar	12
missense	1 clinvar	1 clinvar	134 clinvar	13 clinvar	4 clinvar	153
nonsense	3 clinvar	2 clinvar	1 clinvar			6
start loss						0
frameshift	2 clinvar	1 clinvar	3 clinvar			6
splice donor/acceptor (+/-2bp)		2 clinvar	7 clinvar			9
Total	6	6	148	18	8	186

Highest pathogenic variant AF is 0.0000037808231

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 353 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001130053.5	RefSeq	NP_001123525.3	8	MANE Select
ENST00000618139.4	Ensembl	ENSP00000484536.2	8	MANE Select
NM_001130055.4	RefSeq	NP_001123527.1	7	Standard
NM_001130056.5	RefSeq	NP_001123528.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Herpes simplex infection - Homo sapiens (human)
Translation Factors
Translation
Metabolism of proteins
Eukaryotic Translation Elongation

Biological Process

translational elongation
positive regulation of I-kappaB kinase/NF-kappaB signaling
cellular response to ionizing radiation

Molecular Function

DNA binding
translation elongation factor activity
protein binding
translation factor activity, RNA binding
cadherin binding

Cellular Component

fibrillar center
nucleus
cytoplasm
endoplasmic reticulum
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000423316
Coding exons: 8
Length: 19845
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125746
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0820	409	404	1.01	0.0000280	4113
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Intolerance Scores

LoFtool: 0.00868
RVIS EVS: 0.34
RVIS percentile EVS: 73.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.970

Gene Damage Prediction

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